From 0d4771a1177b4e06b2f87ac24cdd1f374c4f3069 Mon Sep 17 00:00:00 2001 From: sacha schutz Date: Sun, 21 Jan 2018 17:47:02 +0100 Subject: [PATCH] first commit --- bamviewer.cpp | 48 + bamviewer.h | 31 + bamviewer.pro | 39 + main.cpp | 11 + mainwindow.cpp | 18 + mainwindow.h | 20 + mainwindow.ui | 24 + seqan/LICENSE | 27 + seqan/align.h | 224 + seqan/align/align_base.h | 740 +++ seqan/align/align_cols.h | 429 ++ seqan/align/align_config.h | 395 ++ seqan/align/align_interface_wrapper.h | 179 + seqan/align/align_iterator_base.h | 527 ++ seqan/align/align_metafunctions.h | 115 + seqan/align/align_traceback.h | 161 + seqan/align/alignment_algorithm_tags.h | 165 + seqan/align/alignment_operations.h | 149 + seqan/align/dp_algorithm_impl.h | 1599 ++++++ seqan/align/dp_align_simd_helper.h | 517 ++ seqan/align/dp_band.h | 384 ++ seqan/align/dp_cell.h | 283 + seqan/align/dp_cell_affine.h | 208 + seqan/align/dp_cell_dynamic.h | 249 + seqan/align/dp_cell_linear.h | 125 + seqan/align/dp_context.h | 187 + seqan/align/dp_formula.h | 220 + seqan/align/dp_formula_affine.h | 636 +++ seqan/align/dp_formula_dynamic.h | 689 +++ seqan/align/dp_formula_linear.h | 291 + seqan/align/dp_matrix.h | 644 +++ seqan/align/dp_matrix_navigator.h | 230 + .../align/dp_matrix_navigator_score_matrix.h | 407 ++ .../dp_matrix_navigator_score_matrix_sparse.h | 369 ++ .../align/dp_matrix_navigator_trace_matrix.h | 517 ++ seqan/align/dp_matrix_sparse.h | 150 + seqan/align/dp_meta_info.h | 485 ++ seqan/align/dp_profile.h | 571 ++ seqan/align/dp_scout.h | 340 ++ seqan/align/dp_scout_simd.h | 454 ++ seqan/align/dp_setup.h | 332 ++ seqan/align/dp_trace_segment.h | 341 ++ seqan/align/dp_traceback_adaptor.h | 321 ++ seqan/align/dp_traceback_impl.h | 611 +++ seqan/align/evaluate_alignment.h | 331 ++ seqan/align/fragment.h | 571 ++ seqan/align/gap_anchor.h | 380 ++ seqan/align/gapped_value_type.h | 87 + seqan/align/gaps_anchor.h | 938 ++++ seqan/align/gaps_array.h | 917 ++++ seqan/align/gaps_base.h | 1234 +++++ seqan/align/gaps_iterator_anchor.h | 781 +++ seqan/align/gaps_iterator_array.h | 783 +++ seqan/align/gaps_iterator_base.h | 525 ++ seqan/align/global_alignment_banded.h | 786 +++ .../align/global_alignment_hirschberg_impl.h | 694 +++ .../global_alignment_myers_hirschberg_impl.h | 762 +++ seqan/align/global_alignment_myers_impl.h | 201 + seqan/align/global_alignment_specialized.h | 201 + seqan/align/global_alignment_unbanded.h | 841 +++ seqan/align/local_alignment_banded.h | 298 + ...al_alignment_banded_waterman_eggert_impl.h | 601 ++ seqan/align/local_alignment_enumeration.h | 220 + .../local_alignment_enumeration_banded.h | 126 + .../local_alignment_enumeration_unbanded.h | 122 + seqan/align/local_alignment_unbanded.h | 381 ++ .../local_alignment_waterman_eggert_impl.h | 751 +++ seqan/align/matrix_base.h | 1103 ++++ seqan/align_extend.h | 48 + seqan/align_extend/align_extend.h | 647 +++ seqan/align_extend/align_extend_base.h | 201 + seqan/align_extend/dp_scout_xdrop.h | 206 + seqan/align_profile.h | 57 + seqan/align_profile/add_to_profile.h | 165 + seqan/align_profile/score_profile_seq.h | 536 ++ seqan/align_split.h | 55 + seqan/align_split/align_split_interface.h | 751 +++ seqan/align_split/dp_scout_split.h | 137 + seqan/alignment_free.h | 63 + seqan/alignment_free/af_d2.h | 124 + seqan/alignment_free/af_d2star.h | 224 + seqan/alignment_free/af_d2z.h | 631 +++ seqan/alignment_free/af_n2.h | 641 +++ seqan/alignment_free/alignment_free_base.h | 340 ++ .../alignment_free_comparison.h | 106 + seqan/alignment_free/kmer_functions.h | 965 ++++ seqan/arg_parse.h | 79 + seqan/arg_parse/arg_parse_argument.h | 1164 ++++ seqan/arg_parse/arg_parse_ctd_support.h | 594 ++ seqan/arg_parse/arg_parse_doc.h | 1056 ++++ seqan/arg_parse/arg_parse_exceptions.h | 89 + seqan/arg_parse/arg_parse_option.h | 492 ++ seqan/arg_parse/arg_parse_parse.h | 395 ++ seqan/arg_parse/arg_parse_type_support.h | 236 + seqan/arg_parse/arg_parse_version_check.h | 480 ++ seqan/arg_parse/argument_parser.h | 1192 ++++ seqan/arg_parse/tool_doc.h | 1613 ++++++ seqan/arg_parse/xml_support.h | 95 + seqan/bam_io.h | 96 + seqan/bam_io/bam_alignment_record.h | 612 +++ seqan/bam_io/bam_alignment_record_util.h | 253 + seqan/bam_io/bam_file.h | 363 ++ seqan/bam_io/bam_header_record.h | 483 ++ seqan/bam_io/bam_index_bai.h | 794 +++ seqan/bam_io/bam_io_context.h | 353 ++ seqan/bam_io/bam_sam_conversion.h | 369 ++ seqan/bam_io/bam_scanner_cache.h | 309 ++ seqan/bam_io/bam_tags_dict.h | 890 +++ seqan/bam_io/cigar.h | 696 +++ seqan/bam_io/read_bam.h | 279 + seqan/bam_io/read_sam.h | 399 ++ seqan/bam_io/write_bam.h | 276 + seqan/bam_io/write_sam.h | 221 + seqan/basic.h | 112 + seqan/basic/aggregate_concept.h | 132 + seqan/basic/allocator_chunkpool.h | 245 + seqan/basic/allocator_interface.h | 432 ++ seqan/basic/allocator_multipool.h | 262 + seqan/basic/allocator_simple.h | 239 + seqan/basic/allocator_singlepool.h | 250 + seqan/basic/allocator_to_std.h | 206 + seqan/basic/alphabet_adapt_builtins.h | 236 + seqan/basic/alphabet_bio.h | 101 + seqan/basic/alphabet_concept.h | 586 ++ seqan/basic/alphabet_math.h | 294 + seqan/basic/alphabet_profile.h | 382 ++ seqan/basic/alphabet_qualities.h | 129 + seqan/basic/alphabet_residue.h | 1493 +++++ seqan/basic/alphabet_residue_funcs.h | 87 + seqan/basic/alphabet_residue_tabs.h | 461 ++ seqan/basic/alphabet_simple_type.h | 1092 ++++ seqan/basic/alphabet_storage.h | 291 + seqan/basic/array_construct_destruct.h | 1272 +++++ seqan/basic/basic_aggregate.h | 62 + seqan/basic/basic_allocator.h | 64 + seqan/basic/basic_alphabet.h | 98 + seqan/basic/basic_concept.h | 67 + seqan/basic/basic_container.h | 59 + seqan/basic/basic_debug.h | 60 + seqan/basic/basic_device.h | 152 + seqan/basic/basic_exception.h | 378 ++ seqan/basic/basic_functors.h | 214 + seqan/basic/basic_fundamental.h | 88 + seqan/basic/basic_iterator.h | 92 + seqan/basic/basic_math.h | 58 + seqan/basic/basic_metaprogramming.h | 64 + seqan/basic/basic_parallelism.h | 76 + seqan/basic/basic_proxy.h | 59 + seqan/basic/basic_simd_vector.h | 1671 ++++++ seqan/basic/basic_smart_pointer.h | 59 + seqan/basic/basic_stream.h | 1303 +++++ seqan/basic/basic_tangle.h | 166 + seqan/basic/basic_type.h | 543 ++ seqan/basic/basic_view.h | 190 + seqan/basic/boost_preprocessor_subset.h | 4850 +++++++++++++++++ seqan/basic/builtin_functions.h | 63 + seqan/basic/concept_checking.h | 731 +++ seqan/basic/container_concept.h | 633 +++ seqan/basic/debug_helper.h | 243 + seqan/basic/debug_test_system.h | 2392 ++++++++ seqan/basic/fundamental_chunking.h | 148 + seqan/basic/fundamental_comparison.h | 149 + seqan/basic/fundamental_concepts.h | 1018 ++++ seqan/basic/fundamental_conversion.h | 154 + seqan/basic/fundamental_metafunctions.h | 314 ++ seqan/basic/fundamental_tags.h | 658 +++ seqan/basic/fundamental_transport.h | 244 + seqan/basic/holder_base.h | 443 ++ seqan/basic/holder_simple.h | 297 + seqan/basic/holder_tristate.h | 955 ++++ seqan/basic/hosted_type_interface.h | 291 + seqan/basic/iterator_adapt_pointer.h | 96 + seqan/basic/iterator_adapt_std.h | 601 ++ seqan/basic/iterator_adaptor.h | 759 +++ seqan/basic/iterator_base.h | 375 ++ seqan/basic/iterator_concept.h | 866 +++ seqan/basic/iterator_counting.h | 359 ++ seqan/basic/iterator_interface.h | 512 ++ seqan/basic/iterator_position.h | 276 + seqan/basic/iterator_range.h | 398 ++ seqan/basic/iterator_zip.h | 657 +++ seqan/basic/macro_deprecated.h | 78 + seqan/basic/math_functions.h | 206 + seqan/basic/math_log_space_value.h | 481 ++ seqan/basic/metaprogramming_control.h | 280 + seqan/basic/metaprogramming_enable_if.h | 363 ++ seqan/basic/metaprogramming_logic.h | 536 ++ seqan/basic/metaprogramming_math.h | 187 + seqan/basic/metaprogramming_type.h | 338 ++ seqan/basic/metaprogramming_type_algebra.h | 274 + seqan/basic/pair_base.h | 482 ++ seqan/basic/pair_bit_compressed.h | 174 + seqan/basic/pair_packed.h | 180 + seqan/basic/profiling.h | 604 ++ seqan/basic/property_map_concept.h | 169 + seqan/basic/proxy_base.h | 475 ++ seqan/basic/proxy_iterator.h | 335 ++ seqan/basic/test_system.h | 419 ++ seqan/basic/triple_base.h | 533 ++ seqan/basic/triple_packed.h | 184 + seqan/basic/tuple_base.h | 625 +++ seqan/basic/tuple_bit_compressed.h | 549 ++ seqan/basic/volatile_ptr.h | 225 + seqan/bed_io.h | 59 + seqan/bed_io/bed_file.h | 127 + seqan/bed_io/bed_record.h | 432 ++ seqan/bed_io/read_bed.h | 279 + seqan/bed_io/write_bed.h | 148 + seqan/blast.h | 73 + seqan/blast/blast_base.h | 426 ++ seqan/blast/blast_io_context.h | 286 + seqan/blast/blast_record.h | 464 ++ seqan/blast/blast_report_out.h | 865 +++ seqan/blast/blast_statistics.h | 1167 ++++ seqan/blast/blast_tabular.h | 689 +++ seqan/blast/blast_tabular_in.h | 1010 ++++ seqan/blast/blast_tabular_lowlevel.h | 325 ++ seqan/blast/blast_tabular_out.h | 746 +++ seqan/consensus.h | 70 + seqan/consensus/consensus_aligner.h | 186 + seqan/consensus/consensus_aligner_interface.h | 150 + seqan/consensus/consensus_alignment_options.h | 145 + seqan/consensus/consensus_base.h | 1871 +++++++ seqan/consensus/consensus_builder.h | 494 ++ seqan/consensus/consensus_library.h | 574 ++ seqan/consensus/consensus_realign.h | 794 +++ seqan/consensus/consensus_score.h | 541 ++ seqan/consensus/overlap_info_computation.h | 425 ++ seqan/consensus/overlapper.h | 395 ++ seqan/file.h | 94 + seqan/file/file_base.h | 645 +++ seqan/file/file_cstyle.h | 278 + seqan/file/file_forwards.h | 57 + seqan/file/file_interface.h | 335 ++ seqan/file/file_mapping.h | 790 +++ seqan/file/file_page.h | 1583 ++++++ seqan/file/string_external.h | 2210 ++++++++ seqan/file/string_mmap.h | 712 +++ seqan/find.h | 106 + seqan/find/find_abndm.h | 649 +++ seqan/find/find_ahocorasick.h | 311 ++ seqan/find/find_base.h | 1004 ++++ seqan/find/find_begin.h | 400 ++ seqan/find/find_bndm.h | 254 + seqan/find/find_bom.h | 215 + seqan/find/find_hamming_simple.h | 259 + seqan/find/find_horspool.h | 454 ++ seqan/find/find_lambda.h | 239 + seqan/find/find_multi.h | 150 + seqan/find/find_multiple_bfam.h | 365 ++ seqan/find/find_multiple_shiftand.h | 427 ++ seqan/find/find_myers_ukkonen.h | 1660 ++++++ seqan/find/find_pattern_base.h | 471 ++ seqan/find/find_pex.h | 737 +++ seqan/find/find_score.h | 467 ++ seqan/find/find_set_horspool.h | 259 + seqan/find/find_shiftand.h | 239 + seqan/find/find_shiftor.h | 278 + seqan/find/find_simple.h | 135 + seqan/find/find_wild_shiftand.h | 642 +++ seqan/find/find_wumanber.h | 441 ++ seqan/gff_io.h | 56 + seqan/gff_io/gff_file.h | 165 + seqan/gff_io/gff_io_base.h | 655 +++ seqan/graph_algorithms.h | 72 + .../all_pairs_shortest_path.h | 202 + seqan/graph_algorithms/bellman_ford.h | 136 + seqan/graph_algorithms/bipartite_matching.h | 116 + seqan/graph_algorithms/breadth_first_search.h | 138 + seqan/graph_algorithms/connected_components.h | 150 + seqan/graph_algorithms/depth_first_search.h | 177 + seqan/graph_algorithms/dijkstra.h | 144 + seqan/graph_algorithms/floyd_warshall.h | 122 + seqan/graph_algorithms/ford_fulkerson.h | 220 + .../graph_algorithm_heap_tree.h | 490 ++ seqan/graph_algorithms/graph_algorithm_hmm.h | 1171 ++++ .../graph_algorithm_lis_his.h | 449 ++ seqan/graph_algorithms/kruskal.h | 137 + seqan/graph_algorithms/path_growing.h | 134 + seqan/graph_algorithms/prim.h | 194 + .../single_source_shortest_path.h | 233 + .../strongly_connected_compnents.h | 180 + seqan/graph_algorithms/topological_sort.h | 120 + seqan/graph_algorithms/transitive_closure.h | 107 + .../weakly_connected_components.h | 121 + .../weighted_bipartite_matching.h | 323 ++ seqan/graph_align.h | 69 + .../graph_algorithm_refine_align.h | 195 + .../graph_algorithm_refine_aligngraph.h | 289 + .../graph_algorithm_refine_annotation.h | 355 ++ .../graph_algorithm_refine_exact.h | 555 ++ .../graph_algorithm_refine_exact_iterative.h | 683 +++ .../graph_algorithm_refine_fragment.h | 201 + .../graph_algorithm_refine_inexact.h | 331 ++ .../graph_algorithm_refine_scoring.h | 52 + seqan/graph_align/graph_impl_align.h | 2109 +++++++ seqan/graph_align/graph_impl_align_adapt.h | 409 ++ seqan/graph_msa.h | 54 + seqan/graph_msa/graph_align_tcoffee_base.h | 1075 ++++ .../graph_msa/graph_align_tcoffee_distance.h | 213 + .../graph_msa/graph_align_tcoffee_guidetree.h | 898 +++ seqan/graph_msa/graph_align_tcoffee_io.h | 1140 ++++ seqan/graph_msa/graph_align_tcoffee_kmer.h | 153 + seqan/graph_msa/graph_align_tcoffee_library.h | 1086 ++++ seqan/graph_msa/graph_align_tcoffee_msa.h | 660 +++ .../graph_align_tcoffee_progressive.h | 485 ++ .../graph_align_tcoffee_refinement.h | 516 ++ seqan/graph_types.h | 82 + seqan/graph_types/graph_base.h | 321 ++ seqan/graph_types/graph_drawing.h | 914 ++++ seqan/graph_types/graph_edgestump.h | 1031 ++++ seqan/graph_types/graph_idmanager.h | 458 ++ seqan/graph_types/graph_impl_automaton.h | 961 ++++ seqan/graph_types/graph_impl_directed.h | 1034 ++++ seqan/graph_types/graph_impl_hmm.h | 983 ++++ seqan/graph_types/graph_impl_oracle.h | 233 + seqan/graph_types/graph_impl_tree.h | 1085 ++++ seqan/graph_types/graph_impl_trie.h | 232 + seqan/graph_types/graph_impl_undirected.h | 835 +++ seqan/graph_types/graph_impl_wordgraph.h | 327 ++ seqan/graph_types/graph_interface.h | 760 +++ seqan/graph_types/graph_iterator.h | 95 + seqan/graph_types/graph_iterator_adjacency.h | 340 ++ seqan/graph_types/graph_iterator_bfs.h | 298 + seqan/graph_types/graph_iterator_dfs.h | 302 + seqan/graph_types/graph_iterator_edge.h | 465 ++ seqan/graph_types/graph_iterator_outedge.h | 1152 ++++ seqan/graph_types/graph_iterator_vertex.h | 345 ++ seqan/graph_types/graph_utility_parsing.h | 94 + seqan/graph_types/property_map_generic.h | 223 + seqan/graph_types/property_map_internal.h | 227 + .../property_map_internal_pointer.h | 232 + seqan/index.h | 243 + seqan/index/find2_backtracking.h | 1359 +++++ seqan/index/find2_base.h | 241 + seqan/index/find2_functors.h | 200 + seqan/index/find2_index.h | 266 + 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159 + seqan/pipe/pipe_edit_environment.h | 355 ++ seqan/pipe/pipe_filter.h | 139 + seqan/pipe/pipe_iterator.h | 264 + seqan/pipe/pipe_joiner.h | 133 + seqan/pipe/pipe_namer.h | 149 + seqan/pipe/pipe_sampler.h | 647 +++ seqan/pipe/pipe_shifter.h | 171 + seqan/pipe/pipe_source.h | 420 ++ seqan/pipe/pipe_tupler.h | 482 ++ seqan/pipe/pool_base.h | 1410 +++++ seqan/pipe/pool_mapper.h | 636 +++ seqan/pipe/pool_sorter.h | 469 ++ seqan/platform.h | 465 ++ seqan/random.h | 63 + seqan/random/random_base.h | 119 + seqan/random/random_beta.h | 351 ++ seqan/random/random_util.h | 133 + seqan/realign.h | 57 + seqan/realign/realign_base.h | 1823 +++++++ seqan/realign/realign_helper_functions.h | 205 + seqan/reduced_aminoacid.h | 55 + .../reduced_aminoacid_base.h | 131 + .../reduced_aminoacid_base_late.h | 107 + .../reduced_aminoacid_cluster_red_base.h | 135 + ...aminoacid_cluster_red_tables_20_to_n_b62.h | 1853 +++++++ ...aminoacid_cluster_red_tables_22_to_n_b62.h | 2074 +++++++ ...aminoacid_cluster_red_tables_24_to_n_b62.h | 2296 ++++++++ .../reduced_aminoacid_murphy10_base.h | 122 + .../reduced_aminoacid_murphy10_tables.h | 154 + seqan/rna_io.h | 73 + seqan/rna_io/bpseq_read_write.h | 240 + seqan/rna_io/connect_read_write.h | 302 + seqan/rna_io/dot_bracket_read_write.h | 409 ++ seqan/rna_io/ebpseq_read_write.h | 672 +++ seqan/rna_io/rna_header.h | 121 + seqan/rna_io/rna_io_context.h | 134 + seqan/rna_io/rna_record.h | 279 + seqan/rna_io/rna_struct_file.h | 347 ++ seqan/rna_io/stockholm_read_write.h | 339 ++ seqan/rna_io/vienna_read_write.h | 280 + seqan/roi_io.h | 59 + seqan/roi_io/read_roi.h | 252 + seqan/roi_io/roi_file.h | 147 + seqan/roi_io/roi_io_context.h | 71 + seqan/roi_io/roi_record.h | 119 + seqan/roi_io/write_roi.h | 122 + seqan/score.h | 56 + seqan/score/score_base.h | 344 ++ seqan/score/score_edit.h | 133 + seqan/score/score_matrix.h | 217 + seqan/score/score_matrix_data.h | 945 ++++ seqan/score/score_matrix_dyn.h | 240 + seqan/score/score_matrix_io.h | 329 ++ seqan/score/score_simd_wrapper.h | 183 + seqan/score/score_simple.h | 291 + seqan/seeds.h | 90 + seqan/seeds/banded_chain_alignment.h | 474 ++ seqan/seeds/banded_chain_alignment_impl.h | 1288 +++++ seqan/seeds/banded_chain_alignment_profile.h | 267 + seqan/seeds/banded_chain_alignment_scout.h | 370 ++ .../seeds/banded_chain_alignment_traceback.h | 393 ++ seqan/seeds/basic_iter_indirect.h | 180 + seqan/seeds/seeds_base.h | 42 + seqan/seeds/seeds_combination.h | 461 ++ seqan/seeds/seeds_extension.h | 873 +++ seqan/seeds/seeds_global_chaining.h | 291 + seqan/seeds/seeds_global_chaining_base.h | 44 + seqan/seeds/seeds_global_chaining_gusfield.h | 48 + seqan/seeds/seeds_seed_base.h | 670 +++ seqan/seeds/seeds_seed_chained.h | 503 ++ seqan/seeds/seeds_seed_diagonal.h | 187 + seqan/seeds/seeds_seed_set_base.h | 301 + seqan/seeds/seeds_seed_set_non_scored.h | 56 + seqan/seeds/seeds_seed_set_scored.h | 56 + seqan/seeds/seeds_seed_set_unordered.h | 385 ++ seqan/seeds/seeds_seed_simple.h | 278 + seqan/seq_io.h | 75 + seqan/seq_io/bam_sam.h | 554 ++ seqan/seq_io/fai_index.h | 695 +++ seqan/seq_io/fasta_fastq.h | 497 ++ seqan/seq_io/genomic_region.h | 283 + seqan/seq_io/read_embl.h | 223 + seqan/seq_io/read_genbank.h | 248 + seqan/seq_io/sequence_file.h | 556 ++ seqan/sequence.h | 142 + seqan/sequence/adapt_array_pointer.h | 771 +++ seqan/sequence/adapt_stl_container.h | 1335 +++++ seqan/sequence/container_view.h | 724 +++ seqan/sequence/container_view_zip.h | 295 + seqan/sequence/iter_concat_virtual.h | 563 ++ seqan/sequence/segment_base.h | 839 +++ seqan/sequence/segment_infix.h | 699 +++ seqan/sequence/segment_prefix.h | 642 +++ seqan/sequence/segment_suffix.h | 649 +++ seqan/sequence/segment_utils.h | 130 + seqan/sequence/sequence_concatenator.h | 288 + seqan/sequence/sequence_forwards.h | 199 + seqan/sequence/sequence_interface.h | 1293 +++++ seqan/sequence/sequence_lexical.h | 763 +++ seqan/sequence/sequence_shortcuts.h | 257 + seqan/sequence/string_alloc.h | 446 ++ seqan/sequence/string_array.h | 289 + seqan/sequence/string_base.h | 2083 +++++++ seqan/sequence/string_block.h | 545 ++ seqan/sequence/string_cstyle.h | 853 +++ seqan/sequence/string_packed.h | 2039 +++++++ seqan/sequence/string_packed_old.h | 1278 +++++ seqan/sequence/string_set_base.h | 1844 +++++++ seqan/sequence/string_set_concat_direct.h | 700 +++ .../sequence/string_set_dependent_generous.h | 332 ++ seqan/sequence/string_set_dependent_tight.h | 378 ++ seqan/sequence/string_set_owner.h | 437 ++ seqan/sequence/string_set_segment.h | 511 ++ seqan/sequence/string_set_view.h | 96 + seqan/sequence_journaled.h | 63 + .../journal_entries_sorted_array.h | 750 +++ seqan/sequence_journaled/journal_entry.h | 161 + seqan/sequence_journaled/sequence_journaled.h | 1105 ++++ .../sequence_journaled_iterator.h | 1236 +++++ .../sequence_journaled_iterator_fast.h | 383 ++ seqan/simple_intervals_io.h | 54 + .../simple_intervals_file.h | 176 + 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seqan/stream/iostream_bzip2.h | 302 + seqan/stream/iostream_bzip2_impl.h | 429 ++ seqan/stream/iostream_zip.h | 383 ++ seqan/stream/iostream_zip_impl.h | 386 ++ seqan/stream/iostream_zutil.h | 229 + seqan/stream/iter_stream.h | 738 +++ seqan/stream/lexical_cast.h | 287 + seqan/stream/stream_base.h | 232 + seqan/stream/stream_compressor.h | 489 ++ seqan/stream/tokenization.h | 688 +++ seqan/stream/virtual_stream.h | 692 +++ seqan/system.h | 91 + seqan/system/file_async.h | 1259 +++++ seqan/system/file_directory.h | 315 ++ seqan/system/file_forwards.h | 162 + seqan/system/file_sync.h | 495 ++ seqan/system/system_base.h | 65 + seqan/system/system_event_win.h | 236 + seqan/system/system_forwards.h | 81 + seqan/tabix_io.h | 59 + seqan/tabix_io/tabix_index_tbi.h | 532 ++ seqan/translation.h | 48 + seqan/translation/translation.h | 682 +++ seqan/translation/translation_tables.h | 884 +++ seqan/ucsc_io.h | 45 + seqan/ucsc_io/ucsc_file.h | 182 + seqan/ucsc_io/ucsc_io.h | 446 ++ 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seqan/file/file_base.h create mode 100644 seqan/file/file_cstyle.h create mode 100644 seqan/file/file_forwards.h create mode 100644 seqan/file/file_interface.h create mode 100644 seqan/file/file_mapping.h create mode 100644 seqan/file/file_page.h create mode 100644 seqan/file/string_external.h create mode 100644 seqan/file/string_mmap.h create mode 100644 seqan/find.h create mode 100644 seqan/find/find_abndm.h create mode 100644 seqan/find/find_ahocorasick.h create mode 100644 seqan/find/find_base.h create mode 100644 seqan/find/find_begin.h create mode 100644 seqan/find/find_bndm.h create mode 100644 seqan/find/find_bom.h create mode 100644 seqan/find/find_hamming_simple.h create mode 100644 seqan/find/find_horspool.h create mode 100644 seqan/find/find_lambda.h create mode 100644 seqan/find/find_multi.h create mode 100644 seqan/find/find_multiple_bfam.h create mode 100644 seqan/find/find_multiple_shiftand.h create mode 100644 seqan/find/find_myers_ukkonen.h create mode 100644 seqan/find/find_pattern_base.h create mode 100644 seqan/find/find_pex.h create mode 100644 seqan/find/find_score.h create mode 100644 seqan/find/find_set_horspool.h create mode 100644 seqan/find/find_shiftand.h create mode 100644 seqan/find/find_shiftor.h create mode 100644 seqan/find/find_simple.h create mode 100644 seqan/find/find_wild_shiftand.h create mode 100644 seqan/find/find_wumanber.h create mode 100644 seqan/gff_io.h create mode 100644 seqan/gff_io/gff_file.h create mode 100644 seqan/gff_io/gff_io_base.h create mode 100644 seqan/graph_algorithms.h create mode 100644 seqan/graph_algorithms/all_pairs_shortest_path.h create mode 100644 seqan/graph_algorithms/bellman_ford.h create mode 100644 seqan/graph_algorithms/bipartite_matching.h create mode 100644 seqan/graph_algorithms/breadth_first_search.h create mode 100644 seqan/graph_algorithms/connected_components.h create mode 100644 seqan/graph_algorithms/depth_first_search.h create mode 100644 seqan/graph_algorithms/dijkstra.h create mode 100644 seqan/graph_algorithms/floyd_warshall.h create mode 100644 seqan/graph_algorithms/ford_fulkerson.h create mode 100644 seqan/graph_algorithms/graph_algorithm_heap_tree.h create mode 100644 seqan/graph_algorithms/graph_algorithm_hmm.h create mode 100644 seqan/graph_algorithms/graph_algorithm_lis_his.h create mode 100644 seqan/graph_algorithms/kruskal.h create mode 100644 seqan/graph_algorithms/path_growing.h create mode 100644 seqan/graph_algorithms/prim.h create mode 100644 seqan/graph_algorithms/single_source_shortest_path.h create mode 100644 seqan/graph_algorithms/strongly_connected_compnents.h create mode 100644 seqan/graph_algorithms/topological_sort.h create mode 100644 seqan/graph_algorithms/transitive_closure.h create mode 100644 seqan/graph_algorithms/weakly_connected_components.h create mode 100644 seqan/graph_algorithms/weighted_bipartite_matching.h create mode 100644 seqan/graph_align.h create mode 100644 seqan/graph_align/graph_algorithm_refine_align.h create mode 100644 seqan/graph_align/graph_algorithm_refine_aligngraph.h create mode 100644 seqan/graph_align/graph_algorithm_refine_annotation.h create mode 100644 seqan/graph_align/graph_algorithm_refine_exact.h create mode 100644 seqan/graph_align/graph_algorithm_refine_exact_iterative.h create mode 100644 seqan/graph_align/graph_algorithm_refine_fragment.h create mode 100644 seqan/graph_align/graph_algorithm_refine_inexact.h create mode 100644 seqan/graph_align/graph_algorithm_refine_scoring.h create mode 100644 seqan/graph_align/graph_impl_align.h create mode 100644 seqan/graph_align/graph_impl_align_adapt.h create mode 100644 seqan/graph_msa.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_base.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_distance.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_guidetree.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_io.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_kmer.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_library.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_msa.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_progressive.h create mode 100644 seqan/graph_msa/graph_align_tcoffee_refinement.h create mode 100644 seqan/graph_types.h create mode 100644 seqan/graph_types/graph_base.h create mode 100644 seqan/graph_types/graph_drawing.h create mode 100644 seqan/graph_types/graph_edgestump.h create mode 100644 seqan/graph_types/graph_idmanager.h create mode 100644 seqan/graph_types/graph_impl_automaton.h create mode 100644 seqan/graph_types/graph_impl_directed.h create mode 100644 seqan/graph_types/graph_impl_hmm.h create mode 100644 seqan/graph_types/graph_impl_oracle.h create mode 100644 seqan/graph_types/graph_impl_tree.h create mode 100644 seqan/graph_types/graph_impl_trie.h create mode 100644 seqan/graph_types/graph_impl_undirected.h create mode 100644 seqan/graph_types/graph_impl_wordgraph.h create mode 100644 seqan/graph_types/graph_interface.h create mode 100644 seqan/graph_types/graph_iterator.h create mode 100644 seqan/graph_types/graph_iterator_adjacency.h create mode 100644 seqan/graph_types/graph_iterator_bfs.h create mode 100644 seqan/graph_types/graph_iterator_dfs.h create mode 100644 seqan/graph_types/graph_iterator_edge.h create mode 100644 seqan/graph_types/graph_iterator_outedge.h create mode 100644 seqan/graph_types/graph_iterator_vertex.h create mode 100644 seqan/graph_types/graph_utility_parsing.h create mode 100644 seqan/graph_types/property_map_generic.h create mode 100644 seqan/graph_types/property_map_internal.h create mode 100644 seqan/graph_types/property_map_internal_pointer.h create mode 100644 seqan/index.h create mode 100644 seqan/index/find2_backtracking.h create mode 100644 seqan/index/find2_base.h create mode 100644 seqan/index/find2_functors.h create mode 100644 seqan/index/find2_index.h create mode 100644 seqan/index/find2_index_multi.h create mode 100644 seqan/index/find2_vstree_factory.h create mode 100644 seqan/index/find_backtracking.h create mode 100644 seqan/index/find_index.h create mode 100644 seqan/index/find_index_approx.h create mode 100644 seqan/index/find_index_binary.h create mode 100644 seqan/index/find_index_esa.h create mode 100644 seqan/index/find_index_lambda.h create mode 100644 seqan/index/find_index_qgram.h create mode 100644 seqan/index/find_pigeonhole.h create mode 100644 seqan/index/find_quasar.h create mode 100644 seqan/index/find_swift.h create mode 100644 seqan/index/index_base.h create mode 100644 seqan/index/index_bidirectional.h create mode 100644 seqan/index/index_bidirectional_stree.h create mode 100644 seqan/index/index_bifm.h create mode 100644 seqan/index/index_bifm_stree.h create mode 100644 seqan/index/index_bwt.h create mode 100644 seqan/index/index_childtab.h create mode 100644 seqan/index/index_device.h create mode 100644 seqan/index/index_dfi.h create mode 100644 seqan/index/index_esa_algs.h create mode 100644 seqan/index/index_esa_algs_multi.h create mode 100644 seqan/index/index_esa_base.h create mode 100644 seqan/index/index_esa_drawing.h create mode 100644 seqan/index/index_esa_stree.h create mode 100644 seqan/index/index_fm.h create mode 100644 seqan/index/index_fm_compressed_sa.h create mode 100644 seqan/index/index_fm_compressed_sa_iterator.h create mode 100644 seqan/index/index_fm_dox.h create mode 100644 seqan/index/index_fm_lf_table.h create mode 100644 seqan/index/index_fm_rank_dictionary_base.h create mode 100644 seqan/index/index_fm_rank_dictionary_levels.h create mode 100644 seqan/index/index_fm_rank_dictionary_naive.h create mode 100644 seqan/index/index_fm_rank_dictionary_wt.h create mode 100644 seqan/index/index_fm_right_array_binary_tree.h create mode 100644 seqan/index/index_fm_right_array_binary_tree_iterator.h create mode 100644 seqan/index/index_fm_sparse_string.h create mode 100644 seqan/index/index_fm_stree.h create mode 100644 seqan/index/index_forwards.h create mode 100644 seqan/index/index_lcp.h create mode 100644 seqan/index/index_lcp_tree.h create mode 100644 seqan/index/index_pizzachili.h create mode 100644 seqan/index/index_pizzachili_find.h create mode 100644 seqan/index/index_pizzachili_string.h create mode 100644 seqan/index/index_qgram.h create mode 100644 seqan/index/index_qgram_bucketrefinement.h create mode 100644 seqan/index/index_qgram_openaddressing.h create mode 100644 seqan/index/index_qgram_stree.h create mode 100644 seqan/index/index_sa_btree.h create mode 100644 seqan/index/index_sa_bwtwalk.h create mode 100644 seqan/index/index_sa_lss.h create mode 100644 seqan/index/index_sa_mm.h create mode 100644 seqan/index/index_sa_qsort.h create mode 100644 seqan/index/index_sa_stree.h create mode 100644 seqan/index/index_sa_truncated.h create mode 100644 seqan/index/index_shawarma.h create mode 100644 seqan/index/index_shims.h create mode 100644 seqan/index/index_skew3.h create mode 100644 seqan/index/index_skew7.h create mode 100644 seqan/index/index_skew7_multi.h create mode 100644 seqan/index/index_view.h create mode 100644 seqan/index/index_wotd.h create mode 100644 seqan/index/pipe_merger3.h create mode 100644 seqan/index/pipe_merger7.h create mode 100644 seqan/index/pizzachili_api.h create mode 100644 seqan/index/pump_extender3.h create mode 100644 seqan/index/pump_extender7.h create mode 100644 seqan/index/pump_lcp_core.h create mode 100644 seqan/index/pump_separator7.h create mode 100644 seqan/index/radix.h create mode 100644 seqan/index/repeat_base.h create mode 100644 seqan/index/shape_base.h create mode 100644 seqan/index/shape_gapped.h create mode 100644 seqan/index/shape_minimizer.h create mode 100644 seqan/index/shape_onegapped.h create mode 100644 seqan/index/shape_predefined.h create mode 100644 seqan/index/shape_threshold.h create mode 100644 seqan/journaled_set.h create mode 100644 seqan/journaled_set/journal_alignment_interface.h create mode 100644 seqan/journaled_set/journal_alignment_traceback_adaptor.h create mode 100644 seqan/journaled_set/journaled_set_base.h create mode 100644 seqan/journaled_set/journaled_set_impl.h create mode 100644 seqan/journaled_set/journaled_set_join.h create mode 100644 seqan/journaled_set/journaled_set_join_config.h create mode 100644 seqan/journaled_set/journaled_set_join_global_align_compact.h create mode 100644 seqan/journaled_set/journaled_set_join_global_align_manhatten.h create mode 100644 seqan/journaled_set/journaled_set_journal_trace_descriptor.h create mode 100644 seqan/journaled_set/score_biaffine.h create mode 100644 seqan/journaled_string_tree.h create mode 100644 seqan/journaled_string_tree/delta_map.h create mode 100644 seqan/journaled_string_tree/delta_map_entry.h create mode 100644 seqan/journaled_string_tree/delta_map_iterator.h create mode 100644 seqan/journaled_string_tree/delta_store.h create mode 100644 seqan/journaled_string_tree/journaled_string_tree_base.h create mode 100644 seqan/journaled_string_tree/journaled_string_tree_impl.h create mode 100644 seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h create mode 100644 seqan/journaled_string_tree/journaled_string_tree_traverser.h create mode 100644 seqan/journaled_string_tree/journaled_string_tree_traverser_node.h create mode 100644 seqan/journaled_string_tree/journaled_string_tree_traverser_util.h create mode 100644 seqan/journaled_string_tree/jst_extension_base.h create mode 100644 seqan/journaled_string_tree/jst_extension_horspool.h create mode 100644 seqan/journaled_string_tree/jst_extension_myers_ukkonen.h create mode 100644 seqan/journaled_string_tree/jst_extension_shiftand.h create mode 100644 seqan/journaled_string_tree/jst_extension_shiftor.h create mode 100644 seqan/journaled_string_tree/observable.h create mode 100644 seqan/journaled_string_tree/stack_observer.h create mode 100644 seqan/map.h create mode 100644 seqan/map/map_adapter_stl.h create mode 100644 seqan/map/map_base.h create mode 100644 seqan/map/map_chooser.h create mode 100644 seqan/map/map_skiplist.h create mode 100644 seqan/map/map_vector.h create mode 100644 seqan/map/sumlist.h create mode 100644 seqan/map/sumlist_mini.h create mode 100644 seqan/map/sumlist_skip.h create mode 100644 seqan/math.h create mode 100644 seqan/math/math_common_factor.h create mode 100644 seqan/math/math_operators.h create mode 100644 seqan/math/math_rational.h create mode 100644 seqan/misc/accumulators.h create mode 100644 seqan/misc/base.h create mode 100644 seqan/misc/bit_twiddling.h create mode 100644 seqan/misc/bit_twiddling_functors.h create mode 100644 seqan/misc/dequeue.h create mode 100644 seqan/misc/edit_environment.h create mode 100644 seqan/misc/interval_tree.h create mode 100644 seqan/misc/map.h create mode 100644 seqan/misc/memset.h create mode 100644 seqan/misc/name_store_cache.h create mode 100644 seqan/misc/priority_type_base.h create mode 100644 seqan/misc/priority_type_heap.h create mode 100644 seqan/misc/set.h create mode 100644 seqan/misc/svg.h create mode 100644 seqan/misc/terminal.h create mode 100644 seqan/misc/union_find.h create mode 100644 seqan/modifier.h create mode 100644 seqan/modifier/cyclic_shape.h create mode 100644 seqan/modifier/modifier_alphabet.h create mode 100644 seqan/modifier/modifier_alphabet_expansion.h create mode 100644 seqan/modifier/modifier_cyclic_shape.h create mode 100644 seqan/modifier/modifier_functors.h create mode 100644 seqan/modifier/modifier_iterator.h create mode 100644 seqan/modifier/modifier_padding.h create mode 100644 seqan/modifier/modifier_position.h create mode 100644 seqan/modifier/modifier_reverse.h create mode 100644 seqan/modifier/modifier_shortcuts.h create mode 100644 seqan/modifier/modifier_string.h create mode 100644 seqan/modifier/modifier_view.h create mode 100755 seqan/parallel.h create mode 100644 seqan/parallel/parallel_algorithms.h create mode 100644 seqan/parallel/parallel_atomic_misc.h create mode 100644 seqan/parallel/parallel_atomic_primitives.h create mode 100644 seqan/parallel/parallel_lock.h create mode 100644 seqan/parallel/parallel_macros.h create mode 100644 seqan/parallel/parallel_queue.h create mode 100644 seqan/parallel/parallel_queue_suspendable.h create mode 100644 seqan/parallel/parallel_resource_pool.h create mode 100644 seqan/parallel/parallel_sequence.h create mode 100644 seqan/parallel/parallel_serializer.h create mode 100644 seqan/parallel/parallel_splitting.h create mode 100644 seqan/parallel/parallel_tags.h create mode 100644 seqan/parse_lm.h create mode 100644 seqan/parse_lm/local_match_store.h create mode 100644 seqan/parse_lm/parse_blastn_tabular.h create mode 100644 seqan/parse_lm/parse_lastz_general.h create mode 100644 seqan/parse_lm/parse_stellar_gff.h create mode 100644 seqan/pipe.h create mode 100644 seqan/pipe/pipe_base.h create mode 100644 seqan/pipe/pipe_caster.h create mode 100644 seqan/pipe/pipe_counter.h create mode 100644 seqan/pipe/pipe_echoer.h create mode 100644 seqan/pipe/pipe_edit_environment.h create mode 100644 seqan/pipe/pipe_filter.h create mode 100644 seqan/pipe/pipe_iterator.h create mode 100644 seqan/pipe/pipe_joiner.h create mode 100644 seqan/pipe/pipe_namer.h create mode 100644 seqan/pipe/pipe_sampler.h create mode 100644 seqan/pipe/pipe_shifter.h create mode 100644 seqan/pipe/pipe_source.h create mode 100644 seqan/pipe/pipe_tupler.h create mode 100644 seqan/pipe/pool_base.h create mode 100644 seqan/pipe/pool_mapper.h create mode 100644 seqan/pipe/pool_sorter.h create mode 100644 seqan/platform.h create mode 100644 seqan/random.h create mode 100644 seqan/random/random_base.h create mode 100644 seqan/random/random_beta.h create mode 100644 seqan/random/random_util.h create mode 100644 seqan/realign.h create mode 100644 seqan/realign/realign_base.h create mode 100644 seqan/realign/realign_helper_functions.h create mode 100644 seqan/reduced_aminoacid.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_base.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_base_late.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h create mode 100644 seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h create mode 100644 seqan/rna_io.h create mode 100644 seqan/rna_io/bpseq_read_write.h create mode 100644 seqan/rna_io/connect_read_write.h create mode 100644 seqan/rna_io/dot_bracket_read_write.h create mode 100644 seqan/rna_io/ebpseq_read_write.h create mode 100644 seqan/rna_io/rna_header.h create mode 100644 seqan/rna_io/rna_io_context.h create mode 100644 seqan/rna_io/rna_record.h create mode 100644 seqan/rna_io/rna_struct_file.h create mode 100644 seqan/rna_io/stockholm_read_write.h create mode 100644 seqan/rna_io/vienna_read_write.h create mode 100644 seqan/roi_io.h create mode 100644 seqan/roi_io/read_roi.h create mode 100644 seqan/roi_io/roi_file.h create mode 100644 seqan/roi_io/roi_io_context.h create mode 100644 seqan/roi_io/roi_record.h create mode 100644 seqan/roi_io/write_roi.h create mode 100644 seqan/score.h create mode 100644 seqan/score/score_base.h create mode 100644 seqan/score/score_edit.h create mode 100644 seqan/score/score_matrix.h create mode 100644 seqan/score/score_matrix_data.h create mode 100644 seqan/score/score_matrix_dyn.h create mode 100644 seqan/score/score_matrix_io.h create mode 100644 seqan/score/score_simd_wrapper.h create mode 100644 seqan/score/score_simple.h create mode 100644 seqan/seeds.h create mode 100644 seqan/seeds/banded_chain_alignment.h create mode 100644 seqan/seeds/banded_chain_alignment_impl.h create mode 100644 seqan/seeds/banded_chain_alignment_profile.h create mode 100644 seqan/seeds/banded_chain_alignment_scout.h create mode 100644 seqan/seeds/banded_chain_alignment_traceback.h create mode 100644 seqan/seeds/basic_iter_indirect.h create mode 100644 seqan/seeds/seeds_base.h create mode 100644 seqan/seeds/seeds_combination.h create mode 100644 seqan/seeds/seeds_extension.h create mode 100644 seqan/seeds/seeds_global_chaining.h create mode 100644 seqan/seeds/seeds_global_chaining_base.h create mode 100644 seqan/seeds/seeds_global_chaining_gusfield.h create mode 100644 seqan/seeds/seeds_seed_base.h create mode 100644 seqan/seeds/seeds_seed_chained.h create mode 100644 seqan/seeds/seeds_seed_diagonal.h create mode 100644 seqan/seeds/seeds_seed_set_base.h create mode 100644 seqan/seeds/seeds_seed_set_non_scored.h create mode 100644 seqan/seeds/seeds_seed_set_scored.h create mode 100644 seqan/seeds/seeds_seed_set_unordered.h create mode 100644 seqan/seeds/seeds_seed_simple.h create mode 100644 seqan/seq_io.h create mode 100644 seqan/seq_io/bam_sam.h create mode 100644 seqan/seq_io/fai_index.h create mode 100644 seqan/seq_io/fasta_fastq.h create mode 100644 seqan/seq_io/genomic_region.h create mode 100644 seqan/seq_io/read_embl.h create mode 100644 seqan/seq_io/read_genbank.h create mode 100644 seqan/seq_io/sequence_file.h create mode 100644 seqan/sequence.h create mode 100644 seqan/sequence/adapt_array_pointer.h create mode 100644 seqan/sequence/adapt_stl_container.h create mode 100644 seqan/sequence/container_view.h create mode 100644 seqan/sequence/container_view_zip.h create mode 100644 seqan/sequence/iter_concat_virtual.h create mode 100644 seqan/sequence/segment_base.h create mode 100644 seqan/sequence/segment_infix.h create mode 100644 seqan/sequence/segment_prefix.h create mode 100644 seqan/sequence/segment_suffix.h create mode 100644 seqan/sequence/segment_utils.h create mode 100644 seqan/sequence/sequence_concatenator.h create mode 100644 seqan/sequence/sequence_forwards.h create mode 100644 seqan/sequence/sequence_interface.h create mode 100644 seqan/sequence/sequence_lexical.h create mode 100644 seqan/sequence/sequence_shortcuts.h create mode 100644 seqan/sequence/string_alloc.h create mode 100644 seqan/sequence/string_array.h create mode 100644 seqan/sequence/string_base.h create mode 100644 seqan/sequence/string_block.h create mode 100644 seqan/sequence/string_cstyle.h create mode 100644 seqan/sequence/string_packed.h create mode 100644 seqan/sequence/string_packed_old.h create mode 100644 seqan/sequence/string_set_base.h create mode 100644 seqan/sequence/string_set_concat_direct.h create mode 100644 seqan/sequence/string_set_dependent_generous.h create mode 100644 seqan/sequence/string_set_dependent_tight.h create mode 100644 seqan/sequence/string_set_owner.h create mode 100644 seqan/sequence/string_set_segment.h create mode 100644 seqan/sequence/string_set_view.h create mode 100644 seqan/sequence_journaled.h create mode 100644 seqan/sequence_journaled/journal_entries_sorted_array.h create mode 100644 seqan/sequence_journaled/journal_entry.h create mode 100644 seqan/sequence_journaled/sequence_journaled.h create mode 100644 seqan/sequence_journaled/sequence_journaled_iterator.h create mode 100644 seqan/sequence_journaled/sequence_journaled_iterator_fast.h create mode 100644 seqan/simple_intervals_io.h create mode 100644 seqan/simple_intervals_io/simple_intervals_file.h create mode 100644 seqan/simple_intervals_io/simple_intervals_io.h create mode 100644 seqan/statistics.h create mode 100644 seqan/statistics/statistics_base.h create mode 100644 seqan/statistics/statistics_markov_model.h create mode 100644 seqan/store.h create mode 100644 seqan/store/store_align.h create mode 100644 seqan/store/store_align_intervals.h create mode 100644 seqan/store/store_all.h create mode 100644 seqan/store/store_annotation.h create mode 100644 seqan/store/store_base.h create mode 100644 seqan/store/store_contig.h create mode 100644 seqan/store/store_intervaltree.h create mode 100644 seqan/store/store_io.h create mode 100644 seqan/store/store_io_gff.h create mode 100644 seqan/store/store_io_sam.h create mode 100644 seqan/store/store_io_ucsc.h create mode 100644 seqan/store/store_library.h create mode 100644 seqan/store/store_matepair.h create mode 100644 seqan/store/store_read.h create mode 100644 seqan/stream.h create mode 100644 seqan/stream/adapt_ios.h create mode 100644 seqan/stream/buffered_stream.h create mode 100644 seqan/stream/file_stream.h create mode 100644 seqan/stream/formatted_file.h create mode 100644 seqan/stream/guess_format.h create mode 100644 seqan/stream/iostream_bgzf.h create mode 100644 seqan/stream/iostream_bzip2.h create mode 100644 seqan/stream/iostream_bzip2_impl.h create mode 100644 seqan/stream/iostream_zip.h create mode 100644 seqan/stream/iostream_zip_impl.h create mode 100644 seqan/stream/iostream_zutil.h create mode 100644 seqan/stream/iter_stream.h create mode 100644 seqan/stream/lexical_cast.h create mode 100644 seqan/stream/stream_base.h create mode 100644 seqan/stream/stream_compressor.h create mode 100644 seqan/stream/tokenization.h create mode 100644 seqan/stream/virtual_stream.h create mode 100644 seqan/system.h create mode 100644 seqan/system/file_async.h create mode 100644 seqan/system/file_directory.h create mode 100644 seqan/system/file_forwards.h create mode 100644 seqan/system/file_sync.h create mode 100644 seqan/system/system_base.h create mode 100644 seqan/system/system_event_win.h create mode 100644 seqan/system/system_forwards.h create mode 100644 seqan/tabix_io.h create mode 100644 seqan/tabix_io/tabix_index_tbi.h create mode 100644 seqan/translation.h create mode 100644 seqan/translation/translation.h create mode 100644 seqan/translation/translation_tables.h create mode 100644 seqan/ucsc_io.h create mode 100644 seqan/ucsc_io/ucsc_file.h create mode 100755 seqan/ucsc_io/ucsc_io.h create mode 100644 seqan/ucsc_io/ucsc_record.h create mode 100644 seqan/vcf_io.h create mode 100644 seqan/vcf_io/read_vcf.h create mode 100644 seqan/vcf_io/vcf_file.h create mode 100644 seqan/vcf_io/vcf_header.h create mode 100644 seqan/vcf_io/vcf_header_record.h create mode 100644 seqan/vcf_io/vcf_io_context.h create mode 100644 seqan/vcf_io/vcf_record.h create mode 100644 seqan/vcf_io/write_vcf.h create mode 100644 seqan/version.h diff --git a/bamviewer.cpp b/bamviewer.cpp new file mode 100644 index 0000000..5723d47 --- /dev/null +++ b/bamviewer.cpp @@ -0,0 +1,48 @@ +#include "bamviewer.h" + +BamViewer::BamViewer(QObject *parent) +{ + + + +} + +void BamViewer::setFilename(const QString &filename) +{ + QFileInfo info(filename); + mFilename = info.absoluteFilePath(); + + QString s = "/home/sacha/exemple.sam"; + qDebug()< +#include +#include +#include + +#include "seqan/bam_io.h" +#include + +#define SEQAN_HAS_ZLIB 1 + +using namespace seqan; + +class BamViewer : public QAbstractScrollArea +{ +public: + BamViewer(QObject * parent = nullptr); + + void setFilename(const QString& filename); + +protected: + + void paintEvent(QPaintEvent * event) override; + +private: + QString mFilename; + +}; + +#endif // BAMVIEWER_H diff --git a/bamviewer.pro b/bamviewer.pro new file mode 100644 index 0000000..e32f43c --- /dev/null +++ b/bamviewer.pro @@ -0,0 +1,39 @@ +#------------------------------------------------- +# +# Project created by QtCreator 2018-01-21T16:57:25 +# +#------------------------------------------------- + +QT += core gui + +greaterThan(QT_MAJOR_VERSION, 4): QT += widgets + +TARGET = bamviewer +TEMPLATE = app + +# The following define makes your compiler emit warnings if you use +# any feature of Qt which has been marked as deprecated (the exact warnings +# depend on your compiler). Please consult the documentation of the +# deprecated API in order to know how to port your code away from it. +DEFINES += QT_DEPRECATED_WARNINGS + +# You can also make your code fail to compile if you use deprecated APIs. +# In order to do so, uncomment the following line. +# You can also select to disable deprecated APIs only up to a certain version of Qt. +#DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x060000 # disables all the APIs deprecated before Qt 6.0.0 + +CONFIG+= c++14 + +SOURCES += \ + main.cpp \ + mainwindow.cpp \ + bamviewer.cpp + +HEADERS += \ + mainwindow.h \ + bamviewer.h + +FORMS += \ + mainwindow.ui + +LIBS+= -lz diff --git a/main.cpp b/main.cpp new file mode 100644 index 0000000..b48f94e --- /dev/null +++ b/main.cpp @@ -0,0 +1,11 @@ +#include "mainwindow.h" +#include + +int main(int argc, char *argv[]) +{ + QApplication a(argc, argv); + MainWindow w; + w.show(); + + return a.exec(); +} diff --git a/mainwindow.cpp b/mainwindow.cpp new file mode 100644 index 0000000..ea070db --- /dev/null +++ b/mainwindow.cpp @@ -0,0 +1,18 @@ +#include "mainwindow.h" +#include "ui_mainwindow.h" + +MainWindow::MainWindow(QWidget *parent) : + QMainWindow(parent) +{ + + mViewer = new BamViewer; + + mViewer->setFilename("/home/sacha/exemple.bam"); + + + setCentralWidget(mViewer); +} + +MainWindow::~MainWindow() +{ +} diff --git a/mainwindow.h b/mainwindow.h new file mode 100644 index 0000000..10f3776 --- /dev/null +++ b/mainwindow.h @@ -0,0 +1,20 @@ +#ifndef MAINWINDOW_H +#define MAINWINDOW_H + +#include +#include "bamviewer.h" + + +class MainWindow : public QMainWindow +{ + Q_OBJECT + +public: + explicit MainWindow(QWidget *parent = 0); + ~MainWindow(); + +private: + BamViewer * mViewer; +}; + +#endif // MAINWINDOW_H diff --git a/mainwindow.ui b/mainwindow.ui new file mode 100644 index 0000000..6050363 --- /dev/null +++ b/mainwindow.ui @@ -0,0 +1,24 @@ + + MainWindow + + + + 0 + 0 + 400 + 300 + + + + MainWindow + + + + + + + + + + + diff --git a/seqan/LICENSE b/seqan/LICENSE new file mode 100644 index 0000000..3d08d0d --- /dev/null +++ b/seqan/LICENSE @@ -0,0 +1,27 @@ +Copyright (c) 2006-2016, Knut Reinert, FU Berlin +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + * Neither the name of Knut Reinert or the FU Berlin nor the names of + its contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +DAMAGE. + diff --git a/seqan/align.h b/seqan/align.h new file mode 100644 index 0000000..8e5858e --- /dev/null +++ b/seqan/align.h @@ -0,0 +1,224 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_H_ + +// TODO(holtgrew): Usage of gapped value in align module is not consistent, need proxies in many places, reference not cleanly implemented everywhere yet. +// TODO(holtgrew): The Author: tag at the top has to be corrected in the headers of this module. +// TODO(holtgrew): Anchor Gaps must be integrated completely. +// TODO(holtgrew): Local alignments & Fragments don't work nicely together at the moment, multiLocalAlignments() needs an equivalent in the new align module. +// TODO(holtgrew): Align<>, AlignCol<> need some love and documentation. +// TODO(holtgrew): Gaps need better documentation. +// TODO(holtgrew): refinement should become graph_align and also host Graph> +// TODO(holtgrew): graph_msa should become align_msa, or so, see whitepaper. +// TODO(holtgrew): The documentation and Tutorial need heavy updates, clipping alignments howto can go away. + +// ============================================================================ +// Prerequisites +// ============================================================================ + +#include +#include + +#include +#include // ModifiedAlphabet<>. +#include +#include // TODO(holtgrew): We should not have to depend on this. + +// TODO(holtgrew): Why not use priority queue from STL? +#include +#include + +// ============================================================================ +// Support +// ============================================================================ + +#include +#include +#include +#include + +// ============================================================================ +// Gaps & Gaps Iterator Data Structures +// ============================================================================ + +#include + +#include +#include + +#include +#include + +#include +#include +#include + +// ============================================================================ +// Alignment Data Structures and Columns +// ============================================================================ + +#include +#include + +// ============================================================================ +// Alignment Algorithm Implementations. +// ============================================================================ + +//################################################################################ +// New module +//################################################################################ + +// The tags have to be available everywhere so we define them centrally. +#include + +// Defines all tags needed for the DP alignment. +#include + +// The DP Band +#include + +// Stores the score value of a particular cell in the dp matrix. +// If affine gap costs are selected one cell stores the three values +// for all three dp matrices. +#include +#include +#include +#include + +// The DP Scout +#include + +// Stores the actual trace segment that was detected during traceback. +// The trace segments can be adapted into any alignment representation +// form. +#include +#include + +// Implements the different recursion formula of the alignment algorithms. +#include +#include +#include +#include + +// Defines meta informations which determine how to compute a column and a +// certain cell for different profiles. +#include + +// Actual matrix to store the values. Uses the matrix_base.h definitions +// as a host. +#include +#include + +// The navigator that based on the selected profile and band chooses the +// correct way to navigate through the matrix. +#include +#include +#include +#include + +// Ensures the backwards compatibility for the global interfaces of the +// alignment algorithms. Based on the called function this selects the +// correct parameters for the new alignment module. +#include +#include + +#ifdef SEQAN_SIMD_ENABLED +#include +#include +#endif // SEQAN_SIMD_ENABLED + +// The actual implementations of the traceback and the dynamic programming that +// is used by all different alignment algorithms. +#include +#include + +//################################################################################ +// Old module +//################################################################################ + +// Also, we have an implementation of Hirschberg's algorithm to compute +// alignments. +#include + +// The implementations of Myers' bitvector algorithm for alignments can only +// compute alignment scores. The combination of Hirschberg's and Myers' +// algorithm is limited in the same way. +#include +#include + +// Implementations of the local alignment algorithms with declumping. We also +// use them for the localAlignment() calls and return the best local alignment +// only. +// TODO(rmaerker): Replace this with a new implementation based on the new alignment module. +#include +#include + +// We carry around this implementation of Smith-Waterman because it supports +// aligning into fragment strings and alignment graphs. Eventually, it could +// go away if Waterman-Eggert supports them. +//#include + +// ============================================================================ +// Alignment Algorithm Interfaces +// ============================================================================ + +#include + +// The front-end functions for global alignments. +#include +#include + +// The front-end functions for local alignments. +#include +#include + +// The front-end for enumeration of local alignments. +#include // documentation +#include +#include + +// The front-end functions for the more specialized alignment algorithms such as +// Hirschberg, Myers and Myers-Hirschberg. +#include + +// ============================================================================ +// Operations On Alignments +// ============================================================================ + +#include +#include + +#endif // SEQAN_INCLUDE_SEQAN_ALIGN_H_ diff --git a/seqan/align/align_base.h b/seqan/align/align_base.h new file mode 100644 index 0000000..a23afff --- /dev/null +++ b/seqan/align/align_base.h @@ -0,0 +1,740 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// The Align class provides tabular alignments. It contains multiple +// Gap objects, one for each row of the alignment. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class Align +// ---------------------------------------------------------------------------- + +/*! + * @class Align + * @implements EqualityComparableConcept + * @headerfile + * @brief Tabular alignment of same-type sequences. + * + * @signature template + * class Align; + * + * @tparam TSequence Type of the underlying sequence. + * @tparam TGapSpec Tag for selecting the @link Gaps @endlink specialization. + * + * The Alignment class is for storing tabular alignments of sequences having the same type. They do so by being a + * container of @link Gaps @endlink objects. The most common use case is storing pairwise alignments that are + * generated by one of the dynamic programming alignment algorithms. + * + * @section Example + * + * Here is an example of using an Align object with @link globalAlignment @endlink. + * + * @include demos/dox/align/align.cpp + * + * The output is as follows: + * + * @include demos/dox/align/align.cpp.stdout + * + * @see globalAlignment + * @see localAlignment + * @see Gaps + */ + +template +class Align +{ +public: + typedef Gaps TGaps; + typedef String TRows; + typedef typename Size::Type TRowsSize; + + TRows data_rows; + + Align() {} + + template + Align(StringSet & stringset) + { + setStrings(*this, stringset); + } + + Align & operator=(Align const & other) + { + data_rows = other.data_rows; + return *this; + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Cols +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#Cols + * @brief Return the type representing a column in an Align object. + * + * @signature Cols::Type + * + * @tparam TAlign The Align object to get the column type for. + * + * @return Type The resulting column type. + */ + +template +struct Cols > +{ + typedef AlignCols > Type; +}; + +template +struct Cols const> +{ + typedef AlignCols const> Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#Value + * @brief Return the value type for an Align object. + * + * @signature Value::Type + * + * @tparam TAlign The Align object to get the value type for. + * + * @return Type The resulting value type. + */ + +template +struct Value >: + Value > +{}; +template +struct Value const>: + Value const> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction GetValue +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#GetValue + * @brief Return the get-value type for an Align object. + * + * @signature GetValue::Type + * + * @tparam TAlign The Align object to get the get-value type for. + * + * @return Type The resulting get-value type. + */ + +template +struct GetValue >: + GetValue > +{}; +template +struct GetValue const>: + GetValue const> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#Reference + * @brief Return the reference type for an Align object. + * + * @signature GetValue::Type + * + * @tparam TAlign The Align object to get the reference type for. + * + * @return Type The resulting reference type. + */ + +template +struct Reference >: + Reference > +{}; +template +struct Reference const>: + Reference const> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Rows +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#Row + * @brief Return the row type (@link Gaps @endlink specialization). + * + * @signature Row::Type + * + * @tparam TAlign The Align object to get the row type for. + * + * @return Type The resulting row type. + */ + +/*! + * @mfn Align#Rows + * @brief Return the type used for rows in an Align object (a Gaps specialization). + * + * @signature Rows::Type + * + * @tparam TAlign The Align object to get the rows type for. + * + * @return Type The resulting rows type. + */ + +template +struct Rows > +{ + typedef String > Type; +}; +template +struct Rows const> +{ + typedef String > const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Source +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#Source + * @brief Return the type of the underlying sequence. + * + * @signature Rows::Type; + * + * @tparam TAlign The Align object to get the underlying sequence type for. + * + * @return Type The resulting sequence type. + */ + +template +struct Source > +{ + typedef TSource Type; +}; +template +struct Source const> +{ + typedef TSource Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction StringSetType +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#StringSetType + * @brief Return the type that would be used for a string set of the sources. + * + * @signature Rows::Type + * + * @tparam TAlign The Align object to get the string set type for. + * + * @return Type The resulting string set type. + */ + +template +struct StringSetType > +{ + typedef StringSet > Type; +}; + +template +struct StringSetType const> +{ + typedef StringSet > Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function move() +// ---------------------------------------------------------------------------- + +template +inline +void move(Align & target, Align & source) +{ + move(target.data_rows, source.data_rows); +} + +// ---------------------------------------------------------------------------- +// Function rows() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#rows + * @brief Returns the rows of an Align object. + * + * @signature TRows rows(align); + * + * @param[in] align The Align object to get the rows for. + * + * @return TRows A container with the Gaps of the Align object. + */ + +template +inline typename Rows >::Type & +rows(Align & me) +{ + return me.data_rows; +} + +template +inline typename Rows const>::Type & +rows(Align const & me) +{ + return me.data_rows; +} + +// ---------------------------------------------------------------------------- +// Function row() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#row + * @brief Returns a single row of an Align object. + * + * @signature TRow row(align, pos); + * + * @param[in] align The Align object to get the row of. + * @param[in] pos The number of the row to get. + * + * @return TRow Reference to the given row of align (Metafunction: @link Align#Row @endlink). + */ + +template +inline typename Row >::Type & +row(Align & me, + TPosition _pos) +{ + return value(rows(me), _pos); +} + +template +inline typename Row const>::Type & +row(Align const & me, + TPosition _pos) +{ + return value(rows(me), _pos); +} + +// ---------------------------------------------------------------------------- +// Function cols() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#cols + * @brief Returns the columns of an Align object. + * + * @signature TCols cols(align); + * + * @param[in] align The Align object to get the cols of. + * + * @return TCols The columns of the Align object (Metafunction: @link Align#Cols @endlink). + */ + +template +inline typename Cols >::Type +cols(Align & me) +{ + return typename Cols >::Type(me); +} + +template +inline typename Cols const>::Type +cols(Align const & me) +{ + return typename Cols const>::Type(me); +} + +// ---------------------------------------------------------------------------- +// Function col() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#col + * @brief Returns the columns of an Align object. + * + * @signature TCol col(align); + * + * @param[in] align The Align object to get the cols of. + * + * @return TCol The column of the Align object (Metafunction: @link Align#Col @endlink). + */ + +template +inline typename Col >::Type +col(Align & me, + TPosition _pos) +{ + return value(cols(me), _pos); +} + +template +inline typename Col const>::Type +col(Align const & me, + TPosition _pos) +{ + return value(cols(me), _pos); +} + +// ---------------------------------------------------------------------------- +// Function detach() +// ---------------------------------------------------------------------------- + +template +inline void +detach(Align & me) +{ + typedef Align TAlign; + typedef typename Rows::Type TRows; + typedef typename Iterator::Type TRowsIterator; + + TRowsIterator it = begin(rows(me)); + TRowsIterator it_end = end(rows(me)); + + while (it != it_end) + { + detach(*it); + ++it; + } +} + +// ---------------------------------------------------------------------------- +// Function write() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#write + * @deprecated Old-style I/O. + * @brief Writing of Gaps to Streams in human-readable format. + * + * @signature void write(stream, align); + * + * @param[in,out] stream The Stream to write to. + * @param[in] align The Align object to write out. + */ + +template +inline void +write(TFile & target, + Align const & source) +{ + typedef Align const TAlign; + typedef typename Row::Type TRow; + typedef typename Position::Type>::Type TRowsPosition; + typedef typename Position::Type TPosition; + + TRowsPosition row_count = length(rows(source)); + TPosition begin_ = 0; + TPosition end_ = std::min(length(row(source, 0)), length(row(source, 1))); + + unsigned int baseCount = 0; + unsigned int leftSpace = 6; + while (begin_ < end_) + { + unsigned int windowSize_ = 50; + if ((begin_ + windowSize_) > end_) + windowSize_ = end_ - begin_; + + // Print header line + char buffer[20]; + int len = snprintf(buffer, 20, "%7u", (unsigned)baseCount); + write(target, buffer, len); + baseCount += windowSize_; + writeValue(target, ' '); + for (TPosition i = 1; i <= windowSize_; ++i) + { + if ((i % 10) == 0) + writeValue(target, ':'); + else if ((i % 5) == 0) + writeValue(target, '.'); + else + writeValue(target, ' '); + } + writeValue(target, ' '); + writeValue(target, '\n'); + + // Print sequences + for (TRowsPosition i = 0; i < 2 * row_count - 1; ++i) + { + for (unsigned int j = 0; j < leftSpace + 2; ++j) + writeValue(target, ' '); + if ((i % 2) == 0) + { + TRow & row_ = row(source, i / 2); + typedef typename Iterator::Type const, Standard>::Type TIter; + TIter begin1_ = iter(row_, begin_); + TIter end1_ = iter(row_, begin_ + windowSize_); + for (; begin1_ != end1_; ++begin1_) + { + if (isGap(begin1_)) + writeValue(target, gapValue()); + else + writeValue(target, getValue(begin1_)); + } + } + else + { + for (unsigned int j = 0; j < windowSize_; ++j) + { + if ((!isGap(row(source, (i - 1) / 2), begin_ + j)) && + (!isGap(row(source, (i + 1) / 2), begin_ + j)) && + (row(source, (i - 1) / 2)[begin_ + j] == row(source, (i + 1) / 2)[begin_ + j])) + { + writeValue(target, '|'); + } + else + { + writeValue(target, ' '); + } + } + } + writeValue(target, '\n'); + } + writeValue(target, '\n'); + begin_ += 50; + } + writeValue(target, '\n'); +} + +// ---------------------------------------------------------------------------- +// Function clearClipping() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#clearClipping + * @brief Clear clipping on all rows. + * + * @signature void clearClipping(align); + * + * @param[in,out] align Align object to clear clippings of. + */ + +// TODO(holtgrew): Undocumented. + +template +inline void +clearClipping(Align & align_) +{ + typedef typename Rows >::Type TRows; + typedef typename Iterator::Type TRowsIterator; + + for (TRowsIterator it = begin(rows(align_)); it != end(rows(align_)); goNext(it)) + clearClipping(*it); +} + +// ---------------------------------------------------------------------------- +// Function operator<<() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#operator<< + * @brief Stream-output for Align objects. + * + * @signature TStream operator<<(stream, align); + * + * @param[in,out] stream std::ostream to write to. + * @param[in] align Align object to write out. + * + * @return TStream Reference to stream after output of align. + */ + +// stream operators + +template +inline TStream & +operator<<(TStream & target, + Align const & source) +{ + typename DirectionIterator::Type it = directionIterator(target, Output()); + write(it, source); + return target; +} + +// ---------------------------------------------------------------------------- +// Function setStrings() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#setStrings + * @brief Loads the sequences of a string set into an alignment. + * + * @signature void setStrings(align, stringSet); + * + * @param[in,out] align Align object to set underlying sequence of. + * @param[in] stringSet The @link StringSet @endlink with the data. + */ + +template +inline void +setStrings(Align & me, + StringSet & stringset) +{ + typedef Align TAlign; + typedef StringSet TStringset; + + typedef typename Rows::Type TRows; + typedef typename Iterator::Type TRowsIterator; + typedef typename Size::Type TStringsetSize; + + clear(me.data_rows); + resize(me.data_rows, length(stringset)); + TRowsIterator it = begin(rows(me)); + TStringsetSize stringset_length = length(stringset); + for (TStringsetSize i = 0; i < stringset_length; ++i) + { + setSource(*it, value(stringset, i)); + ++it; + } +} + +// ---------------------------------------------------------------------------- +// Function clearGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#clearGaps + * @brief Clear gaps of all Align rows. + * + * @signature void clearGaps(align); + * + * @param[in] align The Align object to clear all all gaps from. + */ + +template +inline void +clearGaps(Align & me) +{ + typedef Align TAlign; + typedef typename Rows::Type TRows; + typedef typename Iterator::Type TRowsIterator; + + for (TRowsIterator it = begin(rows(me)); it != end(rows(me)); goNext(it)) + clearGaps(*it); +} + +// ---------------------------------------------------------------------------- +// Function stringSet() +// ---------------------------------------------------------------------------- + +/*! + * @fn Align#stringSet + * @brief Return string set with all ungapped sequences. + * + * @signature TStringSet stringSet(align); + * + * @param[in] align Align object to get sequences of. + * + * @return TStringSet The set of ungapped sequences (Metafunction: @link Align#StringSetType @endlink). + */ + +template +inline typename StringSetType >::Type +stringSet(Align & me) +{ + typedef Align TAlign; + typedef typename StringSetType::Type TStringSet; + + typedef typename Rows::Type TRows; + typedef typename Iterator::Type TRowsIterator; + + TStringSet ss; + + for (TRowsIterator it = begin(rows(me)); it != end(rows(me)); goNext(it)) + appendValue(ss, source(*it)); + return ss; +} + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool operator==(Align const & lhs, + Align const & rhs) +{ + if (length(lhs.data_rows) != length(rhs.data_rows)) + return false; + typedef typename Align::TGaps TGaps; + typedef typename Iterator::Type TIter; + for (unsigned i = 0; i < length(rhs.data_rows); ++i) + for (TIter itL = begin(lhs.data_rows[i], Rooted()), itR = begin(rhs.data_rows[i], Rooted()); !atEnd(itL); goNext(itL), goNext(itR)) + if (*itL != *itR) + return false; + return true; +} + +// ---------------------------------------------------------------------------- +// Function operator!=() +// ---------------------------------------------------------------------------- + +template +inline bool operator!=(Align const & lhs, + Align const & rhs) +{ + return !(lhs == rhs); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_BASE_H_ diff --git a/seqan/align/align_cols.h b/seqan/align/align_cols.h new file mode 100644 index 0000000..00b625b --- /dev/null +++ b/seqan/align/align_cols.h @@ -0,0 +1,429 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// AlignCols is a wrapper around Align that allows the virtual access to the +// rows of an alignment. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class AlignCols +// ---------------------------------------------------------------------------- + +/*! + * @class AlignCols + * @implements EqualityComparableConcept + * @implements RandomAccessContainerConcept + * @headerfile + * @brief Pseudo columns container for row-based Align class. + * + * @signature template + * class AlignCols; + * + * @tparam TAlign The Align type. + */ + +template +struct AlignCols +{ + // TODO(holtgrew): Do we need this mutable? + mutable TAlign * data_align; + + AlignCols() : + data_align(0) + {} + + + AlignCols(TAlign & align) : data_align(&align) + {} + + template + inline typename Value::Type + operator[](TPosition _pos) + { + return value(*this, _pos); + } + + template + inline typename Value::Type + operator[](TPosition _pos) const + { + return value(*this, _pos); + } +}; + +// ---------------------------------------------------------------------------- +// Specialization AlignCols +// ---------------------------------------------------------------------------- + +template +struct AlignColIterator; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Host +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Add HostedTypeConcept and make AlignCols object implement the concept. + +template +struct Host > +{ + typedef TAlign Type; +}; +template +struct Host const> +{ + typedef TAlign Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction AlignColIterator +// ---------------------------------------------------------------------------- + +template +struct Iterator, TIteratorSpec> +{ + typedef Iter > Type; +}; +template +struct Iterator const, TIteratorSpec> +{ + typedef Iter > Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +// Iterator is also used as Value + +template +struct Value >: + Iterator, Standard> +{}; + +template +struct Value const>: + Iterator const, Standard> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Size +// ---------------------------------------------------------------------------- + +template +struct Size >: + Size::Type> +{}; + +template +struct Size const>: + Size::Type> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Position +// ---------------------------------------------------------------------------- + +template +struct Position >: + Position::Type> +{}; + +template +struct Position const>: + Position::Type> +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function host() +// ---------------------------------------------------------------------------- + +template +inline typename Host >::Type & +host(AlignCols & me) +{ + SEQAN_ASSERT(me.data_align != 0); + return *me.data_align; +} + +template +inline typename Host const>::Type & +host(AlignCols const & me) +{ + SEQAN_ASSERT(me.data_align != 0); + return *me.data_align; +} + +// ---------------------------------------------------------------------------- +// Function iter() +// ---------------------------------------------------------------------------- + +/*! + * @fn AlignCols#iter + * @headerfile + * @brief Iterator to the item at the given position in the alignment columns. + * + * @signature TIterator iter(cols, pos[, tag]); + * + * @param[in] cols The AlignCols object to get the iterator for. + * @param[in] pos The position to get the iterator for. + * @param[in] tag The tag to pick the type of the iterator. + * + * @return TIterator The resulting iterator. If TTag is the type of tag and TAlignCols the + * type of cols then TIterator is of the type Iterator<TAlignCols, + * TTag>::Type. + * + * @section Remarks + * + * If pos is out of range then the iterator is invalid. + */ + +template +inline typename Iterator, Tag const>::Type +iter(AlignCols & me, + TPosition pos_, + Tag const) +{ + return typename Iterator, Tag const>::Type(host(me), pos_); +} + +template +inline typename Iterator const, Tag const>::Type +iter(AlignCols const & me, + TPosition pos_, + Tag const) +{ + return typename Iterator const, Tag const>::Type(host(me), pos_); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +/*! + * @fn AlignCols#value + * @headerfile + * @brief Returns AlignCols value at a position. + * + * @signature TColumn value(alignCols, pos); + * + * @return TColumn The column, as determined by Value metafunction. + */ + +template +inline typename Value >::Type +value(AlignCols & me, + TPosition _pos) +{ + return iter(me, _pos); +} + +template +inline typename Value const>::Type +value(AlignCols const & me, + TPosition _pos) +{ + return iter(me, _pos); +} + +// ---------------------------------------------------------------------------- +// Function beginPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position::Type +_beginPositionAlignCols(TAlignCols const & me) +{ + typedef typename Host::Type TAlign; + typename Position::Type>::Type _i = length(rows(host(me))); + + if (!_i) + { + return 0; + } + + --_i; + typename Position::Type _pos = beginPosition(row(host(me), _i)); + + while (_i > 0) + { + --_i; + typename Position::Type _pos2 = beginPosition(row(host(me), _i)); + if (_pos2 < _pos) + { + _pos = _pos2; + } + } + return _pos; +} + +template +inline typename Position >::Type +beginPosition(AlignCols const & me) +{ + return _beginPositionAlignCols(me); +} + +template +inline typename Position >::Type +beginPosition(AlignCols & me) +{ + return _beginPositionAlignCols(me); +} + +// ---------------------------------------------------------------------------- +// Function begin() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator, Tag const>::Type +begin(AlignCols & me, + Tag const tag_) +{ + return iter(me, beginPosition(me), tag_); +} + +template +inline typename Iterator const, Tag const>::Type +begin(AlignCols const & me, + Tag const tag_) +{ + return iter(me, beginPosition(me), tag_); +} + +// ---------------------------------------------------------------------------- +// Function endPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position::Type +_endPositionAlignCols(TAlignCols const & me) +{ + typedef typename Host::Type TAlign; + + typename Position::Type>::Type _i = length(rows(host(me))); + typename Position::Type _pos = 0; + + while (_i > 0) + { + --_i; + typename Position::Type _pos2 = endPosition(row(host(me), _i)); + if (_pos2 > _pos) + { + _pos = _pos2; + } + } + return _pos; +} + +template +inline typename Position >::Type +endPosition(AlignCols & me) +{ + return _endPositionAlignCols(me); +} + +template +inline typename Position const>::Type +endPosition(AlignCols const & me) +{ + return _endPositionAlignCols(me); +} + +// ---------------------------------------------------------------------------- +// Function end() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator, Tag const>::Type +end(AlignCols & me, + Tag const tag_) +{ + return iter(me, endPosition(me), tag_); +} + +template +inline typename Iterator const, Tag const>::Type +end(AlignCols const & me, + Tag const tag_) +{ + return iter(me, endPosition(me), tag_); +} + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +template +inline typename Size >::Type +length(AlignCols const & me) +{ + return endPosition(me) - beginPosition(me); +} + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool +operator==(AlignCols const & left, + AlignCols const & right) +{ + return left.data_align == right.data_align; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_COLS_H_ diff --git a/seqan/align/align_config.h b/seqan/align/align_config.h new file mode 100644 index 0000000..b76e683 --- /dev/null +++ b/seqan/align/align_config.h @@ -0,0 +1,395 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Tobias Rausch +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class AlignConfig +// ---------------------------------------------------------------------------- + +/*! + * @class AlignConfig + * @headerfile + * @brief Indication of whether begin/end gaps are free for DP alignment algorithms. + * + * @signature template + * struct AlignConfig; + * + * @tparam TOP Whether or not the begin gaps in the vertical sequence are free. + * @tparam LEFT Whether or not the begin gaps in the horizontal sequence are free. + * @tparam RIGHT Whether or not the end gaps in the horizontal sequence are free. + * @tparam BOTTOM Whether or not the end gap sin the vertical sequence are free. + * @tparam TSpec Tag for specializing the AlignConfig object (default: Default). + * + * Used in the DP alignment algorithms to configure the begin/end gap free-nes. + * + * @see globalAlignment + * + * @section Specialization List + * + * The following gives an (incomplete) list of useful AlignConfig specializations. + * + *
+ *
AlignConfig<false, false, false, false>
+ *
ordinary global alignment
+ *
AlignConfig<true, false, false, true>
+ *
semiglobal alignment, free begin and end gaps in second/vertical sequence
+ *
AlignConfig<false, true, true, false>
+ *
semiglobal alignment, free begin and end gaps in first/horizontal sequence
+ *
AlignConfig<false, true, false, true>
+ *
overlap alignment with second/vertical sequence overhanging to the left of first/horizontal
+ *
AlignConfig<true, false, true, false>
+ *
overlap alignment with first/horizontal sequence overhanging to the left of second/vertical
+ *
AlignConfig<false, true, false, false>
+ *
free begin gaps in second/vertical sequence only
+ *
AlignConfig<false, false, true, false>
+ *
free end gaps in second/vertical sequence only
+ *
+ */ + +template +class AlignConfig +{}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// TODO(holtgrew): Make this follow the header structure. + +template +inline void +_initFirstColumn(AlignConfig const, + TElement& element, + TCost const cost) +{ + element = cost; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_initFirstColumn(AlignConfig const, + TElement& element, + TCost const) +{ + element = 0; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_initFirstRow(AlignConfig const, + TElement& element, + TCost const cost) +{ + element = cost; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_initFirstRow(AlignConfig const, + TElement& element, + TCost const) +{ + element = 0; +} + +////////////////////////////////////////////////////////////////////////////// + + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastRow(AlignConfig const, + TValue1&, + TIndex1&, + TValue2 const, + TIndex2 const) +{ + // Nop +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastRow(AlignConfig const, + TValue1& maxValue, + TIndex1& maxIndex, + TValue2 const val, + TIndex2 const index) +{ + if (val > maxValue[0]) { + maxValue[0] = val; + maxIndex[0] = index; + } +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastColumn(AlignConfig const, + TValue1& maxValue, + TIndex1&, + TColumn const& column) +{ + maxValue[1] = column[length(column) - 1]; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastColumn(AlignConfig const, + TValue1& maxValue, + TIndex1& maxIndex, + TColumn const& column) +{ + typedef typename Size::Type TSize; + typedef typename Iterator::Type TColIter; + TSize limit = length(column) - 1; + maxValue[1] = column[limit]; + TColIter itCol = begin(column, Standard()); + TColIter itColEnd = end(column, Standard()); + for(TSize i = 0;itCol != itColEnd; ++i, ++itCol) { + if (*itCol > maxValue[1]) { + maxValue[1] = *itCol; + maxIndex[1] = i; + } + } +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline TScoreValue +_maxOfAlignment(AlignConfig const, + TValue& maxValue, + TIndex&, + TSize const, + TSize const) +{ + return maxValue[1]; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline TScoreValue +_maxOfAlignment(AlignConfig const, + TValue& maxValue, + TIndex& maxIndex, + TSize const len1, + TSize const) +{ + maxIndex[0] = len1; + return maxValue[1]; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline TScoreValue +_maxOfAlignment(AlignConfig const, + TValue& maxValue, + TIndex& maxIndex, + TSize const, + TSize const len2) +{ + maxIndex[1] = len2; + return maxValue[0]; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline TScoreValue +_maxOfAlignment(AlignConfig const, + TValue& maxValue, + TIndex& maxIndex, + TSize const len1, + TSize const len2) +{ + // Find the maximum + if (maxValue[1] > maxValue[0]) maxIndex[0] = len1; + else maxIndex[1] = len2; + return (maxValue[0] > maxValue[1]) ? maxValue[0] : maxValue[1]; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastColumn(AlignConfig const, + TValue1& maxValue, + TIndex1& maxIndex, + TValue2 const val, + TIndex2 const row, + TIndex2 const col) +{ + maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastColumn(AlignConfig const, + TValue1& maxValue, + TIndex1& maxIndex, + TValue2 const val, + TIndex2 const row, + TIndex2 const col) +{ + if (val > maxValue[1]) {maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col; } +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastRow(AlignConfig const, + TValue1& maxValue, + TIndex1& maxIndex, + TValue2 const val, + TIndex2 const row, + TIndex2 const col) +{ + maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +_lastRow(AlignConfig const, + TValue1& maxValue, + TIndex1& maxIndex, + TValue2 const val, + TIndex2 const row, + TIndex2 const col) +{ + if (val > maxValue[0]) {maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col; } +} + + +////////////////////////////////////////////////////////////////////////////// + +template +inline bool +_configValueTop(AlignConfig const) +{ + return true; +} + +template +inline bool +_configValueTop(AlignConfig const) +{ + return false; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline bool +_configValueLeft(AlignConfig const) +{ + return true; +} + +template +inline bool +_configValueLeft(AlignConfig const) +{ + return false; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline bool +_configValueRight(AlignConfig const) +{ + return true; +} + +template +inline bool +_configValueRight(AlignConfig const) +{ + return false; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline bool +_configValueBottom(AlignConfig const) +{ + return true; +} + +template +inline bool +_configValueBottom(AlignConfig const) +{ + return false; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_CONFIG_H_ diff --git a/seqan/align/align_interface_wrapper.h b/seqan/align/align_interface_wrapper.h new file mode 100644 index 0000000..177d0ae --- /dev/null +++ b/seqan/align/align_interface_wrapper.h @@ -0,0 +1,179 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_ALIGN_INTERFACE_WRAPPER_H_ +#define INCLUDE_SEQAN_ALIGN_ALIGN_INTERFACE_WRAPPER_H_ + +namespace seqan +{ + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _alignWrapperSequential(); Score; StringSet vs. StringSet +// ---------------------------------------------------------------------------- + +template +inline auto +_alignWrapperSequential(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + TAlignConfig const & config, + TGapModel const & /*gaps*/) + +{ + String results; + resize(results, length(stringsV)); + + auto zipCont = makeZipView(results, stringsH, stringsV); + forEach(zipCont, + [&] (auto tuple) + { + using namespace seqan; + DPScoutState_ dpScoutState; + String > traceSegments; // Dummy segments. + std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, + std::get<1>(tuple), std::get<2>(tuple), scoringScheme, + config, TGapModel()); + }); + return results; +} + +// ---------------------------------------------------------------------------- +// Function _alignWrapperSequential(); Score; String vs. StringSet +// ---------------------------------------------------------------------------- + +template +inline auto +_alignWrapperSequential(TString1 const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + TAlignConfig const & config, + TGapModel const & /*gaps*/) + +{ + String results; + resize(results, length(stringsV)); + + auto zipCont = makeZipView(results, stringsV); + forEach(zipCont, + [&] (auto tuple) + { + using namespace seqan; + DPScoutState_ dpScoutState; + String > traceSegments; // Dummy segments. + std::get<0>(tuple) = _setUpAndRunAlignment(traceSegments, dpScoutState, stringH, std::get<1>(tuple), + scoringScheme, config, TGapModel()); + }); + return results; +} + +// ---------------------------------------------------------------------------- +// Function _alignWrapperSequential(); Gaps +// ---------------------------------------------------------------------------- + +template +inline auto +_alignWrapperSequential(StringSet, TSetSpecH> & gapSeqSetH, + StringSet, TSetSpecV> & gapSeqSetV, + Score const & scoringScheme, + TAlignConfig const & config, + TGapModel const & /*gaps*/) + +{ + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + + String results; + resize(results, length(gapSeqSetH)); + + auto zipCont = makeZipView(results, gapSeqSetH, gapSeqSetV); + forEach(zipCont, + [&] (auto tuple) + { + using namespace seqan; + String trace; + DPScoutState_ dpScoutState; + std::get<0>(tuple) = _setUpAndRunAlignment(trace, dpScoutState, source(std::get<1>(tuple)), + source(std::get<2>(tuple)), scoringScheme, config, + TGapModel()); + _adaptTraceSegmentsTo(std::get<1>(tuple), std::get<2>(tuple), trace); + }); + return results; +} + +// ---------------------------------------------------------------------------- +// Function _alignWrapper() +// ---------------------------------------------------------------------------- + +template +inline auto _alignWrapper(TArgs && ...args) +{ +#ifdef SEQAN_SIMD_ENABLED + return _alignWrapperSimd(std::forward(args)...); +#else + return _alignWrapperSequential(std::forward(args)...); +#endif +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_ALIGN_ALIGN_INTERFACE_WRAPPER_H_ diff --git a/seqan/align/align_iterator_base.h b/seqan/align/align_iterator_base.h new file mode 100644 index 0000000..4eef6b5 --- /dev/null +++ b/seqan/align/align_iterator_base.h @@ -0,0 +1,527 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== + +#ifndef SEQAN_HEADER_ALIGN_ITERATOR_BASE_H +#define SEQAN_HEADER_ALIGN_ITERATOR_BASE_H + +namespace seqan +{ + +////////////////////////////////////////////////////////////////////////////// +// Align Iterator for Gaps alignment +////////////////////////////////////////////////////////////////////////////// + +// TODO(holtgrew): Extend class Iter? +/*! + * @class AlignColIterator + * @extends Iter + * @headerfile + * @brief Iterator for alignment columns. + * + * @signature template + * class Iter >; + * + * @tparam TAlign Align object to iterate columns of. + * @tparam TSpec Tag for specializing the class further. + */ + +template +class Iter > +{ +public: + typedef typename Rows::Type TRows; + typedef typename Row::Type TRow; + typedef typename Iterator::Type TRowIterator; + typedef typename Position::Type TRowPosition; + typedef String TIterators; + + TAlign * data_host; + TIterators data_iterators; + +public: + Iter() + { + } + Iter(TAlign & _align): + data_host(& _align) + { + typename Position::Type _i = length(rows(_align)); + resize(data_iterators, _i, Exact()); + } + Iter(TAlign & _align, TRowPosition _pos): + data_host(& _align) + { + typename Position::Type _i = length(rows(_align)); + resize(data_iterators, _i, Exact()); + + while (_i > 0) + { + --_i; + data_iterators[_i] = iter(row(_align, _i), _pos); + } + } + Iter(Iter const & _other): + data_host(_other.data_host), + data_iterators(_other.data_iterators) + { + } + ~Iter() + { + } + + Iter const & + operator = (Iter const & _other) + { + data_host = _other.data_host; + data_iterators = _other.data_iterators; + return *this; + } +//____________________________________________________________________________ +}; + +////////////////////////////////////////////////////////////////////////////// + +// TODO(holtgrew); Document as dox/hosted? + +template +inline TAlign & +host(Iter > & me) +{ + return *me.data_host; +} +template +inline TAlign & +host(Iter > const & me) +{ + return *me.data_host; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +setHost(Iter > & me, TAlign & _host) +{ + me.data_host = & _host; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Cols::Type +container(Iter > & me) +{ + return cols(*me.data_host); +} +template +inline typename Cols::Type +container(Iter > const & me) +{ + return cols(*me.data_host); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +goNext(Iter > & me) +{ + typedef typename Row::Type TRow; + typedef typename Iterator::Type TRowIterator; + typedef String TIterators; + typedef typename Iterator::Type TIteratorsIterator; + + TIteratorsIterator _it = begin(me.data_iterators); + TIteratorsIterator _it_end = end(me.data_iterators); + + while (_it != _it_end) + { + goNext(*_it); + ++_it; + } +} +//____________________________________________________________________________ + +template +inline Iter > & +operator ++(Iter > & me) +{ + goNext(me); + return me; +} +//____________________________________________________________________________ + +template +inline Iter > +operator ++(Iter > & me, int) +{ + Iter > ret = me; + goNext(me); + return ret; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +goPrevious(Iter > & me) +{ + typedef typename Row::Type TRow; + typedef typename Iterator::Type TRowIterator; + typedef String TIterators; + typedef typename Iterator::Type TIteratorsIterator; + + TIteratorsIterator _it = begin(me.data_iterators); + TIteratorsIterator _it_end = end(me.data_iterators); + + while (_it != _it_end) + { + goPrevious(*_it); + ++_it; + } +} +//____________________________________________________________________________ + +template +inline Iter > & +operator --(Iter > & me) +{ + goPrevious(me); + return me; +} +//____________________________________________________________________________ + +template +inline Iter > +operator --(Iter > & me, int) +{ + Iter > ret = me; + goPrevious(me); + return ret; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline bool +operator ==(Iter > & _left, + Iter > & _right) +{ + return getValue(_left.data_iterators, 0) == getValue(_right.data_iterators, 0); +} +template +inline bool +operator ==(Iter > const & _left, + Iter > & _right) +{ + return value(_left.data_iterators, 0) == value(_right.data_iterators, 0); +} +template +inline bool +operator ==(Iter > & _left, + Iter > const & _right) +{ + return value(_left.data_iterators, 0) == value(_right.data_iterators, 0); +} +template +inline bool +operator ==(Iter > const & _left, + Iter > const & _right) +{ + return value(_left.data_iterators, 0) == value(_right.data_iterators, 0); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline bool +operator !=(Iter > & _left, + Iter > & _right) +{ + return value(_left.data_iterators, 0) != value(_right.data_iterators, 0); +} +template +inline bool +operator !=(Iter > const & _left, + Iter > & _right) +{ + return value(_left.data_iterators, 0) != value(_right.data_iterators, 0); +} +template +inline bool +operator !=(Iter > & _left, + Iter > const & _right) +{ + return value(_left.data_iterators, 0) != value(_right.data_iterators, 0); +} +template +inline bool +operator !=(Iter > const & _left, + Iter > const & _right) +{ + return value(_left.data_iterators, 0) != value(_right.data_iterators, 0); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Reference::Type +value(Iter > & me, + TPosition pos_) +{ + return value(me.data_iterators[pos_]); +} +template +inline typename Reference::Type +value(Iter > const & me, + TPosition pos_) +{ + return value(me.data_iterators[pos_]); +} +////////////////////////////////////////////////////////////////////////////// + +template +inline typename GetValue::Type +getValue(Iter > & me, + TPosition pos_) +{ + return getValue(me.data_iterators[pos_]); +} +template +inline typename GetValue::Type +getValue(Iter > const & me, + TPosition pos_) +{ + return getValue(me.data_iterators[pos_]); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +assignValue(Iter > & me, + TPosition pos_, + TValue & val) +{ + return assignValue(me.data_iterators[pos_], val); +} +template +inline void +assignValue(Iter > & me, + TPosition pos_, + TValue const & val) +{ + return assignValue(me.data_iterators[pos_], val); +} +template +inline void +assignValue(Iter > const & me, + TPosition pos_, + TValue & val) +{ + return assignValue(me.data_iterators[pos_], val); +} +template +inline void +assignValue(Iter > const & me, + TPosition pos_, + TValue const & val) +{ + return assignValue(me.data_iterators[pos_], val); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +moveValue(Iter > & me, + TPosition pos_, + TValue & val) +{ + return moveValue(me.data_iterators[pos_], val); +} +template +inline void +moveValue(Iter > & me, + TPosition pos_, + TValue const & val) +{ + return moveValue(me.data_iterators[pos_], val); +} +template +inline void +moveValue(Iter > const & me, + TPosition pos_, + TValue & val) +{ + return moveValue(me.data_iterators[pos_], val); +} +template +inline void +moveValue(Iter > const & me, + TPosition pos_, + TValue const & val) +{ + return moveValue(me.data_iterators[pos_], val); +} + +////////////////////////////////////////////////////////////////////////////// + +//??? TODO +//disabled since GapsIterator has no operator - and + +/* +template +inline Iter > & +operator +=(Iter > & me, + TSize size) +{ + typedef typename Row::Type TRow; + typedef typename Iterator::Type TRowIterator; + typedef String TIterators; + typedef typename Iterator::Type TIteratorsIterator; + + TIteratorsIterator _it = begin(me.data_iterators); + TIteratorsIterator _it_end = end(me.data_iterators); + + while (_it != _it_end) + { + *_it += size; + ++_it; + } + return me; +} + + +////////////////////////////////////////////////////////////////////////////// + +template +inline Iter > +operator +(Iter > & me, + TSize size) +{ + Iter > ret = me; + me += size; + return me; +} +template +inline Iter > +operator +(Iter > const & me, + TSize size) +{ + Iter > ret = me; + me += size; + return me; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline Iter > & +operator -=(Iter > & me, + TSize size) +{ + typedef typename Row::Type TRow; + typedef typename Iterator::Type TRowIterator; + typedef String TIterators; + typedef typename Iterator::Type TIteratorsIterator; + + TIteratorsIterator _it = begin(me.data_iterators); + TIteratorsIterator _it_end = end(me.data_iterators); + + while (_it != _it_end) + { + *_it -= size; + ++_it; + } + return me; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline Iter > +operator -(Iter > & me, + TSize size) +{ + Iter > ret = me; + me -= size; + return me; +} +template +inline Iter > +operator -(Iter > const & me, + TSize size) +{ + Iter > ret = me; + me -= size; + return me; +} + +//____________________________________________________________________________ + +template +inline typename Difference::Type +operator -(Iter > const & left, + Iter > const & right) +{ + SEQAN_ASSERT_GT(length(left.data_iterators), 0u); + SEQAN_ASSERT_GT(length(right.data_iterators), 0u); + + return (left.data_iterators[0] - right.data_iterators[0]); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Position::Type +position(Iter > & me) +{ + return position(me.data_iterators[0], row(host(me), 0)); +} +template +inline typename Position::Type +position(Iter > const & me) +{ + return position(me.data_iterators[0], row(host(me), 0)); +} +*/ +////////////////////////////////////////////////////////////////////////////// + + + +////////////////////////////////////////////////////////////////////////////// + +}// namespace seqan + +#endif //#ifndef SEQAN_HEADER_... diff --git a/seqan/align/align_metafunctions.h b/seqan/align/align_metafunctions.h new file mode 100644 index 0000000..5ae233c --- /dev/null +++ b/seqan/align/align_metafunctions.h @@ -0,0 +1,115 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Align-specific metafunctions. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Cols +// ---------------------------------------------------------------------------- + +template +struct Cols; + +// ---------------------------------------------------------------------------- +// Metafunction Col +// ---------------------------------------------------------------------------- + +/*! + * @mfn Align#Col + * @headerfile + * @brief The column type for @link Align @endlink objects. + * + * @signature Col::Type + * + * @tparam TAlign The @link Align @endlink object to query for its column type. + * + * @return Type The resulting type. + */ + +template +struct Col : Value::Type> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Rows +// ---------------------------------------------------------------------------- + +template +struct Rows; + +// ---------------------------------------------------------------------------- +// Metafunction Row +// ---------------------------------------------------------------------------- + +template +struct Row : Value::Type> +{}; + +template +struct Row +{ + typedef typename Row::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction StringSetType +// ---------------------------------------------------------------------------- + +template +struct StringSetType; + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_METAFUNCTIONS_H_ diff --git a/seqan/align/align_traceback.h b/seqan/align/align_traceback.h new file mode 100644 index 0000000..6b9ea34 --- /dev/null +++ b/seqan/align/align_traceback.h @@ -0,0 +1,161 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// Author: Tobias Rausch +// ========================================================================== +// AlignTraceback object for storing the alignment traceback results. +// +// The _pump* functions for converting from AlignTrace to Gaps and Fragment +// String objects are defined where Gaps / the Alignment Graph spec is +// defined. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Specialization TraceBack +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Mark as internal with underscore? + +/*! + * @typedef TraceBack + * @headerfile + * @brief Traceback value. + * + * @signature struct TraceBack_; + * @signature typedef SimpleType TraceBack. + * + * The ValueSize of TraceBack is 3. The values are defined in the following way: + * + *
    + *
  • 0 - Diagonal Move
    • + *
  • 1 - Horizontal Move
    • + *
  • 2 - Vertical Move
    • + *
+ */ + +struct TraceBack_ {}; +typedef SimpleType TraceBack; + +template <> struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 3; +}; + +template <> struct BitsPerValue +{ + typedef uint8_t Type; + static const Type VALUE = 2; +}; + +// ---------------------------------------------------------------------------- +// Helper Class AlignTraceback +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Mark as internal with underscore? + +/*! + * @class AlignTraceback + * @headerfile + * @brief Data structure for storing alignment traceback. + * + * @signature template + * struct AlignTraceback; + * + * @tparam TSize Size type to use in the traceback. + */ + +/*! + * @var TSizes AlignTraceback::sizes + * @brief The traceback lengths. + */ + +/*! + * @var TLengths AlignTraceback::tsv + * @brief The traceback lengths. + */ + +template +struct AlignTraceback +{ + // Run lengths in the align matrix. + String sizes; + // Trace values: 0 = diagonal, 1 = horizontal, 2 = vertical. + String tvs; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _alignTracePrint() +// ---------------------------------------------------------------------------- + +// _alignTracePrint: this function is called by various alignment algorithm to build up the alignment during traceback + +template +inline void +_alignTracePrint(AlignTraceback & tb, + TSequenceH const &, + TSequenceV const &, + TId const, + TPos const, + TId const, + TPos const, + TPos const segLen, + TTraceValue const tv) +{ + appendValue(tb.sizes, segLen); + appendValue(tb.tvs, tv); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGN_TRACEBACK_H_ diff --git a/seqan/align/alignment_algorithm_tags.h b/seqan/align/alignment_algorithm_tags.h new file mode 100644 index 0000000..741645a --- /dev/null +++ b/seqan/align/alignment_algorithm_tags.h @@ -0,0 +1,165 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// We put the tag definition into its own header so we can include them +// independently from the algorithms. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Global Alignment Algorithm Tags +// ---------------------------------------------------------------------------- + +/*! + * @defgroup AlignmentAlgorithmTags Alignment Algorithm Tags + * @brief Tags for selecting algorithms. + */ + +// TODO(holtgrew): Rename MyersBitVector to Myers? Clashes with find module at the moment. + +/*! + * @tag AlignmentAlgorithmTags#Gotoh + * @headerfile + * @brief Tag for selecting Gotoh DP algorithm. + * + * @signature struct Gotoh_; + * @signature typedef Tag Gotoh; + */ + +struct Gotoh_; +typedef Tag Gotoh; + +/*! + * @tag AlignmentAlgorithmTags#NeedlemanWunsch + * @headerfile + * @brief Tag for selecting NeedlemanWunsch DP algorithm. + * + * @signature struct Hirschberg_; + * @signature typedef Tag NeedlemanWunsch; + */ + +struct NeedlemanWunsch_; +typedef Tag NeedlemanWunsch; + +/*! + * @tag AlignmentAlgorithmTags#Hirschberg + * @headerfile + * @brief Tag for selecting Hirschberg's DP algorithm. + * + * @signature struct Hirschberg_; + * @signature typedef Tag Hirschberg; + */ + +struct Hirschberg_; +typedef Tag Hirschberg; + +/*! + * @tag AlignmentAlgorithmTags#MyersBitVector + * @headerfile + * @brief Tag for selecting Myers' bit-vector algorithm. + * + * @signature struct MyersBitVector_; + * @signature typedef Tag MyersBitVector; + */ + +struct MyersBitVector_; +typedef Tag MyersBitVector; + +/*! + * @tag AlignmentAlgorithmTags#MyersHirschberg + * @headerfile + * @brief Tag for selecting a combination of Myers' bit-vector algorithm with Hirschberg's algorithm. + * + * @signature struct MyersHirschberg_; + * @signature typedef Tag MyersHirschberg; + */ + +struct MyersHirschberg_; +typedef Tag MyersHirschberg; + +// ---------------------------------------------------------------------------- +// Local Alignment Algorithm Tags +// ---------------------------------------------------------------------------- + +/*! + * @defgroup PairwiseLocalAlignmentAlgorithms Pairwise Local Alignment Algorithms + * @brief Tags for selecting algorithms. + */ + +/*! + * @tag PairwiseLocalAlignmentAlgorithms#SmithWaterman + * @headerfile + * @brief Tag for selecting the Smith-Waterman algorithm. + * + * @signature struct SmithWaterman_; + * @signature typedef Tag SmithWaterman; + */ + +struct SmithWaterman_; +typedef Tag SmithWaterman; + +/*! + * @tag PairwiseLocalAlignmentAlgorithms#WatermanEggert + * @headerfile + * @brief Tag for selecting the Waterman-Eggert algorithm. + * + * @signature struct WatermanEggert_; + * @signature typedef Tag WatermanEggert; + */ + +struct WatermanEggert_; +typedef Tag WatermanEggert; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_ALGORITHM_TAGS_H_ diff --git a/seqan/align/alignment_operations.h b/seqan/align/alignment_operations.h new file mode 100644 index 0000000..fccc61a --- /dev/null +++ b/seqan/align/alignment_operations.h @@ -0,0 +1,149 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Birte Kehr +// ========================================================================== +// Operations on alignments such as integration +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +template +inline void +integrateGaps(Gaps & targetRow, + Gaps const & sourceRow, + TPos const viewPos) +{ + typedef typename Iterator, Standard>::Type TTargetIt; + typedef typename Iterator const, Standard>::Type TSourceIt; + + // This assertion ensures that the number of sequence characters after viewPos is greater than or equal to + // the number of source characters in the clipped infix row. + SEQAN_ASSERT_GEQ(endPosition(targetRow) - toSourcePosition(targetRow, viewPos), + endPosition(sourceRow) - beginPosition(sourceRow)); + + // init iterators + TTargetIt it = iter(targetRow, viewPos); + + // walk through Gaps containers and copy gaps + for (TSourceIt sIt = begin(sourceRow, Standard()), sItEnd = end(sourceRow, Standard()); sIt != sItEnd;) + { + TPos gapSize = countGaps(sIt); + insertGaps(it, gapSize); + goFurther(it, gapSize+1); + goFurther(sIt, gapSize+1); + } +} + +template +inline void +integrateGaps(Gaps & targetRow, + Gaps const & sourceRow) +{ + typename Position::Type viewPos = beginPosition(source(sourceRow)) // correct for infixes + - beginPosition(source(targetRow)) // ... + + beginPosition(sourceRow); // respect source clipping + + integrateGaps(targetRow, sourceRow, toViewPosition(targetRow, viewPos)); +} + +// ---------------------------------------------------------------------------- +// Function integrateAlign() +// ---------------------------------------------------------------------------- + +/*! + * @fn integrateAlign + * @headerfile + * @brief Integrates an alignment into another by copying the gaps. + * + * @signature void integrateAlign(align1, align2[, positions]); + * + * @param[in,out] align1 Target Alignment object into which align2 is to be integrated. + * @param[in] align2 Alignment object that is to be integrated into align1. + * @param[in] positions The integration positions in align1 for all rows (view positions), String of positions. + * + * @section Examples + * + * @include demos/dox/align/integrate_align.cpp + * + * The output is as follows: + * + * @include demos/dox/align/integrate_align.cpp.stdout + */ + +template +void integrateAlign(Align & align, + Align const & infixAlign, + String const & viewPos) +{ + SEQAN_ASSERT_EQ_MSG(length(rows(infixAlign)), length(rows(align)), "Both align objects need same number of rows."); + typedef typename Size >::Type TSize; + //NOTE(h-2): could be parallelized + for (TSize i = 0; i < length(rows(align)); ++i) + integrateGaps(row(align, i), row(infixAlign, i), viewPos[i]); +} + +template +void integrateAlign(Align & align, + Align const & infixAlign) +{ + SEQAN_ASSERT_EQ_MSG(length(rows(infixAlign)), length(rows(align)), "Both align objects need same number of rows."); + typedef typename Size >::Type TSize; + //NOTE(h-2): could be parallelized + for (TSize i = 0; i < length(rows(align)); ++i) + integrateGaps(row(align, i), row(infixAlign, i)); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_ALIGNMENT_OPERATIONS_H_ diff --git a/seqan/align/dp_algorithm_impl.h b/seqan/align/dp_algorithm_impl.h new file mode 100644 index 0000000..39ae3d8 --- /dev/null +++ b/seqan/align/dp_algorithm_impl.h @@ -0,0 +1,1599 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the core of the dp algorithms. +// This is the crucial part of the refactoring of the alignment algorithms. +// It implements - at the moment only a column wise approach - the core +// loop structure for all alignment profiles. We generally differ between an +// unbanded alignment which is very easy, a banded alignment and a special +// case of the banded alignment the Hamming distance, where upper diagonal +// equals lower diagonal. +// +// The unbanded alignment: +// The computation of the unbanded alignment is divided into three parts. +// In the following we refer to a track as the part where the inner loop +// is iterating (in case of column wise navigation a track is equivalent +// to a column). +// First we compute the initial track. Afterwards we continue with all +// inner tracks of the dp matrix and in the end we compute the last track +// separately. This is because all three types have a special property that +// is different from the other track types. +// Each track itself is further divided into three parts, namely the first cell +// the inner cell and the last cell, corresponding to the initial row, +// all inner rows and the last row of a typical dp matrix. This partition of +// the dp matrix allows us to easily change the behavior of different cells +// according to the chosen dp profile at compile time. +// See alignment_dp_meta_info.h to learn about the different meta objects +// that manage the characteristics of each cell of a particular track type. +// +// The banded alignment: +// In the banded alignment we generally divide the dp matrix into the same +// partition as for the unbanded alignment. The only difference is that we, +// additionally add a specific information of how the current track is +// located within the dp matrix. Since we only consider a band we do not +// necessarily span over the full matrix size for a particular column. +// We distinguish between the locations: PartialColumnTop, +// PartialColumnMiddle, PartialColumnBottom and FullColumn (which is the +// default location for unbanded alignments). Each location of the column +// implies a different composition of the cells contained within a +// particular track. Thus, we are able to set different recursion +// directions and tracking informations for each cell independent from the +// runtime. The only difference is that the outer for-loop (iterating over +// the tracks) is split up into three loops. The first loop then only +// iterates over these tracks that are located at the top of the matrix. +// The second for-loop iterates over the tracks that either are of type +// PartialColumnMiddle or FullColumn (wide bands, where the upper diagonal +// begins behind the track where the lower diagonal crosses the last row of +// the dp matrix). And the last for-loop iterates over the tail of the band +// which is located at the PartialColumnBottom. +// +// The Hamming distance: +// In the special case where upper diagonal equals lower diagonal we only +// have to parse one diagonal of the matrix so we have a special +// implementation for that, though it works for all dp profiles. +// +// Restricitons: +// At the moment we have implemented a restriction such that not all bands +// are accepted. If the dp profile consists of the standard global alignment +// algorithm (NeedlemanWunsch or Gotoh), the band is required to go through +// the sink and the source of the dp matrix. If this is not given the +// alignment algorithm is aborted and the score MinValue::VALUE +// is returned. +// There are no further restrictions. +// +// GapCosts: +// Another detail of the new module is the selection of the gap functions, +// which is also now part of the compile time configuration. Whenever an +// algorithm is implemented it would automatically work for both gap +// functions (linear gaps and affine gaps). +// +// Navigation: +// It is possible to a certain degree to change the behavior of how to parse +// through the dp matrix. Using the new navigators one can implement +// different behaviors for different matrices. At the moment we only support +// column wise navigation for full and sparse score matrices and for full +// traceback matrices. Another detail of this navigators comes into account, +// when we want to compute only the score. We actually create a navigator +// for the dp matrix but implemented it this way that it gets never actually +// called when the traceback is disabled. Thus we do not store the traceback +// matrix if it is not necessary. +// +// Traceback: +// The traceback is now implemented as a single function that is used by all +// alignment profiles. Here we prefer the diagonal direction before the +// vertical before the horizontal direction. +// All tracebacks are first stored within the String object +// and afterwards, when the traceback is finished adapted to its given +// target object such as Align, Graph, Fragments, etc. +// +// Tracing: +// We use now an object called DPScout to keep track of the maximal score. +// This object scouts for the best value and can be overloaded to implement +// different strategies of how the score should be traced. Togehter with +// the meta_info file it only traces thus cells that are allowed to be +// traced given the current dp profile. Since this is also a compile time +// property we do not need to track every cell for the global alignment, +// while we do in the local alignment. +// +// Structure: +// The sequences within the matrix are marked as horizontal and vertical +// sequence to determine there orientation within the matrix. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function prepareAlign() +// ---------------------------------------------------------------------------- + +template +inline void +prepareAlign(StringSet > & align, + TSequence const & strH, + StringSet const & setV) +{ + size_t numAlignments = length(setV); + + SEQAN_ASSERT_EQ(length(align), 0u); + SEQAN_ASSERT_GT(numAlignments, 0u); + + resize(align, numAlignments); + for(size_t i = 0; i < numAlignments; ++i) + { + resize(rows(align[i]), 2); + assignSource(row(align[i], 0), strH); + assignSource(row(align[i], 1), setV[i]); + } +} + +// ---------------------------------------------------------------------------- +// Function _checkBandProperties() +// ---------------------------------------------------------------------------- + +// Checks whether the chosen band fits the dp profile. +template +inline bool _checkBandProperties(TSequenceH const & /*seqH*/, + TSequenceV const & /*seqV*/, + DPBandConfig const & /*band*/, + TAlignmentProfile const & /*alignProfile*/) +{ + return true; +} + +template +inline bool _checkBandProperties(TSequenceH const & seqH, + TSequenceV const & seqV, + DPBandConfig const & band, + TAlignmentProfile const & /*alignProfile*/) +{ + typedef typename MakeSigned::Type>::Type TSignedSize; + + // Check if the intersection between band and DP matrix is empty. + if (upperDiagonal(band) < (0 - static_cast(length(seqV))) || + lowerDiagonal(band) > static_cast(length(seqH))) + { + return false; + } + + // If the band begins before the beginning of the horizontal sequence + // then check if free end-gaps are enabled at the beginning of the vertical sequence. + if (upperDiagonal(band) < 0 && !IsFreeEndGap_::VALUE) + return false; + + // If the band begins before the beginning of the vertical sequence + // then check if free end-gaps are enabled at the beginning of the horizontal sequence. + if (lowerDiagonal(band) > 0 && !IsFreeEndGap_::VALUE) + return false; + + // If the band ends behind the end of the vertical sequence + // then check if free end-gaps are enabled at the end of the horizontal sequence. + if (upperDiagonal(band) + static_cast(length(seqV)) < static_cast(length(seqH)) && + !IsFreeEndGap_::VALUE) + { + return false; + } + + // If the band ends behind the end of the horizontal sequence + // then check if free end-gaps are enabled at the end of the vertical sequence. + if (lowerDiagonal(band) + static_cast(length(seqV)) > static_cast(length(seqH)) && + !IsFreeEndGap_::VALUE) + { + return false; + } + + return true; +} + +// ---------------------------------------------------------------------------- +// Function _invalidDPSettings() +// ---------------------------------------------------------------------------- + + +// Checks if the settings for the dp algorithm are valid. +// Returns true if they are valid, false otherwise. +template +inline bool _isValidDPSettings(TSequenceH const & seqH, + TSequenceV const & seqV, + TBand const & band, + TAlignmentProfile const & alignProfile) +{ + // Check if the sequences are empty. + if (empty(seqH) || empty(seqV)) + { + return false; + } + + return _checkBandProperties(seqH, seqV, band, alignProfile); +} + +// ---------------------------------------------------------------------------- +// Function _isBandEnabled() +// ---------------------------------------------------------------------------- + +// Returns true if a band is selected, otherwise false. +template +inline bool +_isBandEnabled(DPBandConfig const & /*band*/) +{ + return IsSameType::VALUE; +} + +// ---------------------------------------------------------------------------- +// Function _computeCell() +// ---------------------------------------------------------------------------- + +// Computes the score and tracks it if enabled. +template +inline void +_computeCell(TDPScout & scout, + TTraceMatrixNavigator & traceMatrixNavigator, + DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + TColumnDescriptor const &, + TCellDescriptor const &, // One of FirstCell, InnerCell or LastCell. + TDPProfile const &) +{ + typedef DPMetaColumn_ TMetaColumn; + assignValue(traceMatrixNavigator, + _computeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, seqHVal, seqVVal, + scoringScheme, typename RecursionDirection_::Type(), + TDPProfile())); + + if (TrackingEnabled_::VALUE) + { + typedef typename LastColumnEnabled_::Type TIsLastColumn; + typedef typename LastRowEnabled_::Type TIsLastRow; + _scoutBestScore(scout, activeCell, traceMatrixNavigator, + TIsLastColumn(), TIsLastRow()); + } +} + +// ---------------------------------------------------------------------------- +// Function _precomputeScoreMatrixOffset() +// ---------------------------------------------------------------------------- + +// Default fallback if scoring scheme is not a matrix. +template +inline TSeqValue const & +_precomputeScoreMatrixOffset(TSeqValue const & seqVal, + TScoringScheme const & /*score*/) +{ + return seqVal; +} + +// ---------------------------------------------------------------------------- +// Function _computeTrack() +// ---------------------------------------------------------------------------- + +// Computes one track of the dp algorithm. A track is defined as the area that is filled by the inner loop and +// iterated by the outer loop. For the column-wise navigation the track is equivalent with the column. +template +inline void +_computeTrack(TDPScout & scout, + TDPScoreMatrixNavigator & dpScoreMatrixNavigator, + TDPTraceMatrixNavigator & dpTraceMatrixNavigator, + TSeqHValue const & seqHValue, + TSeqVValue const & seqVValue, + TSeqVIterator const & seqBegin, + TSeqVIterator const & seqEnd, + TScoringScheme const & scoringScheme, + TColumnDescriptor const &, + TDPProfile const &) +{ + // Set the iterator to the begin of the track. + _goNextCell(dpScoreMatrixNavigator, TColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), FirstCell()); + + // Precompute the row of the scoring matrix for future look-ups. + TSeqHValue tmpSeqH = _precomputeScoreMatrixOffset(seqHValue, scoringScheme); + + // Initilaize SIMD version with multiple end points. + _preInitScoutVertical(scout); + + // Compute the first cell. + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), tmpSeqH, seqVValue, scoringScheme, + TColumnDescriptor(), FirstCell(), TDPProfile()); + + TSeqVIterator iter = seqBegin; + TSeqVIterator itEnd = (seqEnd - 1); + // Compute the inner cells of the current track. + for (; iter != itEnd; ++iter) + { + // Set the iterator to the next cell within the track. + _goNextCell(dpScoreMatrixNavigator, TColumnDescriptor(), InnerCell()); + _goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), InnerCell()); + // Compute the inner cell. + // If we have variable length simd, we need to check if we reached the end of one of the sequences. + // For all other cases, the function returns always false. + if (SEQAN_UNLIKELY(_reachedVerticalEndPoint(scout, iter))) + { + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), tmpSeqH, + sequenceEntryForScore(scoringScheme, container(iter), position(iter)), scoringScheme, + TColumnDescriptor(), LastCell(), TDPProfile()); + _nextVerticalEndPos(scout); + } + else + { + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), tmpSeqH, + sequenceEntryForScore(scoringScheme, container(iter), position(iter)), scoringScheme, + TColumnDescriptor(), InnerCell(), TDPProfile()); + } + _incVerticalPos(scout); + } + // Set the iterator to the last cell of the track. + _goNextCell(dpScoreMatrixNavigator, TColumnDescriptor(), LastCell()); + _goNextCell(dpTraceMatrixNavigator, TColumnDescriptor(), LastCell()); + // Compute the last cell. + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), tmpSeqH, + sequenceEntryForScore(scoringScheme, container(iter), position(iter)), scoringScheme, + TColumnDescriptor(), LastCell(), TDPProfile()); +} + +// ---------------------------------------------------------------------------- +// Function _computeUnbandedAlignmentHelperTerminate() +// ---------------------------------------------------------------------------- + +template +inline bool //TODO(C++11) constexpr +_computeAlignmentHelperCheckTerminate(DPScout_ const & /**/) +{ + return false; +} + +template +inline bool +_computeAlignmentHelperCheckTerminate(DPScout_ > const & s) +{ + return _terminationCriteriumIsMet(s); +} + +// ---------------------------------------------------------------------------- +// Function _computeUnbandedAlignment() +// ---------------------------------------------------------------------------- + +// Computes the standard DP-algorithm. +template +inline void +_computeUnbandedAlignment(TDPScout & scout, + TDPScoreMatrixNavigator & dpScoreMatrixNavigator, + TDPTraceMatrixNavigator & dpTraceMatrixNavigator, + TSequenceH const & seqH, + TSequenceV const & seqV, + TScoringScheme const & scoringScheme, + DPProfile_ const & dpProfile) +{ + typedef typename Iterator::Type TConstSeqHIterator; + typedef typename Iterator::Type TConstSeqVIterator; + + // Initilaize SIMD version with multiple end points. + _preInitScoutHorizontal(scout); + + // ============================================================================ + // PREPROCESSING + // ============================================================================ + + TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); + TConstSeqVIterator seqVEnd = end(seqV, Rooted()); + + SEQAN_ASSERT_GT(length(seqH), 0u); + SEQAN_ASSERT_GT(length(seqV), 0u); + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, 0), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + + // ============================================================================ + // MAIN DP + // ============================================================================ + + TConstSeqHIterator seqHIter = begin(seqH, Rooted()); + TConstSeqHIterator seqHIterEnd = end(seqH, Rooted()) - 1; + for (; seqHIter != seqHIterEnd; ++seqHIter) + { + // We might only select it if SIMD version is available. + if (SEQAN_UNLIKELY(_reachedHorizontalEndPoint(scout, seqHIter))) + { + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + _nextHorizontalEndPos(scout); + } + else + { + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + } + if (_computeAlignmentHelperCheckTerminate(scout)) + { + return; + } + _incHorizontalPos(scout); + } + + // ============================================================================ + // POSTPROCESSING + // ============================================================================ + + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + + // If we compute only the single option. we need to check if there are other possibilities at the end. + // Traceback only from Diagonal, but could also come from vertical or horizontal. + +// for (unsigned i = 0; i < length(recMatrix); ++i) +// { +// std::cout << recMatrix[i]._score << "\t"; +// } +// std::cout << std::endl; +} + +// ---------------------------------------------------------------------------- +// Function _computeBandedAlignment() +// ---------------------------------------------------------------------------- + +// Computes the banded DP-algorithm. +template +inline void +_computeBandedAlignment(TDPScout & scout, + TDPScoreMatrixNavigator & dpScoreMatrixNavigator, + TDPTraceMatrixNavigator & dpTraceMatrixNavigator, + TSequenceH const & seqH, + TSequenceV const & seqV, + TScoringScheme const & scoringScheme, + TBand const & band, + DPProfile_ const & dpProfile) +{ + typedef DPProfile_ TDPProfile; + typedef typename MakeSigned::Type>::Type TSignedSizeSeqH; + typedef typename MakeSigned::Type>::Type TSignedSizeSeqV; + typedef typename Iterator::Type TConstSeqHIterator; + typedef typename Iterator::Type TConstSeqVIterator; + + + // Now we have the problem of not knowing when we are in the last cell. + + // ============================================================================ + // PREPROCESSING + // ============================================================================ + TSignedSizeSeqH seqHlength = static_cast(length(seqH)); + TSignedSizeSeqH seqVlength = static_cast(length(seqV)); + + TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); + TConstSeqVIterator seqVEnd = begin(seqV, Rooted()) - _min(0, _max(-seqVlength, lowerDiagonal(band))); + + // We have to distinguish two band sizes. Some which spans the whole matrix in between and thus who not. + // This can be distinguished, if UpperDiagonal > length(seqV) + LowerDiagonal + + // We start at least at the first position of the horizontal sequence or wherever the lower diagonal begins first. + TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); + + // The horizontal initial phase ends after the upper diagonal but at most after the horizontal sequence, or there is no horizontal initialization phase. + TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); + + // The middle band phase ends after the lower diagonal crosses the bottom of the alignment matrix or after the horizontal sequence if it is smaller. + TConstSeqHIterator seqHIterEndColumnMiddle = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, seqVlength + lowerDiagonal(band))); + // Swap the two iterators if we are in a band that spans over the full column. + if (upperDiagonal(band) > seqVlength + lowerDiagonal(band)) + std::swap(seqHIterEndColumnTop, seqHIterEndColumnMiddle); + + // The bottom band phase ends after the upper diagonal of the band crosses the bottom of the matrix or after the horizontal sequence if it is smaller. + TConstSeqHIterator seqHIterEndColumnBottom = begin(seqH, Rooted()) + _max(0, _min(seqHlength, + upperDiagonal(band) + seqVlength) - 1); + + // The Initial column can be PartialColumnTop which is given if the upper diagonal is >= 0, + // otherwise it only can be PartialColumnMiddle or PartialColumnBottom depending where the lower diagonal is. + + // Check for single initialization cells in InitialColumn and FinalColumn. + if (seqHIterBegin == end(seqH, Rooted()) - 1) + { + // Set the iterator to the begin of the track. + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + // Only one cell + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), + sequenceEntryForScore(scoringScheme, seqH, position(seqHIterBegin)), + sequenceEntryForScore(scoringScheme, seqV, 0), scoringScheme, + MetaColumnDescriptor(), FirstCell(), TDPProfile()); + // we might need to additionally track this point. + if (TrackingEnabled_ >, FirstCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), False()); + return; + } + if (seqHIterEndColumnBottom == begin(seqH, Rooted())) + { + // Set the iterator to the begin of the track. + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + // Only one cell + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), + sequenceEntryForScore(scoringScheme, seqH, 0), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), scoringScheme, + MetaColumnDescriptor(), FirstCell(), TDPProfile()); + // We might need to additionally track this point. + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True()); + return; + } + + if (upperDiagonal(band) < 0) + { + ++seqVBegin; + if (lowerDiagonal(band) > -seqVlength) + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, 0), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + else + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, 0), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + } + else if (lowerDiagonal(band) >= 0) + { + // Set the iterator to the begin of the track. + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + // Should we not just compute the cell? + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), + sequenceEntryForScore(scoringScheme, seqH, position(seqHIterBegin)), + sequenceEntryForScore(scoringScheme, seqV, 0), + scoringScheme, + MetaColumnDescriptor(), FirstCell(), TDPProfile()); + // we might need to additionally track this point. + if (TrackingEnabled_ >, FirstCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), False()); + } + else // Upper diagonal >= 0 and lower Diagonal < 0 + if (lowerDiagonal(band) <= -seqVlength) // The band is bounded by the top and bottom of the matrix. + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, 0), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + else // The band is bounded by the top but not the bottom of the matrix. + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, 0), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + + if (_computeAlignmentHelperCheckTerminate(scout)) + { + return; + } + + // ============================================================================ + // MAIN DP + // ============================================================================ + + TConstSeqHIterator seqHIter = seqHIterBegin; + // Compute the first part of the band, where the band is bounded by the top but not by the bottom of the matrix. + for (; seqHIter != seqHIterEndColumnTop; ++seqHIter) + { + ++seqVEnd; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + if (_computeAlignmentHelperCheckTerminate(scout)) + { + return; + } + } + + // TODO(rmaerker): Check if putting the if-statement before the actual algorithm can speedup the code. + // Check whether the band spans over the full column or not at some point. + if (upperDiagonal(band) > seqVlength + lowerDiagonal(band)) + { + // Compute the second part of the band, where the band is bounded by the top and the bottom of the matrix. + // We might want to track the current cell here, since this is the first cell that crosses the bottom but is + // not part of the FullColumn tracks. + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True()); + for (; seqHIter != seqHIterEndColumnMiddle; ++seqHIter) + { + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + + if (_computeAlignmentHelperCheckTerminate(scout)) + { + return; + } + } + } + else // Compute the second part of the band, where the band is not bounded by the top and bottom of the matrix + { + for (; seqHIter != seqHIterEndColumnMiddle; ++seqHIter) + { + ++seqVBegin; + ++seqVEnd; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + if (_computeAlignmentHelperCheckTerminate(scout)) + { + return; + } + } // We might want to track the current cell here, since this is the first cell that crosses the bottom. + if (TrackingEnabled_ >, LastCell>::VALUE) + { + if (lowerDiagonal(band) + seqVlength < seqHlength) + { + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True()); + } + } + + } + // Compute the third part of the band, where the band, is bounded by the bottom but not by the top of the matrix. + for (; seqHIter != seqHIterEndColumnBottom; ++seqHIter) + { + ++seqVBegin; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + if (_computeAlignmentHelperCheckTerminate(scout)) + { + return; + } + } + + // ============================================================================ + // POSTPROCESSING + // ============================================================================ + + // Check where the last track of the column is located. + if (seqHIter - begin(seqH, Rooted()) < seqHlength - 1) // Case 1: The band ends before the final column is reached. + { + // Set the iterator to the begin of the track. + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), + scoringScheme, + MetaColumnDescriptor(), FirstCell(), TDPProfile()); + // We might need to additionally track this point. + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, False(), True()); + } + else if (seqHIter == end(seqH, Rooted()) - 1) // Case 2: The band ends somewhere in the final column of the matrix. + { + // Case2a: The band ends in the last cell of the final column. + if (upperDiagonal(band) == seqHlength - seqVlength) + { + // Set the iterator to the begin of the track. + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + + _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), + previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), + previousCellVertical(dpScoreMatrixNavigator), + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), + scoringScheme, + MetaColumnDescriptor(), FirstCell(), TDPProfile()); + // we might need to additionally track this point. + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), True()); + } + else // Case2b: At least two cells intersect between the band and the matrix in the final column of the matrix. + { + if (upperDiagonal(band) >= seqHlength) // The band is bounded by the top of the matrix only or by the top and the bottom. + { + if (lowerDiagonal(band) + seqVlength > seqHlength) // The band is bounded by the top of the matrix + { + ++seqVEnd; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + } + else // The band is bounded by the top and the bottom of the matrix. + { + if (lowerDiagonal(band) + seqVlength + 1 > seqHlength) // We have to go into the last cell. + { + ++seqVEnd; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), True()); + } + else + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, 0), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + } + + } + else // The band is bounded by bottom of matrix or completely unbounded. + { + ++seqVBegin; + if (lowerDiagonal(band) + seqVlength <= seqHlength) // The band is bounded by the bottom of the matrix. + { + if (lowerDiagonal(band) + seqVlength == seqHlength) // We have to go into the last cell. + { + ++seqVEnd; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator, True(), True()); + } + else + { + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + } + } + else // The band is unbounded by the matrix. + { + ++seqVEnd; + _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, + sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), + sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin) - 1), + seqVBegin, seqVEnd, scoringScheme, + MetaColumnDescriptor(), dpProfile); + } + + } + } + } +} + +// TODO(rmaerker): This is denbug code only. +//template +//inline void +//_debugBandedAlignment(TDPScout & scout, +// TDPScoreMatrixNavigator & dpScoreMatrixNavigator, +// TDPTraceMatrixNavigator & dpTraceMatrixNavigator, +// TSequenceH const & seqH, +// TSequenceV const & seqV, +// TScoringScheme const & scoringScheme, +// TBand const & band, +// DPProfile_ const & dpProfile) +//{ +// typedef DPProfile_ TDPProfile; +// typedef typename Value::Type TSeqHValue; +// typedef typename Value::Type TSeqVValue; +// typedef typename Iterator::Type TConstSeqHIterator; +// typedef typename Iterator::Type TConstSeqVIterator; +// +// +// String testMatrix; +// resize(testMatrix, (length(seqH) + 1) * (length(seqV)+1)); +// // Now we have the problem of not knowing when we are in the last cell. +// +// // INITIALIZATION +// TConstSeqVIterator seqVBegin = begin(seqV, Standard()) - _min(0, 1+upperDiagonal(band)); +// TConstSeqVIterator seqVEnd = begin(seqV, Standard()) - _min(0, _max(-static_cast(length(seqV)), lowerDiagonal(band))); +// +//// std::cout << "Begin Pos: " << seqVBegin - begin(seqV) << "\n"; +//// std::cout << "End Pos: " << seqVEnd - begin(seqV) << "\n"; +// +// // We have to distinguish two band sizes. Some which spans the whole matrix in between and thus who not. +// // This can be distinguished, if UpperDiagonal > length(seqV) + LowerDiagonal +// +// // We start at the least at the first sequence or wherever the lower diagonal begins first. +// TConstSeqHIterator seqHIterBegin = begin(seqH, Standard()) + _max(0, _min(static_cast(length(seqH) - 1), lowerDiagonal(band))); +// // TODO(rmaerker): Cehck if this assertion is correct. +//// SEQAN_ASSERT_NEQ(seqHIterBegin, end(seqH, Standard())); // The iterator never points to the end of the horizontal sequence. +// +// // The horizontal initial phase ends after the upper diagonal but at most after the horizontal sequence, or there is no horizontal initialization phase. +// TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Standard()) + _min(static_cast(length(seqH))-1, _max(0, upperDiagonal(band))); +// +// // The middle band phase ends after the lower diagonal crosses the bottom of the alignment matrix or after the horizontal sequence if it is smaller. +// TConstSeqHIterator seqHIterEndColumnMiddle = begin(seqH, Standard()) + _min(static_cast(length(seqH))-1, _max(0,static_cast(length(seqV)) + lowerDiagonal(band))); +// // Swap the two iterators if we are in a band that spans over the full column. +// if (upperDiagonal(band) > static_cast(length(seqV)) + lowerDiagonal(band)) +// std::swap(seqHIterEndColumnTop, seqHIterEndColumnMiddle); +// +// // The bottom band phase ends after the upper diagonal of the band crosses the bottom of the matrix or after the horizontal sequence if it is smaller. +// TConstSeqHIterator seqHIterEndColumnBottom = begin(seqH, Standard()) + _max(0, _min(static_cast(length(seqH)), +// upperDiagonal(band) + static_cast(length(seqV))) -1); +// +//// std::cout << "seqHIterBegin Pos H: " << seqHIterBegin - begin(seqH) << "\n"; +//// std::cout << "seqHIterEndColumnTop Pos H: " << seqHIterEndColumnTop - begin(seqH) << "\n"; +//// std::cout << "seqHIterEndColumnMiddle Pos H: " << seqHIterEndColumnMiddle - begin(seqH) << "\n"; +//// std::cout << "seqHIterEndColumnBottom Pos H: " << seqHIterEndColumnBottom - begin(seqH) << "\n"; +//// +//// std::cout << "_activeColIterator Pos: " << dpScoreMatrixNavigator._activeColIterator - begin(*dpScoreMatrixNavigator._ptrDataContainer) << "\n"; +//// std::cout << "_prevColIterator Pos: " << dpScoreMatrixNavigator._prevColIterator - begin(*dpScoreMatrixNavigator._ptrDataContainer) << "\n"; +// +// // The Initial column can be PartialColumnTop which is given if the upper diagonal is >= 0, +// // otherwise it only can be PartialColumnMiddle or PartialColumnBottom depending where the lower diagonal is. +// +// // Have to check for single initialization cells in InitialColumn and FinalColumn. +// if (seqHIterBegin == end(seqH)-1) +// { +// // Set the iterator to the begin of the track. +// _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// // Only one cell +// _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), +// previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), +// previousCellVertical(dpScoreMatrixNavigator), value(seqHIterBegin), TSeqVValue(), scoringScheme, +// MetaColumnDescriptor(), FirstCell(), TDPProfile()); +//// std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n"; +// std::stringstream stream; +// stream << _scoreOfCell(value(dpScoreMatrixNavigator)); +// testMatrix[length(seqH) * length(seqV)] = stream.str(); +// // we might need to additionally track this point. +// if (TrackingEnabled_ >, FirstCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// return; +// } +// if (seqHIterEndColumnBottom == begin(seqH)) +// { +// // Set the iterator to the begin of the track. +// _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// // Only one cell +// _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), +// previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), +// previousCellVertical(dpScoreMatrixNavigator), TSeqHValue(), value(seqVBegin), scoringScheme, +// MetaColumnDescriptor(), FirstCell(), TDPProfile()); +//// std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n"; +// std::stringstream stream; +// stream << _scoreOfCell(value(dpScoreMatrixNavigator)); +// testMatrix[length(seqH) * length(seqV)] = stream.str(); +// // We might need to additionally track this point. +// if (TrackingEnabled_ >, LastCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// return; +// } +// +// if (upperDiagonal(band) < 0) +// { +// ++seqVBegin; +// if (lowerDiagonal(band) > -static_cast(length(seqV))) +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// TSeqHValue(), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, 0, seqVBegin - begin(seqV) + 1, testMatrix); +// else +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// TSeqHValue(), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, 0, seqVBegin - begin(seqV) + 1, testMatrix); +// } +// else if (lowerDiagonal(band) >= 0) +// { +// // Set the iterator to the begin of the track. +// _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// // Should we not just compute the cell? +// _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), +// previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), +// previousCellVertical(dpScoreMatrixNavigator), value(seqHIterBegin), TSeqVValue(), scoringScheme, +// MetaColumnDescriptor(), FirstCell(), TDPProfile()); +// // we might need to additionally track this point. +//// std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n"; +// int col = lowerDiagonal(band); +// std::stringstream stream; +// stream << _scoreOfCell(value(dpScoreMatrixNavigator)); +// testMatrix[col * (length(seqV) + 1)] = stream.str(); +// if (TrackingEnabled_ >, FirstCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// } +// else // Upper diagonal >= 0 and lower Diagonal < 0 +// if (lowerDiagonal(band) <= -static_cast(length(seqV))) // The band is bounded by the top and bottom of the matrix. +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// TSeqHValue(), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, 0, 0, testMatrix); +// else // The band is bounded by the top but not the bottom of the matrix. +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// TSeqHValue(), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, 0,0, testMatrix); +// +// +// // RECURSION +// TConstSeqHIterator seqHIter = seqHIterBegin; +// // Compute the first part of the band, where the band is bounded by the top but not by the bottom of the matrix. +// for (;seqHIter != seqHIterEndColumnTop; ++seqHIter) +// { +//// std::cout << value(seqHIter) << ":\t"; +// ++seqVEnd; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, ((seqHIter - begin(seqH)) + 1)*(length(seqV) +1), 0, testMatrix); +// } +// +// // Check whether the band spans over the full column or not at some point. +// if (upperDiagonal(band) > static_cast(length(seqV)) + lowerDiagonal(band)) +// { +// // Compute the second part of the band, where the band is bounded by the top and the bottom of the matrix. +// // We might want to track the current cell here, since this is the first cell that crosses the bottom. +// // TODO(rmaerker): We have to check if the initial column/ row can be tracked!!! +// if (TrackingEnabled_ >, LastCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// for (;seqHIter != seqHIterEndColumnMiddle; ++seqHIter) +// { +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, (seqHIter - begin(seqH) + 1) * (length(seqV) + 1), 0, testMatrix); +// } +// } +// else // Compute the second part of the band, where the band is not bounded by the top and bottom of the matrix +// { +// for (;seqHIter != seqHIterEndColumnMiddle; ++seqHIter) +// { +// ++seqVBegin; +// ++seqVEnd; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, (seqHIter - begin(seqH) +1) * (length(seqV)+1), seqVBegin - begin(seqV), testMatrix); +// } // We might want to track the current cell here, since this is the first cell that crosses the bottom. +// if (TrackingEnabled_ >, LastCell>::VALUE) +// { +// // TODO(rmaerker): This is only a hot fix. +// if (lowerDiagonal(band) + length(seqV) < length(seqH)) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// } +// } +// // Compute the third part of the band, where the band, is bounded by the bottom but not by the top of the matrix. +// for (;seqHIter != seqHIterEndColumnBottom; ++seqHIter) +// { +// ++seqVBegin; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, (seqHIter - begin(seqH) + 1) * (length(seqV) + 1), seqVBegin - begin(seqV), testMatrix); +// } +// +// // Where ends the last cell? +// if(seqHIter - begin(seqH) < static_cast(length(seqH))-1) // Case 1: The band ends before the final column is reached. +// { +// // Set the iterator to the begin of the track. +// _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// +// _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), +// previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), +// previousCellVertical(dpScoreMatrixNavigator), value(seqHIter), value(seqVBegin), scoringScheme, +// MetaColumnDescriptor(), FirstCell(), TDPProfile()); +//// std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n"; +// std::stringstream stream; +// stream << _scoreOfCell(value(dpScoreMatrixNavigator)); +// testMatrix[(seqHIter - begin(seqH) + 1) * (length(seqV) + 1) + length(seqV)] = stream.str(); +// // We might need to additionally track this point. +// if (TrackingEnabled_ >, LastCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// } +// else if(seqHIter == end(seqH)-1) // Case 2: The band ends somewhere in the final column of the matrix. +// { +// if (upperDiagonal(band) == static_cast(length(seqH))-static_cast(length(seqV))) // Case2a: The band ends in the last cell of the final column. // He should be here.... +// { +// // Set the iterator to the begin of the track. +// _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); +// +// _computeCell(scout, dpTraceMatrixNavigator, value(dpScoreMatrixNavigator), +// previousCellDiagonal(dpScoreMatrixNavigator), previousCellHorizontal(dpScoreMatrixNavigator), +// previousCellVertical(dpScoreMatrixNavigator), value(seqHIter), value(seqVBegin), scoringScheme, +// MetaColumnDescriptor(), FirstCell(), TDPProfile()); +//// std::cout << _scoreOfCell(value(dpScoreMatrixNavigator)) << "\n"; +// std::stringstream stream; +// stream << _scoreOfCell(value(dpScoreMatrixNavigator)); +// testMatrix[(length(seqH) * (length(seqV) + 1)) + length(seqV)] = stream.str(); +// // we might need to additionally track this point. +// if (TrackingEnabled_ >, LastCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// } +// else // Case2b: At least two cells intersect between the band and the matrix in the final column of the matrix. +// { +// if (upperDiagonal(band) >= static_cast(length(seqH))) // The band is bounded by the top of the matrix only or by the top and the bottom. +// { +// if (lowerDiagonal(band) + static_cast(length(seqV)) > static_cast(length(seqH))) // The band is bounded by the top of the matrix +// { +// ++seqVEnd; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, length(seqH) * (length(seqV) + 1), 0, testMatrix); +// } +// else // The band is bounded by the top and the bottom of the matrix. +// { +// if (lowerDiagonal(band) + static_cast(length(seqV)) + 1 > static_cast(length(seqH)) ) +// { +// ++seqVEnd; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, length(seqH) * (length(seqV) + 1), 0, testMatrix); +// if (TrackingEnabled_ >, LastCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// } +// else +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), TSeqVValue(), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, length(seqH) * (length(seqV) +1), 0, testMatrix); +// +// } +// +// } +// else // The band is bounded by bottom of matrix or completely unbounded. +// { +// ++seqVBegin; +// if (lowerDiagonal(band) + length(seqV) <= length(seqH)) // The band is bounded by the bottom of the matrix. +// { +// if (lowerDiagonal(band) + length(seqV) == length(seqH)) +// { +// ++seqVEnd; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, length(seqH) * (length(seqV)+1), seqVBegin - begin(seqV), testMatrix); +// if (TrackingEnabled_ >, LastCell>::VALUE) +// _scoutBestScore(scout, _scoreOfCell(value(dpScoreMatrixNavigator)), dpTraceMatrixNavigator); +// } +// else +// { +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, length(seqH) * (length(seqV) + 1), seqVBegin - begin(seqV), testMatrix); +// } +// } +// else // The band is unbounded by the matrix. +// { +// ++seqVEnd; +// _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, +// value(seqHIter), value(seqVBegin-1), seqVBegin, seqVEnd, scoringScheme, +// MetaColumnDescriptor(), dpProfile, length(seqH) * (length(seqV)+1), seqVBegin - begin(seqV), testMatrix); +// } +// +// } +// } +// } +// +// for (unsigned i = 0; i <= length(seqV); ++i) +// { +// for (unsigned j = 0; j <= length(seqH); ++j) +// { +// unsigned pos = j * (length(seqV) + 1) + i; +// //if (!testMatrix[pos].empty()) +// std::cout << testMatrix[pos] << "\t" << std::flush; +// } +// std::cout << std::endl; +// } +// +//} + +// ---------------------------------------------------------------------------- +// Function _computeHammingDistance() +// ---------------------------------------------------------------------------- + +// Computes the Hamming-Distance if the band-size is 1. +template +inline void +_computeHammingDistance(TDPScout & scout, + TDPScoreMatrixNavigator & dpScoreMatrixNavigator, + TDPTraceMatrixNavigator & dpTraceMatrixNavigator, + TSequenceH const & seqH, + TSequenceV const & seqV, + TScoringScheme const & scoringScheme, + TBand const & band, + DPProfile_ const &) +{ + typedef typename MakeSigned::Type>::Type TSignedSizeSeqH; + typedef typename MakeSigned::Type>::Type TSignedSizeSeqV; + typedef typename Iterator::Type TConstSeqHIterator; + typedef typename Iterator::Type TConstSeqVIterator; + typedef typename Value::Type TDPCell; + typedef DPProfile_ TDPProfile; + + // ============================================================================ + // PREPROCESSING + // ============================================================================ + + TSignedSizeSeqH seqHlength = static_cast(length(seqH)); + TSignedSizeSeqH seqVlength = static_cast(length(seqV)); + + TConstSeqHIterator itH = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, upperDiagonal(band))); + TConstSeqHIterator itHEnd = begin(seqH, Rooted()) + _min(seqHlength - 1, upperDiagonal(band) + seqVlength); + + TConstSeqVIterator itV = begin(seqV, Rooted()) + _max(0, _min(seqVlength - 1, -lowerDiagonal(band))); + TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); + + assignValue(dpTraceMatrixNavigator, + _computeScore(value(dpScoreMatrixNavigator), TDPCell(), TDPCell(), TDPCell(), + sequenceEntryForScore(scoringScheme, seqH, position(itH)), + sequenceEntryForScore(scoringScheme, seqV, position(itV)), + scoringScheme, RecursionDirectionZero(), TDPProfile())); + + if (upperDiagonal(band) < 0) + { + if (upperDiagonal(band) == -seqVlength) + { + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + return; + } + else + { + if (TrackingEnabled_ >, InnerCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + } + } + else if (lowerDiagonal(band) > 0) + { + if (lowerDiagonal(band) == seqHlength) + { + if (TrackingEnabled_ >, FirstCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + return; + } + else + { + if (TrackingEnabled_ >, FirstCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + } + } + else + { + if (TrackingEnabled_ >, FirstCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + } + + TDPCell prevDiagonal = value(dpScoreMatrixNavigator); + + // ============================================================================ + // MAIN DP + // ============================================================================ + + while (itH != itHEnd && itV != itVEnd) + { + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + assignValue(dpTraceMatrixNavigator, + _computeScore(value(dpScoreMatrixNavigator), prevDiagonal, TDPCell(), TDPCell(), + sequenceEntryForScore(scoringScheme, seqH, position(itH)), + sequenceEntryForScore(scoringScheme, seqV, position(itV)), + scoringScheme, RecursionDirectionDiagonal(), TDPProfile())); + if (TrackingEnabled_ >, InnerCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + prevDiagonal = value(dpScoreMatrixNavigator); + ++itH; + ++itV; + } + + // ============================================================================ + // POSTPROCESSING + // ============================================================================ + + _goNextCell(dpScoreMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + _goNextCell(dpTraceMatrixNavigator, MetaColumnDescriptor(), FirstCell()); + + assignValue(dpTraceMatrixNavigator, + _computeScore(value(dpScoreMatrixNavigator), prevDiagonal, TDPCell(), TDPCell(), + sequenceEntryForScore(scoringScheme, seqH, position(itH)), + sequenceEntryForScore(scoringScheme, seqV, position(itV)), + scoringScheme, RecursionDirectionDiagonal(), TDPProfile())); + + if (itH == itHEnd) + { + if (itV == itVEnd) // Is in the last cell of final column + { + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + } + if (TrackingEnabled_ >, LastCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + } + else + { + if (TrackingEnabled_ >, InnerCell>::VALUE) + _scoutBestScore(scout, value(dpScoreMatrixNavigator), dpTraceMatrixNavigator); + } +} + +// ---------------------------------------------------------------------------- +// Function _printTracebackMatrix() +// ---------------------------------------------------------------------------- + +template +void _printTracebackMatrix(TTraceMatrix & dpTraceMatrix) +{ + typedef typename Size::Type TSize; + TSize dimH = length(dpTraceMatrix, +DPMatrixDimension_::HORIZONTAL); + TSize dimV = length(dpTraceMatrix, +DPMatrixDimension_::VERTICAL); + + for (unsigned row = 0; row < dimV; ++row) + { + for (unsigned column = 0; column < dimH; ++column) + std::cout << _translateTraceValue(value(dpTraceMatrix, row + column * dimV)) << "\t"; + std::cout << std::endl; + } + std::cout << std::endl; +} + +template +void _printTracebackMatrix(TTraceMatrix & dpTraceMatrix, TPosition const simdLane) +{ + typedef typename Size::Type TSize; + TSize dimH = length(dpTraceMatrix, +DPMatrixDimension_::HORIZONTAL); + TSize dimV = length(dpTraceMatrix, +DPMatrixDimension_::VERTICAL); + + for (unsigned row = 0; row < dimV; ++row) + { + for (unsigned column = 0; column < dimH; ++column) + std::cout << _translateTraceValue(value(dpTraceMatrix, row + column * dimV)[simdLane]) << "\t"; + std::cout << std::endl; + } + std::cout << std::endl; +} + +// ---------------------------------------------------------------------------- +// Function _correctTraceValue() +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, void) +_correctTraceValue(TTraceNavigator &, + DPScout_, TDPScoutSpec> const &) +{ + // Nothing to do. +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +_correctTraceValue(TTraceNavigator &, + DPScout_, TDPScoutSpec> const &) +{ + // Nothing to do. +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, void) +_correctTraceValue(TTraceNavigator & traceNavigator, + DPScout_, TDPScoutSpec> const & dpScout) +{ + _setToPosition(traceNavigator, maxHostPosition(dpScout)); + + if (_verticalScoreOfCell(dpScout._maxScore) == _scoreOfCell(dpScout._maxScore)) + { + value(traceNavigator) &= ~TraceBitMap_::DIAGONAL; + value(traceNavigator) |= TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; + } + else if (_horizontalScoreOfCell(dpScout._maxScore) == _scoreOfCell(dpScout._maxScore)) + { + value(traceNavigator) &= ~TraceBitMap_::DIAGONAL; + value(traceNavigator) |= TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +_correctTraceValue(TTraceNavigator & traceNavigator, + DPScout_, TDPScoutSpec> const & dpScout) +{ + _setToPosition(traceNavigator, maxHostPosition(dpScout)); + TScoreValue cmpV = cmpEq(_verticalScoreOfCell(dpScout._maxScore), _scoreOfCell(dpScout._maxScore)); + TScoreValue cmpH = cmpEq(_horizontalScoreOfCell(dpScout._maxScore), _scoreOfCell(dpScout._maxScore)); + value(traceNavigator) = blend(value(traceNavigator), + value(traceNavigator) & ~TraceBitMap_::DIAGONAL, + cmpV | cmpH); + value(traceNavigator) = blend(value(traceNavigator), + value(traceNavigator) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + cmpV); + value(traceNavigator) = blend(value(traceNavigator), + value(traceNavigator) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmpH); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, void) +_correctTraceValue(TTraceNavigator & traceNavigator, + DPScout_, TDPScoutSpec> const & dpScout) +{ + _setToPosition(traceNavigator, maxHostPosition(dpScout)); + if (isGapExtension(dpScout._maxScore, DynamicGapExtensionVertical())) + { + value(traceNavigator) &= ~TraceBitMap_::DIAGONAL; + value(traceNavigator) |= TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; + } + else if (isGapExtension(dpScout._maxScore, DynamicGapExtensionHorizontal())) + { + value(traceNavigator) &= ~TraceBitMap_::DIAGONAL; + value(traceNavigator) |= TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +_correctTraceValue(TTraceNavigator & traceNavigator, + DPScout_, TDPScoutSpec> const & dpScout) +{ + _setToPosition(traceNavigator, maxHostPosition(dpScout)); + TScoreValue cmpV = isGapExtension(dpScout._maxScore, DynamicGapExtensionVertical()); + TScoreValue cmpH = isGapExtension(dpScout._maxScore, DynamicGapExtensionHorizontal()); + value(traceNavigator) = blend(value(traceNavigator), + value(traceNavigator) & ~TraceBitMap_::DIAGONAL, + cmpV | cmpH); + value(traceNavigator) = blend(value(traceNavigator), + value(traceNavigator) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + cmpV); + value(traceNavigator) = blend(value(traceNavigator), + value(traceNavigator) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmpH); +} + +// ---------------------------------------------------------------------------- +// Function _finishAlignment() +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not >, TScoreValue) +_finishAlignment(TTraceTarget & /*traceSegments*/, + TTraceMatNavigator & /*dpTraceMatrixNavigator*/, + DPScout_, TDPScoutSpec> & dpScout, + TSeqH const & /*seqH*/, + TSeqV const & /*seqV*/, + DPBandConfig const & /*band*/, + DPProfile_ const & /*dpProfile*/) +{ + return maxScore(dpScout); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And >, IsTracebackEnabled_ >, TScoreValue) +_finishAlignment(TTraceTarget & traceSegments, + TTraceMatNavigator & dpTraceMatrixNavigator, + DPScout_, TDPScoutSpec> & scout, + TSeqH const & seqH, + TSeqV const & seqV, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + typedef typename Size::Type TSize; + + for(TSize i = 0; i < length(traceSegments); ++i) + { + _setSimdLane(dpTraceMatrixNavigator, i); + _setSimdLane(scout, i); + + if (IsSingleTrace_::VALUE) + { + _correctTraceValue(dpTraceMatrixNavigator, scout); + } + _computeTraceback(traceSegments[i], dpTraceMatrixNavigator, scout, _hostLengthH(scout, seqH), + _hostLengthV(scout, seqV), band, dpProfile); + } + return maxScore(scout); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And > >, IsTracebackEnabled_ >, TScoreValue) +_finishAlignment(TTraceTarget & traceSegments, + TTraceMatNavigator & dpTraceMatrixNavigator, + DPScout_, TDPScoutSpec> & dpScout, + TSeqH const & seqH, + TSeqV const & seqV, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + if (IsSingleTrace_::VALUE) + _correctTraceValue(dpTraceMatrixNavigator, dpScout); + + _computeTraceback(traceSegments, dpTraceMatrixNavigator, dpScout, seqH, seqV, band, dpProfile); + return maxScore(dpScout); +} + +// ---------------------------------------------------------------------------- +// Function _computeAligmnment() +// ---------------------------------------------------------------------------- + +template +inline typename Value::Type +_computeAlignment(DPContext & dpContext, + TTraceTarget & traceSegments, + TScoutState & scoutState, + TSequenceH const & seqH, + TSequenceV const & seqV, + TScoreScheme const & scoreScheme, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + typedef typename GetDPScoreMatrix >::Type TDPScoreMatrixHost; + typedef typename Value::Type TDPScoreValue; + + typedef typename GetDPTraceMatrix >::Type TDPTraceMatrixHost; + typedef typename Value::Type TTraceValue; + + typedef typename DefaultScoreMatrixSpec_::Type TScoreMatrixSpec; + + typedef DPMatrix_ TDPScoreMatrix; + typedef DPMatrix_ TDPTraceMatrix; + + typedef DPMatrixNavigator_ TDPScoreMatrixNavigator; + typedef DPMatrixNavigator_, NavigateColumnWise> TDPTraceMatrixNavigator; + + typedef typename ScoutSpecForAlignmentAlgorithm_::Type TDPScoutSpec; + typedef DPScout_ TDPScout; + + // Check if current dp settings are valid. If not return infinity value for dp score value. + if (!_isValidDPSettings(seqH, seqV, band, dpProfile)) + return createVector(MinValue::Type>::VALUE); // NOTE(rrahn): In case of non-simd version, createVector returns just a scalar. + + TDPScoreMatrix dpScoreMatrix; + TDPTraceMatrix dpTraceMatrix; + + // TODO(rmaerker): Check whether the matrix allocation can be reduced if upperDiagonal < 0? + setLength(dpScoreMatrix, +DPMatrixDimension_::HORIZONTAL, length(seqH) + 1 - std::max(0, lowerDiagonal(band))); + setLength(dpTraceMatrix, +DPMatrixDimension_::HORIZONTAL, length(seqH) + 1 - std::max(0, lowerDiagonal(band))); + + if (IsSameType::VALUE) + { + setLength(dpScoreMatrix, +DPMatrixDimension_::VERTICAL, length(seqV) + 1); + setLength(dpTraceMatrix, +DPMatrixDimension_::VERTICAL, length(seqV) + 1); + } + else + { + int bandSize = _min(static_cast(length(seqH)), upperDiagonal(band)) - _max(lowerDiagonal(band), -static_cast(length(seqV))) + 1; + setLength(dpScoreMatrix, +DPMatrixDimension_::VERTICAL, _min(static_cast(length(seqV)) + 1, bandSize)); + setLength(dpTraceMatrix, +DPMatrixDimension_::VERTICAL, _min(static_cast(length(seqV)) + 1, bandSize)); + } + + // We set the host to the score matrix and the dp matrix. + setHost(dpScoreMatrix, getDpScoreMatrix(dpContext)); + setHost(dpTraceMatrix, getDpTraceMatrix(dpContext)); + + resize(dpScoreMatrix); + // We do not need to allocate the memory for the trace matrix if the traceback is disabled. + if (IsTracebackEnabled_::VALUE) + resize(dpTraceMatrix); + + TDPScoreMatrixNavigator dpScoreMatrixNavigator; + TDPTraceMatrixNavigator dpTraceMatrixNavigator; + + _init(dpScoreMatrixNavigator, dpScoreMatrix, band); + _init(dpTraceMatrixNavigator, dpTraceMatrix, band); + + TDPScout dpScout(scoutState); +#if SEQAN_ALIGN_SIMD_PROFILE + profile.preprTimer += sysTime() - timer; + timer = sysTime(); +#endif + // Execute the alignment. + if (!_isBandEnabled(band)) + _computeUnbandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); + else if (upperDiagonal(band) == lowerDiagonal(band)) + _computeHammingDistance(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfile); + else + _computeBandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, + band, dpProfile); +#if SEQAN_ALIGN_SIMD_PROFILE + profile.alignTimer += sysTime() - timer; + timer = sysTime(); +#endif + return _finishAlignment(traceSegments, dpTraceMatrixNavigator, dpScout, seqH, seqV, band, dpProfile); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_ALGORITHM_IMPL_H_ diff --git a/seqan/align/dp_align_simd_helper.h b/seqan/align/dp_align_simd_helper.h new file mode 100644 index 0000000..8fd634a --- /dev/null +++ b/seqan/align/dp_align_simd_helper.h @@ -0,0 +1,517 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_DP_ALIGN_SIMD_HELPER_H_ +#define INCLUDE_SEQAN_ALIGN_DP_ALIGN_SIMD_HELPER_H_ + +namespace seqan +{ + +#if SEQAN_ALIGN_SIMD_PROFILE +struct AlignSimdProfile_ +{ + double preprTimer = 0.0; + double alignTimer = 0.0; + double traceTimer = 0.0; + + void clear() + { + preprTimer = 0.0; + alignTimer = 0.0; + traceTimer = 0.0; + } +}; + + double timer = 0.0; + +AlignSimdProfile_ profile; +#endif + +// ============================================================================ +// Forwards +// ============================================================================ + +template +struct VectorLength_; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +template +struct SimdAlignVariableLengthTraits +{ + using TSimdVector = TSimdVector_; + using TSeqH = TSeqH_; + using TSeqV = TSeqV_; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _createSimdRepImpl() +// ---------------------------------------------------------------------------- + +#define SEQAN_CREATE_SIMD_REP_IMPL_2(data, strPos, chrPos) getValue(data[strPos + 1], chrPos), getValue(data[strPos], chrPos) +#define SEQAN_CREATE_SIMD_REP_IMPL_4(data, strPos, chrPos) SEQAN_CREATE_SIMD_REP_IMPL_2(data, strPos + 2, chrPos), SEQAN_CREATE_SIMD_REP_IMPL_2(data, strPos, chrPos) +#define SEQAN_CREATE_SIMD_REP_IMPL_8(data, strPos, chrPos) SEQAN_CREATE_SIMD_REP_IMPL_4(data, strPos + 4, chrPos), SEQAN_CREATE_SIMD_REP_IMPL_4(data, strPos, chrPos) +#define SEQAN_CREATE_SIMD_REP_IMPL_16(data, strPos, chrPos) SEQAN_CREATE_SIMD_REP_IMPL_8(data, strPos + 8, chrPos), SEQAN_CREATE_SIMD_REP_IMPL_8(data, strPos, chrPos) +#define SEQAN_CREATE_SIMD_REP_IMPL_32(data, strPos, chrPos) SEQAN_CREATE_SIMD_REP_IMPL_16(data, strPos + 16, chrPos), SEQAN_CREATE_SIMD_REP_IMPL_16(data, strPos, chrPos) + +#define SEQAN_CREATE_SIMD_REP_FILL_IMPL_2(MACRO, data, chrPos) MACRO(data, 0, chrPos) +#define SEQAN_CREATE_SIMD_REP_FILL_IMPL(data, chrPos, SIZE) SEQAN_CREATE_SIMD_REP_FILL_IMPL_2(SEQAN_CREATE_SIMD_REP_IMPL_##SIZE, data, chrPos) + +#define SEQAN_CREATE_SIMD_REP_IMPL(SIZE) \ +template \ +inline void _createSimdRepImpl(TSimdVecs & simdStr, \ + TStrings const & strings, \ + VectorLength_ const & /*size*/) \ +{ \ + auto itB = begin(simdStr, Standard()); \ + auto itE = end(simdStr, Standard()); \ + for (auto it = itB; it != itE; ++it) \ + fillVector(*it, SEQAN_CREATE_SIMD_REP_FILL_IMPL(strings, it - itB, SIZE)); \ +} + +SEQAN_CREATE_SIMD_REP_IMPL(2) +SEQAN_CREATE_SIMD_REP_IMPL(4) +SEQAN_CREATE_SIMD_REP_IMPL(8) +SEQAN_CREATE_SIMD_REP_IMPL(16) +SEQAN_CREATE_SIMD_REP_IMPL(32) + +template +inline void _createSimdRepImpl(TSimdVecs & simdStr, + TStrings const & strings) +{ + _createSimdRepImpl(simdStr, strings, VectorLength_::Type>::VALUE>()); +} + +// Actually precompute value if scoring scheme is score matrix and simd version. +template +inline SEQAN_FUNC_ENABLE_IF(And >, IsScoreMatrix_ >, TSeqValue) +_precomputeScoreMatrixOffset(TSeqValue const & seqVal, + Score > const & /*score*/) +{ + return createVector(TScore::VALUE_SIZE) * seqVal; +} + +// ---------------------------------------------------------------------------- +// Function _prepareAndRunSimdAlignment() +// ---------------------------------------------------------------------------- + +template +inline void +_prepareAndRunSimdAlignment(TResult & results, + TTraces & traces, + TSequencesH const & seqH, + TSequencesV const & seqV, + TScore const & scoringScheme, + AlignConfig2 const & alignConfig, + TGapModel const & /*gapModel*/, + SimdAlignEqualLength const & /*tag*/) +{ + String > stringSimdH; + String > stringSimdV; + + resize(stringSimdH, length(seqH[0])); + resize(stringSimdV, length(seqV[0])); + _createSimdRepImpl(stringSimdH, seqH); + _createSimdRepImpl(stringSimdV, seqV); + + DPScoutState_ state; + results = _setUpAndRunAlignment(traces, state, stringSimdH, stringSimdV, scoringScheme, alignConfig, TGapModel()); +} + +template +inline void +_prepareAndRunSimdAlignment(TResult & results, + TTraces & traces, + TSequencesH const & seqH, + TSequencesV const & seqV, + TScore const & scoringScheme, + AlignConfig2 const & alignConfig, + TGapModel const & /*gapModel*/, + SimdAlignVariableLength const /*tag*/) +{ + SEQAN_ASSERT_EQ(length(seqH), length(seqV)); + SEQAN_ASSERT_EQ(static_cast(LENGTH::VALUE), length(seqH)); + + using TPadStringH = ModifiedString::Type, ModPadding>; + using TPadStringV = ModifiedString::Type, ModPadding>; + + String > stringSimdH; + String > stringSimdV; + + DPScoutState_ > > state; + + String lengthsH; + String lengthsV; + + resize(lengthsH, length(seqH)); + resize(lengthsV, length(seqV)); + resize(state.endsH, length(seqH)); + resize(state.endsV, length(seqV)); + + for (unsigned i = 0; i < length(seqH); ++i) + { + lengthsH[i] = length(seqH[i]) - 1; + lengthsV[i] = length(seqV[i]) - 1; + state.endsH[i] = i; + state.endsV[i] = i; + } + + setHost(state.sortedEndsH, lengthsH); + setHost(state.sortedEndsV, lengthsV); + setCargo(state.sortedEndsH, state.endsH); + setCargo(state.sortedEndsV, state.endsV); + + auto maxLengthLambda = [](auto& lengthLhs, auto& lengthRhs) { return lengthLhs < lengthRhs; }; + sort(state.sortedEndsH, maxLengthLambda, Serial()); + sort(state.sortedEndsV, maxLengthLambda, Serial()); + + size_t maxH = back(state.sortedEndsH) + 1; + size_t maxV = back(state.sortedEndsV) + 1; + + // and we have to prepare the bit masks of the DPScoutState + resize(state.masks, maxV, createVector(0)); + resize(state.masksV, maxV, createVector(0)); + resize(state.masksH, maxH, createVector(0)); + + // Create Stringset with padded strings. + StringSet paddedH; + StringSet paddedV; + resize(paddedH, length(seqH)); + resize(paddedV, length(seqV)); + + for(unsigned i = 0; i < length(seqH); ++i) + { + setHost(paddedH[i], seqH[i]); + setHost(paddedV[i], seqV[i]); + expand(paddedH[i], maxH); + expand(paddedV[i], maxV); + + // mark the original end position of the alignment in the masks (with -1, all bits set) + assignValue(state.masksH[lengthsH[i]], i, -1); + assignValue(state.masksV[lengthsV[i]], i, -1); + } + + // now create SIMD representation + resize(stringSimdH, maxH); + resize(stringSimdV, maxV); + _createSimdRepImpl(stringSimdH, paddedH); + _createSimdRepImpl(stringSimdV, paddedV); + + state.dimV = length(stringSimdV); + state.isLocalAlignment = IsLocalAlignment_::VALUE; + state.right = IsFreeEndGap_::VALUE; + state.bottom = IsFreeEndGap_::VALUE; + + results = _setUpAndRunAlignment(traces, state, stringSimdH, stringSimdV, scoringScheme, alignConfig, TGapModel()); +} + +template +inline void +_prepareAndRunSimdAlignment(TResult & results, + TTraces & traces, + TSequencesH const & seqH, + TSequencesV const & seqV, + TScore const & scoringScheme, + AlignConfig2 const & alignConfig, + TGapModel const & /*gapModel*/) +{ + auto seqLengthH = length(seqH[0]); + auto seqLengthV = length(seqV[0]); + auto zipView = makeZipView(seqH, seqV); + bool allSameLength = std::all_of(begin(zipView, Standard()), end(zipView, Standard()), + [seqLengthH, seqLengthV](auto param) + { + return (length(std::get<0>(param)) == seqLengthH) && + (length(std::get<1>(param)) == seqLengthV); + }); + if(allSameLength) + _prepareAndRunSimdAlignment(results, traces, seqH, seqV, scoringScheme, alignConfig, TGapModel(), SimdAlignEqualLength()); + else + _prepareAndRunSimdAlignment(results, traces, seqH, seqV, scoringScheme, alignConfig, TGapModel(), + SimdAlignVariableLength()); +} + +// ---------------------------------------------------------------------------- +// Function _alignWrapperSimd(); Score; StringSet vs. StringSet +// ---------------------------------------------------------------------------- + +template +inline auto +_alignWrapperSimd(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + TAlignConfig const & config, + TGapModel const & /*gaps*/) +{ + typedef typename SimdVector::Type TSimdAlign; + + unsigned const numAlignments = length(stringsV); + unsigned const sizeBatch = LENGTH::VALUE; + unsigned const fullSize = sizeBatch * ((numAlignments + sizeBatch - 1) / sizeBatch); + + String results; + resize(results, numAlignments); + + StringSet > trace; // We need to declare it, but it will not be used. + + // Create a SIMD scoring scheme. + Score > > simdScoringScheme(scoringScheme); + + for (auto pos = 0u; pos < fullSize; pos += sizeBatch) + { + TSimdAlign resultsBatch; + if (SEQAN_UNLIKELY(numAlignments < pos + sizeBatch)) + { + StringSet > depSetH; + StringSet > depSetV; + for (unsigned i = pos; i < fullSize; ++i) + { + if (i >= numAlignments) + { + appendValue(depSetH, back(stringsH)); + appendValue(depSetV, back(stringsV)); + } + else + { + appendValue(depSetH, stringsH[i]); + appendValue(depSetV, stringsV[i]); + } + } + SEQAN_ASSERT_EQ(length(depSetH), sizeBatch); + SEQAN_ASSERT_EQ(length(depSetV), sizeBatch); + + _prepareAndRunSimdAlignment(resultsBatch, trace, depSetH, depSetV, simdScoringScheme, config, TGapModel()); + } + else + { + auto infSetH = infixWithLength(stringsH, pos, sizeBatch); + auto infSetV = infixWithLength(stringsV, pos, sizeBatch); + + _prepareAndRunSimdAlignment(resultsBatch, trace, infSetH, infSetV, simdScoringScheme, config, TGapModel()); + } + + // TODO(rrahn): Could be parallelized! + for(auto x = pos; x < pos + sizeBatch && x < numAlignments; ++x) + results[x] = resultsBatch[x - pos]; + } + return results; +} + +// ---------------------------------------------------------------------------- +// Function _alignWrapperSimd(); Score; String vs. StringSet +// ---------------------------------------------------------------------------- + +template +inline auto +_alignWrapperSimd(TString1 const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + TAlignConfig const & config, + TGapModel const & /*gaps*/) +{ + typedef typename SimdVector::Type TSimdAlign; + + unsigned const numAlignments = length(stringsV); + unsigned const sizeBatch = LENGTH::VALUE; + unsigned const fullSize = sizeBatch * ((numAlignments + sizeBatch - 1) / sizeBatch); + + String results; + resize(results, numAlignments); + + // Prepare strings. + StringSet > setH; + for (auto i = 0u; i < sizeBatch; ++i) + appendValue(setH, stringH); + + StringSet > trace; // We need to declare it, but it will not be used. + + // Create a SIMD scoring scheme. + Score > > simdScoringScheme(scoringScheme); + + for (auto pos = 0u; pos < fullSize; pos += sizeBatch) + { + TSimdAlign resultsBatch; + if (SEQAN_UNLIKELY(numAlignments < pos + sizeBatch)) + { + StringSet > depSetV; + for (unsigned i = pos; i < fullSize; ++i) + { + if (i >= numAlignments) + appendValue(depSetV, back(stringsV)); + else + appendValue(depSetV, stringsV[i]); + } + SEQAN_ASSERT_EQ(length(depSetV), sizeBatch); + + _prepareAndRunSimdAlignment(resultsBatch, trace, setH, depSetV, simdScoringScheme, config, TGapModel()); + } + else + { + auto infSetV = infixWithLength(stringsV, pos, sizeBatch); + _prepareAndRunSimdAlignment(resultsBatch, trace, setH, infSetV, simdScoringScheme, config, TGapModel()); + } + // TODO(rrahn): Could be parallelized! + for(auto x = pos; x < pos + sizeBatch && x < numAlignments; ++x) + results[x] = resultsBatch[x - pos]; + } + return results; +} + +// ---------------------------------------------------------------------------- +// Function _alignWrapperSimd(); Gaps +// ---------------------------------------------------------------------------- + +template +inline auto +_alignWrapperSimd(StringSet, TSetSpecH> & gapSeqSetH, + StringSet, TSetSpecV> & gapSeqSetV, + Score const & scoringScheme, + TAlignConfig const & config, + TGapModel const & /*gaps*/) +{ + typedef Gaps TGapSequenceH; + typedef Gaps TGapSequenceV; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + + typedef typename SimdVector::Type TSimdAlign; + +#if SEQAN_ALIGN_SIMD_PROFILE + timer = sysTime(); +#endif + + unsigned const numAlignments = length(gapSeqSetH); + unsigned const sizeBatch = LENGTH::VALUE; + unsigned const fullSize = sizeBatch * ((numAlignments + sizeBatch - 1) / sizeBatch); + + String results; + resize(results, numAlignments); + + // Create a SIMD scoring scheme. + Score > > simdScoringScheme(scoringScheme); + + // Prepare string sets with sequences. + StringSet::Type, Dependent<> > depSetH; + StringSet::Type, Dependent<> > depSetV; + reserve(depSetH, fullSize); + reserve(depSetV, fullSize); + for (unsigned i = 0; i < fullSize; ++i) + { + if (i >= numAlignments) + { + appendValue(depSetH, source(back(gapSeqSetH))); + appendValue(depSetV, source(back(gapSeqSetV))); + } + else + { + appendValue(depSetH, source(gapSeqSetH[i])); + appendValue(depSetV, source(gapSeqSetV[i])); + } + } + + // Run alignments in batches. + for (auto pos = 0u; pos < fullSize; pos += sizeBatch) + { + auto infSetH = infixWithLength(depSetH, pos, sizeBatch); + auto infSetV = infixWithLength(depSetV, pos, sizeBatch); + + TSimdAlign resultsBatch; + + StringSet > trace; + resize(trace, sizeBatch, Exact()); + + _prepareAndRunSimdAlignment(resultsBatch, trace, infSetH, infSetV, simdScoringScheme, config, TGapModel()); + + // copy results and finish traceback + // TODO(rrahn): Could be parallelized! + // to for_each call + for(auto x = pos; x < pos + sizeBatch && x < numAlignments; ++x) + { + results[x] = resultsBatch[x - pos]; + _adaptTraceSegmentsTo(gapSeqSetH[x], gapSeqSetV[x], trace[x - pos]); + } +#if SEQAN_ALIGN_SIMD_PROFILE + profile.traceTimer += sysTime() - timer; + timer = sysTime(); +#endif + } + return results; +} + +} // namespace seqan +#endif // #ifndef INCLUDE_SEQAN_ALIGN_DP_ALIGN_SIMD_HELPER_H_ + diff --git a/seqan/align/dp_band.h b/seqan/align/dp_band.h new file mode 100644 index 0000000..b636d50 --- /dev/null +++ b/seqan/align/dp_band.h @@ -0,0 +1,384 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// This class stores the band information as well as the meta-inforation, +// whether a band was selected or not. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_BAND_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_BAND_H_ + +namespace seqan +{ + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @defgroup DPBandSwitch + * @brief Tags used to switch between banded and unbanded alignment. + * + * @tag DPBandSwitch#BandOn + * @brief Switches banded alignment on. + * @headerfile + * @signature struct BandOn_; + * @signature typedef Tag BandOn; + * + * @tag DPBandSwitch#BandOff + * @brief Switches banded alignment off. + * @headerfile + * @signature struct BandOff_; + * @signature typedef Tag BandOff; + */ + +// ---------------------------------------------------------------------------- +// Tag BandOff +// ---------------------------------------------------------------------------- + +// Used when computing unbanded alignments. +struct BandOff_; +typedef Tag BandOff; + +// ---------------------------------------------------------------------------- +// Tag BandOn +// ---------------------------------------------------------------------------- + +// Used when computing banded alignments. +struct BandOn_; +typedef Tag BandOn; + +// ---------------------------------------------------------------------------- +// Class DPBandConfig +// ---------------------------------------------------------------------------- + +/*! + * @class DPBandConfig + * @headerfile + * @brief Simple class to configure banded alignments. + * + * @signature template + * class DPBandConfig; + * + * @tparam TSwitch Tag to switch between banded and unbanded alignments. + * One of @link DPBandSwitch @endlink. Defaults to @link DPBandSwitch#BandOff @endlink. + * + * To compute banded alignments use @link DPBand @endlink as a shortcut for the DPBandConfig with + * band switched on. + */ + +// Simple band class. +template +struct DPBandConfig {}; + +// ---------------------------------------------------------------------------- +// Class DPBandConfig [BandOff] +// ---------------------------------------------------------------------------- + +// The specialization when using no band. +// Per default the member variables _lowerDiagonal and _upperDiagonal are +// always 0. +template <> +struct DPBandConfig +{ + typedef int TPosition; +}; + +// ---------------------------------------------------------------------------- +// Class DPBandConfig [BandOn] +// ---------------------------------------------------------------------------- + +// The specialization when using a band. +// On construction the diagonals are set to 0. +template <> +struct DPBandConfig +{ + typedef int TPosition; + + int _lowerDiagonal; + int _upperDiagonal; + +/*! + * @fn DPBandConfig::DPBandConfig + * @brief Constructor. + * + * @signature DPBandConfig(); + * @signature DPBandConfig(lowerDiag, upperDiag); + * + * @tparam TSwitch Tag to switch between banded and unbanded alignments. One of @link DPBandSwitch @endlink. + * The second constructor is only supported when @link DPBandConfig @endlink is specialized with + * @link DPBandSwitch#BandOn @endlink. + * + * @param lowerDiag The value for the lower diagonal of the band. + * @param upperDiag The value for the upper diagonal of the band. + * + * A negative value for the diagonals indicates an intersection of the diagonal with the vertical sequence (y-axis) + * and a positive value indicates an intersection with the horizontal sequence (x-axis). + * The value of the lower diagonal has to compare less or equal to the value of the upper diagonal. + */ + + DPBandConfig() : + _lowerDiagonal(0), _upperDiagonal(0) {} + + DPBandConfig(int lowerDiagonal, int upperDiagonal) : + _lowerDiagonal(lowerDiagonal), _upperDiagonal(upperDiagonal) + { + SEQAN_ASSERT_LEQ(lowerDiagonal, upperDiagonal); + } +}; + +/*! + * @typedef DPBand + * @headerfile + * @brief Global typedef used for @link DPBandConfig @endlink specialized with @link DPBandSwitch#BandOn @endlink. + * + * @signature typedef DPBandConfig DPBand; + */ + +// Typedef for Band. +typedef DPBandConfig DPBand; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +/*! + * @mfn DPBandConfig#Position + * @headerfile + * @brief Metafunction returning the position type. + * + * @signature typename Position::Type; + * + * @tparam T The type @link DPBandConfig @endlink to query the position type for. + * @return TPosition The position type. + */ + +// ---------------------------------------------------------------------------- +// Metafunction Position +// ---------------------------------------------------------------------------- + +template +struct Position > +{ + typedef typename DPBandConfig::TPosition Type; +}; + +template +struct Position const>: + Position >{}; + +// ---------------------------------------------------------------------------- +// Metafunction Size +// ---------------------------------------------------------------------------- + +/*! + * @mfn DPBandConfig#Size + * @headerfile + * @brief Metafunction returning the size type. + * + * @signature typename Size::Type; + * + * @tparam T The type @link DPBandConfig @endlink to query the size type for. + * @return TSize The size type. + */ + +template +struct Size > +{ + typedef unsigned Type; +}; + + +template +struct Size const>: + Size >{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function setLowerDiagonal +// ---------------------------------------------------------------------------- + +/*! + * @fn DPBandConfig#setLowerDiagonal + * @headerfile + * @brief Sets the value of the lower diagonal. + * + * @signature setLowerDiagonal(obj, val); + * + * @param obj The object of type @link DPBandConfig @endlink to set the lower diagonal for. + * @param val The new value for the lower diagonal. + * + * @note If the band is switched off, this function defaults to no-op. + */ + +inline void +setLowerDiagonal(DPBandConfig & /*dpBand*/, int /*newLowerDiagonal*/) +{ + //no-op +} + +inline void +setLowerDiagonal(DPBandConfig & dpBand, int newLowerDiagonal) +{ + dpBand._lowerDiagonal = newLowerDiagonal; +} + +// ---------------------------------------------------------------------------- +// Function lowerDiagonal +// ---------------------------------------------------------------------------- + +/*! + * @fn DPBandConfig#lowerDiagonal + * @headerfile + * @brief Returns the value of the lower diagonal. + * + * @signature TPosition lowerDiagonal(obj); + * + * @param obj The object of type @link DPBandConfig @endlink to query the lower diagonal for. + * + * @note If the band is switched off this function always returns 0. + * @return TPosition The value of the lower diagonal. + */ + +inline Position >::Type +lowerDiagonal(DPBandConfig const & /*dpBand*/) +{ + return 0; +} + +template +inline typename Position >::Type +lowerDiagonal(DPBandConfig const & dpBand) +{ + return dpBand._lowerDiagonal; +} + +// ---------------------------------------------------------------------------- +// Function setUpperDiagonal +// ---------------------------------------------------------------------------- + +/*! + * @fn DPBandConfig#setUpperDiagonal + * @headerfile + * @brief Sets the value of the upper diagonal. + * + * @signature setUpperDiagonal(obj, val); + * + * @param obj The object of type @link DPBandConfig @endlink to set the upper diagonal for. + * @param val The new value for the upper diagonal. + * + * @note If the band is switched off, this function defaults to no-op. + */ + +inline void +setUpperDiagonal(DPBandConfig & /*dpBand*/, int /*newUpperDiagonal*/) +{ + //no-op +} + +inline void +setUpperDiagonal(DPBandConfig & dpBand, int newUpperDiagonal) +{ + dpBand._upperDiagonal = newUpperDiagonal; +} + +// ---------------------------------------------------------------------------- +// Function upperDiagonal +// ---------------------------------------------------------------------------- + +/*! + * @fn DPBandConfig#upperDiagonal + * @headerfile + * @brief Returns the value of the upper diagonal. + * + * @signature TPosition upperDiagonal(obj); + * + * @param obj The object of type @link DPBandConfig @endlink to query the upper diagonal for. + * + * @note If the band is switched off this function always returns 0. + * @return TPosition The value of the upper diagonal. + */ + +inline Position >::Type +upperDiagonal(DPBandConfig const & /*dpBand*/) +{ + return 0; +} + +template +inline typename Position >::Type +upperDiagonal(DPBandConfig const & dpBand) +{ + return dpBand._upperDiagonal; +} + +// ---------------------------------------------------------------------------- +// Function bandSize() +// ---------------------------------------------------------------------------- + +/*! + * @fn DPBandConfig#bandSize + * @headerfile + * @brief Returns the size of the band. + * + * @signature TSize bandSize(obj); + * + * @param obj The object of type @link DPBandConfig @endlink to query the band size for. + * + * @note If the band is switched off this function always returns 0. + * @return TSize The number of diagonals covered by the band. + */ + +inline Size >::Type +bandSize(DPBandConfig const &) +{ + return 0; +} + +template +inline typename Size >::Type +bandSize(DPBandConfig const & band) +{ + return upperDiagonal(band) - lowerDiagonal(band) + 1; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_BAND_H_ diff --git a/seqan/align/dp_cell.h b/seqan/align/dp_cell.h new file mode 100644 index 0000000..49f3b85 --- /dev/null +++ b/seqan/align/dp_cell.h @@ -0,0 +1,283 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Declares the DPCell, which is used to substitute the score of each cell. +// Thus, we are able to add additional features to an alignment cell such as +// a flag to indicate if it is forbidden or not. Or to store two additional +// scores necessary for the affine gap function. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class DPCell_ +// ---------------------------------------------------------------------------- + +// Used to store the score of a particular cell of the score matrix. +// It can be specialized for linear and affine gap costs. +// For affine gap costs it stores the values of all three matrices at a particular +// position of the matrix. +template +class DPCell_; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +template +struct Value > +{ + typedef TScoreValue Type; +}; + +template +struct Value const> +{ + typedef TScoreValue const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +template +struct Reference > +{ + typedef TScoreValue & Type; +}; + +template +struct Reference const> +{ + typedef TScoreValue const & Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction DPCellDefaultInfinity +// ---------------------------------------------------------------------------- + +// Defines the default infinity value for a DPCell. +template +struct DPCellDefaultInfinity +{ + static const int VALUE; +}; + +template +const int DPCellDefaultInfinity::VALUE = MinValue::VALUE; + +// We use the min value of the score type and shift it one bits to the left. This way we can use "infinity" without +// checking for it during the computation. +template +struct DPCellDefaultInfinity > +{ + static const TScoreValue VALUE; +}; + +template + const TScoreValue DPCellDefaultInfinity >::VALUE = + createVector(MinValue::Type>::VALUE) / createVector(2); + +template +struct DPCellDefaultInfinity const> : + public DPCellDefaultInfinity >{}; + +// ---------------------------------------------------------------------------- +// Metafunction StringSpecForValue_ +// ---------------------------------------------------------------------------- + +// Defines the default infinity value for a DPCell. +template +struct StringSpecForValue_ > +{ + typedef typename If >, Alloc, Alloc<> >::Type Type; +}; + +template +struct StringSpecForValue_ const> : + StringSpecForValue_ > +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _scoreOfCell +// ---------------------------------------------------------------------------- + +// Returns the score value for a given cell. +template +inline typename Reference >::Type +_scoreOfCell(DPCell_ & dpCell) +{ + return dpCell._score; +} + +template +inline typename Reference const>::Type +_scoreOfCell(DPCell_ const & dpCell) +{ + return dpCell._score; +} + +// ---------------------------------------------------------------------------- +// Function _setScoreOfCell +// ---------------------------------------------------------------------------- + +template +inline void +_setScoreOfCell(DPCell_ & dpCell, TScoreValue const & newScore) +{ + dpCell._score = newScore; +} + +template +inline void +_setScoreOfCell(DPCell_ & dpCell, TScoreValue const & newScore, TScoreValue const & mask) +{ + dpCell._score = blend(dpCell._score, newScore, mask); +} + +// ---------------------------------------------------------------------------- +// Function _verticalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for vertical-gaps of the given cell. +template +inline typename Reference >::Type +_verticalScoreOfCell(DPCell_ & dpCell) +{ + return dpCell._score; +} + +template +inline typename Reference const>::Type +_verticalScoreOfCell(DPCell_ const & dpCell) +{ + return dpCell._score; +} + +// ---------------------------------------------------------------------------- +// Function _setVerticalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for vertical-gaps of the given cell. +template +inline void +_setVerticalScoreOfCell(DPCell_ & /*dpCell*/, TScoreValue const & /*newVerticalScore*/) +{ + // no-op +} + +template +inline void +_setVerticalScoreOfCell(DPCell_ & /*dpCell*/, TScoreValue const & /*newVerticalScore*/, TScoreValue const & /*mask*/) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function _horizontalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for horizontal-gaps of the given cell. +template +inline typename Reference >::Type +_horizontalScoreOfCell(DPCell_ & dpCell) +{ + return dpCell._score; +} + +template +inline typename Reference const>::Type +_horizontalScoreOfCell(DPCell_ const & dpCell) +{ + return dpCell._score; +} + +// ---------------------------------------------------------------------------- +// Function _setHorizontalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for vertical-gaps of the given cell. +template +inline void +_setHorizontalScoreOfCell(DPCell_ & /*dpCell*/, TScoreValue const & /*newHorizontalScore*/) +{ + // no-op +} + +template +inline void +_setHorizontalScoreOfCell(DPCell_ & /*dpCell*/, TScoreValue const & /*newHorizontalScore*/, TScoreValue const & /*mask*/) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function setGapExtension() +// ---------------------------------------------------------------------------- + +template +inline void +setGapExtension(DPCell_ & /*dpCell*/, TF1 , TF2) +{ + // no-op +} + +template +inline void +setGapExtension(DPCell_ & /*dpCell*/, TF1 , TF2, TScoreValue) +{ + // no-op +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_ diff --git a/seqan/align/dp_cell_affine.h b/seqan/align/dp_cell_affine.h new file mode 100644 index 0000000..c12990c --- /dev/null +++ b/seqan/align/dp_cell_affine.h @@ -0,0 +1,208 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the DPCell for affine gap functions. It stores the score +// values for the three matrices: diagonal, vertical and horizontal. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class DPCell [AffineGaps] +// ---------------------------------------------------------------------------- + +// Specialization for the affine gap cost function. +// This class stores three values belonging to the matrix storing the current +// maximum, the matrix for horizontal gaps and the matrix for vertical gaps. +template +class DPCell_ +{ +public: + TScoreValue _score = DPCellDefaultInfinity::VALUE; + TScoreValue _horizontalScore = DPCellDefaultInfinity::VALUE; + TScoreValue _verticalScore = DPCellDefaultInfinity::VALUE; + + DPCell_() = default; + // Copy c'tor. + DPCell_(DPCell_ const & other) : + _score(other._score), + _horizontalScore(other._horizontalScore), + _verticalScore(other._verticalScore) + {} + + // Move c-tor + DPCell_(DPCell_ && other) : DPCell_() + { + swap(*this, other); + } + + // The assignment operator. + DPCell_ & + operator=(DPCell_ other) + { + swap(*this, other); + return *this; + } + + // Assign score to cell. + DPCell_ & + operator=(TScoreValue const & score) + { + _score = score; + return *this; + } + + ~DPCell_() = default; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function operator<() +// ---------------------------------------------------------------------------- + +// Needed for banded chain alignment for the set. +template +inline bool operator<(DPCell_ const & left, + DPCell_ const & right) +{ + return left._score < right._score && left._horizontalScore < right._horizontalScore && + left._verticalScore < right._verticalScore; +} + +// ---------------------------------------------------------------------------- +// Function _verticalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for vertical-gaps of the given cell. +template +inline typename Reference >::Type +_verticalScoreOfCell(DPCell_ & dpCell) +{ + return dpCell._verticalScore; +} + +template +inline typename Reference const>::Type +_verticalScoreOfCell(DPCell_ const & dpCell) +{ + return dpCell._verticalScore; +} + +// ---------------------------------------------------------------------------- +// Function _setVerticalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for vertical-gaps of the given cell. +template +inline SEQAN_FUNC_ENABLE_IF(Not > >,void) +_setVerticalScoreOfCell(DPCell_ & dpCell, TScoreValue const & newVerticalScore) +{ + dpCell._verticalScore = newVerticalScore; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >,void) +_setVerticalScoreOfCell(DPCell_ & dpCell, TScoreValue const & newVerticalScore, TScoreValue const & mask) +{ + dpCell._verticalScore = blend(dpCell._verticalScore, newVerticalScore, mask); +} + +// ---------------------------------------------------------------------------- +// Function _horizontalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for horizontal-gaps of the given cell. +template +inline typename Reference >::Type +_horizontalScoreOfCell(DPCell_ & dpCell) +{ + return dpCell._horizontalScore; +} + +template +inline typename Reference const>::Type +_horizontalScoreOfCell(DPCell_ const & dpCell) +{ + return dpCell._horizontalScore; +} + +// ---------------------------------------------------------------------------- +// Function _setHorizontalScoreOfCell() +// ---------------------------------------------------------------------------- + +// Returns the score of the matrix for vertical-gaps of the given cell. +template +inline SEQAN_FUNC_ENABLE_IF(Not > >,void) +_setHorizontalScoreOfCell(DPCell_ & dpCell, TScoreValue const & newHorizontalScore) +{ + dpCell._horizontalScore = newHorizontalScore; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >,void) +_setHorizontalScoreOfCell(DPCell_ & dpCell, TScoreValue const & newHorizontalScore, TScoreValue const & mask) +{ + dpCell._horizontalScore = blend(dpCell._horizontalScore, newHorizontalScore, mask); +} + +template +inline void +swap(DPCell_ & lhs, + DPCell_ & rhs) +{ + std::swap(lhs._score, rhs._score); + std::swap(lhs._horizontalScore, rhs._horizontalScore); + std::swap(lhs._verticalScore, rhs._verticalScore); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_ diff --git a/seqan/align/dp_cell_dynamic.h b/seqan/align/dp_cell_dynamic.h new file mode 100644 index 0000000..567d5f9 --- /dev/null +++ b/seqan/align/dp_cell_dynamic.h @@ -0,0 +1,249 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the dynamic gap model published in "Dynamic Gaps Selector: +// A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model +// Optimization" by Gianvito Urgese et al. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_ +#define INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction GetFlagMaskType +// ---------------------------------------------------------------------------- + +namespace impl +{ +namespace dp_cell +{ +template +struct FlagMaskType +{ + using Type = typename If >, + TScoreValue, + uint8_t>::Type; +}; +} // namespace dp_cell +} // namespace impl + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +struct DynamicGapExtensionHorizontal_; +typedef Tag DynamicGapExtensionHorizontal; + +struct DynamicGapExtensionVertical_; +typedef Tag DynamicGapExtensionVertical; + +enum DynamicGapsMask +{ + MASK_VERTICAL_GAP = 1, + MASK_HORIZONTAL_GAP = 2 +}; + +// ---------------------------------------------------------------------------- +// Class DPCell [DynamicGaps] +// ---------------------------------------------------------------------------- + +// The specialization for linear gap cost function. +// It solely stores the maximal score. +template +class DPCell_ +{ +public: + using TFlagMaskType = typename impl::dp_cell::FlagMaskType::Type; + + TScoreValue _score = DPCellDefaultInfinity::VALUE; + TFlagMaskType _flagMask = TFlagMaskType(); + + DPCell_() = default; + + // Copy c'tor. + DPCell_(DPCell_ const & other) : _score(other._score), _flagMask(other._flagMask) + {} + + // Move c'tor. + DPCell_(DPCell_ && other) : DPCell_() + { + swap(*this, other); + } + + // Construct with score. + DPCell_(TScoreValue const & pScore) : _score(pScore) + {} + + // Assignment and move operator. + DPCell_& operator=(DPCell_ other) + { + swap(*this, other); + return *this; + } + + // Assignment of score. + DPCell_ & + operator=(TScoreValue const & score) + { + _score = score; + return *this; + } + + ~DPCell_() = default; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +template +struct SetGapExtension; + +template +struct SetGapExtension, False, False> +{ + static const char VALUE = 0; +}; + +template +struct SetGapExtension, False, True> +{ + static const char VALUE = MASK_HORIZONTAL_GAP; +}; + +template +struct SetGapExtension, True, False> +{ + static const char VALUE = MASK_VERTICAL_GAP; +}; + +template +struct SetGapExtension, True, True> +{ + static const char VALUE = MASK_HORIZONTAL_GAP | MASK_VERTICAL_GAP; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +template +inline void _setBit(DPCell_ & cell, + TFlag const & /*flag*/, + DynamicGapExtensionVertical const & /*tag*/) +{ + if (IsSameType::VALUE) + cell._flagMask |= MASK_VERTICAL_GAP; + else + cell._flagMask &= ~MASK_VERTICAL_GAP; +} + +template +inline void _setBit(DPCell_ & cell, + TFlag const & /*flag*/, + DynamicGapExtensionHorizontal const & /*tag*/) +{ + if (IsSameType::VALUE) + cell._flagMask |= MASK_HORIZONTAL_GAP; + else + cell._flagMask &= ~MASK_HORIZONTAL_GAP; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >,bool) +isGapExtension(DPCell_ const & cell, + TSpec const & /*spec*/) +{ + if (IsSameType::VALUE) + return cell._flagMask & MASK_HORIZONTAL_GAP; + else + return cell._flagMask & MASK_VERTICAL_GAP; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >,TScoreValue) +isGapExtension(DPCell_ const & cell, + TSpec const & /*spec*/) +{ + return blend(cell._flagMask & createVector(MASK_VERTICAL_GAP), + cell._flagMask & createVector(MASK_HORIZONTAL_GAP), + createVector(IsSameType::VALUE)); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, void) +setGapExtension(DPCell_ & cell, + TFlagV const & /*vert*/, TFlagH const & /*hori*/) +{ + cell._flagMask = SetGapExtension, TFlagV, TFlagH>::VALUE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +setGapExtension(DPCell_ & cell, + TFlagV const & /*vert*/, TFlagH const & /*hori*/, + TScoreValue const & cmp) +{ + cell._flagMask = blend(cell._flagMask, createVector(SetGapExtension, TFlagV, TFlagH>::VALUE), cmp); +} + +// ---------------------------------------------------------------------------- +// Function operator<() +// ---------------------------------------------------------------------------- + +// Needed for banded chain alignment for the std::set. +template +inline bool operator<(DPCell_ const & left, + DPCell_ const & right) +{ + return left._score < right._score; +} + +template +inline void +swap(DPCell_ & lhs, + DPCell_ & rhs) +{ + std::swap(lhs._score, rhs._score); + std::swap(lhs._flagMask, rhs._flagMask); +} + +} // namespace seqan + +#endif // INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_ diff --git a/seqan/align/dp_cell_linear.h b/seqan/align/dp_cell_linear.h new file mode 100644 index 0000000..1a46fbe --- /dev/null +++ b/seqan/align/dp_cell_linear.h @@ -0,0 +1,125 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the DPCell for linear gap cost functions. This requires only +// one matrix, such that we only need to store one score value per matrix +// entry. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + + +// ---------------------------------------------------------------------------- +// Class DPCell [LinearGaps] +// ---------------------------------------------------------------------------- + +// The specialization for linear gap cost function. +// It solely stores the maximal score. +template +class DPCell_ +{ +public: + TScoreValue _score = DPCellDefaultInfinity::VALUE; + + DPCell_() = default; + + // Copy c'tor. + DPCell_(DPCell_ const & other) : _score(other._score) + {} + + // Move c'tor. + DPCell_(DPCell_ && other) : DPCell_() + { + swap(*this, other); + } + + // Assignment & move operator + DPCell_& operator=(DPCell_ other) + { + swap(*this, other); + return *this; + } + + // Assignment of score. + DPCell_ & + operator=(TScoreValue const & score) + { + _score = score; + return *this; + } + + ~DPCell_() = default; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function operator<() +// ---------------------------------------------------------------------------- + +// Needed for banded chain alignment for the std::set. +template +inline bool operator<(DPCell_ const & left, + DPCell_ const & right) +{ + return left._score < right._score; +} + +template +inline void +swap(DPCell_ & lhs, + DPCell_ & rhs) +{ + std::swap(lhs._score, rhs._score); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_LINEAR_H_ diff --git a/seqan/align/dp_context.h b/seqan/align/dp_context.h new file mode 100644 index 0000000..3049369 --- /dev/null +++ b/seqan/align/dp_context.h @@ -0,0 +1,187 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the context that can be passed to the dp functions in order +// to reuse memory blocks in mutliple calls of the same function. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_ +#define INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_ + +namespace seqan +{ + +// ============================================================================ +// Forwards +// ============================================================================ + +template +struct GetDPScoreMatrix +{}; + +template +struct GetDPTraceMatrix +{}; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +template +struct DPContext +{ + typedef typename GetDPScoreMatrix::Type TScoreMatrixHost; + typedef typename GetDPTraceMatrix::Type TTraceMatrixHost; + + TScoreMatrixHost _scoreMatrix; + TTraceMatrixHost _traceMatrix; + + DPContext() : _scoreMatrix(), _traceMatrix() + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction GetDPScoreMatrix +// ---------------------------------------------------------------------------- + +template +struct GetDPScoreMatrix > +{ + typedef DPCell_ TDPScoreValue_; + typedef DPMatrix_ TDPScoreMatrix_; + + typedef typename Host::Type Type; +}; + +template +struct GetDPScoreMatrix const > +{ + typedef DPCell_ TDPScoreValue_; + typedef DPMatrix_ TDPScoreMatrix_; + + typedef typename Host::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction GetDPTraceMatrix +// ---------------------------------------------------------------------------- + +template +struct GetDPTraceMatrix > +{ + typedef typename TraceBitMap_::Type TTraceValue_; + typedef DPMatrix_ TDPScoreMatrix_; + + typedef typename Host::Type Type; +}; + +template +struct GetDPTraceMatrix const > +{ + typedef typename TraceBitMap_::Type TTraceValue_; + typedef DPMatrix_ TDPScoreMatrix_; + + typedef typename Host::Type const Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function dpScoreMatrix() +// ---------------------------------------------------------------------------- + +template +inline typename GetDPScoreMatrix >::Type & +getDpScoreMatrix(DPContext & dpContext) +{ + return dpContext._scoreMatrix; +} + +template +inline typename GetDPScoreMatrix const >::Type & +getDpScoreMatrix(DPContext const & dpContext) +{ + return dpContext._scoreMatrix; +} + +// ---------------------------------------------------------------------------- +// Function dpTraceMatrix() +// ---------------------------------------------------------------------------- + +template +inline typename GetDPTraceMatrix >::Type & +getDpTraceMatrix(DPContext & dpContext) +{ + return dpContext._traceMatrix; +} + +template +inline typename GetDPTraceMatrix const >::Type & +getDpTraceMatrix(DPContext const & dpContext) +{ + return dpContext._traceMatrix; +} + +// ---------------------------------------------------------------------------- +// Function setDpScoreMatrix() +// ---------------------------------------------------------------------------- + +template +inline void +setDpTraceMatrix(DPContext & dpContext, + typename GetDPScoreMatrix >::Type const & scoreMatrix) +{ + dpContext._scoreMatrix = scoreMatrix; +} + +// ---------------------------------------------------------------------------- +// Function setDpTraceMatrix() +// ---------------------------------------------------------------------------- + +template +inline void +setDpTraceMatrix(DPContext & dpContext, + typename GetDPTraceMatrix >::Type const & traceMatrix) +{ + dpContext._tarceMatrix = traceMatrix; +} + +} + +#endif // INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_ diff --git a/seqan/align/dp_formula.h b/seqan/align/dp_formula.h new file mode 100644 index 0000000..9ecd0ab --- /dev/null +++ b/seqan/align/dp_formula.h @@ -0,0 +1,220 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Defines the recursion formula for the dp-alignment algorithms. +// ========================================================================== + +// TODO(holtgrew): Documentation in this header necessary or internal only? + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionDiagonal +// ---------------------------------------------------------------------------- + +struct RecursionDirectionDiagonal_; +typedef Tag RecursionDirectionDiagonal; + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionHorizontal +// ---------------------------------------------------------------------------- + +struct RecursionDirectionHorizontal_; +typedef Tag RecursionDirectionHorizontal; + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionVertical +// ---------------------------------------------------------------------------- + +struct RecursionDirectionVertical_; +typedef Tag RecursionDirectionVertical; + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionAll +// ---------------------------------------------------------------------------- + +struct RecursionDirectionAll_; +typedef Tag RecursionDirectionAll; + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionUpperDiagonal +// ---------------------------------------------------------------------------- + +struct RecursionDirectionUpperDiagonal_; +typedef Tag RecursionDirectionUpperDiagonal; + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionLowerDiagonal +// ---------------------------------------------------------------------------- + +struct RecursionDirectionLowerDiagonal_; +typedef Tag RecursionDirectionLowerDiagonal; + +// ---------------------------------------------------------------------------- +// Tag RecursionDirectionZero +// ---------------------------------------------------------------------------- + +struct RecursionDirectionZero_; +typedef Tag RecursionDirectionZero; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _computeScore +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_computeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + TRecursionDirection const & recDir, + TDPProfile const & dpProfile) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + TTraceValue traceDir = _doComputeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, seqHVal, + seqVVal, scoringScheme, recDir, dpProfile); + if (IsLocalAlignment_::VALUE) + if (activeCell._score <= 0) + { + _setScoreOfCell(activeCell, static_cast(0)); + _setHorizontalScoreOfCell(activeCell, static_cast(0)); + _setVerticalScoreOfCell(activeCell, static_cast(0)); + return TraceBitMap_::NONE; + } + + return traceDir; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_computeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + TRecursionDirection const & recDir, + TDPProfile const & dpProfile) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + TTraceValue traceDir = _doComputeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, seqHVal, + seqVVal, scoringScheme, recDir, dpProfile); + if (IsLocalAlignment_::VALUE) + { + TScoreValue cmp = cmpGt(createVector(1), activeCell._score); + _setScoreOfCell(activeCell, TraceBitMap_::NONE, cmp); + _setHorizontalScoreOfCell(activeCell, TraceBitMap_::NONE, cmp); + _setVerticalScoreOfCell(activeCell, TraceBitMap_::NONE, cmp); + return blend(traceDir, TraceBitMap_::NONE, cmp); + } + + return traceDir; +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionDiagonal] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionDiagonal const &, + TDPProfile const &) +{ + activeCell._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + setGapExtension(activeCell, False(), False(), createVector(-1)); + + if (!IsTracebackEnabled_::VALUE) + return TraceBitMap_::NONE; + + return TraceBitMap_::DIAGONAL; +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionZero] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & /*seqHVal*/, + TSequenceVValue const & /*seqVVal*/, + TScoringScheme const & /*scoringScheme*/, + RecursionDirectionZero const &, + DPProfile_ const &) +{ + _scoreOfCell(activeCell) = createVector(0); + return TraceBitMap_::NONE; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_ diff --git a/seqan/align/dp_formula_affine.h b/seqan/align/dp_formula_affine.h new file mode 100644 index 0000000..2e22c0c --- /dev/null +++ b/seqan/align/dp_formula_affine.h @@ -0,0 +1,636 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the affine gap cost functions. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [RecursionDirectionDiagonal, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueGap, + TracebackOff const &, + RecursionDirectionDiagonal const &) +{ + if(activeCell._score < rightCompare) + activeCell._score = rightCompare; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueGap, + TracebackOff const &, + RecursionDirectionDiagonal const &) +{ + activeCell._score = blend(activeCell._score, rightCompare, cmpGt(rightCompare, activeCell._score)); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueGap gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + if(activeCell._score <= rightCompare) + { + activeCell._score = rightCompare; + return TraceBitMap_::DIAGONAL | leftTrace; + } + return leftTrace | gapTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL const & leftTrace, + TTraceValueGap const & gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + TScoreValue cmp = cmpGt(activeCell._score, rightCompare); + activeCell._score = blend(rightCompare, activeCell._score, cmp); + return blend(TraceBitMap_::DIAGONAL | leftTrace, + leftTrace | gapTrace, + cmp); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueGap gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + if(activeCell._score < rightCompare) + { + activeCell._score = rightCompare; // Maximal score comes from diagonal. + return TraceBitMap_::DIAGONAL | leftTrace; // Return trace for Diagonal. + } + if (activeCell._score == rightCompare) // Maximal score comes from previous computed directions and diagonal. + return leftTrace | TraceBitMap_::DIAGONAL | gapTrace; // Return all directions inclusively the flag indicating max from gap. + return leftTrace | gapTrace; // Maximum comes from gap. Return gap value inclusively the flag indicating max from gap. +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL const & leftTrace, + TTraceValueGap const & gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + TScoreValue cmpG = cmpGt(rightCompare, activeCell._score); + TScoreValue cmpE = cmpEq(rightCompare, activeCell._score); + TScoreValue result = leftTrace | gapTrace; + activeCell._score = blend(activeCell._score, rightCompare, cmpG); + result = blend(result, TraceBitMap_::DIAGONAL | leftTrace, cmpG); + return blend(result, leftTrace | TraceBitMap_::DIAGONAL | gapTrace, cmpE); +} + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [RecursionDirectionHorizontal, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueR, + TracebackOff const &, + RecursionDirectionHorizontal const &) +{ + if(activeCell._horizontalScore < rightCompare) + activeCell._score = activeCell._horizontalScore = rightCompare; + else + activeCell._score = activeCell._horizontalScore; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueR, + TracebackOff const &, + RecursionDirectionHorizontal const &) +{ + TScoreValue cmp = cmpGt(rightCompare, activeCell._horizontalScore); + activeCell._horizontalScore = blend(activeCell._horizontalScore, rightCompare, cmp); + activeCell._score = activeCell._horizontalScore; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &, + RecursionDirectionHorizontal const &) +{ + if(activeCell._horizontalScore < rightCompare) + { + activeCell._score = activeCell._horizontalScore = rightCompare; + return rightTrace; + } + activeCell._score = activeCell._horizontalScore; + return leftTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &, + RecursionDirectionHorizontal const &) +{ + TScoreValue cmp = cmpGt(rightCompare, activeCell._horizontalScore); + activeCell._horizontalScore = blend(activeCell._horizontalScore, rightCompare, cmp); + activeCell._score = activeCell._horizontalScore; + return blend(leftTrace, rightTrace, cmp); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &, + RecursionDirectionHorizontal const &) +{ + if(activeCell._horizontalScore < rightCompare) + { + activeCell._score = activeCell._horizontalScore = rightCompare; + return rightTrace; + } + activeCell._score = activeCell._horizontalScore; + if (activeCell._horizontalScore == rightCompare) + return leftTrace | rightTrace; + return leftTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL const & leftTrace, + TTraceValueR const & rightTrace, + TracebackOn > const &, + RecursionDirectionHorizontal const &) +{ + TScoreValue cmpG = cmpGt(rightCompare, activeCell._horizontalScore); + TScoreValue cmpE = cmpEq(rightCompare, activeCell._horizontalScore); + activeCell._horizontalScore = blend(activeCell._horizontalScore, rightCompare, cmpG); + activeCell._score = activeCell._horizontalScore; + + TScoreValue result = leftTrace; + result = blend(result, rightTrace, cmpG); + return blend(result, leftTrace | rightTrace, cmpE); +} + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [RecursionDirectionVertical, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueR, + TracebackOff const &, + RecursionDirectionVertical const &) +{ + if(activeCell._verticalScore < rightCompare) + activeCell._score = activeCell._verticalScore = rightCompare; + else + activeCell._score = activeCell._verticalScore; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueR, + TracebackOff const &, + RecursionDirectionVertical const &) +{ + TScoreValue cmp = cmpGt(rightCompare, activeCell._verticalScore); + activeCell._verticalScore = blend(activeCell._verticalScore, rightCompare, cmp); + activeCell._score = activeCell._verticalScore; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &, + RecursionDirectionVertical const &) +{ + if(activeCell._verticalScore < rightCompare) + { + activeCell._score = activeCell._verticalScore = rightCompare; + return rightTrace; + } + activeCell._score = activeCell._verticalScore; + return leftTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL const & leftTrace, + TTraceValueR const & rightTrace, + TracebackOn > const &, + RecursionDirectionVertical const &) +{ + TScoreValue cmp = cmpGt(rightCompare, activeCell._verticalScore); + activeCell._verticalScore = blend(activeCell._verticalScore, rightCompare, cmp); + activeCell._score = activeCell._verticalScore; + return blend(leftTrace, rightTrace, cmp); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &, + RecursionDirectionVertical const &) +{ + if(activeCell._verticalScore < rightCompare) + { + activeCell._score = activeCell._verticalScore = rightCompare; + return rightTrace; + } + activeCell._score = activeCell._verticalScore; + if (activeCell._verticalScore == rightCompare) + return leftTrace | rightTrace; + return leftTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &, + RecursionDirectionVertical const &) +{ + TScoreValue cmpG = cmpGt(rightCompare, activeCell._verticalScore); + TScoreValue cmpE = cmpEq(rightCompare, activeCell._verticalScore); + activeCell._verticalScore = blend(activeCell._verticalScore, rightCompare, cmpG); + activeCell._score = activeCell._verticalScore; + + TScoreValue result = leftTrace; + result = blend(result, rightTrace, cmpG); + return blend(result, leftTrace | rightTrace, cmpE); +} + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [Vertical vs Horizontal, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TracebackOff const &) +{ + if(activeCell._score < activeCell._horizontalScore) + activeCell._score = activeCell._horizontalScore; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TracebackOff const &) +{ + activeCell._score = blend(activeCell._score, activeCell._horizontalScore, + cmpGt(activeCell._horizontalScore, activeCell._score)); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TracebackOn > const &) +{ + if(activeCell._score < activeCell._horizontalScore) + { + activeCell._score = activeCell._horizontalScore; + return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } + return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TracebackOn > const &) +{ + TScoreValue cmp = cmpGt(activeCell._horizontalScore, activeCell._score); + activeCell._score = blend(activeCell._score, activeCell._horizontalScore, cmp); + return blend(TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmp); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TracebackOn > const &) +{ + if(activeCell._score < activeCell._horizontalScore) + { + activeCell._score = activeCell._horizontalScore; + return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } + if (activeCell._score == activeCell._horizontalScore) + return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TracebackOn > const &) +{ + TScoreValue cmpG = cmpGt(activeCell._horizontalScore, activeCell._score); + TScoreValue cmpE = cmpEq(activeCell._horizontalScore, activeCell._score); + activeCell._score = blend(activeCell._score, activeCell._horizontalScore, cmpG); + + return blend(blend(TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmpG), + TraceBitMap_::MAX_FROM_VERTICAL_MATRIX | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmpE); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionAllDirection, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionAll const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + // Now we have to find a smart version to solve this problem. Which is not as easy I would think. + activeCell._horizontalScore = _horizontalScoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + TScoreValue tmpScore = _scoreOfCell(previousHorizontal) + scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal); + TTraceValue tvGap = _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::HORIZONTAL, + TraceBitMap_::HORIZONTAL_OPEN, + TTracebackConfig(), + RecursionDirectionHorizontal()); + + // Now we can decide for the optimal score in horizontal score or not? + activeCell._verticalScore = _verticalScoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + tmpScore = _scoreOfCell(previousVertical) + scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal); + tvGap |= _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::VERTICAL, + TraceBitMap_::VERTICAL_OPEN, + TTracebackConfig(), + RecursionDirectionVertical()); + + // Finds the maximum between the vertical and the horizontal matrix. Stores the flag for coming from a potential direction. + TTraceValue tvMax = _internalComputeScore(activeCell, TTracebackConfig()); // Stores from where the maximal score comes. + tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, tmpScore, tvGap, tvMax, TTracebackConfig(), RecursionDirectionDiagonal()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionUpperDiagonalDirection, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionUpperDiagonal const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + activeCell._horizontalScore = _horizontalScoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + activeCell._verticalScore = DPCellDefaultInfinity >::VALUE; + TScoreValue tmpScore = _scoreOfCell(previousHorizontal) + scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal); + TTraceValue tv = _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::HORIZONTAL, + TraceBitMap_::HORIZONTAL_OPEN, + TTracebackConfig(), + RecursionDirectionHorizontal()); + tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, + tmpScore, + tv, + TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + TTracebackConfig(), + RecursionDirectionDiagonal()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionLowerDiagonal, AffineGaps] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionLowerDiagonal const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + activeCell._verticalScore = _verticalScoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + TScoreValue tmpScore = _scoreOfCell(previousVertical) + scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal); + + activeCell._horizontalScore = DPCellDefaultInfinity >::VALUE; + // This computes the difference between the vertical extend and vertical open. + TTraceValue tv = _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::VERTICAL, + TraceBitMap_::VERTICAL_OPEN, + TTracebackConfig(), + RecursionDirectionVertical()); + + // Up to here, activeCell stores the highest value of vertical or vertical open. + tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, + tmpScore, + tv, + TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TTracebackConfig(), + RecursionDirectionDiagonal()); // Now we have this problem. How do we determine if the max comes from the vertical distance. +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionHorizontalDirection] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionHorizontal const &, + DPProfile_ const &) +{ + TScoreValue tmpGapOpenHorizontal = _scoreOfCell(previousHorizontal) + scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal); + activeCell._horizontalScore = _horizontalScoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + + activeCell._verticalScore = DPCellDefaultInfinity >::VALUE; + return _internalComputeScore(activeCell, + tmpGapOpenHorizontal, + TraceBitMap_::HORIZONTAL, + TraceBitMap_::HORIZONTAL_OPEN, + TTracebackConfig(), + RecursionDirectionHorizontal()) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionVerticalDirection] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionVertical const &, + DPProfile_ const &) +{ + TScoreValue tmpGapOpenVertical = _scoreOfCell(previousVertical) + scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal); + activeCell._verticalScore = _verticalScoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + + // Here we distinguish between vertical and vertical open. + activeCell._horizontalScore = DPCellDefaultInfinity >::VALUE; + return _internalComputeScore(activeCell, + tmpGapOpenVertical, + TraceBitMap_::VERTICAL, + TraceBitMap_::VERTICAL_OPEN, + TTracebackConfig(), + RecursionDirectionVertical()) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_ diff --git a/seqan/align/dp_formula_dynamic.h b/seqan/align/dp_formula_dynamic.h new file mode 100644 index 0000000..1c8fe8b --- /dev/null +++ b/seqan/align/dp_formula_dynamic.h @@ -0,0 +1,689 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the score function for dynamic gap costs published in +// "Dynamic Gaps Selector: A Smith Waterman Sequence Alignment Algorithm with +// Affine Gap Model Optimization" by Gianvito Urgese et al. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_DP_FORMULA_DYNAMIC_H_ +#define INCLUDE_SEQAN_ALIGN_DP_FORMULA_DYNAMIC_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [RecursionDirectionDiagonal, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & diagCompare, + TTraceValueL, + TTraceValueGap, + TracebackOff const &, + RecursionDirectionDiagonal const &) +{ + if(_scoreOfCell(activeCell) < diagCompare) + { + activeCell._score = diagCompare; + setGapExtension(activeCell, False(), False()); + return TraceBitMap_::NONE; + } + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & diagCompare, + TTraceValueL, + TTraceValueGap, + TracebackOff const &, + RecursionDirectionDiagonal const &) +{ + TScoreValue cmp = cmpGt(diagCompare, _scoreOfCell(activeCell)); + activeCell._score = blend(activeCell._score, diagCompare, cmp); + setGapExtension(activeCell, False(), False(), cmp); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & diagCompare, + TTraceValueL leftTrace, + TTraceValueGap gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + if(_scoreOfCell(activeCell) <= diagCompare) + { + activeCell._score = diagCompare; + setGapExtension(activeCell, False(), False()); + return TraceBitMap_::DIAGONAL | leftTrace; + } + return leftTrace | gapTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & diagCompare, + TTraceValueL const & leftTrace, + TTraceValueGap const & gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + TScoreValue cmp = cmpGt(_scoreOfCell(activeCell), diagCompare); + activeCell._score = blend(diagCompare, activeCell._score, cmp); + setGapExtension(activeCell, False(), False(), cmp); + return blend(TraceBitMap_::DIAGONAL | leftTrace, + leftTrace | gapTrace, + cmp); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & diagCompare, + TTraceValueL leftTrace, + TTraceValueGap gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + if(_scoreOfCell(activeCell) < diagCompare) + { + activeCell._score = diagCompare; // Maximal score comes from diagonal. + setGapExtension(activeCell, False(), False()); + return TraceBitMap_::DIAGONAL | leftTrace; // Return trace for Diagonal. + } + if (_scoreOfCell(activeCell) == diagCompare) // Maximal score comes from previous computed directions and diagonal. + return leftTrace | TraceBitMap_::DIAGONAL | gapTrace; // Return all directions inclusively the flag indicating max from gap. + + return leftTrace | gapTrace; // Maximum comes from gap. Return gap value inclusively the flag indicating max from gap. +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & diagCompare, + TTraceValueL const & leftTrace, + TTraceValueGap const & gapTrace, + TracebackOn > const &, + RecursionDirectionDiagonal const &) +{ + TScoreValue cmp = cmpGt(diagCompare, _scoreOfCell(activeCell)); + activeCell._score = blend(activeCell._score, diagCompare, cmp); + setGapExtension(activeCell, False(), False(), cmp); + return blend(blend(leftTrace | gapTrace, + TraceBitMap_::DIAGONAL | leftTrace, + cmp), + leftTrace | TraceBitMap_::DIAGONAL | gapTrace, + cmpEq(_scoreOfCell(activeCell), diagCompare)); +} + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [RecursionDirectionHorizontal, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOff const &, + RecursionDirectionHorizontal const &) +{ + if(!isGapExtension(prevCell, DynamicGapExtensionHorizontal())) + activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenHorizontal(score, valH, valV); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOff const &, + RecursionDirectionHorizontal const &) +{ + activeCell._score = blend(_scoreOfCell(prevCell) + scoreGapOpenHorizontal(score, valH, valV), activeCell._score, + isGapExtension(prevCell, DynamicGapExtensionHorizontal())); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOn const &, + RecursionDirectionHorizontal const &) +{ + if (!isGapExtension(prevCell, DynamicGapExtensionHorizontal())) + { + activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenHorizontal(score, valH, valV); + return TraceBitMap_::HORIZONTAL_OPEN; + } + return TraceBitMap_::HORIZONTAL; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOn const &, + RecursionDirectionHorizontal const &) +{ + activeCell._score = blend(_scoreOfCell(prevCell) + scoreGapOpenHorizontal(score, valH, valV), activeCell._score, + isGapExtension(prevCell, DynamicGapExtensionHorizontal())); + return TraceBitMap_::HORIZONTAL; +} + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [RecursionDirectionVertical, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOff const &, + RecursionDirectionVertical const &) +{ + if(!isGapExtension(prevCell, DynamicGapExtensionVertical())) + activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenVertical(score, valH, valV); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOff const &, + RecursionDirectionVertical const &) +{ + activeCell._score = blend(_scoreOfCell(prevCell) + scoreGapOpenVertical(score, valH, valV), activeCell._score, + isGapExtension(prevCell, DynamicGapExtensionVertical())); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOn const &, + RecursionDirectionVertical const &) +{ + if (!isGapExtension(prevCell, DynamicGapExtensionVertical())) + { + activeCell._score = _scoreOfCell(prevCell) + scoreGapOpenVertical(score, valH, valV); + return TraceBitMap_::VERTICAL_OPEN; + } + return TraceBitMap_::VERTICAL; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + DPCell_ const & prevCell, + TValueH const & valH, + TValueV const & valV, + TScore const & score, + TracebackOn const &, + RecursionDirectionVertical const &) +{ + TScoreValue cmp = isGapExtension(prevCell, DynamicGapExtensionVertical()); + activeCell._score = blend(_scoreOfCell(prevCell) + scoreGapOpenVertical(score, valH, valV), activeCell._score, cmp); + return blend(TraceBitMap_::VERTICAL_OPEN, + TraceBitMap_::VERTICAL, + cmp); +} + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore [Vertical vs Horizontal, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & horizontalComp, + TracebackOff const &) +{ + if(_scoreOfCell(activeCell) < horizontalComp) + { + activeCell._score = horizontalComp; + setGapExtension(activeCell, False(), True()); + return TraceBitMap_::NONE; + } + setGapExtension(activeCell, True(), False()); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & horizontalComp, + TracebackOff const &) +{ + TScoreValue cmp = cmpGt(horizontalComp, _scoreOfCell(activeCell)); + activeCell._score = blend(activeCell._score, horizontalComp, cmp); + setGapExtension(activeCell, False(), True(), cmp); + setGapExtension(activeCell, True(), False(), cmpEq(cmp, TraceBitMap_::NONE)); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & horizontalComp, + TracebackOn > const &) +{ + if(_scoreOfCell(activeCell) < horizontalComp) + { + activeCell._score = horizontalComp; + setGapExtension(activeCell, False(), True()); + return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } + setGapExtension(activeCell, True(), False()); + return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & horizontalComp, + TracebackOn > const &) +{ + TScoreValue cmp = cmpGt(horizontalComp, _scoreOfCell(activeCell)); + activeCell._score = blend(activeCell._score, horizontalComp, cmp); + setGapExtension(activeCell, False(), True(), cmp); + setGapExtension(activeCell, True(), False(), cmpEq(cmp, TraceBitMap_::NONE)); + return blend(TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmp); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & horizontalComp, + TracebackOn > const &) +{ + if(_scoreOfCell(activeCell) < horizontalComp) + { + setGapExtension(activeCell, False(), True()); + activeCell._score = horizontalComp; + return TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } + if (_scoreOfCell(activeCell) == horizontalComp) + { + setGapExtension(activeCell, True(), True()); + return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; + } + setGapExtension(activeCell, True(), False()); + return TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & horizontalComp, + TracebackOn > const &) +{ + TScoreValue cmpG = cmpGt(horizontalComp, _scoreOfCell(activeCell)); + TScoreValue cmpE = cmpEq(horizontalComp, _scoreOfCell(activeCell)); + setGapExtension(activeCell, True(), False(), createVector(-1)); + setGapExtension(activeCell, False(), True(), cmpG); + setGapExtension(activeCell, True(), True(), cmpE); + + TScoreValue result = TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; + result = blend(result, + TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmpG); + return blend(result, + TraceBitMap_::MAX_FROM_VERTICAL_MATRIX + | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + cmpE); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionAllDirection, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionAll const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + typedef typename std::decay::type TCell; + + // Compute best alignment from either horizontal open or extension. + TCell tmpScore(_scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal)); + TTraceValue tvGap = _internalComputeScore(tmpScore, previousHorizontal, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionHorizontal()); + + // Compute best alignment between vertical and vertical open gap. + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + tvGap |= _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionVertical()); + + // Finds the maximum between the vertical and the horizontal matrix. Stores the flag for coming from a potential direction. + TTraceValue tvMax = _internalComputeScore(activeCell, tmpScore._score, TTracebackConfig()); // Stores from where the maximal score comes. + tmpScore._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, tmpScore._score, tvGap, tvMax, TTracebackConfig(), RecursionDirectionDiagonal()); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionAll const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + typedef typename std::decay::type TCell; + + // Compute best alignment from either horizontal open or extension. + TCell tmpScore = {_scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal), + typename TCell::TFlagMaskType()}; + TTraceValue tvGap = _internalComputeScore(tmpScore, previousHorizontal, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionHorizontal()); + + // Compute best alignment between vertical and vertical open gap. + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + tvGap |= _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionVertical()); + + // Finds the maximum between the vertical and the horizontal matrix. Stores the flag for coming from a potential direction. + TTraceValue tvMax = _internalComputeScore(activeCell, tmpScore._score, TTracebackConfig()); // Stores from where the maximal score comes. + tmpScore._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, tmpScore._score, tvGap, tvMax, TTracebackConfig(), RecursionDirectionDiagonal()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionUpperDiagonalDirection, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionUpperDiagonal const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + // This computes the difference between the horizontal extend and horizontal open. + activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + TTraceValue tv = _internalComputeScore(activeCell, previousHorizontal, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionHorizontal()); + + setGapExtension(activeCell, False(), True()); + TScoreValue tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, tmpScore, tv, TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + TTracebackConfig(),RecursionDirectionDiagonal()); +} + + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionUpperDiagonal const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + // This computes the difference between the horizontal extend and horizontal open. + activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + TTraceValue tv = _internalComputeScore(activeCell, previousHorizontal, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionHorizontal()); + + setGapExtension(activeCell, False(), True(), createVector(-1)); + TScoreValue tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, + tmpScore, + tv, + TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + TTracebackConfig(), + RecursionDirectionDiagonal()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionLowerDiagonal, DynamicGaps] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionLowerDiagonal const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + // This computes the difference between the vertical extend and vertical open. + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + TTraceValue tv = _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionVertical()); + setGapExtension(activeCell, True(), False()); + TScoreValue tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, tmpScore, tv, TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TTracebackConfig(), RecursionDirectionDiagonal()); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionLowerDiagonal const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + + // This computes the difference between the vertical extend and vertical open. + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + TTraceValue tv = _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), RecursionDirectionVertical()); + setGapExtension(activeCell, True(), False(), createVector(-1)); + TScoreValue tmpScore = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, + tmpScore, + tv, + TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TTracebackConfig(), + RecursionDirectionDiagonal()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionHorizontalDirection] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionHorizontal const & tag, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + setGapExtension(activeCell, False(), True()); + return _internalComputeScore(activeCell, previousHorizontal, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), tag) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionHorizontal const & tag, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + setGapExtension(activeCell, False(), True(), createVector(-1)); + return _internalComputeScore(activeCell, previousHorizontal, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), tag) | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionVerticalDirection] +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionVertical const & tag, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + setGapExtension(activeCell, True(), False()); + return _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), tag) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionVertical const & tag, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + setGapExtension(activeCell, True(), False(), createVector(-1)); + return _internalComputeScore(activeCell, previousVertical, seqHVal, seqVVal, scoringScheme, + TTracebackConfig(), tag) | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +} // namespace seqan + +#endif // INCLUDE_SEQAN_ALIGN_DP_FORMULA_DYNAMIC_H_ diff --git a/seqan/align/dp_formula_linear.h b/seqan/align/dp_formula_linear.h new file mode 100644 index 0000000..45ed936 --- /dev/null +++ b/seqan/align/dp_formula_linear.h @@ -0,0 +1,291 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Defines the methods to compute the score when using linear gap costs. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _internalComputeScore() +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueR, + TracebackOff const &) +{ + if (activeCell._score < rightCompare) + activeCell._score = rightCompare; + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL, + TTraceValueR, + TracebackOff const &) +{ + TScoreValue cmp = cmpGt(rightCompare, activeCell._score); + activeCell._score = blend(activeCell._score, rightCompare, cmp); + return TraceBitMap_::NONE; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &) +{ + if (activeCell._score < rightCompare) + { + activeCell._score = rightCompare; + return rightTrace; + } + return leftTrace; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL const & leftTrace, + TTraceValueR const & rightTrace, + TracebackOn > const &) +{ + TScoreValue cmp = cmpGt(rightCompare, activeCell._score); + activeCell._score = blend(activeCell._score, rightCompare, cmp); + return blend(leftTrace, rightTrace, cmp); +} + +template + inline SEQAN_FUNC_ENABLE_IF(Not > >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL leftTrace, + TTraceValueR rightTrace, + TracebackOn > const &) +{ + if (activeCell._score < rightCompare) + { + activeCell._score = rightCompare; + return rightTrace; + } + return (activeCell._score == rightCompare) ? (rightTrace | leftTrace) : (leftTrace); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename TraceBitMap_::Type) +_internalComputeScore(DPCell_ & activeCell, + TScoreValue const & rightCompare, + TTraceValueL const & leftTrace, + TTraceValueR const & rightTrace, + TracebackOn > const &) +{ + // Check for greater values. + TScoreValue cmp = cmpGt(activeCell._score, rightCompare); // cmp greater + activeCell._score = blend(rightCompare, activeCell._score, cmp); // activeCell._score + + // Check for equality. + return blend(blend(rightTrace, leftTrace, cmp), leftTrace | rightTrace, cmpEq(rightCompare, activeCell._score)); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionAll, LinearGaps] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionAll const &, + DPProfile_ const &) +{ + typedef typename TraceBitMap_::Type TTraceValue; + activeCell._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + + TScoreValue tmpScore = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + + TTraceValue tv = _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::DIAGONAL, + TraceBitMap_::VERTICAL | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TTracebackConfig()); + tmpScore = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, + tmpScore, + tv, + TraceBitMap_::HORIZONTAL | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + TTracebackConfig()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionUpperDiagonal, LinearGaps] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionUpperDiagonal const &, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + TScoreValue tmpScore = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + return _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::DIAGONAL, + TraceBitMap_::HORIZONTAL | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX, + TTracebackConfig()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionLowerDiagonal, LinearGaps] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionLowerDiagonal const &, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal); + TScoreValue tmpScore = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + + return _internalComputeScore(activeCell, + tmpScore, + TraceBitMap_::DIAGONAL, + TraceBitMap_::VERTICAL | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX, + TTracebackConfig()); +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionHorizontal] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & previousHorizontal, + DPCell_ const & /*previousVertical*/, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionHorizontal const &, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal); + + if (!IsTracebackEnabled_::VALUE) + return TraceBitMap_::NONE; + + return TraceBitMap_::HORIZONTAL + | TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX; +} + +// ---------------------------------------------------------------------------- +// Function _doComputeScore [RecursionDirectionVertical] +// ---------------------------------------------------------------------------- + +template +inline typename TraceBitMap_::Type +_doComputeScore(DPCell_ & activeCell, + DPCell_ const & /*previousDiagonal*/, + DPCell_ const & /*previousHorizontal*/, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + RecursionDirectionVertical const &, + DPProfile_ const &) +{ + activeCell._score = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal); + + if (!IsTracebackEnabled_::VALUE) + return TraceBitMap_::NONE; + + return TraceBitMap_::VERTICAL + | TraceBitMap_::MAX_FROM_VERTICAL_MATRIX; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_ diff --git a/seqan/align/dp_matrix.h b/seqan/align/dp_matrix.h new file mode 100644 index 0000000..1e853c5 --- /dev/null +++ b/seqan/align/dp_matrix.h @@ -0,0 +1,644 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Ren� Rahn +// ========================================================================== +// This file implements the class DPMatrix and its specialization +// FullDPMatrix. The DPMatrix is a wrapper class around the Matrix +// class. Thus we can implement different specializations for the dp-matrix +// that are used through the different dp-algorithms. For example, we need +// a full dp matrix to store the traceback or the score for the Waterman- +// Eggert algorithm, while for the other dp-algorithms we only need one +// column vector to compute the scores. The default dp-matrix specialization +// can be selected using a special meta-function. +// ========================================================================== + +// TODO(holtgrew): Documentation in this header necessary or internal only? + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +struct DefaultScoreMatrixSpec_; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag MatrixMember +// ---------------------------------------------------------------------------- + +struct DPMatrixMember_; +typedef Tag DPMatrixMember; + +// ---------------------------------------------------------------------------- +// Tag SparseDPMatrix +// ---------------------------------------------------------------------------- + +struct SparseDPMatrix_; +typedef Tag SparseDPMatrix; + +// ---------------------------------------------------------------------------- +// Tag FullDPMatrix +// ---------------------------------------------------------------------------- + +struct FullDPMatrix_; +typedef Tag FullDPMatrix; + +// ---------------------------------------------------------------------------- +// Enum DPMatrixDimension +// ---------------------------------------------------------------------------- + +// Used to globally specify the correct dimension and the correct size of +// dimension for the dp matrix. +struct DPMatrixDimension_ +{ + typedef unsigned int TValue; + + static const TValue VERTICAL = 0u; + static const TValue HORIZONTAL = 1u; + static const TValue DIMENSION = 2u; +}; + +// ---------------------------------------------------------------------------- +// Class DPMatrix_ +// ---------------------------------------------------------------------------- + +// The dp matrix used as a score matrix and as a trace-back matrix. +template +class DPMatrix_ +{}; + + +// Default dp matrix implementation stores all cells of the dp matrix in the +// underlying two-dimensional matrix. +template +class DPMatrix_ +{ +public: + + typedef typename Member::Type THost; + + Holder data_host; // The host containing the actual matrix. + + DPMatrix_() : + data_host() + { + create(data_host); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction DefaultScoreMatrixSpec_ +// ---------------------------------------------------------------------------- + +// This meta-function determines the default specialization of dp matrix +// based on the given algorithm tag. +template +struct DefaultScoreMatrixSpec_ +{ + typedef SparseDPMatrix Type; +}; + +// TODO(rmaerker): Move to WatermanEggert implementation? +template <> +struct DefaultScoreMatrixSpec_ > +{ + typedef FullDPMatrix Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction DataHost_ +// ---------------------------------------------------------------------------- + +// Returns the type of the underlying matrix. +template +struct Member, DPMatrixMember> +{ + typedef Matrix Type; +}; + +template +struct Member const, DPMatrixMember> +{ + typedef Matrix const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction SizeArr_ +// ---------------------------------------------------------------------------- + +// Returns the type of the containers to store the dimensions and the factors +// in order to move properly in the matrix. +template +struct SizeArr_ {}; + +template +struct SizeArr_ > +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Member::Type TDataHost_; + typedef typename SizeArr_::Type Type; +}; + +template +struct SizeArr_ const> +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Member::Type TDataHost_; + typedef typename SizeArr_::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Spec +// ---------------------------------------------------------------------------- + +template +struct Spec > +{ + typedef TMatrixSpec Type; +}; + +template +struct Spec const>: + Spec >{}; + + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +template +struct Value > +{ + typedef TValue Type; +}; + +template +struct Value const> +{ + typedef TValue const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +template +struct Reference > +{ + typedef TValue & Type; +}; + +template +struct Reference const> +{ + typedef TValue const & Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction GetValue +// ---------------------------------------------------------------------------- + +template +struct GetValue >: + Reference >{}; + +template +struct GetValue const>: + Reference const>{}; + +// ---------------------------------------------------------------------------- +// Metafunction Position +// ---------------------------------------------------------------------------- + +template +struct Position > +{ + typedef typename DPMatrix_::THost TDataMatrix_; + typedef typename Position::Type Type; +}; + +template +struct Position const>: + Position >{}; + +// ---------------------------------------------------------------------------- +// Metafunction Size +// ---------------------------------------------------------------------------- + +template +struct Size > +{ + typedef typename DPMatrix_::THost TDataMatrix_; + typedef typename Size::Type Type; +}; + +template +struct Size const>: + Size >{}; + +// ---------------------------------------------------------------------------- +// Metafunction Host +// ---------------------------------------------------------------------------- + +template +struct Host > +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Member::Type TDataMatrix_; + typedef typename Host::Type Type; +}; + +template +struct Host const> +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Member::Type TDataMatrix_; + typedef typename Host::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Iterator +// ---------------------------------------------------------------------------- + +// There are two iterator types. The standard iterator returns a +// non-rooted iterator to the underlying vector of the hosted two-dimensional +// matrix. The rooted iterator returns the iterator defined by the +// hosted matrix object which is a position iterator. +template +struct Iterator, Standard const> +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Host::Type THost_; + typedef typename Iterator::Type Type; +}; + +template +struct Iterator const, Standard const> +{ + typedef DPMatrix_ const TDPMatrix_; + typedef typename Host::Type THost_; + typedef typename Iterator::Type Type; +}; + +template +struct Iterator, Rooted const> +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Member::Type TDataMatrix_; + typedef typename Iterator::Type Type; +}; + +template +struct Iterator const, Rooted const> +{ + typedef DPMatrix_ TDPMatrix_; + typedef typename Member::Type TDataMatrix_; + typedef typename Iterator::Type Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _checkCorrectDimension() +// ---------------------------------------------------------------------------- + +// Checks whether a given value applies to the correct dimension. +inline bool _checkCorrectDimension(DPMatrixDimension_::TValue dim) +{ + return dim < DPMatrixDimension_::DIMENSION; +} + +// ---------------------------------------------------------------------------- +// Function _dataHost() +// ---------------------------------------------------------------------------- + +// Returns a reference to the hosted matrix. +template +inline Holder >::Type> & +_dataHost(DPMatrix_& dpMatrix) +{ + return _dataHost(value(dpMatrix.data_host)); +} + +template +inline Holder >::Type> const & +_dataHost(DPMatrix_ const & dpMatrix) +{ + return _dataHost(value(dpMatrix.data_host)); +} + +// ---------------------------------------------------------------------------- +// Function _dataLengths() +// ---------------------------------------------------------------------------- + +// Returns a reference to the _dataLengths container of the hosted matrix. +template +inline typename SizeArr_ >::Type & +_dataLengths(DPMatrix_&dpMatrix) +{ + return _dataLengths(value(dpMatrix.data_host)); +} + +template +inline typename SizeArr_ const>::Type & +_dataLengths(DPMatrix_ const & dpMatrix) +{ + return _dataLengths(value(dpMatrix.data_host)); +} + +// ---------------------------------------------------------------------------- +// Function _dataFactors() +// ---------------------------------------------------------------------------- + +// Returns a reference to the _dataFactors container of the hosted matrix. +template +inline typename SizeArr_ >::Type & +_dataFactors(DPMatrix_&dpMatrix) +{ + return _dataFactors(value(dpMatrix.data_host)); +} + +template +inline typename SizeArr_ const>::Type & +_dataFactors(DPMatrix_ const & dpMatrix) +{ + return _dataFactors(value(dpMatrix.data_host)); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +// Returns the value of the matrix at the given host position. +template +inline typename Reference >::Type +value(DPMatrix_ & dpMatrix, + TPosition const & pos) +{ + return value(value(dpMatrix.data_host), pos); +} + +template +inline typename Reference const>::Type +value(DPMatrix_ const & dpMatrix, + TPosition const & pos) +{ + return value(value(dpMatrix.data_host), pos); +} + +// Returns the value of the matrix at the two given coordinates. +template +inline typename Reference >::Type +value(DPMatrix_ & dpMatrix, + TPositionV const & posDimV, + TPositionH const & posDimH) +{ + return value(value(dpMatrix.data_host), posDimV, posDimH); +} + +template +inline typename Reference const>::Type +value(DPMatrix_ const & dpMatrix, + TPositionV const & posDimV, + TPositionH const & posDimH) +{ + return value(value(dpMatrix.data_host), posDimV, posDimH); +} + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +// Returns the length of a given dimension. +template +inline typename Size const>::Type +length(DPMatrix_ const & dpMatrix, + unsigned int dimension) +{ + SEQAN_ASSERT(_checkCorrectDimension(dimension)); + + return length(value(dpMatrix.data_host), dimension); +} + +// Returns the overall length of the underlying vector of the hosted matrix. +template +inline typename Size const>::Type +length(DPMatrix_ const & dpMatrix) +{ + return length(value(dpMatrix.data_host)); // Note that even if the dimensional lengths are set but the matrix was not resized + // this function returns 0 or the previous length of the host before the resize. +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +inline void +clear(DPMatrix_ & dpMatrix) +{ + clear(_dataLengths(dpMatrix)); + resize(_dataLengths(dpMatrix), 2, 0); + clear(_dataFactors(dpMatrix)); + resize(_dataFactors(dpMatrix), 2, 0); + _dataFactors(dpMatrix)[DPMatrixDimension_::VERTICAL] = 1u; + clear(host(dpMatrix)); +} + +// ---------------------------------------------------------------------------- +// Function empty() +// ---------------------------------------------------------------------------- + +template +inline bool +empty(DPMatrix_ const & dpMatrix) +{ + return empty(host(dpMatrix)); +} + +// ---------------------------------------------------------------------------- +// Function setLength() +// ---------------------------------------------------------------------------- + +// Sets the new length of a given dimension. +template +inline void +setLength(DPMatrix_ & dpMatrix, + unsigned int dimension, + TSize const & newLength) +{ + SEQAN_ASSERT(_checkCorrectDimension(dimension)); + setLength(value(dpMatrix.data_host), dimension, newLength); +} + +// ---------------------------------------------------------------------------- +// Function updateFactors() +// ---------------------------------------------------------------------------- + +template +inline typename Size >::Type +updateFactors(DPMatrix_ & dpMatrix) +{ + typedef typename Size >::Type TSize; + + TSize factor_ = _dataFactors(dpMatrix)[0] * length(dpMatrix, 0); + for (unsigned int i = 1; (factor_ > 0) && (i < dimension(value(dpMatrix.data_host))); ++i) + { + _dataFactors(dpMatrix)[i] = factor_; + factor_ *= length(dpMatrix, i); + } + return factor_; +} + +// ---------------------------------------------------------------------------- +// Function resize() +// ---------------------------------------------------------------------------- + +// Resizes the matrix. Note, the lengths of the dimensions have to be set before. +template +inline void +resize(DPMatrix_ & dpMatrix) +{ + typedef typename Size >::Type TSize; + + TSize reqSize = updateFactors(dpMatrix); + if (reqSize >= length(dpMatrix)) + resize(host(dpMatrix), reqSize, Exact()); +} + +template +inline void +resize(DPMatrix_ & dpMatrix, + TValue const & fillValue) +{ + typedef typename Size >::Type TSize; + + TSize reqSize = updateFactors(dpMatrix); + if (reqSize >= length(dpMatrix)) + resize(host(dpMatrix), reqSize, fillValue, Exact()); +} + +// ---------------------------------------------------------------------------- +// Function begin() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator, Standard const>::Type +begin(DPMatrix_ & dpMatrix, Standard const) +{ + return begin(host(dpMatrix)); +} + +template +inline typename Iterator const, Standard const>::Type +begin(DPMatrix_ const & dpMatrix, Standard const) +{ + return begin(host(dpMatrix)); +} + +template +inline typename Iterator, Rooted const>::Type +begin(DPMatrix_ & dpMatrix, Rooted const) +{ + return begin(value(dpMatrix.data_host)); +} + +template +inline typename Iterator const, Rooted const>::Type +begin(DPMatrix_ const & dpMatrix, Rooted const) +{ + return begin(value(dpMatrix.data_host)); +} + +// ---------------------------------------------------------------------------- +// Function end() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator, Standard const>::Type +end(DPMatrix_ & dpMatrix, Standard const) +{ + return end(host(dpMatrix)); +} + +template +inline typename Iterator const, Standard const>::Type +end(DPMatrix_ const & dpMatrix, Standard const) +{ + return end(host(dpMatrix)); +} + +template +inline typename Iterator, Rooted const>::Type +end(DPMatrix_ & dpMatrix, Rooted const) +{ + return end(value(dpMatrix.data_host)); +} + +template +inline typename Iterator const, Rooted const>::Type +end(DPMatrix_ const & dpMatrix, Rooted const) +{ + return end(value(dpMatrix.data_host)); +} + +// ---------------------------------------------------------------------------- +// Function coordinate() +// ---------------------------------------------------------------------------- + +// Returns the coordinate of a host positio in a given dimension. +template +inline typename Position >::Type +coordinate(DPMatrix_ const & dpMatrix, + TPosition hostPos, + typename DPMatrixDimension_::TValue dimension) +{ + return coordinate(value(dpMatrix.data_host), hostPos, dimension); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_H_ diff --git a/seqan/align/dp_matrix_navigator.h b/seqan/align/dp_matrix_navigator.h new file mode 100644 index 0000000..a39100b --- /dev/null +++ b/seqan/align/dp_matrix_navigator.h @@ -0,0 +1,230 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Implements the DPMatrixNavigator. +// This is the parent class for all navigators that parse over a dp-matrix. +// This class facilitates the correct navigation through the dp-matrix for +// all kind of standard dp-algorithms. At the moment there only exists the +// NavigateColumnWise but this can be complemented by other navigation +// structures like anti-diagonals or in tiles. +// The Navigator can be specialized with three parameters. The first one is +// the used specialization of the dp-matrix (FullDPMatrix or SparseDPMatrix). +// the second parameter decides if it is a navigator for a score matrix or +// a trace matrix. And the last parameter determines the sort of navigation. +// ========================================================================== + +// TODO(holtgrew): Documentation in this header necessary or internal only? + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag DPScoreMatrix +// ---------------------------------------------------------------------------- + +// Used to select a navigator for the score matrix. +struct DPScoreMatrix_; +typedef Tag DPScoreMatrix; + +// ---------------------------------------------------------------------------- +// Tag DPTraceMatrix +// ---------------------------------------------------------------------------- + +// Used to select a navigator for the trace matrix. +template +struct DPTraceMatrix {}; + +// ---------------------------------------------------------------------------- +// Tag NavigateColumnWise +// ---------------------------------------------------------------------------- + +// Facilitates column wise navigation through the dp-matrix. +struct NavigateColumnWise_; +typedef Tag NavigateColumnWise; + +// ---------------------------------------------------------------------------- +// Class DPMatrixNavigator_ +// ---------------------------------------------------------------------------- + +template +class DPMatrixNavigator_; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +template +struct Value > +{ + typedef typename Value::Type Type; +}; + +template +struct Value const> +{ + typedef typename Value::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +template +struct Reference > +{ + typedef typename Reference::Type Type; +}; + +template +struct Reference const> +{ + typedef typename Reference::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Container +// ---------------------------------------------------------------------------- + +template +struct Container > +{ + typedef TDPMatrix Type; +}; + +template +struct Container const> +{ + typedef TDPMatrix const Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function assignValue() +// ---------------------------------------------------------------------------- + +template +inline void +assignValue(DPMatrixNavigator_ & dpNavigator, + TValue const & element) +{ + assignValue(dpNavigator._activeColIterator, element); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +template +inline typename Reference >::Type +value(DPMatrixNavigator_ & dpNavigator) +{ + return value(dpNavigator._activeColIterator); +} + +template +inline typename Reference const>::Type +value(DPMatrixNavigator_ const & dpNavigator) +{ + return value(dpNavigator._activeColIterator); +} + +template +inline typename Reference >::Type +value(DPMatrixNavigator_ & dpNavigator, + TCoordinateH const & coordinateV, + TCoordinateV const & coordinateH) +{ + return value(container(dpNavigator), coordinateV, coordinateH); +} + +template +inline typename Reference const>::Type +value(DPMatrixNavigator_ const & dpNavigator, + TCoordinateV const & coordinateV, + TCoordinateH const & coordinateH) +{ + return value(container(dpNavigator), coordinateV, coordinateH); +} + +// ---------------------------------------------------------------------------- +// Function coordinate() +// ---------------------------------------------------------------------------- + +template +inline typename DPMatrixDimension_::TValue +coordinate(DPMatrixNavigator_ const & dpNavigator, + typename DPMatrixDimension_::TValue const & dimension) +{ + // Simply delegate to coordinate of underlying matrix. + return coordinate(value(dpNavigator._ptrDataContainer), + dpNavigator._activeColIterator - begin(*dpNavigator._ptrDataContainer, Standard()), dimension); +} + +// ---------------------------------------------------------------------------- +// Function container() +// ---------------------------------------------------------------------------- + +template +inline typename Container >::Type & +container(DPMatrixNavigator_ & dpNavigator) +{ + return *dpNavigator._ptrDataContainer; +} + +template +inline typename Container const>::Type & +container(DPMatrixNavigator_ const & dpNavigator) +{ + return *dpNavigator._ptrDataContainer; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_H_ diff --git a/seqan/align/dp_matrix_navigator_score_matrix.h b/seqan/align/dp_matrix_navigator_score_matrix.h new file mode 100644 index 0000000..9110b49 --- /dev/null +++ b/seqan/align/dp_matrix_navigator_score_matrix.h @@ -0,0 +1,407 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// The navigator for the full score dp-matrix. We need two iterators over the +// current column and the previous column. We also store the three neighboring +// cells needed for the recursion formula. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class DPMatrixNavigator [FullDPMatrix, ScoreMatrix] +// ---------------------------------------------------------------------------- + +// The navigator for the score matrix. +// +// This navigator runs on a FullDPMatrix while it navigates column wise. +template +class DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> +{ +public: + typedef DPMatrix_ TDPMatrix_; + typedef typename Pointer_::Type TDPMatrixPointer_; + typedef typename Iterator::Type TDPMatrixIterator; + + TDPMatrixPointer_ _ptrDataContainer = nullptr; // Pointer to the matrix this navigator is working on. + int _laneLeap = 0; // Stores the jump to the next column + TDPMatrixIterator _activeColIterator = TDPMatrixIterator(); // The active column iterator. + TDPMatrixIterator _prevColIterator = TDPMatrixIterator(); // The previous column iterator. + TValue _prevCellDiagonal = TValue(); // The previous diagonal cell + TValue _prevCellHorizontal = TValue(); // The previous Horizontal cell + TValue _prevCellVertical = TValue(); // The previous Vertical cell +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _init() +// ---------------------------------------------------------------------------- + +// Initializes the navigator for an unbanded alignment. +template +inline void +_init(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & navigator, + DPMatrix_ & dpMatrix, + DPBandConfig const &) +{ + navigator._ptrDataContainer = &dpMatrix; + navigator._activeColIterator = begin(dpMatrix, Standard()); + navigator._prevColIterator = navigator._activeColIterator - _dataFactors(dpMatrix)[DPMatrixDimension_::HORIZONTAL]; + navigator._laneLeap = 1; + assignValue(navigator._activeColIterator, TValue()); +} + +// Initializes the navigator for a banded alignment. +template +inline void +_init(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & navigator, + DPMatrix_ & dpMatrix, + DPBandConfig const & band) +{ + typedef typename Size >::Type TMatrixSize; + typedef typename MakeSigned::Type TSignedSize; + navigator._ptrDataContainer = &dpMatrix; + + + // Band begins within the first row. + if (lowerDiagonal(band) >= 0) + { + navigator._laneLeap = _min(length(dpMatrix, DPMatrixDimension_::VERTICAL), bandSize(band)); + navigator._activeColIterator = begin(dpMatrix, Standard()) + _dataLengths(dpMatrix)[DPMatrixDimension_::VERTICAL] - 1; + } + else if (upperDiagonal(band) <= 0) // Band begins within the first column. + { + navigator._laneLeap = 1; + navigator._activeColIterator = begin(dpMatrix, Standard()); + } + else // Band intersects with the point of origin. + { + TMatrixSize lengthVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL); + int lastPos = _max(-static_cast(lengthVertical - 1), lowerDiagonal(band)); + navigator._laneLeap = lengthVertical + lastPos; + navigator._activeColIterator = begin(dpMatrix, Standard()) + navigator._laneLeap - 1; + } + // Set previous iterator to same position, one column left. + navigator._prevColIterator = navigator._activeColIterator - _dataFactors(dpMatrix)[DPMatrixDimension_::HORIZONTAL]; + assignValue(navigator._activeColIterator, TValue()); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [DPInitialColumn, FirstCell] +// ---------------------------------------------------------------------------- + +// In the initial column we don't need to do anything because, the navigagtor is already initialized. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [PartialColumnTop, FirstCell] +// ---------------------------------------------------------------------------- + +// We are in the banded case, where the band crosses the first row. +// The left cell of the active cell is not valid, beacause we only can come from horizontal direction. +// The lower left cell of the active cell is the horizontal direction. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + --dpNavigator._laneLeap; + dpNavigator._activeColIterator += dpNavigator._laneLeap; + dpNavigator._prevColIterator += dpNavigator._laneLeap; + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [FullColumn, FirstCell] +// ---------------------------------------------------------------------------- + +// We are in the unbanded case or in the middle phase of the wide band. +// The left cell of the active cell represents horizontal direction. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + dpNavigator._activeColIterator += dpNavigator._laneLeap; + dpNavigator._prevColIterator += dpNavigator._laneLeap; + dpNavigator._prevCellHorizontal = value(dpNavigator._prevColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [PartialColumnMiddle, PartialColumnBottom, FirstCell] +// ---------------------------------------------------------------------------- + +// We are in the banded case. +// The left cell of the active cell represents diagonal direction. The lower left diagonal represents the horizontal direction. + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + dpNavigator._activeColIterator += dpNavigator._laneLeap; + dpNavigator._prevColIterator += dpNavigator._laneLeap; + dpNavigator._prevCellDiagonal = value(dpNavigator._prevColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, InnerCell] +// ---------------------------------------------------------------------------- + +// If we are in the initial column, we only need to represent the vertical direction. +// But we still have to update the previous column iterator. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; + ++dpNavigator._prevColIterator; // Do we have to increase the prevColIterator.... +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [AnyColumn, InnerCell] +// ---------------------------------------------------------------------------- + +// For any other column type and location we can use the same navigation procedure. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, LastCell] +// ---------------------------------------------------------------------------- + +// If we are in the initial column we only need to represent the vertical direction. +// But we still have to update the previous column iterator. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; + ++dpNavigator._prevColIterator; +} + +// We need this function to avoid ambiguous function calls. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; + ++dpNavigator._prevColIterator; +} + +// We need this function to avoid ambiguous function calls. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; + ++dpNavigator._prevColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [FullColumn, LastCell] +// ---------------------------------------------------------------------------- + +// If we are in a full column the values correspond to standard dp directions. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [PartialColumnBottom, LastCell] +// ---------------------------------------------------------------------------- + +// If we are in banded case and are the band crosses the last row, we have to update +// the additional leap for the current track. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); + ++dpNavigator._activeColIterator; + ++dpNavigator._laneLeap; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [PartialColumnTop & PartialColumnBottom, LastCell] +// ---------------------------------------------------------------------------- + +// If we are in the banded case the left cell of the active represents the diagonal direction. +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function previousCellDiagonal() +// ---------------------------------------------------------------------------- + +template +inline typename Reference >::Type +previousCellDiagonal(DPMatrixNavigator_ & dpNavigator) +{ + return dpNavigator._prevCellDiagonal; +} + +template +inline typename Reference const>::Type +previousCellDiagonal(DPMatrixNavigator_ const & dpNavigator) +{ + return dpNavigator._prevCellDiagonal; +} + +// ---------------------------------------------------------------------------- +// Function previousCellHorizontal() +// ---------------------------------------------------------------------------- + +template +inline typename Reference >::Type +previousCellHorizontal(DPMatrixNavigator_ & dpNavigator) +{ + return dpNavigator._prevCellHorizontal; +} + +template +inline typename Reference const>::Type +previousCellHorizontal(DPMatrixNavigator_ const & dpNavigator) +{ + return dpNavigator._prevCellHorizontal; +} + +// ---------------------------------------------------------------------------- +// Function previousCellVertical() +// ---------------------------------------------------------------------------- + +template +inline typename Reference >::Type +previousCellVertical(DPMatrixNavigator_ & dpNavigator) +{ + return dpNavigator._prevCellVertical; +} + +template +inline typename Reference const>::Type +previousCellVertical(DPMatrixNavigator_ const & dpNavigator) +{ + return dpNavigator._prevCellVertical; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_ diff --git a/seqan/align/dp_matrix_navigator_score_matrix_sparse.h b/seqan/align/dp_matrix_navigator_score_matrix_sparse.h new file mode 100644 index 0000000..acc3267 --- /dev/null +++ b/seqan/align/dp_matrix_navigator_score_matrix_sparse.h @@ -0,0 +1,369 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// The navigator for the sparse score dp-matrix. This class also provides an +// iterator for the active and the previous column. It stores the neighbouring +// cells needed for the recursion formula. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class DPMatrixNavigator [SparseDPMatrix, ScoreMatrix] +// ---------------------------------------------------------------------------- + +// Specialization of the score matrix navigator for a sparse dp matrix. +template +class DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> +{ +public: + typedef DPMatrix_ TDPMatrix_; + typedef typename Pointer_::Type TDPMatrixPointer_; + typedef typename Iterator::Type TDPMatrixIterator; + + TDPMatrixPointer_ _ptrDataContainer = nullptr; // Pointer to the underlying matrix to navigate on. + int _laneLeap = 0; // The distance to leap when going to the next column. + TDPMatrixIterator _activeColIterator = TDPMatrixIterator(); // The iterator over the active column. + TDPMatrixIterator _prevColIterator = TDPMatrixIterator(); // The iterator over the previous column. + TValue _prevCellDiagonal = TValue(); // The previous value in diagonal direction. + TValue _prevCellHorizontal = TValue(); // The previous value in horizontal direction. + TValue _prevCellVertical = TValue(); // The previous value in vertical direction. +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _init() +// ---------------------------------------------------------------------------- + + +// Initializes the navigator for unbanded alignments +template +inline void +_init(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & navigator, + DPMatrix_ & dpMatrix, + DPBandConfig const &) +{ + navigator._ptrDataContainer = &dpMatrix; + navigator._activeColIterator = begin(dpMatrix, Standard()); + navigator._prevColIterator = navigator._activeColIterator; + navigator._laneLeap = 1 - _dataLengths(dpMatrix)[DPMatrixDimension_::VERTICAL]; + assignValue(navigator._activeColIterator, TValue()); +} + +// Initializes the navigator for banded alignments +template +inline void +_init(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & navigator, + DPMatrix_ & dpMatrix, + DPBandConfig const & band) +{ + typedef DPMatrix_ TSparseDPMatrix; + typedef typename Size::Type TSize; + typedef typename MakeSigned::Type TSignedSize; + navigator._ptrDataContainer = &dpMatrix; + + // Band begins within the first row. + if (lowerDiagonal(band) >= 0) + { + navigator._laneLeap = 0; + navigator._activeColIterator = begin(dpMatrix, Standard()) + length(dpMatrix, DPMatrixDimension_::VERTICAL) - 1; + } + else if (upperDiagonal(band) <= 0) // Band begins within the first column + { + navigator._laneLeap = 1 - _dataLengths(dpMatrix)[DPMatrixDimension_::VERTICAL]; + navigator._activeColIterator = begin(dpMatrix, Standard()); + } + else // Band intersects with the point of origin. + { + navigator._laneLeap = _max(lowerDiagonal(band), 1 - static_cast(length(dpMatrix, DPMatrixDimension_::VERTICAL))); + navigator._activeColIterator = begin(dpMatrix, Standard()) + length(dpMatrix, DPMatrixDimension_::VERTICAL) + navigator._laneLeap - 1; + } + navigator._prevColIterator = navigator._activeColIterator; + assignValue(navigator._activeColIterator, TValue()); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [DPInitialColumn, PartialColumnTop, FirstCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [DPInitialColumn, FullColumn, FirstCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [DPInitialColumn, FirstCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [PartialColumnTop, FirstCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + --dpNavigator._laneLeap; + dpNavigator._activeColIterator += dpNavigator._laneLeap; + dpNavigator._prevColIterator = dpNavigator._activeColIterator; + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [FullColumn, FirstCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + dpNavigator._activeColIterator += dpNavigator._laneLeap; + dpNavigator._prevCellHorizontal = value(dpNavigator._activeColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [FirstCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + dpNavigator._activeColIterator += dpNavigator._laneLeap; + dpNavigator._prevColIterator = dpNavigator._activeColIterator; + dpNavigator._prevCellDiagonal = value(dpNavigator._prevColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, InnerCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, FullColumn, InnerCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [InnerCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [FullColumn, InnerCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._activeColIterator); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, LastCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, PartialColumnBottom, LastCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [DPInitialColumn, FullColumn, LastCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [LastCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [PartialColumnBottom, LastCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._prevColIterator); + ++dpNavigator._activeColIterator; + ++dpNavigator._laneLeap; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [FullColumn, LastCell] +// ---------------------------------------------------------------------------- + + +template +inline void +_goNextCell(DPMatrixNavigator_, DPScoreMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + dpNavigator._prevCellDiagonal = dpNavigator._prevCellHorizontal; + dpNavigator._prevCellVertical = value(dpNavigator._activeColIterator); + dpNavigator._prevCellHorizontal = value(++dpNavigator._activeColIterator); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_SPARSE_H_ diff --git a/seqan/align/dp_matrix_navigator_trace_matrix.h b/seqan/align/dp_matrix_navigator_trace_matrix.h new file mode 100644 index 0000000..0fc7233 --- /dev/null +++ b/seqan/align/dp_matrix_navigator_trace_matrix.h @@ -0,0 +1,517 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// This specialization is used to navigate through the traceback matrix +// of any standard dp-alignment algorithm. The DPTraceMatrix gets the +// traceback flag TracebackOn or TracebackOff. A traceback is only computed +// if the traceback is switched on. If this is not the case, the void +// functions will be compiled as no-op functions, while in functions that try +// to access a value of the underlying matrix via the navigator an assertion +// is thrown. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class DPMatrixNavigator [FullDPMatrix, DPTraceMatrix] +// ---------------------------------------------------------------------------- + +// The matrix navigator for the trace-back matrix. +// +// It takes three types to be specialized. The first type defines the underlying +// dp-matrix it is working on. This has to be a FullDPMatrix. The second type, +// specifies that this is a trace-matrix navigator while the TTraceFlag can either +// be TracebackOn to enable the navigator or TracebackOff to disable it. +// The last parameter specifies the kind of navigation. +template +class DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> +{ +public: + + typedef DPMatrix_ TDPMatrix_; + typedef typename Pointer_::Type TDPMatrixPointer_; + typedef typename Iterator::Type TDPMatrixIterator; + + TDPMatrixPointer_ _ptrDataContainer = nullptr; // The pointer to the underlying Matrix. + int _laneLeap = 0; // Keeps track of the jump size from one column to another. + unsigned _simdLane = 0; // Used for tracing the correct cell in case of simd vectors. + TDPMatrixIterator _activeColIterator = TDPMatrixIterator(); // The current column iterator. +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _init() +// ---------------------------------------------------------------------------- + +// Initializes the navigator for unbanded alignments. +template +inline void +_init(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & navigator, + DPMatrix_ & dpMatrix, + DPBandConfig const &) +{ + if (IsSameType::VALUE) + return; // Leave navigator uninitialized because it is never used. + + navigator._ptrDataContainer = &dpMatrix; + navigator._activeColIterator = begin(dpMatrix, Standard()); + navigator._laneLeap = 1; + assignValue(navigator._activeColIterator, TValue()); +} + +// Initializes the navigator for banded alignments. +// Note, the band size has a maximal width of length of the vertical sequence. +template +inline void +_init(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & navigator, + DPMatrix_ & dpMatrix, + DPBandConfig const & band) +{ + typedef typename Size >::Type TMatrixSize; + typedef typename MakeSigned::Type TSignedSize; + + if (IsSameType::VALUE) + return; // Leave navigator as is because it should never be used. + + navigator._ptrDataContainer = &dpMatrix; + + // Band begins within the first row. + if (lowerDiagonal(band) >= 0) + { + // The first cell of the first column starts at the last cell in the matrix of the current column. + navigator._laneLeap = _min(length(dpMatrix, DPMatrixDimension_::VERTICAL), bandSize(band)); + navigator._activeColIterator = begin(dpMatrix, Standard()) + _dataLengths(dpMatrix)[DPMatrixDimension_::VERTICAL] - 1; + } + else if (upperDiagonal(band) <= 0) // Band begins within the first column. + { + // The first cell starts at the beginning of the current column. + navigator._laneLeap = 1; + navigator._activeColIterator = begin(dpMatrix, Standard()); + } + else // Band intersects with the point of origin. + { + // First cell starts at position i, such that i + abs(lowerDiagonal) = length(seqV). + TMatrixSize lengthVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL); + int lastPos = _max(-static_cast(lengthVertical - 1), lowerDiagonal(band)); + navigator._laneLeap = lengthVertical + lastPos; + navigator._activeColIterator = begin(dpMatrix, Standard()) + navigator._laneLeap - 1; + } + assignValue(navigator._activeColIterator, TValue()); +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [DPInitialColumn, FirstCell] +// ---------------------------------------------------------------------------- + +// In the initial column we don't need to do anything because, the navigagtor is already initialized. +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & /*dpNavigator*/, + MetaColumnDescriptor const &, + FirstCell const &) +{ + // no-op +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [PartialColumnTop, FirstCell] +// ---------------------------------------------------------------------------- + +// We are in the banded case, where the band crosses the first row. +// The left cell of the active cell is not valid, beacause we only can come from horizontal direction. +// The lower left cell of the active cell is the horizontal direction. + +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + --dpNavigator._laneLeap; + dpNavigator._activeColIterator += dpNavigator._laneLeap; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell() [other column types, FirstCell] +// ---------------------------------------------------------------------------- + +// We are in the banded case. +// The left cell of the active cell represents diagonal direction. The lower left diagonal represents the horizontal direction. + +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + FirstCell const &) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + dpNavigator._activeColIterator += dpNavigator._laneLeap; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [any column, InnerCell] +// ---------------------------------------------------------------------------- + +// For any other column type and location we can use the same navigation procedure. +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + InnerCell const &) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [PartialColumnBottom, LastCell] +// ---------------------------------------------------------------------------- + +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + ++dpNavigator._activeColIterator; +} + +// If we are in banded case and the band crosses the last row, we have to update +// the additional leap for the current track. +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + ++dpNavigator._activeColIterator; + ++dpNavigator._laneLeap; +} + +// ---------------------------------------------------------------------------- +// Function _goNextCell [any other column, LastCell] +// ---------------------------------------------------------------------------- + +// If we are in the banded case the left cell of the active represents the diagonal direction. +template +inline void +_goNextCell(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + MetaColumnDescriptor const &, + LastCell const &) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + ++dpNavigator._activeColIterator; +} + +// ---------------------------------------------------------------------------- +// Function _traceHorizontal() +// ---------------------------------------------------------------------------- + +template +inline void +_traceHorizontal(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + bool isBandShift) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + if (isBandShift) + dpNavigator._activeColIterator -= _dataFactors(*dpNavigator._ptrDataContainer)[DPMatrixDimension_::HORIZONTAL] - 1; + else + dpNavigator._activeColIterator -= _dataFactors(*dpNavigator._ptrDataContainer)[DPMatrixDimension_::HORIZONTAL]; + +} + +// ---------------------------------------------------------------------------- +// Function _traceDiagonal() +// ---------------------------------------------------------------------------- + +template +inline void +_traceDiagonal(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + bool isBandShift) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + if (isBandShift) + dpNavigator._activeColIterator -= _dataFactors(*dpNavigator._ptrDataContainer)[DPMatrixDimension_::HORIZONTAL]; + else + dpNavigator._activeColIterator -= _dataFactors(*dpNavigator._ptrDataContainer)[DPMatrixDimension_::HORIZONTAL] + 1; + +} + +// ---------------------------------------------------------------------------- +// Function _traceVertical() +// ---------------------------------------------------------------------------- + +template +inline void +_traceVertical(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + bool /*isBandShift*/) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + dpNavigator._activeColIterator -= _dataFactors(*dpNavigator._ptrDataContainer)[DPMatrixDimension_::VERTICAL]; +} + +// ---------------------------------------------------------------------------- +// Function setToPosition() +// ---------------------------------------------------------------------------- + +template +inline void +_setToPosition(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + TPosition const & hostPosition) +{ + if (IsSameType::VALUE) + return; + + SEQAN_ASSERT_LT(hostPosition, static_cast(length(container(dpNavigator)))); + + dpNavigator._activeColIterator = begin(*dpNavigator._ptrDataContainer, Standard()) + hostPosition; +} + + +// Sets the host position based on the given horizontal and vertical position. Note that the horizontal and +// vertical positions must correspond to the correct size of the underlying matrix. +// For banded matrices the vertical dimension might not equal the length of the vertical sequence. +template +inline void +_setToPosition(DPMatrixNavigator_, DPTraceMatrix, NavigateColumnWise> & dpNavigator, + TPositionH const & horizontalPosition, + TPositionV const & verticalPosition) +{ + if (IsSameType::VALUE) + return; + SEQAN_ASSERT_LT(horizontalPosition, static_cast(length(container(dpNavigator), +DPMatrixDimension_::HORIZONTAL))); + SEQAN_ASSERT_LT(verticalPosition, static_cast(length(container(dpNavigator), +DPMatrixDimension_::VERTICAL))); + + TPositionH hostPosition = horizontalPosition * _dataFactors(container(dpNavigator))[+DPMatrixDimension_::HORIZONTAL] + verticalPosition; + dpNavigator._activeColIterator = begin(*dpNavigator._ptrDataContainer, Standard()) + hostPosition; +} + +// ---------------------------------------------------------------------------- +// Function assignValue() +// ---------------------------------------------------------------------------- + +template +inline void +assignValue(DPMatrixNavigator_, TNavigationSpec> & dpNavigator, + TValue const & element) +{ + if (IsSameType::VALUE) + return; // Do nothing since no trace back is computed. + + assignValue(dpNavigator._activeColIterator, element); +} + +// ---------------------------------------------------------------------------- +// Function scalarValue(); Helper to switch between simd and scalar. +// ---------------------------------------------------------------------------- + +// SIMD Version. Returns always a copy and never a reference. +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename Value::Type) +_scalarValue(TValue const & vec, + TPos const pos) +{ + return value(vec, pos); +} + +// Non-simd variant. Identity version. +template +inline SEQAN_FUNC_ENABLE_IF(Not > >, TValue &) +_scalarValue(TValue & val, + TPos const /*pos*/) +{ + return val; +} + +// Wrapper to get the scalar value. +template +inline auto +scalarValue(DPMatrixNavigator_, TNavigationSpec> const & dpNavigator) +{ + if (IsSameType::VALUE) + SEQAN_ASSERT_FAIL("Try to access uninitialized object!"); + + return _scalarValue(*dpNavigator._activeColIterator, dpNavigator._simdLane); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +// Current position. +template +inline typename Reference, TNavigationSpec> >::Type +value(DPMatrixNavigator_, TNavigationSpec> & dpNavigator) +{ + if (IsSameType::VALUE) + SEQAN_ASSERT_FAIL("Try to access uninitialized object!"); + + return *dpNavigator._activeColIterator; +} + +template +inline typename Reference, TNavigationSpec> const >::Type +value(DPMatrixNavigator_, TNavigationSpec> const & dpNavigator) +{ + if (IsSameType::VALUE) + SEQAN_ASSERT_FAIL("Try to access uninitialized object!"); + + return *dpNavigator._activeColIterator; +} + +// At specified position. +template +inline typename Reference, TNavigationSpec> >::Type +value(DPMatrixNavigator_, TNavigationSpec> & dpNavigator, + TPosition const & position) +{ + if (IsSameType::VALUE) + SEQAN_ASSERT_FAIL("Try to access uninitialized object!"); + + return *(begin(*dpNavigator._ptrDataContainer) + position); +} + +template +inline typename Reference, TNavigationSpec> const >::Type +value(DPMatrixNavigator_, TNavigationSpec> const & dpNavigator, + TPosition const & position) +{ + if (IsSameType::VALUE) + SEQAN_ASSERT_FAIL("Try to access uninitialized object!"); + + return *(begin(*dpNavigator._ptrDataContainer) + position); +} + +// ---------------------------------------------------------------------------- +// Function coordinate() +// ---------------------------------------------------------------------------- + +// Returns the coordinate of the given dimension for the current position of the +// navigator within the matrix. +template +inline typename DPMatrixDimension_::TValue +coordinate(DPMatrixNavigator_, TNavigationSpec> const & dpNavigator, + typename DPMatrixDimension_::TValue const & dimension) +{ + if (IsSameType::VALUE) + SEQAN_ASSERT_FAIL("Try to access uninitialized object!"); + SEQAN_ASSERT_EQ(_checkCorrectDimension(dimension), true); + + if (IsSameType::VALUE) + return _dataLengths(*dpNavigator._ptrDataContainer)[dimension]; // Return lengths of given dimension. + + return coordinate(value(dpNavigator._ptrDataContainer), position(dpNavigator), dimension); // Simply delegate to coordinate of underlying matrix. +} + +// ---------------------------------------------------------------------------- +// Function position() +// ---------------------------------------------------------------------------- + +// Returns the current position of the navigator within the matrix. +template +inline typename Position, TNavigationSpec> >::Type +position(DPMatrixNavigator_, TNavigationSpec> const & dpNavigator) +{ + // Return 0 when traceback is not enabled. This is necessary to still track the score even + // the traceback is not enabled. + if (IsSameType::VALUE) + return 0; + + return position(dpNavigator._activeColIterator, *dpNavigator._ptrDataContainer); +} + +// ---------------------------------------------------------------------------- +// Function _setSimdLane() +// ---------------------------------------------------------------------------- + +template +inline void +_setSimdLane(DPMatrixNavigator_, TNavigationSpec> & dpNavigator, + TPos const pos) +{ + SEQAN_ASSERT_LT(pos, static_cast(LENGTH::Type>::VALUE)); + + dpNavigator._simdLane = pos; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_TRACE_MATRIX_H_ diff --git a/seqan/align/dp_matrix_sparse.h b/seqan/align/dp_matrix_sparse.h new file mode 100644 index 0000000..4666a46 --- /dev/null +++ b/seqan/align/dp_matrix_sparse.h @@ -0,0 +1,150 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class DPMatrix [SparseDPMatrix] +// ---------------------------------------------------------------------------- + +template +class DPMatrix_ +{ +public: + + typedef typename Member::Type THost; + + Holder data_host; // The host containing the actual matrix. + + DPMatrix_() : + data_host() + { + create(data_host); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function resize() +// ---------------------------------------------------------------------------- + +template +inline void +resize(DPMatrix_ & dpMatrix) +{ + typedef DPMatrix_ TDPMatrix; + typedef typename Size::Type TSize; + + TSize _dimVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL); + + if (_dimVertical >= length(dpMatrix)) + resize(host(dpMatrix), _dimVertical, Exact()); +} + +template +inline void +resize(DPMatrix_ & dpMatrix, + TValue const & fillValue) +{ + typedef DPMatrix_ TDPMatrix; + typedef typename Size::Type TSize; + + TSize _dimVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL); + + if (_dimVertical > length(dpMatrix)) + resize(host(dpMatrix), _dimVertical, fillValue, Exact()); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +template +inline typename Reference >::Type +value(DPMatrix_ & dpMatrix, + TPositionV const & posV, + TPositionH const &) +{ + return value(dpMatrix, posV); +} + +template +inline typename Reference const>::Type +value(DPMatrix_ const & dpMatrix, + TPositionV const & posV, + TPositionH const &) +{ + return value(dpMatrix, posV); +} + +// ---------------------------------------------------------------------------- +// Function coordinate() +// ---------------------------------------------------------------------------- + + +template +inline typename Position >::Type +coordinate(DPMatrix_ const & /*dpMatrix*/, + TPosition hostPos, + typename DPMatrixDimension_::TValue dimension) +{ + SEQAN_ASSERT(_checkCorrectDimension(dimension)); + + if (dimension == DPMatrixDimension_::VERTICAL) + return hostPos; + + return 0u; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_ diff --git a/seqan/align/dp_meta_info.h b/seqan/align/dp_meta_info.h new file mode 100644 index 0000000..dab1bdc --- /dev/null +++ b/seqan/align/dp_meta_info.h @@ -0,0 +1,485 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Ren� Rahn +// ========================================================================== +// Here are defined the strategies for the different alignment algorithms. +// All classes are only used to determine the correct computational state +// of a particular alignment algorithm depending on its profile at a +// particular time. +// All classes are only used on a meta-level. +// ========================================================================== + +// TODO(holtgrew): Documentation in this header necessary or internal only? + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag DPInitialColumn +// ---------------------------------------------------------------------------- + +// Specifies the first column of the dp matrix. +struct DPInitialColumn_; +typedef Tag DPInitialColumn; + +// ---------------------------------------------------------------------------- +// Tag DPInnerColumn +// ---------------------------------------------------------------------------- + +// Specifies any inner column of the dp matrix between the first and the last +// column. +struct DPInnerColumn_; +typedef Tag DPInnerColumn; + +// ---------------------------------------------------------------------------- +// Tag DPFinalColumn +// ---------------------------------------------------------------------------- + +// Specifies the last column of a dp matrix. +struct DPFinalColumn_; +typedef Tag DPFinalColumn; + + +// The TColumnProperty determines the property of the column (if it is initial, inner, or last column) +// The TLocation determines how the column is organized in the matrix. +// It can have the values: FullColumn, PartialColumnTop, PartialColumnMiddle, PartialColumnBottom. +template +struct MetaColumnDescriptor +{ + typedef TColumnProperty_ TColumnProperty; + typedef TLocation_ TLocation; +}; + +// ---------------------------------------------------------------------------- +// Tag FullColumn +// ---------------------------------------------------------------------------- + +// Columns that span over the complete dp-matrix. (Unbanded alignemnts) +struct FullColumn_; +typedef Tag FullColumn; + +// ---------------------------------------------------------------------------- +// Tag PartialColumnTop +// ---------------------------------------------------------------------------- + +// Columns that begin in the first row, but does not at the last row of the dp-matrix +struct PartialColumnTop_; +typedef Tag PartialColumnTop; + +// ---------------------------------------------------------------------------- +// Tag PartialColumnMiddle +// ---------------------------------------------------------------------------- + +// Columns that are not attached to the begin or end of the dp-matrix. +struct PartialColumnMiddle_; +typedef Tag PartialColumnMiddle; + +// ---------------------------------------------------------------------------- +// Tag PartialColumnBottom +// ---------------------------------------------------------------------------- + +// Columns that end in the last row of the dp-matrix but do not start in the first row. +struct PartialColumnBottom_; +typedef Tag PartialColumnBottom; + + +// The cell specifiers are used to determine the cell of a column. +// There are three different cell specifiers used for the first cell, the +// inner cell and the last cell of a column. + +// ---------------------------------------------------------------------------- +// Tag FirstCell +// ---------------------------------------------------------------------------- + +struct FirstCell_; +typedef Tag FirstCell; + +// ---------------------------------------------------------------------------- +// Tag InnerCell +// ---------------------------------------------------------------------------- + +struct InnerCell_; +typedef Tag InnerCell; + +// ---------------------------------------------------------------------------- +// Tag LastCell +// ---------------------------------------------------------------------------- + +struct LastCell_; +typedef Tag LastCell; + + +// ---------------------------------------------------------------------------- +// Class DPMetaCell_ +// ---------------------------------------------------------------------------- + +// Keeps meta-information of a cell in the dp-matrix. It stores the recursion direction +// for a particular cell type and whether it can be tracked or not. + +template +struct DPMetaCell_ {}; + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ +// ---------------------------------------------------------------------------- + +// Keeps meta-information of an entire column in the dp-matrix. Depending on the chosen +// DPProfile and the current column descriptor it selects for the different column locations and +// cell specifiers the correct meta-information about how is which cell computed and which cell is +// tracked. + +template +struct DPMetaColumn_ {}; + + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [FullColumn] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_ > +{ + typedef typename IsLocalAlignment_::Type TIsLocal; + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> Horizontal | Zero, All, All + // If FinalColumn -> Horizontal | Zero, All, All + + typedef typename If, + IsFreeEndGap_ >, RecursionDirectionZero, RecursionDirectionHorizontal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeLastCell_; + + // If Local + // If InitialColumn -> True, True, True + // If InnerColumn -> True, True, True + // If FinalColumn -> True, True, True + + // If Global + // If InitialColumn -> False, False, False | True (if DPLastRow) + // If InnerColumn -> False, False, False | True (if DPLastRow) + // If FinalColumn -> False | True, False | True (if DPLastColumn), True + + typedef typename If, + And, + IsFreeEndGap_ > // check this if he is really entitled to find the maximum here. + >, True, False>::Type TrackFlagFirstCell_; + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagInnerCell_; + typedef typename If, + Or, + IsFreeEndGap_ > >, True, False>::Type TrackFlagLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [PartialColumnTop] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_ > +{ + typedef typename IsLocalAlignment_::Type TIsLocal; + + // How does the recursion directions look like? + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> Horizontal | Zero, All, LowerBand + // If FinalColumn -> Horizontal | Zero, All, LowerBand + + typedef typename If, + IsFreeEndGap_ >, RecursionDirectionZero, RecursionDirectionHorizontal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionLowerDiagonal>::Type TRecursionTypeLastCell_; + + // If Local + // If InitialColumn -> True, True, True + // If InnerColumn -> True, True, True + // If FinalColumn -> True, True, True + + // If Global + // If InitialColumn -> False, False, False + // If InnerColumn -> False, False, False + // If FinalColumn -> False | True, False | True, False | True (if DPLastColumn True) + + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagFirstCell_; + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagInnerCell_; + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [PartialColumnMiddle] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_ > +{ + typedef typename IsLocalAlignment_::Type TIsLocal; + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> UpperDiagonal, All, LowerDiagonal + // If FinalColumn -> UpperDiagonal, All, LowerDiagonal + + typedef typename If, RecursionDirectionZero, RecursionDirectionUpperDiagonal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionLowerDiagonal>::Type TRecursionTypeLastCell_; + + // If Local + // If InitialColumn -> True, True, True + // If InnerColumn -> True, True, True + // If FinalColumn -> True, True, True + + // If Global + // If InitialColumn -> False, False, False + // If InnerColumn -> False, False, False + // If FinalColumn -> False | True, False | True, False | True (if DPLastColumn True) + + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagFirstCell_; + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagInnerCell_; + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [PartialColumnBottom] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_ > +{ + typedef typename IsLocalAlignment_::Type TIsLocal; + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> UpperDiagonal, All, All + // If FinalColumn -> UpperDiagonal, All, All + + typedef typename If, RecursionDirectionZero, RecursionDirectionUpperDiagonal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeLastCell_; + + // If Local + // If InitialColumn -> True, True, True + // If InnerColumn -> True, True, True + // If FinalColumn -> True, True, True + + // If Global + // If InitialColumn -> False, False, False | True (if DPLastRow) + // If InnerColumn -> False, False, False | True (if DPLastRow) + // If FinalColumn -> False | True, False | True (if DPLastColumn), True (last is always true) + + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagFirstCell_; + typedef typename If, + And, + IsFreeEndGap_ > + >, True, False>::Type TrackFlagInnerCell_; + typedef typename If, + Or, + IsFreeEndGap_ > >, True, False>::Type TrackFlagLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + + +// ---------------------------------------------------------------------------- +// Metafunction GetRecursionDirection_ +// ---------------------------------------------------------------------------- + +// Returns the type of recursion for a given DPMetaCell object. +template +struct GetRecursionDirection_ +{ + typedef Nothing Type; +}; + +template +struct GetRecursionDirection_ > +{ + typedef TRecursionDirection Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction RecursionDirection_ +// ---------------------------------------------------------------------------- + +// Returns the type of recursion for a given DPMetaColumn object and a given cell specifier. +template +struct RecursionDirection_ {}; + +template +struct RecursionDirection_ +{ + typedef typename GetRecursionDirection_::Type Type; +}; + +template +struct RecursionDirection_ +{ + typedef typename GetRecursionDirection_::Type Type; +}; + +template +struct RecursionDirection_ +{ + typedef typename GetRecursionDirection_::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IsTrackingEnabled_ +// ---------------------------------------------------------------------------- + +// Returns an object that evaluates to true if for a given cell description the +// tracking was enabled. Otherwise the object evaluates to false. +template +struct IsTrackingEnabled_ : + False {}; + +template +struct IsTrackingEnabled_ >: + True {}; + + +template +struct TrackingEnabled_ : + False {}; + +template +struct TrackingEnabled_: + IsTrackingEnabled_{}; + +template +struct TrackingEnabled_: + IsTrackingEnabled_{}; + +template +struct TrackingEnabled_: + IsTrackingEnabled_{}; + +// ---------------------------------------------------------------------------- +// Metafunction LastColumnEnabled_ +// ---------------------------------------------------------------------------- + +template +struct LastColumnEnabled_ +{ + typedef typename IsSameType::Type Type; +}; + +template +struct LastColumnEnabled_, TColumnDescriptor> : + LastColumnEnabled_ +{}; + +// ---------------------------------------------------------------------------- +// Metafunction LastRowEnabled_ +// ---------------------------------------------------------------------------- + +template +struct LastRowEnabled_ +{ + typedef typename And, + Or, + IsSameType > >::Type Type; +}; + +template +struct LastRowEnabled_, TCellDescriptor, TColumnDescriptor> : + LastRowEnabled_ +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_META_INFO_H_ diff --git a/seqan/align/dp_profile.h b/seqan/align/dp_profile.h new file mode 100644 index 0000000..f57e161 --- /dev/null +++ b/seqan/align/dp_profile.h @@ -0,0 +1,571 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// This header contains all tags, structures and meta-functions that are +// used to define the meta-profile of an alignment algorithm. +// With the meta-profile the sort of alignment can be selected such as +// a global or a local alignment. It further structures the different +// specializations of global and local alignments or selects the gap cost +// function, or enables or disables the trace-back function. +// ========================================================================== + +// TODO(holtgrew): Documentation in this header necessary or internal only? + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class FreeEndGaps_ +// ---------------------------------------------------------------------------- + +// Used to determine which end-gaps are free. +template +struct FreeEndGaps_ {}; + +// ---------------------------------------------------------------------------- +// Class SplitBreakpointAlignment +// ---------------------------------------------------------------------------- +// TODO(rmaerker): maybe in a different header +// Used to specify the global alignment for split breakpoint computation. +struct AlignmentSplitBreakpoint_; +typedef Tag SplitBreakpointAlignment; + +// ---------------------------------------------------------------------------- +// Class GlobalAlignment_ +// ---------------------------------------------------------------------------- + +// This is used to select global alignments. The default is the standard global +// dp-algorithm. +// +// Note, all global alignments have to be specialized versions of GlobalAlignment_<> +template > +struct GlobalAlignment_; + +typedef GlobalAlignment_<> DPGlobal; + +// ---------------------------------------------------------------------------- +// Class SuboptimalAlignment +// ---------------------------------------------------------------------------- + +// TODO(rmaerker): maybe in a different header +// Used to specify the WatermanEggert algorithm. +struct AlignmentSuboptimal_; +typedef Tag SuboptimalAlignment; + +// ---------------------------------------------------------------------------- +// Class LocalAlignment_ +// ---------------------------------------------------------------------------- + +// This is used to select local alignments. The default is the standard local +// dp-algorithm. +// +// Note, all local alignments have to be specialized versions of LocalAlignment_<> + +template +struct LocalAlignment_; + +typedef LocalAlignment_<> DPLocal; +typedef LocalAlignment_ DPLocalEnumerate; + +// Use macro expansion to define all possible SIMD initialization types. + +template +struct InitSimdTrace_; + +#define SEQAN_SIMD_INIT_FILL_VALUE_2_ FILL_VALUE, FILL_VALUE +#define SEQAN_SIMD_INIT_FILL_VALUE_4_ SEQAN_SIMD_INIT_FILL_VALUE_2_, SEQAN_SIMD_INIT_FILL_VALUE_2_ +#define SEQAN_SIMD_INIT_FILL_VALUE_8_ SEQAN_SIMD_INIT_FILL_VALUE_4_, SEQAN_SIMD_INIT_FILL_VALUE_4_ +#define SEQAN_SIMD_INIT_FILL_VALUE_16_ SEQAN_SIMD_INIT_FILL_VALUE_8_, SEQAN_SIMD_INIT_FILL_VALUE_8_ +#define SEQAN_SIMD_INIT_FILL_VALUE_32_ SEQAN_SIMD_INIT_FILL_VALUE_16_, SEQAN_SIMD_INIT_FILL_VALUE_16_ + +#define SEQAN_SIMD_TRACE_SETUP_2_(SIZE, ...) \ +template \ +struct InitSimdTrace_ \ +{ \ + static const TVector VALUE; \ +}; \ + \ +template \ +const TVector InitSimdTrace_::VALUE = TVector{__VA_ARGS__}; + +#define SEQAN_SIMD_TRACE_SETUP_1_(SIZE, MACRO) SEQAN_SIMD_TRACE_SETUP_2_(SIZE, MACRO) +#define SEQAN_SIMD_TRACE_SETUP_(SIZE) SEQAN_SIMD_TRACE_SETUP_1_(SIZE, SEQAN_SIMD_INIT_FILL_VALUE_ ## SIZE ## _) + +SEQAN_SIMD_TRACE_SETUP_(2) +SEQAN_SIMD_TRACE_SETUP_(4) +SEQAN_SIMD_TRACE_SETUP_(8) +SEQAN_SIMD_TRACE_SETUP_(16) +SEQAN_SIMD_TRACE_SETUP_(32) + +// Scalar version. +template +struct TraceValue_ +{ + typedef uint8_t Type; + static const Type NONE = 0u; //0000000 + static const Type DIAGONAL = 1u; //0000001 + static const Type HORIZONTAL = 2u; //0000010 + static const Type VERTICAL = 4u; //0000100 + static const Type HORIZONTAL_OPEN = 8u; //0001000 + static const Type VERTICAL_OPEN = 16u; //0010000 + static const Type MAX_FROM_HORIZONTAL_MATRIX = 32u; //0100000 + static const Type MAX_FROM_VERTICAL_MATRIX = 64u; //1000000 + static const Type NO_VERTICAL_TRACEBACK = ~(VERTICAL | VERTICAL_OPEN); + static const Type NO_HORIZONTAL_TRACEBACK = ~(HORIZONTAL | HORIZONTAL_OPEN); +}; + +// SIMD Vector version. +template +struct TraceValue_ +{ + typedef TVector Type; + static const Type NONE; + static const Type DIAGONAL; + static const Type HORIZONTAL; + static const Type VERTICAL; + static const Type HORIZONTAL_OPEN; + static const Type VERTICAL_OPEN; + static const Type MAX_FROM_HORIZONTAL_MATRIX; + static const Type MAX_FROM_VERTICAL_MATRIX; + static const Type NO_HORIZONTAL_TRACEBACK; + static const Type NO_VERTICAL_TRACEBACK; +}; + +// Macro expansion to define out-of-class initialization of static members. + +#define SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(TRACE_VALUE) \ + template \ + const TVector TraceValue_::TRACE_VALUE = InitSimdTrace_::TRACE_VALUE, LENGTH::VALUE>::VALUE; + +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(NONE) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(DIAGONAL) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(HORIZONTAL) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(VERTICAL) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(HORIZONTAL_OPEN) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(VERTICAL_OPEN) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(MAX_FROM_HORIZONTAL_MATRIX) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(MAX_FROM_VERTICAL_MATRIX) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(NO_HORIZONTAL_TRACEBACK) +SEQAN_SIMD_TRACE_OUT_OF_CLASS_INIT_(NO_VERTICAL_TRACEBACK) + +// Type alias to choose between scalar and simd version of trace value. +template +using TraceBitMap_ = TraceValue_ >::Type >; + +// ---------------------------------------------------------------------------- +// Tag GapsLeft +// ---------------------------------------------------------------------------- + +struct GapsLeft_; +typedef Tag GapsLeft; + +// ---------------------------------------------------------------------------- +// Tag GapsRight +// ---------------------------------------------------------------------------- + +struct GapsRight_; +typedef Tag GapsRight; + + +// ---------------------------------------------------------------------------- +// Tag SingleTrace +// ---------------------------------------------------------------------------- + +struct SingleTrace_; +typedef Tag SingleTrace; + +// ---------------------------------------------------------------------------- +// Tag CompleteTrace +// ---------------------------------------------------------------------------- + +struct CompleteTrace_; +typedef Tag CompleteTrace; + +// ---------------------------------------------------------------------------- +// Tag TracebackConfig_ +// ---------------------------------------------------------------------------- + +template +struct TracebackConfig_ {}; + +// ---------------------------------------------------------------------------- +// Tag TracebackOn +// ---------------------------------------------------------------------------- + +template > +struct TracebackOn {}; + +// ---------------------------------------------------------------------------- +// Tag TracebackOff +// ---------------------------------------------------------------------------- + +struct TracebackOff_ {}; +typedef Tag TracebackOff; + +// ---------------------------------------------------------------------------- +// Tag LinearGaps +// ---------------------------------------------------------------------------- + +/*! + * @tag AlignmentAlgorithmTags#LinearGaps + * @headerfile + * @brief Tag for selecting linear gap cost model. This tag can be used for all standard DP algorithms. + * + * @signature struct LinearGaps_; + * @signature typedef Tag LinearGaps; + */ +struct LinearGaps_; +typedef Tag LinearGaps; + +// ---------------------------------------------------------------------------- +// Tag AffineGaps +// ---------------------------------------------------------------------------- + +/*! + * @tag AlignmentAlgorithmTags#AffineGaps + * @headerfile + * @brief Tag for selecting affine gap cost model. This tag can be used for all standard DP algorithms. + * + * @signature struct AffineGaps_; + * @signature typedef Tag AffineGaps; + */ +struct AffineGaps_; +typedef Tag AffineGaps; + +// ---------------------------------------------------------------------------- +// Tag DynamicGaps +// ---------------------------------------------------------------------------- + +/*! + * @tag AlignmentAlgorithmTags#DynamicGaps + * @headerfile + * @brief Tag for selecting dynamic gap cost model. This tag can be used for all standard DP algorithms. + * + * @signature struct DynamicGaps_; + * @signature typedef Tag DynamicGaps; + */ + +struct DynamicGaps_; +typedef Tag DynamicGaps; + +// ---------------------------------------------------------------------------- +// Class DPProfile +// ---------------------------------------------------------------------------- + +// This meta-object takes three types to be specialized. +// +// TAlignment: The type to select the pairwise alignment algorithm. +// TGapCosts: The gap cost function (LinearGaps or AffineGaps). +// TTraceback: The traceback switch (TracebackOn or TracebackOff). +template +struct DPProfile_ {}; + + +// ---------------------------------------------------------------------------- +// Tag DPFirstRow +// ---------------------------------------------------------------------------- + +// These tags are used to specify the four locations of a dp-matrix where +// free gaps can occur. +struct DPFirstRow_; +typedef Tag DPFirstRow; + +// ---------------------------------------------------------------------------- +// Tag DPFirstColumn +// ---------------------------------------------------------------------------- + +struct DPFirstColumn_; +typedef Tag DPFirstColumn; + +// ---------------------------------------------------------------------------- +// Tag DPLastRow +// ---------------------------------------------------------------------------- + +struct DPLastRow_; +typedef Tag DPLastRow; + +// ---------------------------------------------------------------------------- +// Tag DPLastColumn +// ---------------------------------------------------------------------------- + +struct DPLastColumn_; +typedef Tag DPLastColumn; + +template , + typename TTraceConfig = TracebackOn > > +class AlignConfig2 +{ +public: + TBand _band; + + AlignConfig2() : _band() + {} + + template + AlignConfig2(TPosition const & lDiag, TPosition const & uDiag) : _band(lDiag, uDiag) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction IsGlobalAlignment +// ---------------------------------------------------------------------------- + +// Checks if the dp profile is a global alignment. +template +struct IsGlobalAlignment_ : + False {}; + +template +struct IsGlobalAlignment_ >: + True {}; + +template +struct IsGlobalAlignment_ const>: + True {}; + +template +struct IsGlobalAlignment_ >: + IsGlobalAlignment_{}; + +template +struct IsGlobalAlignment_ const>: + IsGlobalAlignment_{}; + +// ---------------------------------------------------------------------------- +// Metafunction TraceTail_ +// ---------------------------------------------------------------------------- + +// define whether to include the 'tail' of an alignment in the trace +template +struct TraceTail_ : + IsGlobalAlignment_{}; + +// ---------------------------------------------------------------------------- +// Metafunction TraceHead_ +// ---------------------------------------------------------------------------- + +// define whether to include the 'head' of an alignment in the trace +template +struct TraceHead_ : + IsGlobalAlignment_{}; + +// ---------------------------------------------------------------------------- +// Metafunction HasTerminationCriterium_ +// ---------------------------------------------------------------------------- + +// check whether an algorithm has an early termination criterium +// if an algorithm has this, it will get a DPscout that can be terminated +// see dp_scout.h for more info +template +struct HasTerminationCriterium_ : + False {}; + +// ---------------------------------------------------------------------------- +// Metafunction IsLocalAlignment_ +// ---------------------------------------------------------------------------- + +// Checks if the dp profile is a local alignment. +template +struct IsLocalAlignment_ : + False {}; + +template +struct IsLocalAlignment_ >: + True {}; + +template +struct IsLocalAlignment_ const>: + True {}; + +template +struct IsLocalAlignment_ >: + IsLocalAlignment_{}; + +template +struct IsLocalAlignment_ const>: + IsLocalAlignment_{}; + +// ---------------------------------------------------------------------------- +// Metafunction IsTracebackEnabled_ +// ---------------------------------------------------------------------------- + +// Checks if the trace-back for the current dp profile is enabled. +template +struct IsTracebackEnabled_ : + False {}; + +template +struct IsTracebackEnabled_ >: + True {}; + +template +struct IsTracebackEnabled_ const>: + True {}; + +template +struct IsTracebackEnabled_ >: + IsTracebackEnabled_{}; + +template +struct IsTracebackEnabled_ const>: + IsTracebackEnabled_{}; + +// ---------------------------------------------------------------------------- +// Metafunction IsGapsLeft_ +// ---------------------------------------------------------------------------- + +template +struct IsGapsLeft_ : False{}; + +template +struct IsGapsLeft_ > > + : True{}; + +template +struct IsGapsLeft_ > + : IsGapsLeft_{}; + +// ---------------------------------------------------------------------------- +// Metafunction IsSingleTrace_ +// ---------------------------------------------------------------------------- + +template +struct IsSingleTrace_ : False{}; + +template +struct IsSingleTrace_ > > +: True{}; + +template +struct IsSingleTrace_ > +: IsSingleTrace_{}; + +// ---------------------------------------------------------------------------- +// Metafunction IsFreeEndGap_ +// ---------------------------------------------------------------------------- + +// Checks if for the current dp profile and a given gap location the algorithm uses free gaps. +template +struct IsFreeEndGap_ : + False {}; + +template +struct IsFreeEndGap_ const, TDPSide>: + IsFreeEndGap_{}; + +template +struct IsFreeEndGap_, TDPSide>: + IsFreeEndGap_{}; + +template +struct IsFreeEndGap_ const, TDPSide>: + True +{}; + +template +struct IsFreeEndGap_, TDPSide>: + True +{}; + +template +struct IsFreeEndGap_ const, TDPSide>: + IsFreeEndGap_ +{}; + +template +struct IsFreeEndGap_, TDPSide>: + IsFreeEndGap_ +{}; + +template +struct IsFreeEndGap_, DPFirstRow>: + True +{}; + +template +struct IsFreeEndGap_ const, DPFirstRow>: + True +{}; + +template +struct IsFreeEndGap_, DPFirstColumn>: + True +{}; + +template +struct IsFreeEndGap_ const, DPFirstColumn>: + True +{}; + +template +struct IsFreeEndGap_, DPLastRow>: + True +{}; + +template +struct IsFreeEndGap_ const, DPLastRow>: + True +{}; + +template +struct IsFreeEndGap_, DPLastColumn>: + True +{}; + +template +struct IsFreeEndGap_ const, DPLastColumn>: + True +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_PROFILE_H_ diff --git a/seqan/align/dp_scout.h b/seqan/align/dp_scout.h new file mode 100644 index 0000000..4642f9d --- /dev/null +++ b/seqan/align/dp_scout.h @@ -0,0 +1,340 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// The dp scout is a structure that stores the current maximal score and its +// host position in the underlying dp-matrix. +// This class can be overloaded to implement different behaviors of tracking +// the maximal score, e.g., for the split breakpoint computation. +// ========================================================================== +// Author: Hannes Hauswedell +// ========================================================================== +// The terminator specialization of dp scout offers the possibility to have +// dp generation stop, if specified criteria are met. +// To do this, define HasTerminationCriterium_<> for your algorithm and +// implement a DPScoutState for your terminator specialization. In your +// overloaded _scoutBestScore() or _computeCell() you can call +// terminateScout() on your Scout to have DP-generation stop. +// see dp_scout_xdrop.h for an example. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class Terminator_ +// ---------------------------------------------------------------------------- + +template +struct Terminator_; + +// ---------------------------------------------------------------------------- +// Class DPScoutState_ +// ---------------------------------------------------------------------------- + +template +class DPScoutState_; + +template <> +class DPScoutState_ : public Nothing // empty member optimization +{}; + +// ---------------------------------------------------------------------------- +// Class DPScout_ +// ---------------------------------------------------------------------------- + +template +class DPScout_; + +// The default implementation of the dp scout simply stores one maximum +// and its corresponding position. +// +// The state must be a Nothing and is left untouched and unused. +template +class DPScout_ +{ +public: + using TScoreValue = typename Value::Type; + + TDPCell _maxScore = TDPCell(); + uint32_t _maxHostPosition = DPCellDefaultInfinity::VALUE; // The corresponding host position within the underlying dp-matrix. + + DPScout_() = default; + + DPScout_(DPScoutState_ const & /*state*/) {} +}; + +// Terminator_ Specialization +template +class DPScout_ > + : public DPScout_ +{ +public: + typedef DPScout_ TParent; + + DPScoutState_ > * state = nullptr; + bool terminationCriteriumMet = false; + + DPScout_() = default; + + DPScout_(DPScoutState_ > & pState) : + DPScout_(), + state(&pState) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction ScoutSpecForAlignmentAlgorithm_ +// ---------------------------------------------------------------------------- + +// Given an alignment algorithm tag such as GlobalAlignment_ or LocalAlignment_, returns the specialization tag for the +// corresponding DPScout_ specialization. + +template +struct ScoutSpecForAlignmentAlgorithm_ +{ + typedef If, + Terminator_<>, + Default> Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction ScoutStateSpecForScout_ +// ---------------------------------------------------------------------------- + +// Given an dp scout this meta-function returns the appropriate specialization for the scout state. + +template +struct ScoutStateSpecForScout_ +{ + typedef Default Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _scoutBestScore() +// ---------------------------------------------------------------------------- + +// Tracks the new score, if it is the new maximum. +template +inline void +_scoutBestScore(DPScout_ & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn const & /**/, + TIsLastRow const & /**/) +{ + if (_scoreOfCell(activeCell) > _scoreOfCell(dpScout._maxScore)) + { + dpScout._maxScore = activeCell; + dpScout._maxHostPosition = position(navigator); + } +} + +// TODO(rmaerker): Why is this needed? +template +inline void +_scoutBestScore(DPScout_ & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn const & /**/) +{ + _scoutBestScore(dpScout, activeCell, navigator, TIsLastColumn(), False()); +} + +// TODO(rmaerker): Why is this needed? +template +inline void +_scoutBestScore(DPScout_ & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator) +{ + _scoutBestScore(dpScout, activeCell, navigator, False(), False()); +} + +// ---------------------------------------------------------------------------- +// Function maxScore() +// ---------------------------------------------------------------------------- + +// Returns the current maximal score. +template +inline typename Value::Type const +maxScore(DPScout_ const & dpScout) +{ + return _scoreOfCell(dpScout._maxScore); +} + +// ---------------------------------------------------------------------------- +// Function maxHostPosition() +// ---------------------------------------------------------------------------- + +// Returns the host position that holds the current maximum score. +template +inline unsigned int +maxHostPosition(DPScout_ const & dpScout) +{ + return dpScout._maxHostPosition; +} + +// ---------------------------------------------------------------------------- +// Function _terminationCriteriumIsMet() +// ---------------------------------------------------------------------------- + +template +inline bool +_terminationCriteriumIsMet(DPScout_ > const & scout) +{ + return scout.terminationCriteriumMet; +} + +// ---------------------------------------------------------------------------- +// Function terminateScout() +// ---------------------------------------------------------------------------- + +template +inline void +terminateScout(DPScout_ > & scout) +{ + scout.terminationCriteriumMet = true; +} + +// ---------------------------------------------------------------------------- +// Function _preInitScoutHorizontal() +// ---------------------------------------------------------------------------- + +template +inline void +_preInitScoutHorizontal(DPScout_ const & /*scout*/) +{ + // no-op. +} + +// ---------------------------------------------------------------------------- +// Function _reachedHorizontalEndPoint() +// ---------------------------------------------------------------------------- + +template +constexpr inline bool +_reachedHorizontalEndPoint(DPScout_ const & /*scout*/, + TIter const & /*hIt*/) +{ + return false; +} + +// ---------------------------------------------------------------------------- +// Function _preInitScoutVertical() +// ---------------------------------------------------------------------------- + +template +inline void +_preInitScoutVertical(DPScout_ const & /*scout*/) +{ + // no-op. +} + +// ---------------------------------------------------------------------------- +// Function _reachedVerticalEndPoint() +// ---------------------------------------------------------------------------- + +template +constexpr inline bool +_reachedVerticalEndPoint(DPScout_ const & /*scout*/, + TIter const & /*iter*/) +{ + return false; +} + +// ---------------------------------------------------------------------------- +// Function _nextHorizontalEndPos() +// ---------------------------------------------------------------------------- + +template +inline void +_nextHorizontalEndPos(DPScout_ const & /*scout*/) +{ + // no-op. +} + +// ---------------------------------------------------------------------------- +// Function _nextVerticalEndPos() +// ---------------------------------------------------------------------------- + +template +inline void +_nextVerticalEndPos(DPScout_ const & /*scout*/) +{ + // no-op. +} + +// ---------------------------------------------------------------------------- +// Function _incHorizontalPos() +// ---------------------------------------------------------------------------- + +template +inline void +_incHorizontalPos(DPScout_ const & /*scout*/) +{ + // no-op. +} + +// ---------------------------------------------------------------------------- +// Function _incVerticalPos() +// ---------------------------------------------------------------------------- + +template +inline void +_incVerticalPos(DPScout_ const & /*scout*/) +{ + // no-op. +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_TEST_ALIGNMENT_DP_SCOUT_H_ diff --git a/seqan/align/dp_scout_simd.h b/seqan/align/dp_scout_simd.h new file mode 100644 index 0000000..92095d2 --- /dev/null +++ b/seqan/align/dp_scout_simd.h @@ -0,0 +1,454 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2015, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stefan Budach +// ========================================================================== +// DPScout_ specialization for the SIMD alignment implementation. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SIMD_DP_SCOUT_SIMD_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_SIMD_DP_SCOUT_SIMD_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +struct SimdAlignEqualLength_; +typedef Tag SimdAlignEqualLength; + +template +struct SimdAlignVariableLength +{}; + +template +struct SimdAlignmentScout {}; + +// ---------------------------------------------------------------------------- +// Class DPScoutState_ +// ---------------------------------------------------------------------------- + +template <> +class DPScoutState_ +{}; + +template +class DPScoutState_ > +{ +public: + using TSizeH = typename Size::Type; + using TSizeV = typename Size::Type; + + String > masksH; + String > masksV; + String > masks; + + String endsH; + String endsV; + ModifiedString, ModPos > > sortedEndsH; + ModifiedString, ModPos > > sortedEndsV; + + decltype(begin(sortedEndsH, Standard())) nextEndsH; + decltype(begin(sortedEndsV, Standard())) nextEndsV; + + size_t dimV; + size_t posH; + size_t posV; + bool right; + bool bottom; + bool isLocalAlignment; + + // ---------------------------------------------------------------------------- + // Function DPScout_#updateMasksRight() + // ---------------------------------------------------------------------------- + + inline void updateMasksRight() + { + for(size_t pos = dimV - 2; pos != MaxValue::VALUE; --pos) + masks[pos] |= masks[pos + 1]; + } + + // ---------------------------------------------------------------------------- + // Function DPScout_#updateMasksBottom() + // ---------------------------------------------------------------------------- + + inline void updateMasksBottom() + { + for (auto posIt = begin(sortedEndsV, Standard()); posIt != end(sortedEndsV, Standard()); ++posIt) + for (auto it = nextEndsH; it != end(sortedEndsH, Standard()); ++it) + { + masks[*posIt] |= (masksH[*it] & masksV[*posIt]); + } + } + + // ---------------------------------------------------------------------------- + // Function DPScout_#updateMasks() + // ---------------------------------------------------------------------------- + + inline void updateMasks() + { + for(size_t pos = 0; pos < dimV; ++pos) + masks[pos] = masksH[posH] & masksV[pos]; + //for local alignments the BOTTOM parameter must be checked first + if(isLocalAlignment) + { + updateMasksBottom(); + updateMasksRight(); + } + else + { + if(right && posH == *nextEndsH) + updateMasksRight(); + if(bottom) + updateMasksBottom(); + } + } +}; + +// ---------------------------------------------------------------------------- +// Class DPScout_ +// ---------------------------------------------------------------------------- + +template +class DPScout_ > : + public DPScout_ +{ +public: + using TBase = DPScout_; + using TScoutState = DPScoutState_; + + //used in the SIMD version to keep track of all host positions + //SIMD register size divided by 16bit is the amount of alignments + //so we need two vectors of type 32bit to save the host for all alignments + + // TODO(rrahn): Abstract into a struct, so we can model different configurations. + SimdVector::Type _maxHostLow; //first half of alignments + SimdVector::Type _maxHostHigh; //other half + TScoutState * state = nullptr; + unsigned _simdLane = 0; + + DPScout_(TScoutState & pState) : TBase(), state(&pState) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction ScoutSpecForSimdAlignment_ +// ---------------------------------------------------------------------------- + +template +struct ScoutSpecForAlignmentAlgorithm_ > +{ + typedef SimdAlignmentScout Type; +}; + +template +struct ScoutSpecForAlignmentAlgorithm_ > > +{ + typedef SimdAlignmentScout > Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _copySimdCell() +// ---------------------------------------------------------------------------- + +template +inline void +_copySimdCell(DPScout_, SimdAlignmentScout > & dpScout, + DPCell_ const & activeCell, + TScoreValue const & cmp) +{ + dpScout._maxScore._score = blend(dpScout._maxScore._score, activeCell._score, cmp); +} + +template +inline void +_copySimdCell(DPScout_, SimdAlignmentScout > & dpScout, + DPCell_ const & activeCell, + TScoreValue const & cmp) +{ + dpScout._maxScore._score = blend(dpScout._maxScore._score, activeCell._score, cmp); + dpScout._maxScore._horizontalScore = blend(dpScout._maxScore._horizontalScore, activeCell._horizontalScore, cmp); + dpScout._maxScore._verticalScore = blend(dpScout._maxScore._verticalScore, activeCell._verticalScore, cmp); +} + +template +inline void +_copySimdCell(DPScout_, SimdAlignmentScout > & dpScout, + DPCell_ const & activeCell, + TScoreValue const & cmp) +{ + dpScout._maxScore._score = blend(dpScout._maxScore._score, activeCell._score, cmp); + dpScout._maxScore._flagMask = blend(dpScout._maxScore._flagMask, activeCell._flagMask, cmp); +} + +// ---------------------------------------------------------------------------- +// Function _updateHostPositions() +// ---------------------------------------------------------------------------- + +template +inline void +_updateHostPositions(DPScout_ & dpScout, + TSimdVec & cmp, + SimdVector::Type positionNavigator) +{ +// TODO(rrahn): Refactor! +#if defined(__AVX2__) + dpScout._maxHostLow = blend(dpScout._maxHostLow, positionNavigator, + _mm256_cvtepi16_epi32(_mm256_castsi256_si128(reinterpret_cast<__m256i&>(cmp)))); + dpScout._maxHostHigh = blend(dpScout._maxHostHigh, positionNavigator, + _mm256_cvtepi16_epi32(_mm256_extractf128_si256(reinterpret_cast<__m256i&>(cmp),1))); +#elif defined(__SSE3__) + dpScout._maxHostLow = blend(dpScout._maxHostLow, positionNavigator, + _mm_unpacklo_epi16(reinterpret_cast<__m128i&>(cmp), reinterpret_cast<__m128i&>(cmp))); + dpScout._maxHostHigh = blend(dpScout._maxHostHigh, positionNavigator, + _mm_unpackhi_epi16(reinterpret_cast<__m128i&>(cmp), reinterpret_cast<__m128i&>(cmp))); +#endif +} + +// ---------------------------------------------------------------------------- +// Function _scoutBestScore() +// ---------------------------------------------------------------------------- + +template +inline void +_scoutBestScore(DPScout_ > & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn const & /**/, + TIsLastRow const & /**/) +{ + auto cmp = cmpGt(_scoreOfCell(activeCell), _scoreOfCell(dpScout._maxScore)); + _copySimdCell(dpScout, activeCell, cmp); + _updateHostPositions(dpScout, cmp, createVector::Type>(position(navigator))); +} + +template +inline void +_scoutBestScore(DPScout_ > > & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn const & /**/, + TIsLastRow const & /**/) +{ + auto cmp = cmpGt(_scoreOfCell(activeCell), _scoreOfCell(dpScout._maxScore)); + cmp &= dpScout.state->masks[dpScout.state->posV]; + _copySimdCell(dpScout, activeCell, cmp); + _updateHostPositions(dpScout, cmp, createVector::Type>(position(navigator))); +} + +// ---------------------------------------------------------------------------- +// Function maxHostPosition() +// ---------------------------------------------------------------------------- + +template +inline unsigned int +maxHostPosition(DPScout_ > const & dpScout) +{ + if(dpScout._simdLane < LENGTH::Type>::VALUE) + return value(dpScout._maxHostLow, dpScout._simdLane); + else + return value(dpScout._maxHostHigh, dpScout._simdLane - LENGTH::Type>::VALUE); +} + +// ---------------------------------------------------------------------------- +// Function _setSimdLane() +// ---------------------------------------------------------------------------- + +template +inline void +_setSimdLane(DPScout_ & dpScout, TPosition const pos) +{ + dpScout._simdLane = pos; +} + +// ---------------------------------------------------------------------------- +// Function _preInitScoutHorizontal() +// ---------------------------------------------------------------------------- + +template +inline void +_preInitScoutHorizontal(DPScout_ > > & scout) +{ + scout.state->nextEndsH = begin(scout.state->sortedEndsH, Standard()); + scout.state->posH = 0; +} + +// ---------------------------------------------------------------------------- +// Function _preInitScoutVertical() +// ---------------------------------------------------------------------------- + +template +inline void +_preInitScoutVertical(DPScout_ > > & scout) +{ + scout.state->updateMasks(); + scout.state->nextEndsV = begin(scout.state->sortedEndsV, Standard()); + scout.state->posV = 0; +} + +// ---------------------------------------------------------------------------- +// Function _reachedHorizontalEndPoint() +// ---------------------------------------------------------------------------- + +template +inline bool +_reachedHorizontalEndPoint(DPScout_ > > & scout, + TIter const & hIt) +{ + return *(scout.state->nextEndsH) == position(hIt); +} + +// ---------------------------------------------------------------------------- +// Function _reachedVerticalEndPoint() +// ---------------------------------------------------------------------------- + +template +inline bool +_reachedVerticalEndPoint(DPScout_ > > & scout, + TIter const & vIt) +{ + return *(scout.state->nextEndsV) == position(vIt); +} + +// ---------------------------------------------------------------------------- +// Function _nextHorizontalEndPos() +// ---------------------------------------------------------------------------- + +template +inline void +_nextHorizontalEndPos(DPScout_ > > & scout) +{ + auto oldLength = *scout.state->nextEndsH; + while (scout.state->nextEndsH != end(scout.state->sortedEndsH, Standard()) && + *scout.state->nextEndsH == oldLength) + { + ++scout.state->nextEndsH; + } +} + +// ---------------------------------------------------------------------------- +// Function _nextVerticalEndPos() +// ---------------------------------------------------------------------------- + +template +inline void +_nextVerticalEndPos(DPScout_ > > & scout) +{ + auto oldLength = *scout.state->nextEndsV; + while (scout.state->nextEndsV != end(scout.state->sortedEndsV, Standard()) && + *scout.state->nextEndsV == oldLength) + { + ++scout.state->nextEndsV; + } +} + +// ---------------------------------------------------------------------------- +// Function _incHorizontalPos() +// ---------------------------------------------------------------------------- + +template +inline void +_incHorizontalPos(DPScout_ > > & scout) +{ + ++scout.state->posH; +} + +// ---------------------------------------------------------------------------- +// Function _incVerticalPos() +// ---------------------------------------------------------------------------- + +template +inline void +_incVerticalPos(DPScout_ > > & scout) +{ + ++scout.state->posV; +} + +// ---------------------------------------------------------------------------- +// Function _hostLengthH() +// ---------------------------------------------------------------------------- + +template +inline auto +_hostLengthH(DPScout_ > const & /*scout*/, + TSeqH const & seqH) +{ + return length(seqH); +} + +template +inline auto +_hostLengthH(DPScout_ > > const & scout, + TSeqH const & /*seqH*/) +{ + return host(scout.state->sortedEndsH)[scout._simdLane] + 1; +} + +// ---------------------------------------------------------------------------- +// Function _hostLengthV() +// ---------------------------------------------------------------------------- + +template +inline auto +_hostLengthV(DPScout_ > const & /*scout*/, + TSeqV const & seqV) +{ + return length(seqV); +} + +template +inline auto +_hostLengthV(DPScout_ > > const & scout, + TSeqV const & /*seqV*/) +{ + return host(scout.state->sortedEndsV)[scout._simdLane] + 1; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SIMD_DP_SCOUT_SIMD_H_ + diff --git a/seqan/align/dp_setup.h b/seqan/align/dp_setup.h new file mode 100644 index 0000000..29bf429 --- /dev/null +++ b/seqan/align/dp_setup.h @@ -0,0 +1,332 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// SubstituteAlignConfig_ +// ---------------------------------------------------------------------------- + +template +struct SubstituteAlignConfig_; + +// 0000 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + +// 0001 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + +// 0010 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 0011 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 0100 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 0101 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 0110 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 0111 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1000 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1001 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1010 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1011 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1100 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1101 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + + +// 1110 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + +// 1111 +template +struct SubstituteAlignConfig_ > +{ + typedef FreeEndGaps_ Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction SubstituteAlgoTag_ +// ---------------------------------------------------------------------------- + +// NOTE(rmaerker): Needed to substitute the global alingment algo tags to the correct gap model. +template +struct SubstituteAlgoTag_ +{ + typedef TTag Type; +}; + +template <> +struct SubstituteAlgoTag_ +{ + typedef LinearGaps Type; +}; + +template <> +struct SubstituteAlgoTag_ +{ + typedef AffineGaps Type; +}; + +// ---------------------------------------------------------------------------- +// SetUpAlignmentProfile +// ---------------------------------------------------------------------------- + +template +struct SetupAlignmentProfile_; + +// Profile for Needleman-Wunsch algorithm. +template +struct SetupAlignmentProfile_ +{ + typedef DPProfile_, TGapCosts, TTraceSwitch> Type; +}; + +// Profile for Smith-Waterman algorithm. +template +struct SetupAlignmentProfile_ +{ + typedef DPProfile_, TGapCosts, TTraceSwitch> Type; +}; + +// Profile for Waterman-Eggert algorithm +template +struct SetupAlignmentProfile_ +{ + typedef DPProfile_, TGapCosts, TracebackOn > > Type; +}; + + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _usesAffineGaps() +// ---------------------------------------------------------------------------- + +template +inline bool +_usesAffineGaps(TScoringScheme const & scoringScheme, + TSeqH const & seqH, + TSeqV const & seqV) +{ + typedef typename SequenceEntryForScore::Type TSequenceHEntry; + typedef typename SequenceEntryForScore::Type TSequenceVEntry; + + TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0); + TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0); + + return (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) != + scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry)) || + (scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) != + scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry)); +} + +// ---------------------------------------------------------------------------- +// Function _setUpAndRunAlignment() +// ---------------------------------------------------------------------------- + +template +typename Value >::Type +_setUpAndRunAlignment(DPContext & dpContext, + TTrace & traceSegments, + DPScoutState_ & dpScoutState, + TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig2 const & alignConfig) +{ + SEQAN_ASSERT_GEQ(length(seqH), 1u); + SEQAN_ASSERT_GEQ(length(seqV), 1u); + + typedef typename SetupAlignmentProfile_::Type TDPProfile; + return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, + TDPProfile()); +} + +template +typename Value >::Type +_setUpAndRunAlignment(TTrace & traceSegments, + DPScoutState_ & dpScoutState, + TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig2 const & alignConfig, + TGapModel const & /**/) +{ + DPContext dpContext; + return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); +} + +template +typename Value >::Type +_setUpAndRunAlignment(TTrace & traceSegments, + DPScoutState_ & dpScoutState, + TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig2 const & alignConfig) +{ + if (_usesAffineGaps(scoringScheme, seqH, seqV)) + return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, AffineGaps()); + else + return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, LinearGaps()); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_ diff --git a/seqan/align/dp_trace_segment.h b/seqan/align/dp_trace_segment.h new file mode 100644 index 0000000..2b591be --- /dev/null +++ b/seqan/align/dp_trace_segment.h @@ -0,0 +1,341 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// +// The TraceSegment structure is used to store the traceback in a common +// structure such that we can easiely adapt them afterwards in the +// user-defined structure, such as Align or AlignmentGraph objects. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class TraceSegment +// ---------------------------------------------------------------------------- + +// TraceSegments are used as a common interface to all structures that can represent an alignment. +// +// See alignment_dp_traceback_adaptor.h to find methods for adaption. +template +class TraceSegment_ +{ +public: + typedef typename TraceBitMap_<>::Type TTraceValue; + + TPosition _horizontalBeginPos; // the begin position in horizontal dimension + TPosition _verticalBeginPos; // the begin position in vertical dimension + TSize _length; // the length of the segment + TTraceValue _traceValue; // the trace direction + + TraceSegment_() : + _horizontalBeginPos(0), _verticalBeginPos(0), _length(0), _traceValue(+TraceBitMap_::NONE){} + + TraceSegment_(TraceSegment_ const & other) : + _horizontalBeginPos(other._horizontalBeginPos), + _verticalBeginPos(other._verticalBeginPos), + _length(other._length), + _traceValue(other._traceValue) {} + + TraceSegment_(TPosition const & horizontalBeginPos, TPosition const & verticalBeginPos, TSize const & length, + TTraceValue const & traceValue) : + _horizontalBeginPos(horizontalBeginPos), + _verticalBeginPos(verticalBeginPos), + _length(length), + _traceValue(traceValue) {} + + TraceSegment_ & + operator=(TraceSegment_ const & other) + { + if (this != &other) + { + _horizontalBeginPos = other._horizontalBeginPos; + _verticalBeginPos = other._verticalBeginPos; + _length = other._length; + _traceValue = other._traceValue; + } + return *this; + } + +}; + + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Position +// ---------------------------------------------------------------------------- + +template +struct Position > +{ + typedef TPosition Type; +}; + +template +struct Position const>: + Position >{}; + +// ---------------------------------------------------------------------------- +// Metafunction Size +// ---------------------------------------------------------------------------- + +template +struct Size > +{ + typedef TSize Type; +}; + +template +struct Size const>: + Size >{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _getBeginHorizontal() +// ---------------------------------------------------------------------------- + +// The begin position of the segment in horizontal dimension. +template +inline TPosition +_getBeginHorizontal(TraceSegment_ const & traceSegment) +{ + return traceSegment._horizontalBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function _getBeginVertical() +// ---------------------------------------------------------------------------- + +// The begin position of the segment in vertical dimension. +template +inline TPosition +_getBeginVertical(TraceSegment_ const & traceSegment) +{ + return traceSegment._verticalBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function _getEndHorizontal() +// ---------------------------------------------------------------------------- + +// The end position of the segment in horizontal dimension. +template +inline TPosition +_getEndHorizontal(TraceSegment_ const & traceSegment) +{ + typedef typename std::remove_const::type TTraceValue; + if (traceSegment._traceValue & (TraceBitMap_::HORIZONTAL | TraceBitMap_::DIAGONAL)) + { + return traceSegment._horizontalBeginPos + traceSegment._length; + } + return traceSegment._horizontalBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function _getEndVertical() +// ---------------------------------------------------------------------------- + +// The end position of the segment in vertical dimension. +template +inline TPosition +_getEndVertical(TraceSegment_ const & traceSegment) +{ + typedef typename std::remove_const::type TTraceValue; + if (traceSegment._traceValue & (TraceBitMap_::VERTICAL | TraceBitMap_::DIAGONAL)) + { + return traceSegment._verticalBeginPos + traceSegment._length; + } + return traceSegment._verticalBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function _getTraceValue() +// ---------------------------------------------------------------------------- + +// The end position of the segment in vertical dimension. +template +inline typename TraceSegment_::TTraceValue +_getTraceValue(TraceSegment_ const & traceSegment) +{ + return traceSegment._traceValue; +} + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +// The length of the segment. +template +inline TSize +length(TraceSegment_ const & traceSegment) +{ + return traceSegment._length; +} + +// ---------------------------------------------------------------------------- +// Function _setLength() +// ---------------------------------------------------------------------------- + +// The length of the segment. +template +inline void +_setLength(TraceSegment_ & traceSegment, TSize newLength) +{ + traceSegment._length = newLength; +} + +// ---------------------------------------------------------------------------- +// Function _translateTraceValue() +// ---------------------------------------------------------------------------- + +// Translates the trace value into a human-readable format. +// +// Note, used for debugging reasons only. +template +String _translateTraceValue(TTraceValue const & traceValue) +{ + String transcript; + + if ((traceValue & TraceBitMap_::DIAGONAL) == TraceBitMap_::DIAGONAL) + append(transcript, 'D'); + if ((traceValue & TraceBitMap_::VERTICAL) == TraceBitMap_::VERTICAL) + append(transcript, 'V'); + if ((traceValue & TraceBitMap_::HORIZONTAL) == TraceBitMap_::HORIZONTAL) + append(transcript, 'H'); + if ((traceValue & TraceBitMap_::VERTICAL_OPEN) == TraceBitMap_::VERTICAL_OPEN) + append(transcript, 'v'); + if ((traceValue & TraceBitMap_::HORIZONTAL_OPEN) == TraceBitMap_::HORIZONTAL_OPEN) + append(transcript, 'h'); + if ((traceValue & TraceBitMap_::MAX_FROM_VERTICAL_MATRIX) == TraceBitMap_::MAX_FROM_VERTICAL_MATRIX) + append(transcript, '|'); + if ((traceValue & TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX) == TraceBitMap_::MAX_FROM_HORIZONTAL_MATRIX) + append(transcript, '-'); + + if ((traceValue) == TraceBitMap_::NONE) + append(transcript, '0'); + return transcript; +} + +// ---------------------------------------------------------------------------- +// Function oerpator<<() +// ---------------------------------------------------------------------------- + +template +TStream & operator<<(TStream & stream, TraceSegment_ const & traceSegment) +{ + stream << _translateTraceValue(traceSegment._traceValue) << "-"; + stream << "(" << traceSegment._horizontalBeginPos << ", " << traceSegment._verticalBeginPos << ", " << + traceSegment._length << ")"; + return stream; +} + +// ---------------------------------------------------------------------------- +// Function oerpator==() +// ---------------------------------------------------------------------------- + +template +inline bool operator==(TraceSegment_ const & left, TraceSegment_ const & right) +{ + if (left._horizontalBeginPos != right._horizontalBeginPos) + return false; + + if (left._verticalBeginPos != right._verticalBeginPos) + return false; + + if (left._length != right._length) + return false; + + if (left._traceValue != right._traceValue) + return false; + + return true; +} + +// ---------------------------------------------------------------------------- +// Function oerpator!=() +// ---------------------------------------------------------------------------- + +template +inline bool operator!=(TraceSegment_ const & left, TraceSegment_ const & right) +{ + return !(left == right); +} + +// ---------------------------------------------------------------------------- +// Function recordSegment() +// ---------------------------------------------------------------------------- + +// Records a segment given the horizontal and vertical begin position, the length, +// and the corrsponding trace value. +// +// The first parameter is the container the segment is recorded to. +template +inline void _recordSegment(TTraceSegments & traceSegments, + TPositionH const & horizontalBeginPos, + TPositionV const & verticalBeginPos, + TSize const & segmentLength, + TTraceValue const & traceValue) +{ + typedef typename Value::Type TTraceSegment; + + if (segmentLength == 0) + return; // we don't store empty segments + + if (traceValue & TraceBitMap_::DIAGONAL) + appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, +TraceBitMap_::DIAGONAL)); + else if (traceValue & TraceBitMap_::VERTICAL) + appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, +TraceBitMap_::VERTICAL)); + else if (traceValue & TraceBitMap_::HORIZONTAL) + appendValue(traceSegments, TTraceSegment(horizontalBeginPos, verticalBeginPos, segmentLength, +TraceBitMap_::HORIZONTAL)); + // everything else is not tracked. +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACE_SEGMENT_H_ diff --git a/seqan/align/dp_traceback_adaptor.h b/seqan/align/dp_traceback_adaptor.h new file mode 100644 index 0000000..f9e495f --- /dev/null +++ b/seqan/align/dp_traceback_adaptor.h @@ -0,0 +1,321 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Rene Rahn +// ========================================================================== +// Adaptor methods to transcribe a set of trace segments into the +// alignment representing structure. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_ + +namespace seqan { + +// ---------------------------------------------------------------------------- +// Function _writeTraceSegmentToFile() +// ---------------------------------------------------------------------------- + +template +inline void _writeTraceSegmentToFile(TFile & file, TSeq0Value const & seq0Val, TSeq1Value const & seq1Val) +{ + file << '(' << seq0Val << ',' << seq1Val << ")\n"; +} + +// ---------------------------------------------------------------------------- +// Function _adaptTraceSegmentsTo() [Gaps] +// ---------------------------------------------------------------------------- + +template +void +_adaptTraceSegmentsTo(Gaps & gapsHorizontal, + Gaps & gapsVertical, + String, TStringSpec> const & traceSegments) +{ + typedef Gaps TGapsHorizontal; + typedef Gaps TGapsVertical; + typedef typename Iterator::Type TIteratorHorizontal; + typedef typename Iterator::Type TIteratorVertical; + typedef TraceSegment_ TTraceSegment; + typedef typename Iterator const>::Type TTraceIterator; + + clearGaps(gapsHorizontal); + clearClipping(gapsHorizontal); + + clearGaps(gapsVertical); + clearClipping(gapsVertical); + + // Set clipping to 0 + if (empty(traceSegments)) + { + setClippedBeginPosition(gapsHorizontal, 0); + setClippedEndPosition(gapsHorizontal, 0); + setClippedBeginPosition(gapsVertical, 0); + setClippedEndPosition(gapsVertical, 0); + return; + } + + TTraceIterator srcIter = end(traceSegments) - 1; + TTraceIterator srcEnd = begin(traceSegments) - 1; + + // we build the gap structure here. + // set the clipped begin position of the alignment. + setBeginPosition(gapsHorizontal, _getBeginHorizontal(value(srcIter))); // begin of source + setBeginPosition(gapsVertical, _getBeginVertical(value(srcIter))); + + TIteratorHorizontal it0 = begin(gapsHorizontal); + TIteratorVertical it1 = begin(gapsVertical); + + while (srcIter != srcEnd) + { + TSize segmentSize = value(srcIter)._length; + switch (value(srcIter)._traceValue) + { + case TraceBitMap_<>::HORIZONTAL: + insertGaps(it1, segmentSize); + break; + + case TraceBitMap_<>::VERTICAL: + insertGaps(it0, segmentSize); + break; + } + goFurther(it0, segmentSize); + goFurther(it1, segmentSize); + --srcIter; + } + setClippedEndPosition(gapsHorizontal, position(it0) + clippedBeginPosition(gapsHorizontal)); + setClippedEndPosition(gapsVertical, position(it1) + clippedBeginPosition(gapsVertical)); +} + +// ---------------------------------------------------------------------------- +// Function _adaptTraceSegmentsTo() [AlignmentGraph] +// ---------------------------------------------------------------------------- + +template +inline void +_adaptTraceSegmentsTo(Graph > & g, + TSequenceIdH const & seqHId, + TSequenceIdV const & seqVId, + String, TStringSpec> const & traceSegments) +{ + typedef TraceSegment_ TTraceSegment; + // check begin and end positions of the graph. + + // Not safe! + + if (empty(traceSegments)) + return; + + // insert leading gaps + TTraceSegment traceBegin = traceSegments[length(traceSegments) - 1]; + if (_getBeginVertical(traceBegin) != 0) + addVertex(g, seqVId, 0, _getBeginVertical(traceBegin)); + if (_getBeginHorizontal(traceBegin) != 0) + addVertex(g, seqHId, 0, _getBeginHorizontal(traceBegin)); + + + for (TSize i = 0; i < length(traceSegments); ++i) + { + + switch (traceSegments[i]._traceValue) + { + case TraceBitMap_<>::DIAGONAL: + addEdge(g, addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length), + addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length)); + break; + + case TraceBitMap_<>::VERTICAL: + addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length); + break; + + case TraceBitMap_<>::HORIZONTAL: + addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length); + } + } + + // insert trailing gaps + TTraceSegment traceEnd = traceSegments[0]; + + if (_getEndVertical(traceEnd) != length(value(stringSet(g), idToPosition(stringSet(g), seqVId)))) + addVertex(g, seqVId, _getEndVertical(traceEnd), + length(value(stringSet(g), idToPosition(stringSet(g), seqVId))) - _getEndVertical(traceEnd)); + + if (_getEndHorizontal(traceEnd) != length(value(stringSet(g), idToPosition(stringSet(g), seqHId)))) + addVertex(g, seqHId, _getEndHorizontal(traceEnd), + length(value(stringSet(g), idToPosition(stringSet(g), seqHId))) - _getEndHorizontal(traceEnd)); +} + +// ---------------------------------------------------------------------------- +// Function _adaptTraceSegmentsTo() [File] +// ---------------------------------------------------------------------------- + +template +inline void +_adaptTraceSegmentsTo(TFile & file, + TSequenceH const & seqH, + TSequenceV const & seqV, + String, TStringSpec> const & traceSegments) +{ + for (TSize k = length(traceSegments); k > (TSize) 0; --k) + { + switch (traceSegments[k - 1]._traceValue) + { + case TraceBitMap_<>::DIAGONAL: + { + int j = traceSegments[k - 1]._verticalBeginPos; + for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i) + { + _writeTraceSegmentToFile(file, seqH[i], seqV[j]); + ++j; + } + break; + } + + case TraceBitMap_<>::VERTICAL: + { + for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBeginPos + traceSegments[k - 1]._length); ++i) + _writeTraceSegmentToFile(file, gapValue(), seqV[i]); + break; + } + + case TraceBitMap_<>::HORIZONTAL: + { + for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i) + _writeTraceSegmentToFile(file, seqH[i], gapValue()); + } + } + } +} + +// ---------------------------------------------------------------------------- +// Function _adaptTraceSegmentsTo() [Fragments] +// ---------------------------------------------------------------------------- + +template +inline void +_adaptTraceSegmentsTo(String, TStringSpec> & matches, + TSequenceH const & seqHId, + TSequenceV const & seqVId, + String, TStringSpec2> const & traceSegments) +{ + typedef Fragment TFragment; + + for (TSize2 i = 0; i < length(traceSegments); ++i) + if (traceSegments[i]._traceValue == TraceBitMap_<>::DIAGONAL) + appendValue( + matches, + TFragment(seqHId, traceSegments[i]._horizontalBeginPos, seqVId, + traceSegments[i]._verticalBeginPos, traceSegments[i]._length), + Generous()); +} + +// ---------------------------------------------------------------------------- +// Function _adaptTraceSegmentsTo() [VertexDescriptor] +// ---------------------------------------------------------------------------- + +//// TODO (rmaerker): Check if we really need this! +//template +//inline void +//_adaptTraceSegmentsTo(String > & /*nodeString*/, +// TSequence0 const & /*seq0*/, +// TSequence1 const & /*seq1*/, +// String, TStringSpec> const & /*traceSegments*/) +//{ +// typedef String TVertexDescriptorString; +// typedef typename Size::Type TSize; +// typedef typename Iterator::Type TStringIter; +// TVertexDescriptor nilVertex = getNil(); + + +// TODO (rmaerker): see how to adapt this code here for the new structure. +// // TraceBack values +// TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; +// +// if (segLen == 0) return; +// // Number of vertex descriptors in the first string at any position (e.g., group of 5 sequences = group of 5 vertex descriptors) +// TSize len1 = length(getValue(getValue(str,0), 0)); +// // Number of vertex descriptors in the second string at any position (e.g., group of 5 sequences = group of 5 vertex descriptors) +// TSize len2 = length(getValue(getValue(str,1), 0)); +// +// // Resize the node string +// TSize index = length(nodeString); +// resize(nodeString, index + segLen); +// +// if (tv == Horizontal) { +// for (int i = pos1 + segLen - 1; i>= (int) pos1;--i) { +// resize(value(nodeString, index), len1 + len2, nilVertex); +// TStringIter it = begin(value(nodeString, index)); +// for(TPos all = 0;all= (int) pos2;--i) { +// resize(value(nodeString, index), len1 + len2, nilVertex); +// TStringIter it = begin(value(nodeString, index)); +// it+=len1; +// for(TPos all = 0;all= (int) pos1;--i) { +// resize(value(nodeString, index), len1 + len2); +// TStringIter it = begin(value(nodeString, index)); +// for(TPos all = 0;all +// ========================================================================== +// Implements the traceback algorithm. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_ + +// TODO(holtgrew): GapsRight traceback is currently untested. +// TODO(rmaerker): Change Tracback to TraceConfig | TraceBackOff + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class TracebackCoordinator_ +// ---------------------------------------------------------------------------- + +template +class TracebackCoordinator_ +{ +public: + TPosition _currColumn; + TPosition _currRow; + TPosition _endColumn; + TPosition _endRow; + TPosition _breakpoint1; // First breakpoint where banded trace switches to unbanded trace. + TPosition _breakpoint2; // Second breakpoint where unbanded trace switches back to banded trace. Only if begin of upper diagonal is bigger than end of lower diagonal. + bool _isInBand; + + template + TracebackCoordinator_(TPosition currColumn, + TPosition currRow, + DPBandConfig const & band, + TSizeH seqHSize, + TSizeV seqVSize) + : _currColumn(currColumn), + _currRow(currRow), + _endColumn(0u), + _endRow(0u), + _breakpoint1(0u), + _breakpoint2(0u), + _isInBand(false) + { + _initTracebackCoordinator(*this, band, seqHSize, seqVSize); + } + + template + TracebackCoordinator_(TPosition currColumn, + TPosition currRow, + TPosition endColumn, + TPosition endRow, + DPBandConfig const & band, + TSizeH seqHSize, + TSizeV seqVSize) + : _currColumn(currColumn), + _currRow(currRow), + _endColumn(endColumn), + _endRow(endRow), + _breakpoint1(0u), + _breakpoint2(0u), + _isInBand(false) + { + _initTracebackCoordinator(*this, band, seqHSize, seqVSize); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction PreferGapsAtEnd_ +// ---------------------------------------------------------------------------- + +// Checks whether the gaps at the end should be preferred over a matching area. +template +struct PreferGapsAtEnd_ : False{}; + +template +struct PreferGapsAtEnd_ > : True{}; + +template +struct PreferGapsAtEnd_ > > > : True{}; + + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _hasReachedEnd() +// ---------------------------------------------------------------------------- + +template +inline bool +_hasReachedEnd(TracebackCoordinator_ const & coordinator) +{ + return coordinator._currColumn <= coordinator._endColumn || coordinator._currRow <= coordinator._endRow; +} + +// ---------------------------------------------------------------------------- +// Function _initTracebackCoordinator() +// ---------------------------------------------------------------------------- + +template +inline void +_initTracebackCoordinator(TracebackCoordinator_ & coordinator, + DPBandConfig const & band, + TSizeH seqHSize, + TSizeV seqVSize) +{ + typedef typename Position >::Type TBandPosition; + if (IsSameType::VALUE) + { + // Adapt the current column value when the lower diagonal is positive (shift right in horizontal direction). + if (lowerDiagonal(band) >= 0) + coordinator._currColumn += static_cast(lowerDiagonal(band)); + // Adapt the current row value when the current column comes after the upper diagonal (shift down in vertical direction). + if (static_cast(coordinator._currColumn) > upperDiagonal(band)) + coordinator._currRow += coordinator._currColumn - upperDiagonal(band); + // Adapt the end row value when the end column comes after the upper diagonal (shift down in vertical direction). + if (static_cast(coordinator._endColumn) > upperDiagonal(band)) + coordinator._endRow += coordinator._endColumn - upperDiagonal(band); + + coordinator._breakpoint1 = _min(seqHSize, static_cast(_max(0, upperDiagonal(band)))); + coordinator._breakpoint2 = _min(seqHSize, static_cast(_max(0, static_cast(seqVSize) + + lowerDiagonal(band)))); + // Update the current row if the current column is before the upper diagoal or the first column where the maximal band size is reached. + if (coordinator._currColumn < _min(coordinator._breakpoint1, coordinator._breakpoint2)) + coordinator._currRow -= _min(coordinator._breakpoint1, coordinator._breakpoint2) - coordinator._currColumn; + coordinator._isInBand = true; + } +} + +// ---------------------------------------------------------------------------- +// Function _isInBand() +// ---------------------------------------------------------------------------- + +template +inline bool +_isInBand(TracebackCoordinator_ const & coordinator) +{ + if (!coordinator._isInBand) + return coordinator._isInBand; + return (coordinator._currColumn > coordinator._breakpoint1 || coordinator._currColumn <= coordinator._breakpoint2); +} + + +// ---------------------------------------------------------------------------- +// Function _doTracebackGoDiagonal() +// ---------------------------------------------------------------------------- + +template +inline void +_doTracebackGoDiagonal(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + TTraceValue & traceValue, + TTraceValue & lastTraceValue, + TSize & fragmentLength, + TracebackCoordinator_ & tracebackCoordinator, + TGapCosts const &) +{ + if (!(lastTraceValue & TraceBitMap_<>::DIAGONAL)) // the old trace value was not diagonal + { + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, + lastTraceValue); + + lastTraceValue = TraceBitMap_<>::DIAGONAL; + fragmentLength = 0; + } + _traceDiagonal(matrixNavigator, _isInBand(tracebackCoordinator)); + traceValue = scalarValue(matrixNavigator); + --tracebackCoordinator._currColumn; + --tracebackCoordinator._currRow; + ++fragmentLength; +} + +// ---------------------------------------------------------------------------- +// Function _doTracebackGoVertical() +// ---------------------------------------------------------------------------- + +template +inline void +_doTracebackGoVertical(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + TTraceValue & traceValue, + TTraceValue & lastTraceValue, + TSize & fragmentLength, + TracebackCoordinator_ & tracebackCoordinator, + TGapCosts const &) +{ + if (!(lastTraceValue & TraceBitMap_<>::VERTICAL)) // the old trace value was not diagonal + { + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, + lastTraceValue); + + lastTraceValue = TraceBitMap_<>::VERTICAL; + fragmentLength = 0; + } + // We are in a vertical gap. So continue after we reach the end of the vertical gap. + if (IsSameType::VALUE) + { + while ((!(traceValue & TraceBitMap_<>::VERTICAL_OPEN) || (traceValue & TraceBitMap_<>::VERTICAL)) && (tracebackCoordinator._currRow != 1)) + { + _traceVertical(matrixNavigator, _isInBand(tracebackCoordinator)); + traceValue = scalarValue(matrixNavigator); + --tracebackCoordinator._currRow; + ++fragmentLength; + } + // We have to ensure, that we do not continue in vertical direction if we reached a vertical_open sign. + _traceVertical(matrixNavigator, _isInBand(tracebackCoordinator)); + // Forbid continuing in vertical direction. + traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_VERTICAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX); + --tracebackCoordinator._currRow; + ++fragmentLength; + } + else + { + _traceVertical(matrixNavigator, _isInBand(tracebackCoordinator)); + traceValue = scalarValue(matrixNavigator); + --tracebackCoordinator._currRow; + ++fragmentLength; + } +} + +// ---------------------------------------------------------------------------- +// Function _doTracebackMaxFromVertical() +// ---------------------------------------------------------------------------- + +template +inline void +_doTracebackMaxFromVertical(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + TTraceValue & traceValue, + TTraceValue & lastTraceValue, + TSize & fragmentLength, + TracebackCoordinator_ & tracebackCoordinator, + TGapCosts const &) +{ + if (!(lastTraceValue & TraceBitMap_<>::VERTICAL)) // the old trace value was not diagonal + { + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, + lastTraceValue); + lastTraceValue = TraceBitMap_<>::VERTICAL; + fragmentLength = 0; + } + _traceVertical(matrixNavigator, _isInBand(tracebackCoordinator)); + // Forbid continuing in vertical direction. + traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_VERTICAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX); + --tracebackCoordinator._currRow; + ++fragmentLength; +} + +// ---------------------------------------------------------------------------- +// Function _doTracebackGoHorizontal() +// ---------------------------------------------------------------------------- + +template +inline void +_doTracebackGoHorizontal(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + TTraceValue & traceValue, + TTraceValue & lastTraceValue, + TSize & fragmentLength, + TracebackCoordinator_ & tracebackCoordinator, + TGapCosts const &) +{ + if (!(lastTraceValue & TraceBitMap_<>::HORIZONTAL)) // the old trace value was not diagonal + { + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, + lastTraceValue); + + lastTraceValue = TraceBitMap_<>::HORIZONTAL; + fragmentLength = 0; + } + if (IsSameType::VALUE) + { + while ((!(traceValue & TraceBitMap_<>::HORIZONTAL_OPEN) || (traceValue & TraceBitMap_<>::HORIZONTAL)) && (tracebackCoordinator._currColumn != 1)) + { + _traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator)); + traceValue = scalarValue(matrixNavigator); + --tracebackCoordinator._currColumn; + ++fragmentLength; + } + _traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator)); + // Forbid continuing in horizontal direction. + traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_HORIZONTAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX); + --tracebackCoordinator._currColumn; + ++fragmentLength; + } + else + { + _traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator)); + traceValue = scalarValue(matrixNavigator); + --tracebackCoordinator._currColumn; + ++fragmentLength; + } +} + +// ---------------------------------------------------------------------------- +// Function _doTracebackMaxFromHorizontal() +// ---------------------------------------------------------------------------- + +template +inline void +_doTracebackMaxFromHorizontal(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + TTraceValue & traceValue, + TTraceValue & lastTraceValue, + TSize & fragmentLength, + TracebackCoordinator_ & tracebackCoordinator, + TGapCosts const &) +{ + if (!(lastTraceValue & TraceBitMap_<>::HORIZONTAL)) // the old trace value was not diagonal + { + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, + lastTraceValue); + lastTraceValue = TraceBitMap_<>::HORIZONTAL; + fragmentLength = 0; + } + _traceHorizontal(matrixNavigator, _isInBand(tracebackCoordinator)); + // Forbid continuing in horizontal direction. + traceValue = scalarValue(matrixNavigator); // & (TraceBitMap_<>::NO_HORIZONTAL_TRACEBACK | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX); + --tracebackCoordinator._currColumn; + ++fragmentLength; +} + +// ---------------------------------------------------------------------------- +// Function _doTraceback() +// ---------------------------------------------------------------------------- + +template +inline void +_doTraceback(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + TTraceValue & traceValue, + TTraceValue & lastTraceValue, + TSize & fragmentLength, + TracebackCoordinator_ & tracebackCoordinator, + TGapCosts const & gapsCost, + TIsGapsLeft const & /*isGapsLeft*/) +{ + if (TIsGapsLeft::VALUE) // Gaps should be placed on the left. + { + if (traceValue & TraceBitMap_<>::DIAGONAL) + { + _doTracebackGoDiagonal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } // In case of Gotoh we prefer the longest possible way in this direction. + else if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL) + { + _doTracebackGoVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL_OPEN) + { + _doTracebackMaxFromVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL) + { + _doTracebackGoHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL_OPEN) + { + _doTracebackMaxFromHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } // In case of Gotoh we prefer the longest possible way in this direction. + else // the trace back is either NONE or something else + { + if (traceValue == TraceBitMap_<>::NONE) + { + return; + } + SEQAN_ASSERT_FAIL("Reached undefined traceback value!"); + } + } + else // Gaps should be placed on the right. + { + if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL) + { + _doTracebackGoVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX && traceValue & TraceBitMap_<>::VERTICAL_OPEN) + { + _doTracebackMaxFromVertical(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL) + { + _doTracebackGoHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX && traceValue & TraceBitMap_<>::HORIZONTAL_OPEN) + { + _doTracebackMaxFromHorizontal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } // In case of Gotoh we prefer the longest possible way in this direction. + else if (traceValue & TraceBitMap_<>::DIAGONAL) + { + _doTracebackGoDiagonal(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, gapsCost); + } // In case of Gotoh we prefer the longest possible way in this direction. + else // the trace back is either NONE or something else + { + if (traceValue == TraceBitMap_<>::NONE) + { + return; + } + SEQAN_ASSERT_FAIL("Reached undefined traceback value!"); + } + } +} + +// ---------------------------------------------------------------------------- +// Function _retrieveInitialTraceDirection() +// ---------------------------------------------------------------------------- + +template +inline TTraceValue +_retrieveInitialTraceDirection(TTraceValue & traceValue, TDPProfile const & /*dpProfile*/) +{ + if (PreferGapsAtEnd_::VALUE) + { + if (traceValue & TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX) + { + traceValue &= (TraceBitMap_<>::VERTICAL | TraceBitMap_<>::VERTICAL_OPEN | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX); + return TraceBitMap_<>::VERTICAL; + } + else if (traceValue & TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX) + { + traceValue &= (TraceBitMap_<>::HORIZONTAL | TraceBitMap_<>::HORIZONTAL_OPEN | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX); + return TraceBitMap_<>::HORIZONTAL; + } + return TraceBitMap_<>::DIAGONAL; // We set the last value to the + } + + if (traceValue & TraceBitMap_<>::DIAGONAL) + return TraceBitMap_<>::DIAGONAL; + if (traceValue & (TraceBitMap_<>::VERTICAL | TraceBitMap_<>::MAX_FROM_VERTICAL_MATRIX)) + return TraceBitMap_<>::VERTICAL; + if (traceValue & (TraceBitMap_<>::HORIZONTAL | TraceBitMap_<>::MAX_FROM_HORIZONTAL_MATRIX)) + return TraceBitMap_<>::HORIZONTAL; + + return TraceBitMap_<>::NONE; +} + +// ---------------------------------------------------------------------------- +// Function _computeTraceback() +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_DISABLE_IF(Is >, void) +_computeTraceback(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + unsigned maxHostPosition, + TSizeH const & seqHSize, + TSizeV const & seqVSize, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + typedef typename Container::Type TContainer; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef typename TraceBitMap_<>::Type TTraceValue; + + if (IsSameType::VALUE) + return; + + // Determine whether or not we place gaps to the left. + typedef typename IsGapsLeft_::Type TIsGapsLeft; + + // Set the navigator to the position where the maximum was found. + _setToPosition(matrixNavigator, maxHostPosition); + + SEQAN_ASSERT_LEQ(coordinate(matrixNavigator, +DPMatrixDimension_::HORIZONTAL), seqHSize); + SEQAN_ASSERT_LEQ(coordinate(matrixNavigator, +DPMatrixDimension_::VERTICAL), seqVSize); + + TTraceValue traceValue = scalarValue(matrixNavigator); + TTraceValue lastTraceValue = _retrieveInitialTraceDirection(traceValue, dpProfile); + + TracebackCoordinator_ tracebackCoordinator(coordinate(matrixNavigator, +DPMatrixDimension_::HORIZONTAL), + coordinate(matrixNavigator, +DPMatrixDimension_::VERTICAL), + band, seqHSize, seqVSize); + + if (TraceTail_::VALUE) + { + if (tracebackCoordinator._currRow != seqVSize) + _recordSegment(target, seqHSize, tracebackCoordinator._currRow, seqVSize - tracebackCoordinator._currRow, + +TraceBitMap_<>::VERTICAL); + if (tracebackCoordinator._currColumn != seqHSize) + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, seqHSize - + tracebackCoordinator._currColumn, +TraceBitMap_<>::HORIZONTAL); + } + + TSize fragmentLength = 0; + while (!_hasReachedEnd(tracebackCoordinator) && traceValue != TraceBitMap_<>::NONE) + _doTraceback(target, matrixNavigator, traceValue, lastTraceValue, fragmentLength, tracebackCoordinator, TGapCosts(), TIsGapsLeft()); + + // Record last detected fragment. + _recordSegment(target, tracebackCoordinator._currColumn, tracebackCoordinator._currRow, fragmentLength, lastTraceValue); + if (TraceHead_::VALUE) + { + // Record leading gaps if any. + if (tracebackCoordinator._currRow != 0u) + _recordSegment(target, 0, 0, tracebackCoordinator._currRow, +TraceBitMap_<>::VERTICAL); + if (tracebackCoordinator._currColumn != 0u) + _recordSegment(target, 0, 0, tracebackCoordinator._currColumn, +TraceBitMap_<>::HORIZONTAL); + } +} + +//// Needed as a delegation method to allow invocation of both methods with host position and dpScout. +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +_computeTraceback(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + unsigned maxHostPosition, + TSequenceH const & seqH, + TSequenceV const & seqV, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + _computeTraceback(target, matrixNavigator, maxHostPosition, length(seqH), length(seqV), band, dpProfile); +} + +template +inline SEQAN_FUNC_DISABLE_IF(Is >, void) +_computeTraceback(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + DPScout_ const & dpScout, + TSizeH const & seqHSize, + TSizeV const & seqVSize, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + _computeTraceback(target, matrixNavigator, maxHostPosition(dpScout), seqHSize, seqVSize, band, dpProfile); +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +_computeTraceback(TTarget & target, + TDPTraceMatrixNavigator & matrixNavigator, + DPScout_ const & dpScout, + TSequenceH const & seqH, + TSequenceV const & seqV, + DPBandConfig const & band, + DPProfile_ const & dpProfile) +{ + _computeTraceback(target, matrixNavigator, maxHostPosition(dpScout), length(seqH), length(seqV), band, dpProfile); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_IMPL_H_ diff --git a/seqan/align/evaluate_alignment.h b/seqan/align/evaluate_alignment.h new file mode 100644 index 0000000..e242f2e --- /dev/null +++ b/seqan/align/evaluate_alignment.h @@ -0,0 +1,331 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Compute alignment score given a pairwise alignment. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_ +#define INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class AlignmentStats +// ---------------------------------------------------------------------------- + +/*! + * @class AlignmentStats + * @headerfile + * @brief Statistics about a tabular alignment. + * + * @signature struct AlignmentStats; + * + * @see computeAlignmentStats + * + * @fn AlignmentStats::AlignmentStats + * @brief Constructor + * + * @signature AlignmentStats::AlignmentStats(); + * + * All members are initialized to 0. + * + * @var unsigned AlignmentStats::numGaps; + * @brief Number of gap characters (sum of numGapOpens and numGapExtensions) + * + * @var unsigned AlignmentStats::numGapOpens; + * @brief Number of gap open events. + * + * @var unsigned AlignmentStats::numGapExtensions; + * @brief Number of gap extension events. + * + * @var unsigned AlignmentStats::numInsertions; + * @brief Number of gaps in reference relative to query. + * + * @var unsigned AlignmentStats::numDeletions; + * @brief Number of gaps in query relative to reference. + * + * @var unsigned AlignmentStats::numMatches; + * @brief Number of match (identity) events. + * + * @var unsigned AlignmentStats::numMismatches; + * @brief Number of mismatch (not identity) events. + * + * @var unsigned AlignmentStats::numPositiveScores; + * @brief Number of residues aligned with positive score (0 is counted as positive). + * + * @var unsigned AlignmentStats::numNegativeScores; + * @brief Number of residues aligned with negative score. + * + * @var unsigned AlignmentStats::alignmentLength; + * @brief Length of the aligned region + * + * @var float AlignmentStats::alignmentSimilarity; + * @brief The resulting alignment percent similarity (positive). + * + * @var float AlignmentStats::alignmentIdentity; + * @brief The resulting alignment percent identity (match). + * + * @var int AlignmentStats::alignmentScore; + * @brief The resulting alignment score. + */ + +struct AlignmentStats +{ + // Number of gap characters/opens/gap extensions. + unsigned numGaps; + unsigned numGapOpens; + unsigned numGapExtensions; + // Number of insertions and deletions. + unsigned numInsertions; + unsigned numDeletions; + // Number of matches, mismatches. + unsigned numMatches; + unsigned numMismatches; + // Number of aligned residues with positive/negative scores. + unsigned numPositiveScores; + unsigned numNegativeScores; + + // length of the alignment + unsigned alignmentLength; + + // the alignment identity and similarity scores + float alignmentSimilarity; + float alignmentIdentity; + + // The alignment score. + int alignmentScore; + + AlignmentStats() : numGaps(0), numGapOpens(0), numGapExtensions(0), numInsertions(0), numDeletions(0), + numMatches(0), numMismatches(0), numPositiveScores(0), numNegativeScores(0), + alignmentLength(0), alignmentSimilarity(0.0), alignmentIdentity(0.0), alignmentScore(0) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +/*! + * @fn AlignmentStats#clear + * @brief Resets all members to 0. + * + * @signature void clear(stats); + * + * @param[in,out] stats AlignmentStats object to clear. + */ + +inline +void clear(AlignmentStats & stats) +{ + stats.numGaps = 0; + stats.numGapOpens = 0; + stats.numGapExtensions = 0; + stats.numInsertions = 0; + stats.numDeletions = 0; + stats.numMatches = 0; + stats.numMismatches = 0; + stats.numPositiveScores = 0; + stats.numNegativeScores = 0; + stats.alignmentLength = 0; + stats.alignmentSimilarity = 0.0; + stats.alignmentIdentity = 0.0; + stats.alignmentScore = 0; +} + +// ---------------------------------------------------------------------------- +// Function computeAlignmentStats() +// ---------------------------------------------------------------------------- + +/*! + * @fn computeAlignmentStats + * @headerfile + * @brief Compute alignment statistics. + * + * @signature TScoreVal computeAlignmentStats(stats, align, scoringScheme); + * @signature TScoreVal computeAlignmentStats(stats, row0, row1, scoringScheme); + * + * @param[out] stats The @link AlignmentStats @endlink object to store alignment statistics in. + * @param[in] align The @link Align @endlink object to score. + * @param[in] row0 The first row (@link Gaps @endlink object). + * @param[in] row1 The second row (@link Gaps @endlink object). + * @param[in] score The @link Score @endlink object to use for the scoring scheme. + * + * @return TScoreVal The score value of the alignment, of the same type as the value type of scoringScheme + * + * @see AlignmentStats + * + * @section Examples + * + * @include demos/dox/align/compute_alignment_stats.cpp + * + * The output is as follows: + * + * @include demos/dox/align/compute_alignment_stats.cpp.stdout + */ + +template +TScoreVal computeAlignmentStats(AlignmentStats & stats, + Gaps const & row0, + Gaps const & row1, + Score const & scoringScheme) +{ + clear(stats); + + typedef typename Iterator const, Standard>::Type TGapsIter0; + typedef typename Iterator const, Standard>::Type TGapsIter1; + typedef typename Value::Type TAlphabet; + + // Get iterators. + TGapsIter0 it0 = begin(row0); + TGapsIter0 itEnd0 = end(row0); + TGapsIter1 it1 = begin(row1); + TGapsIter1 itEnd1 = end(row1); + + // State whether we have already opened a gap. + bool isGapOpen0 = false, isGapOpen1 = false; + + for (; it0 != itEnd0 && it1 != itEnd1; ++it0, ++it1) + { + if (isGap(it0)) + { + if (!isGapOpen0) + { + stats.numGapOpens += 1; + stats.alignmentScore += scoreGapOpen(scoringScheme); + } + else + { + stats.numGapExtensions += 1; + stats.alignmentScore += scoreGapExtend(scoringScheme); + } + stats.numDeletions += 1; + isGapOpen0 = true; + } + else + { + isGapOpen0 = false; + } + + if (isGap(it1)) + { + if (!isGapOpen1) + { + stats.numGapOpens += 1; + stats.alignmentScore += scoreGapOpen(scoringScheme); + } + else + { + stats.numGapExtensions += 1; + stats.alignmentScore += scoreGapExtend(scoringScheme); + } + stats.numInsertions += 1; + isGapOpen1 = true; + } + else + { + isGapOpen1 = false; + } + + if (!isGap(it0) && !isGap(it1)) + { + // Compute the alignment score and register in stats. + TAlphabet c0 = *it0; + TAlphabet c1 = static_cast(*it1); + TScoreVal scoreVal = score(scoringScheme, c0, c1); + stats.alignmentScore += scoreVal; + // Register other statistics. + bool isMatch = (c0 == c1); + bool isPositive = (scoreVal > 0); + stats.numMatches += isMatch; + stats.numMismatches += !isMatch; + stats.numPositiveScores += isPositive; + stats.numNegativeScores += !isPositive; + } + } + SEQAN_ASSERT(it0 == itEnd0); + SEQAN_ASSERT(it1 == itEnd1); + + stats.numGaps = stats.numGapOpens + stats.numGapExtensions; + + // Finally, compute the alignment similarity from the various counts + stats.alignmentLength = length(row0); + stats.alignmentSimilarity = 100.0 * static_cast(stats.numPositiveScores) + / static_cast(stats.alignmentLength); + stats.alignmentIdentity = 100.0 * static_cast(stats.numMatches) + / static_cast(stats.alignmentLength); + + return stats.alignmentScore; +} + +template +TScoreVal computeAlignmentStats(AlignmentStats & stats, + Align const & align, + Score const & scoringScheme) +{ + SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments."); + SEQAN_ASSERT_EQ_MSG(length(row(align, 0)), length(row(align, 1)), "Invalid alignment!"); + + return computeAlignmentStats(stats, row(align, 0), row(align, 1), scoringScheme); +} + +// NOTE(h-2): this interface is deprecated. Don't use it. +template +TScoreVal computeAlignmentStats(Align const & align, + Score const & scoringScheme) +{ + AlignmentStats stats; + (void)stats; + return computeAlignmentStats(stats, align, scoringScheme); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_ALIGN_EVALUATE_ALIGNMENT_H_ diff --git a/seqan/align/fragment.h b/seqan/align/fragment.h new file mode 100644 index 0000000..de6ae1e --- /dev/null +++ b/seqan/align/fragment.h @@ -0,0 +1,571 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Tobias Rausch +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_FRAGMENT_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_FRAGMENT_H_ + +namespace seqan +{ + +////////////////////////////////////////////////////////////////////////////// +// Fragment Specs +////////////////////////////////////////////////////////////////////////////// + +/*! + * @class ExactFragment + * @extends Fragment + * @headerfile + * @brief A type for ungapped, pairwise segment matches. + * + * @signature template <[typename TSize[, typename TSpec]]> + * class Fragment >; + * + * @tparam TSize The size type of the underlying sequence. Default: Size<CharString>Type. + * @tparam TSpec Specializing type. Default: ExactFragment<>. + */ + +template +struct ExactFragment; + + +/*! + * @class ExactReversableFragment + * @extends Fragment + * @headerfile + * @brief A type for ungapped, pairwise segment matches that maybe in reverse orientation. + * + * Compared to the @link ExactFragment @endlink ExactReversableFragment is a specialized type of @link Fragment @endlink. A @link + * ExactReversableFragment @endlink stores an additional bool value to indicate whether a match is in reverse + * orientation or not. + * + * @signature template <[typename TSize[, typename TSpec]]> + * class Fragment >; + * + * @tparam TSize The size type of the underlying sequence. Default: Size<CharString>Type. + * @tparam TSpec Specializing type. Default: ExactFragment<>. + */ + +template +struct ExactReversableFragment; + + +////////////////////////////////////////////////////////////////////////////// +// Default Fragment is the exact one +////////////////////////////////////////////////////////////////////////////// + +/*! + * @class Fragment + * @headerfile + * @brief A type for pairwise segment matches. + * + * @signature template <[typename TSize[, typename TSpec]]> + * class Fragment; + * + * @tparam TSize The size type of the underlying sequence. Default: Size<CharString>Type. + * @tparam TSpec Specializing type. Default: ExactFragment<>. + * + * @section Examples + * + * @code{.cpp} + * // Construct fragment. + * unsigned seqId1 = 0, beg1 = 0, seqId2 = 32, beg2 = 42, len = 33; + * Fragment<> fragment(seqId1, beg1, seqId2, beg2, len); + * + * // Update fragment's properties. + * fragmentBegin(fragment, 0) = 10; + * fragmentBegin(fragment, 1) = 10; + * sequenceId(fragment, 0) = 33; + * sequenceId(fragment, 1) = 44; + * fragmentLength(fragment) += 42; + * @endcode + */ + + +template >::Type, typename TSpec = ExactFragment<> > +class Fragment; + + +////////////////////////////////////////////////////////////////////////////// +// Size Metafunction +////////////////////////////////////////////////////////////////////////////// + +template +struct Size > { + typedef TSize Type; +}; + + +template +struct Size const> { + typedef TSize Type; +}; + + +////////////////////////////////////////////////////////////////////////////// +// Exact Fragment +////////////////////////////////////////////////////////////////////////////// + + +template +class Fragment > { +public: + typedef typename Id::Type TId; + + TId seqId1; + TSize begin1; + TId seqId2; + TSize begin2; + TSize len; + +/*! + * @fn ExactFragment::Fragment + * @brief Constructor. + * + * @signature Fragment::Fragment(); + * @signature Fragment::Fragment(seqID1, beg1, seqID2, beg2, l); + * + * @param[in] seqID1 ID of the first sequence. Type: TId. + * @param[in] beg1 Begin position of segment match in first sequence. Type: TSize. + * @param[in] seqID2 ID of the second sequence. Type: TId. + * @param[in] beg2 Begin position of segment match in second sequence. Type: TSize. + * @param[in] l The length of the segment match. Type: TSize. + */ + + Fragment() : seqId1(0), begin1(0), seqId2(0), begin2(0), len(0) {} + + Fragment(TId sqId1, TSize beg1, TId sqId2, TSize beg2, TSize l) : + seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l) + {} + +}; + +template +inline bool +operator==(Fragment > const & left, + Fragment > const & right) +{ + return (left.seqId1 == right.seqId1 && + left.begin1 == right.begin1 && + left.seqId2 == right.seqId2 && + left.begin2 == right.begin2 && + left.len == right.len); +} + +template +inline bool +operator<(Fragment > const & left, + Fragment > const & right) +{ + if (left.seqId1 < right.seqId1) + return true; + if (left.seqId1 > right.seqId1) + return false; + if (left.begin1 < right.begin1) + return true; + if (left.begin1 > right.begin1) + return false; + if (left.seqId2 < right.seqId2) + return true; + if (left.seqId2 > right.seqId2) + return false; + if (left.begin2 < right.begin2) + return true; + if (left.begin2 > right.begin2) + return false; + if (left.len < right.len) + return true; + // if (left.len > right.len) + // return false; + return false; +} + +////////////////////////////////////////////////////////////////////////////// +// Exact Fragment that is a forward or reverse match +////////////////////////////////////////////////////////////////////////////// + + +template +class Fragment > { +public: + typedef typename Id::Type TId_; + + TId_ seqId1; + TSize begin1; + TId_ seqId2; + TSize begin2; + TSize len; + bool reversed; + +/*! + * @fn ExactReversableFragment::Fragment + * @brief Constructor. + * + * @signature Fragment::Fragment(); + * @signature Fragment::Fragment(seqID1, beg1, seqID2, beg2, l[, reversed]); + * + * @param[in] seqID1 ID of the first sequence. Type: TId. + * @param[in] beg1 Begin position of segment match in first sequence. Type: TSize. + * @param[in] seqID2 ID of the second sequence. Type: TId. + * @param[in] beg2 Begin position of segment match in second sequence. Type: TSize. + * @param[in] l The length of the segment match. Type: TSize. + * @param[in] reversed A bool; true if the segments match in reverse orientation, false otherwise. + */ + + + Fragment() : seqId1(0), begin1(0), seqId2(0), begin2(0), len(0), reversed(false) {} + + Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l) : + seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l), reversed(false) + {} + + Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l, bool rev) : + seqId1(sqId1), begin1(beg1), seqId2(sqId2), begin2(beg2), len(l), reversed(rev) + {} +}; + +template +inline bool +operator==(Fragment > const & left, + Fragment > const & right) +{ + return (left.seqId1 == right.seqId1 && + left.begin1 == right.begin1 && + left.seqId2 == right.seqId2 && + left.begin2 == right.begin2 && + left.len == right.len && + left.reversed == right.reversed); +} + +template +inline bool +operator<(Fragment > const & left, + Fragment > const & right) +{ + if (left.seqId1 < right.seqId1) + return true; + if (left.seqId1 > right.seqId1) + return false; + if (left.begin1 < right.begin1) + return true; + if (left.begin1 > right.begin1) + return false; + if (left.seqId2 < right.seqId2) + return true; + if (left.seqId2 > right.seqId2) + return false; + if (left.begin2 < right.begin2) + return true; + if (left.begin2 > right.begin2) + return false; + if (left.len < right.len) + return true; + if (left.len > right.len) + return false; + if (left.reversed < right.reversed) + return true; + // if (left.reversed > right.reversed) + // return false; + return false; +} + +////////////////////////////////////////////////////////////////////////////// + +/*! + * @fn Fragment#label + * @brief Access to the Fragment's label. + * + * @signature TInfix label(frag, stringSet, seqID); + * + * @param[in] frag The Fragment to query. + * @param[in] stringSet The @link StringSet @endlink with the sequences. + * @param[in] seqID The id of the sequence for which the label should be retrieved. + */ + +template +inline typename Infix::Type>::Type +label(Fragment const& f, + TStringSet& str, + TVal const seqId) +{ + typedef typename Id >::Type TId; + return ((TId) seqId == (f.seqId1)) ? infix(getValueById(str, (TId) seqId), f.begin1, f.begin1 + f.len) : infix(getValueById(str, (TId) seqId), f.begin2, f.begin2 + f.len); +} + +////////////////////////////////////////////////////////////////////////////// + +/*! + * @fn Fragment#sequenceId + * @brief Access to the sequence ID of a fragment. + * + * @signature TId sequenceId(frag, seqNum); + * + * @param[in] frag A Fragment. + * @param[in] seqNum The sequence number for which the id should be retrieved. Note that @link Fragment @endlink + stores information about exactly two sequences which can be accessed with seqNum 0 or 1 but whose + ids may differ from their seqNum. + * + * @return TId Reference to the sequence fragment id member. + */ + +template +inline typename Id >::Type & +sequenceId(Fragment & f, + TVal const seqId) +{ + return (seqId == (TVal)0) ? f.seqId1 : f.seqId2; +} + +template +inline typename Id >::Type const & +sequenceId(Fragment const & f, + TVal const seqId) +{ + return (seqId == (TVal)0) ? f.seqId1 : f.seqId2; +} + +////////////////////////////////////////////////////////////////////////////// + +/*! + * @fn Fragment#fragmentBegin + * @brief Return fragment begin. + * + * @signature TSize fragmentBegin(frag, seqId); + * + * @param[in] frag The Fragment to query. + * @param[in] seqId The id of the sequence to get the begin for. + * + * @return TSize Reference to the fragment begin position member. + */ + +template +inline TSize& +fragmentBegin(Fragment const& f, + TVal const seqId) +{ + typedef typename Id >::Type TId; + return ((TId) seqId == f.seqId1) ? const_cast(f.begin1) : const_cast(f.begin2); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline TSize& +fragmentLength(Fragment const& f, + TVal const) +{ + return const_cast(f.len); +} + +////////////////////////////////////////////////////////////////////////////// + +/*! + * @fn Fragment#fragmentLength + * @brief Return fragment begin. + * + * @signature TSize fragmentLength(frag); + * + * @param[in] frag The Fragment to query for its length. + * + * @return TSize Reference to the Fragment's length. + */ + +template +inline TSize& +fragmentLength(Fragment const& f) +{ + return const_cast(f.len); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +getProjectedPosition(Fragment > const& f, + TId1 const seqId, + TPosition1 const pos, + TId2& seqId2, + TPosition2& pos2) +{ + typedef typename Id >::Type TId; + + if ((TId) seqId == f.seqId1) { + SEQAN_ASSERT((TPosition1)f.begin1<=pos); + SEQAN_ASSERT(pos - f.begin1 < f.len) ; + pos2 = f.begin2 + (pos - f.begin1); + seqId2 = f.seqId2; + return; + } else { + SEQAN_ASSERT((TPosition1)f.begin2<=pos); + SEQAN_ASSERT(pos - f.begin2 < f.len); + pos2 = f.begin1 + (pos - f.begin2); + seqId2 = f.seqId1; + return; + } +} + + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +getProjectedPosition(Fragment > const& f, + TValue seg_num, + TId1 const seqId, + TPosition1 const pos, + TId2& seqId2, + TPosition2& pos2) +{ + (void) seqId; // When compiled without assertions. + SEQAN_ASSERT((seg_num == 0 && seqId == f.seqId1) || (seg_num == 1 && seqId == f.seqId2)); + + if (seg_num == 0) { + SEQAN_ASSERT((TPosition1)f.begin1<=pos); + SEQAN_ASSERT(pos - f.begin1 < f.len) ; + pos2 = f.begin2 + (pos - f.begin1); + seqId2 = f.seqId2; + return; + } else { + SEQAN_ASSERT((TPosition1)f.begin2<=pos); + SEQAN_ASSERT(pos - f.begin2 < f.len); + pos2 = f.begin1 + (pos - f.begin2); + seqId2 = f.seqId1; + return; + } +} + + + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +getProjectedPosition(Fragment > const& f, + TId1 const seqId, + TPosition1 const pos, + TId2& seqId2, + TPosition2& pos2) +{ + typedef typename Id >::Type TId; + + if ((TId) seqId == f.seqId1) { + SEQAN_ASSERT((TPosition1)f.begin1<=pos); + SEQAN_ASSERT(pos - f.begin1 < f.len) ; + if (f.reversed) pos2 = (f.begin2 + f.len - 1) - (pos - f.begin1); + else pos2 = f.begin2 + (pos - f.begin1); + seqId2 = f.seqId2; + return; + } else { + SEQAN_ASSERT((TPosition1)f.begin2<=pos); + SEQAN_ASSERT(pos - f.begin2 < f.len); + if (f.reversed) pos2 = (f.begin1 + f.len - 1) - (pos - f.begin2); + else pos2 = f.begin1 + (pos - f.begin2); + seqId2 = f.seqId1; + return; + } +} + + +///////////////////////////////////////////////////////////// + +template +inline void +getProjectedPosition(Fragment > const& f, + TValue seg_num, + TId1 const seqId, + TPosition1 const pos, + TId2& seqId2, + TPosition2& pos2) +{ + (void) seqId; // When compiled without assertions. + SEQAN_ASSERT((seg_num == 0 && seqId==f.seqId1) || (seg_num == 1 && seqId==f.seqId2)); + + if (seg_num == 0) { + SEQAN_ASSERT((TPosition1)f.begin1<=pos); + SEQAN_ASSERT(pos - f.begin1 < f.len) ; + if (f.reversed) pos2 = (f.begin2 + f.len - 1) - (pos - f.begin1); + else pos2 = f.begin2 + (pos - f.begin1); + seqId2 = f.seqId2; + return; + } else { + SEQAN_ASSERT((TPosition1)f.begin2<=pos); + SEQAN_ASSERT(pos - f.begin2 < f.len); + if (f.reversed) pos2 = (f.begin1 + f.len - 1) - (pos - f.begin2); + else pos2 = f.begin1 + (pos - f.begin2); + seqId2 = f.seqId1; + return; + } +} + +////////////////////////////////////////////////////////////////////////////// + +/*! + * @fn ExactReversableFragment#isReversed + * @brief Return whether a segment match is in reverse orientation. + * + * @signature bool isReversed(frag); + * + * @param[in] frag The Fragment to query for reverseness. + * + * @return bool true if the fragment is reversed and false otherwise. + */ + +template +inline bool +isReversed(Fragment > const& f) +{ + return f.reversed; +} + +// Compare lexicographically as tuple. + +template +inline bool operator>(Fragment > const & lhs, + Fragment > const & rhs) +{ + if (lhs.seqId1 > rhs.seqId1) + return true; + if (lhs.seqId1 == rhs.seqId1 && lhs.begin1 > rhs.begin1) + return true; + if (lhs.seqId1 == rhs.seqId1 && lhs.begin1 == rhs.begin1 && lhs.seqId2 > rhs.seqId2) + return true; + if (lhs.seqId1 == rhs.seqId1 && lhs.begin1 == rhs.begin1 && lhs.seqId2 == rhs.seqId2 && lhs.begin2 > rhs.begin2) + return true; + if (lhs.seqId1 == rhs.seqId1 && lhs.begin1 == rhs.begin1 && lhs.seqId2 == rhs.seqId2 && lhs.begin2 == rhs.begin2 && lhs.len > rhs.len) + return true; + return false; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_FRAGMENT_H_ diff --git a/seqan/align/gap_anchor.h b/seqan/align/gap_anchor.h new file mode 100644 index 0000000..1a625fd --- /dev/null +++ b/seqan/align/gap_anchor.h @@ -0,0 +1,380 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// TODO(holtgrew): Document? +// Sorting tags (just for lower_bound and upper_bound, positions are always sorted) + +struct SortSeqPos_; +typedef Tag const SortSeqPos; + +struct SortGapPos_; +typedef Tag const SortGapPos; + +// ---------------------------------------------------------------------------- +// Specialization GapAnchor +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Make a class instead of a struct? + +/*! + * @class GapAnchor + * @implements ComparableConcept + * @headerfile + * @brief Stores the position of an alignment character in sequence-space and gap-space in @link AnchorGaps @endlink. + * + * @signature template + * struct GapAnchor; + * + * @tparam TPos Type to store gapped/ungapped positions. + * + * @section Remarks + * + * Used as value type for the gaps strings in @link ReadStoreElement @endlink and @link ContigStoreElement + * @endlink. + * + * @see AnchorGaps + */ + +// We store gap anchors only for the first text character behind a gap or a clipped sequence character + +template +struct GapAnchor +{ +/*! + * @var TPos GapAnchor::seqPos + * @brief Sequence character position in the ungapped sequence. + */ + TPos seqPos; // sequence character position in the ungapped sequence + +/*! + * @var TPos GapAnchor::gapPos + * @brief Sequence character position in the gapped sequence. + */ + TPos gapPos; // sequence character position in the gapped sequence + +/*! + * @fn GapAnchor::GapAnchor + * @brief Constructor. + * + * @signature GapAnchor::GapAnchor([other]); + * @signature GapAnchor::GapAnchor(seqPos, gapPos); + * + * @param[in] other GapAnchor object to copy from. + * @param[in] seqPos Sequence character position in the ungapped sequence (of type TPos). + * @param[in] gapPos Sequence character position in the gapped sequence (of type TPos). + * + * @section Remarks + * + * The default constructor sets both positions to 0. + */ + + GapAnchor() : seqPos(0), gapPos(0) {} + GapAnchor(TPos sP, TPos gP) : seqPos(sP), gapPos(gP) {} + + template + GapAnchor(GapAnchor const &other) + { + seqPos = other.seqPos; + gapPos = other.gapPos; + } + + template + inline GapAnchor const & + operator = (GapAnchor const &other) + { + seqPos = other.seqPos; + gapPos = other.gapPos; + return *this; + } + + template + inline bool + operator == (TOther const &other) const + { + return seqPos == other.seqPos && gapPos == other.gapPos; + } + + template + inline bool + operator != (TOther const &other) const + { + return !(*this == other); + } + + template + inline bool + operator < (TOther const &other) const + { + return seqPos < other.seqPos || gapPos < other.gapPos; + } + + template + inline bool + operator > (TOther const &other) const + { + return seqPos > other.seqPos || gapPos > other.gapPos; + } + + template + inline bool + operator <= (TOther const &other) const + { + return seqPos < other.seqPos || gapPos <= other.gapPos; + } + + template + inline bool + operator >= (TOther const &other) const + { + return seqPos > other.seqPos || gapPos >= other.gapPos; + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Size [GapAnchor] +// ---------------------------------------------------------------------------- + +template +struct Size > +{ + typedef TPos Type; +}; + +template +struct Size const> : public Size > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Position [GapAnchor] +// ---------------------------------------------------------------------------- + +template +struct Position > +{ + typedef TPos Type; +}; + +template +struct Position const> : public Position > +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Functor _LessGapAnchor +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Leading underscore should become a trailing one. + +template +struct _LessGapAnchor; + +template +struct _LessGapAnchor : + public std::binary_function +{ + inline bool + operator() (TGapAnchor const& a1, TGapAnchor const& a2) const { + return (a1.seqPos) < (a2.seqPos); + } +}; + +template +struct _LessGapAnchor : + public std::binary_function +{ + inline bool + operator() (TGapAnchor const& a1, TGapAnchor const& a2) const { + return (a1.gapPos) < (a2.gapPos); + } +}; + +// ---------------------------------------------------------------------------- +// Function lowerBoundGapAnchor() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator::Type +lowerBoundGapAnchor(TGapAnchor const & gaps, + TSearchValue const val, + SortSeqPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.seqPos = val; + return std::lower_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortSeqPos const>() ); +} + +template +inline typename Iterator::Type +lowerBoundGapAnchor(TGapAnchor & gaps, + TSearchValue const val, + SortSeqPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.seqPos = val; + return std::lower_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortSeqPos const>() ); +} + +template +inline typename Iterator::Type +lowerBoundGapAnchor(TGapAnchor const & gaps, + TSearchValue const val, + SortGapPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.gapPos = val; + return std::lower_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortGapPos const>() ); +} + +template +inline typename Iterator::Type +lowerBoundGapAnchor(TGapAnchor & gaps, + TSearchValue const val, + SortGapPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.gapPos = val; + return std::lower_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortGapPos const>() ); +} + +// ---------------------------------------------------------------------------- +// Function upperBoundGapAnchor() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator::Type +upperBoundGapAnchor(TGapAnchors const & gaps, + TSearchValue const val, + SortSeqPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.seqPos = val; + return std::upper_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortSeqPos const>() ); +} + +template +inline typename Iterator::Type +upperBoundGapAnchor(TGapAnchors & gaps, + TSearchValue const val, + SortSeqPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.seqPos = val; + return std::upper_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortSeqPos const>() ); +} + +template +inline typename Iterator::Type +upperBoundGapAnchor(TGapAnchors const & gaps, + TSearchValue const val, + SortGapPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.gapPos = val; + return std::upper_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortGapPos const>() ); +} + +template +inline typename Iterator::Type +upperBoundGapAnchor(TGapAnchors & gaps, + TSearchValue const val, + SortGapPos) +{ + typedef typename Value::Type TGapAnchorElement; + TGapAnchorElement el; + el.gapPos = val; + return std::upper_bound( + begin(gaps, Standard()), + end(gaps, Standard()), + el, + _LessGapAnchor::Type, SortGapPos const>() ); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAP_ANCHOR_H_ diff --git a/seqan/align/gapped_value_type.h b/seqan/align/gapped_value_type.h new file mode 100644 index 0000000..855f1d3 --- /dev/null +++ b/seqan/align/gapped_value_type.h @@ -0,0 +1,87 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +/*! + * @mfn GappedValueType + * @headerfile + * @brief Returns a value type that contains a black value '-'. + * + * @signature GappedValueType::Type + * + * @tparam T The value type that should be expanded (if needed) by '-'. + * + * @return Type A type that can store the values of T and the value '-'. + */ + +// TODO(holtgrew): Would it be enough to define it for Nothing instead of having a default implementation. + +// We need a default implementation since we need it for Nothing. +template +struct GappedValueType +{ + typedef T Type; +}; + +template +struct GappedValueType > +{ + typedef SimpleType THost_; + typedef ModifiedAlphabet > Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPPED_VALUE_TYPE_H_ diff --git a/seqan/align/gaps_anchor.h b/seqan/align/gaps_anchor.h new file mode 100644 index 0000000..c75042d --- /dev/null +++ b/seqan/align/gaps_anchor.h @@ -0,0 +1,938 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// ========================================================================== +// Implementation of Gaps class using pairs of gapped sequence and source +// sequence position as anchors. +// ========================================================================== + +// TODO(holtgrew): Clipping in leading and trailing gaps is not possible right now. Dave and I have to discuss this further. +// TODO(holtgrew): Also, inserting gaps in the front changes the clipped begin position which is unexpected. + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +/*! + * @tag GapsSpecTag#AnchorGaps + * @headerfile + * @brief Tag for the Anchor Gaps specialization. + * + * @signature template + * struct AnchorGaps; + */ + +template +struct AnchorGaps; + +template +inline void _reinitAnchorGaps(Gaps > & gaps); + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Specialization AnchorGaps +// ---------------------------------------------------------------------------- + +/*! + * @class AnchorGaps + * @extends Gaps + * @headerfile + * @brief Stores gaps as anchors of the first characters behind gaps. + * + * @signature template > > + * class Gaps >; + * + * @tparam TSource The type of the underlying sequence. + * @tparam TGapAnchors The type of the string of @link GapAnchor @endlink objects. + */ + +/*! + * @fn AnchorGaps::Gaps + * @brief Constructor + * + * @signature Gaps::Gaps([other]); + * @signature Gaps::Gaps(source[, anchors]); + * @signature Gaps::Gaps(anchors); + * + * @param[in] other Another @link AnchorGaps @endlink object to copy from. + * @param[in] source The underlying sequence to construct the Gaps object from. + * @param[in] anchors The string of anchors to construct with. + * + * An AnchorGaps object has a default constructor, can be constructed from the underlying source, and/or a string of + * gap anchors. + */ + + +template > > +struct AnchorGaps +{}; + +template +class Gaps > +{ +public: + // ----------------------------------------------------------------------- + // Internal Typedefs + // ----------------------------------------------------------------------- + + typedef typename Value::Type TGapAnchor_; + typedef typename Position::Type TViewPosition_; + typedef typename Position::Type TPosition_; + typedef typename Value::Type TValue_; + + typedef typename RemoveReference::Type>::Type TSourceNoConstNoRef; + typedef TSourceNoConstNoRef const & TSourceConstRef; + + // ----------------------------------------------------------------------- + // Member Variables + // ----------------------------------------------------------------------- + + Holder data_source; + Holder data_gaps; + int data_cutBegin; // number of gap positions cut from the beginning + int data_cutEnd; // number of gap positions cut from the end + int data_viewCutBegin; // how many alignment chars should be clipped at the beginning (can be negative too) + int data_viewCutEnd; // how ... end ... + + // ----------------------------------------------------------------------- + // Constructors + // ----------------------------------------------------------------------- + + Gaps() : + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + } + + Gaps(TSource & source) : + data_source(source), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + } + + Gaps(TGapAnchors & anchors) : + data_gaps(anchors), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + } + + Gaps(TGapAnchors const & anchors) : + data_gaps(anchors), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + } + + // everybody has const & constructors + Gaps(TSourceNoConstNoRef const & source, TGapAnchors & anchors) : + data_source(source), + data_gaps(anchors), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + } + + Gaps(TSourceNoConstNoRef const & source, TGapAnchors const & anchors) : + data_source(source), + data_gaps(anchors), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + } + + // if source is not const & (but possibly const) there are also regular & constructors + Gaps(TSourceNoConstNoRef & source, TGapAnchors & anchors, + SEQAN_CTOR_DISABLE_IF(IsSameType)) : + data_source(source), + data_gaps(anchors), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + ignoreUnusedVariableWarning(dummy); + } + + Gaps(TSourceNoConstNoRef & source, TGapAnchors const & anchors, + SEQAN_CTOR_DISABLE_IF(IsSameType)) : + data_source(source), + data_gaps(anchors), + data_cutBegin(0), + data_cutEnd(0), + data_viewCutBegin(0), + data_viewCutEnd(0) + { + ignoreUnusedVariableWarning(dummy); + } + + // ----------------------------------------------------------------------- + // Array Subscript Operator + // ----------------------------------------------------------------------- + + inline typename Reference::Type + operator[](TPosition_ const clippedViewPos) + { + return value(*this, clippedViewPos); + } + + inline typename Reference::Type + operator[](TPosition_ const clippedViewPos) const + { + return value(*this, clippedViewPos); + } + +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function swap() +// ---------------------------------------------------------------------------- + +template +void swap(Gaps > & lhs, + Gaps > & rhs) +{ + swap(lhs.data_source, rhs.data_source); + swap(lhs.data_gaps, rhs.data_gaps); + + std::swap(lhs.data_cutBegin, rhs.data_cutBegin); + std::swap(lhs.data_cutEnd, rhs.data_cutEnd); + std::swap(lhs.data_viewCutBegin, rhs.data_viewCutBegin); + std::swap(lhs.data_viewCutEnd, rhs.data_viewCutEnd); +} + +// ---------------------------------------------------------------------------- +// Helper Function _reinitAnchorGaps() +// ---------------------------------------------------------------------------- + +// Reset the array gaps DS such that represents the ungapped sequence. + +template +inline void _reinitAnchorGaps(Gaps > & gaps) +{ + clear(value(gaps.data_gaps)); + gaps.data_cutBegin = 0; + gaps.data_cutEnd = 0; + gaps.data_viewCutBegin = 0; + gaps.data_viewCutEnd = 0; +} + +// ---------------------------------------------------------------------------- +// Function _dataSource() +// ---------------------------------------------------------------------------- + +template +inline Holder & +_dataSource(Gaps > & me) +{ + return me.data_source; +} + +template +inline Holder const & +_dataSource(Gaps > const & me) +{ + return me.data_source; +} + +// ---------------------------------------------------------------------------- +// Function _assignSourceLength() +// ---------------------------------------------------------------------------- + +template +inline void +_assignSourceLength(TSize & size, Gaps > const & me) +{ + if (IsSameType::VALUE) + size = maxValue() / 2; + else + size = length(value(me.data_source)); +} + +// ---------------------------------------------------------------------------- +// Function _dataAnchors() +// ---------------------------------------------------------------------------- + +template +inline TGapAnchors & +_dataAnchors(Gaps > & me) +{ + return value(me.data_gaps); +} + +template +inline TGapAnchors const & +_dataAnchors(Gaps > const & me) +{ + return value(const_cast &>(me.data_gaps)); +} + +// ---------------------------------------------------------------------------- +// Function _getAnchor() +// ---------------------------------------------------------------------------- + +template +inline void +_getAnchor(TAnchor & anchor, Gaps > const & me, TIdx idx) +{ + if (idx > (TIdx)length(_dataAnchors(me))) + { + _assignSourceLength(anchor.seqPos, me); + if (empty(_dataAnchors(me)) && idx == 1) + anchor.gapPos = anchor.seqPos; + else + { + // for the sick case that an anchor seq position is beyond the sequence end + if (!empty(_dataAnchors(me))) + { + // if there is no sequence but anchors -> assume infinite sequence + if (anchor.seqPos == 0) + anchor.seqPos = maxValue(anchor.gapPos); + // if the sequence has a length > 0, but there is an anchor behind the end + // -> elongate sequence + else if ((int64_t)anchor.seqPos < (int64_t)back(_dataAnchors(me)).seqPos) + anchor.seqPos = back(_dataAnchors(me)).seqPos; + } + anchor.gapPos = maxValue(anchor.gapPos); + } + } + else if (idx > 0) + anchor = _dataAnchors(me)[idx - 1]; + else + { + anchor.seqPos = 0; + if (idx == 0) + anchor.gapPos = 0; + else + anchor.gapPos = minValue(anchor.gapPos); + } +} + +// ---------------------------------------------------------------------------- +// Function _unclippedLength() +// ---------------------------------------------------------------------------- + +template +inline typename Size > >::Type +_unclippedLength(Gaps > const & me) +{ + typedef typename Value::Type TAnchor; + typedef typename Size::Type TSize; + TSize len; + _assignSourceLength(len, me); + if (!empty(_dataAnchors(me))) + { + TAnchor const & last = back(_dataAnchors(me)); + len += last.gapPos - last.seqPos; + } + return len - (me.data_cutBegin + me.data_cutEnd); +} + +// ---------------------------------------------------------------------------- +// Function unclippedLength() +// ---------------------------------------------------------------------------- + +template +inline typename Size > >::Type +unclippedLength(Gaps > const & me) +{ + // TODO(holtgrew): Merge into one public function. + return _unclippedLength(me); +} + +// ---------------------------------------------------------------------------- +// Function clearClipping() +// ---------------------------------------------------------------------------- + +template +inline void +clearClipping(Gaps > & gaps) +{ + gaps.data_viewCutBegin = 0; + gaps.data_viewCutEnd = 0; +} + +// ---------------------------------------------------------------------------- +// Function clearGaps() +// ---------------------------------------------------------------------------- + +template +inline void +clearGaps(Gaps > & gaps) +{ + _reinitAnchorGaps(gaps); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +inline void +clear(Gaps > & gaps) +{ + clear(gaps.data_source); // clear source holder + + // clear gaps, but on holder level + clear(gaps.data_gaps); + gaps.data_cutBegin = 0; + gaps.data_cutEnd = 0; + gaps.data_viewCutBegin = 0; + gaps.data_viewCutEnd = 0; +} + +// ---------------------------------------------------------------------------- +// Function isGap() +// ---------------------------------------------------------------------------- + +template +inline bool +isGap(Gaps > const & gaps, TPosition clippedViewPos) +{ + // TODO(holtgrew): Implement without iterator? + return isGap(iter(gaps, clippedViewPos)); +} + +// ---------------------------------------------------------------------------- +// Function insertGaps() +// ---------------------------------------------------------------------------- + +template +inline void +insertGaps(Gaps > & gaps, TPosition clippedViewPos, TCount count) +{ + // TODO(holtgrew): Implement without iterator? + typedef Gaps > TGaps; + typedef typename Iterator::Type TIter; + + TIter it = iter(gaps, clippedViewPos); + insertGaps(it, count); +} + +// ---------------------------------------------------------------------------- +// Function removeGaps() +// ---------------------------------------------------------------------------- + +template +inline typename Size > >::Type +removeGaps(Gaps > & gaps, TPosition clippedViewPos, TCount count) +{ + // TODO(holtgrew): Implement without iterator? + return removeGaps(iter(gaps, clippedViewPos), count); +} + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We would rather like to have the const version only :( +template +inline typename Size > >::Type +length(Gaps > & me) +{ + return _unclippedLength(me) - (me.data_viewCutBegin + me.data_viewCutEnd); +} + +template +inline typename Size > >::Type +length(Gaps > const & me) +{ + return _unclippedLength(me) - (me.data_viewCutBegin + me.data_viewCutEnd); +} + +// ---------------------------------------------------------------------------- +// Function begin() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator > >::Type +begin(Gaps > & me, Standard) +{ + return typename Iterator > >::Type(me); +} + +template +inline typename Iterator > const>::Type +begin(Gaps > const & me, Standard) +{ + return typename Iterator > const>::Type(me); +} + +template +inline typename Iterator > >::Type +begin(Gaps > & me, Rooted) +{ + return typename Iterator > >::Type(me); +} + +template +inline typename Iterator > const>::Type +begin(Gaps > const & me, Rooted) +{ + return typename Iterator > const>::Type(me); +} + +// ---------------------------------------------------------------------------- +// Function end() +// ---------------------------------------------------------------------------- + +template +inline typename Iterator > >::Type +end(Gaps > & me, Standard) +{ + return typename Iterator > >::Type(me, length(me)); +} + +template +inline typename Iterator > const>::Type +end(Gaps > const & me, Standard) +{ + return typename Iterator > const>::Type(me, length(me)); +} + +template +inline typename Iterator > >::Type +end(Gaps > & me, Rooted) +{ + return typename Iterator > >::Type(me, length(me)); +} + +template +inline typename Iterator > const>::Type +end(Gaps > const & me, Rooted) +{ + return typename Iterator > const>::Type(me, length(me)); +} + +// ---------------------------------------------------------------------------- +// Function beginPosition() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We would rather like to have the const version only :( +template +inline typename Position::Type +beginPosition(Gaps > & gaps) +{ + return toSourcePosition(gaps, 0); +} + +template +inline typename Position::Type +beginPosition(Gaps > const & gaps) +{ + return toSourcePosition(gaps, 0); +} + +// ---------------------------------------------------------------------------- +// Function endPosition() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We would rather like to have the const version only :( +template +inline typename Position::Type +endPosition(Gaps > & gaps) +{ + return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBegin)); +} + +template +inline typename Position::Type +endPosition(Gaps > const & gaps) +{ + return toSourcePosition(gaps, _unclippedLength(gaps) - (gaps.data_viewCutEnd + gaps.data_viewCutBegin)); +} + +// ---------------------------------------------------------------------------- +// Function setBeginPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setBeginPosition(Gaps > & gaps, TPosition sourcePosition) +{ + setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); +} + +// ---------------------------------------------------------------------------- +// Function setEndPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setEndPosition(Gaps > & gaps, TPosition sourcePosition) +{ + setClippedEndPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); +} + +// ---------------------------------------------------------------------------- +// Function createSource() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Remove? Switch to Hosted Type Interface? + +template +inline void createSource(Gaps > & gaps) +{ + create(gaps.data_source); +} + +// ---------------------------------------------------------------------------- +// Function source() +// ---------------------------------------------------------------------------- + +template +inline typename Source > >::Type & +source(Gaps > const & gaps) +{ + return value(gaps.data_source); +} + +// ---------------------------------------------------------------------------- +// Function setSource() +// ---------------------------------------------------------------------------- + +template +inline void +setSource(Gaps > & gaps, TSequence & source) +{ + setValue(gaps.data_source, source); +} + +template +inline void +setSource(Gaps > & gaps, TSequence & source) +{ + setValue(gaps.data_source, source); +} + +// ---------------------------------------------------------------------------- +// Function assignSource() +// ---------------------------------------------------------------------------- + +template +inline void +assignSource(Gaps > & gaps, TSequence2 const & source) +{ + value(gaps.data_source) = source; +} + +// ---------------------------------------------------------------------------- +// Function positionGapToSeq() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Deprecate in favour of toViewPosition/toSourcePosition? + +/*! + * @fn AnchorGaps#positionGapsToSeq + * @brief Convert from gap space in the global alignment to the sequence space on the reference. + * + * @signature TPos positionGapToSeq(gaps, pos); + * + * @param[in] gaps Contig AnchorGaps (e.g. from FragmentStore). + * @param[in] pos Position in gap space. + * + * @return TPos Position in sequence space (Metafunction: @link ContainerConcept#Position @endlink). + * + * See the example below to construct the Gaps object. Note that this construction is fast since it is only a thin wrapper + * around underlying objects. + * + * @section Examples + * + * Convert from gap space to positions pace when the contig required to be loaded. * Converts position aligned read with + * index idx in the aligned read store. + * + * @code{.cpp} + * typedef typename TFragmentStore::TContigStore TContigStore; + * typedef typename Value::Type TContig; + * typedef typename TFragmentStore::TContigSeq TContigSeq; + * typedef Gaps > TContigGaps; + * + * typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore; + * typedef typename Value::Type TAlignedRead; + * typedef typename TAlignedRead::TPos TAlignedReadPos; + * + * unsigned contigId = alignedReadStore[idx].contigId; + * TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps); + * TAlignedRead const & alignedRead = alignedReadStore[idx]; + * // Translate end position from aligned read record to sequence space in reference. + * TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos); + * @endcode + * + * Convert from gap space to position space when the contigs are not required. + * Converts position aligned read with index $idx$ in the aligned read store. + * + * @code{.cpp} + * typedef typename TFragmentStore::TContigStore TContigStore; + * typedef typename Value::Type TContig; + * typedef Gaps > TContigGaps; + * + * typedef typename TFragmentStore::TAlignedReadStore TAlignedReadStore; + * typedef typename Value::Type TAlignedRead; + * typedef typename TAlignedRead::TPos TAlignedReadPos; + * + * unsigned contigId = alignedReadStore[idx].contigId; + * TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps); + * TAlignedRead const & alignedRead = alignedReadStore[idx]; + * // Translate end position from aligned read record to sequence space in reference. + * TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos); + * @endcode + */ + +template +inline TPosition +positionGapToSeq(Gaps > const & me, TPosition const pos, TProjectionDir const & /*dir*/) +{ + typedef typename Position::Type>::Type TAnchorPos; + + GapAnchor prevAnchor, nextAnchor; + TPosition seqPos; + int anchorIdx; + + if (isNegative(pos)) + anchorIdx = -1; + else + { + TGapAnchors const & anchors = _dataAnchors(me); + TAnchorPos seqLength; + _assignSourceLength(seqLength, me); + if (!empty(anchors)) + { + anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard()); + if (anchorIdx < (int)length(anchors)) + if (anchors[anchorIdx].gapPos == (TAnchorPos)pos && anchors[anchorIdx].seqPos != seqLength) + ++anchorIdx; + } + else + anchorIdx = ((TAnchorPos)pos < seqLength) ? 0 : 1; + } + _getAnchor(prevAnchor, me, anchorIdx); + _getAnchor(nextAnchor, me, anchorIdx + 1); + + // View position points to a source. + if (nextAnchor.seqPos - prevAnchor.seqPos > (int)pos - prevAnchor.gapPos) + seqPos = prevAnchor.seqPos + (pos - prevAnchor.gapPos); + else // View position points to a gap + seqPos = (IsSameType::VALUE) ? nextAnchor.seqPos : + (_max(static_cast(nextAnchor.seqPos) - 1, static_cast(0))); + return seqPos; +} + +template +inline TPosition +positionGapToSeq(Gaps > const & me, TPosition pos) +{ + return positionGapToSeq(me, pos, RightOfViewPos()); +} + +// ---------------------------------------------------------------------------- +// Function positionSeqToGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn AnchorGaps#positionSeqToGap + * @brief Convert from sequence space on the reference to gap space in the global alignment. + * + * @signature TPos positionSeqToGap(gaps, pos); + * + * @param[in] gaps The AnchorGaps object to use for the translation. + * @param[in] pos The gap space position to convert to sequence space. + * + * @return TPos The resulting position in sequence space (Metafunction: @link ContainerConcept#Position @endlink). + * + * See the example below to construct the gaps object. Note that this construction is fast since it is only a thin + * wrapper around underlying objects. + * + * @section Example + * + * Convert from gap space to position space on contig $contigId$ when the contigs required to be loaded. + * + * @code{.cpp} + * typedef typename TFragmentStore::TContigStore TContigStore; + * typedef typename Value::Type TContig; + * typedef typename TFragmentStore::TContigSeq TContigSeq; + * typedef Gaps > TContigGaps; + * + * TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps); + * TAlignedReadPos pos = positionGapToSeq(contigGaps, 33); + * @endcode + * + * Convert from gap space to position space on contig $contigId$ when the contigs are not required. + * + * @code{.cpp} + * typedef typename TFragmentStore::TContigStore TContigStore; + * typedef typename Value::Type TContig; + * typedef Gaps > TContigGaps; + * + * TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps); + * TAlignedReadPos endPos = positionGapToSeq(contigGaps, 33); + * @endcode + */ + +template +inline TPosition +positionSeqToGap(Gaps > const & me, TPosition pos) +{ + typedef typename Position::Type>::Type TAnchorPos; + + GapAnchor prevAnchor, nextAnchor; + TPosition gapPos; + int anchorIdx; + + if (isNegative(pos)) + anchorIdx = -1; + else + { + TGapAnchors const & anchors = _dataAnchors(me); + TAnchorPos seqLength; + _assignSourceLength(seqLength, me); + if (!empty(anchors)) + { + anchorIdx = upperBoundGapAnchor(anchors, pos, SortSeqPos()) - begin(anchors, Standard()); + if (anchorIdx < (int)length(anchors)) + if (anchors[anchorIdx].seqPos == (TAnchorPos)pos) + ++anchorIdx; + } + else + anchorIdx = ((TAnchorPos)pos < seqLength) ? 0 : 1; + } + _getAnchor(prevAnchor, me, anchorIdx); + _getAnchor(nextAnchor, me, anchorIdx + 1); + + if (nextAnchor.gapPos - prevAnchor.gapPos > (int)pos - prevAnchor.seqPos) + gapPos = prevAnchor.gapPos + (pos - prevAnchor.seqPos); + else + gapPos = nextAnchor.gapPos; + return gapPos; +} + +// ---------------------------------------------------------------------------- +// Function toViewPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position > >::Type +toViewPosition(Gaps > const & gaps, TPosition const sourcePosition) +{ + return positionSeqToGap(gaps, sourcePosition) - gaps.data_viewCutBegin - gaps.data_cutBegin; +} + +// ---------------------------------------------------------------------------- +// Function toSourcePosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position::Type +toSourcePosition(Gaps > const & gaps, + TPosition const clippedViewPos, + TProjectionDir const /*dir*/) +{ + // TODO(weese): possibly change positionGapToSeq interface to consider a different zero + // shifted by data_cutBegin + return positionGapToSeq(gaps, clippedViewPos + gaps.data_viewCutBegin + gaps.data_cutBegin, TProjectionDir()); +} + +// ---------------------------------------------------------------------------- +// Function setClippedBeginPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setClippedBeginPosition(Gaps > & gaps, TPosition unclippedViewPosition) +{ + gaps.data_viewCutBegin = unclippedViewPosition; +} + +// ---------------------------------------------------------------------------- +// Function setClippedEndPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setClippedEndPosition(Gaps > & gaps, TPosition unclippedViewPosition) +{ + gaps.data_viewCutEnd = _unclippedLength(gaps) - unclippedViewPosition; +} + +// ---------------------------------------------------------------------------- +// Function clippedBeginPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position > >::Type +clippedBeginPosition(Gaps > const & gaps) +{ + return gaps.data_viewCutBegin; +} + +// ---------------------------------------------------------------------------- +// Function clippedEndPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position > >::Type +clippedEndPosition(Gaps > const & gaps) +{ + return _unclippedLength(gaps) - gaps.data_viewCutEnd; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ANCHOR_H_ diff --git a/seqan/align/gaps_array.h b/seqan/align/gaps_array.h new file mode 100644 index 0000000..840cbbb --- /dev/null +++ b/seqan/align/gaps_array.h @@ -0,0 +1,917 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== + +// SEQAN_NO_GENERATED_FORWARDS + +// TODO(holtgrew): Currently, operations are a function of the whole gap count, could be of clipped region only. +// TODO(holtgrew): Problem with the gap value, getValue(), value(). + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// Internally used tag for creating iterators at the begin of containers. +struct Begin__; +typedef Tag Begin_; + +// Internally used tag for creating iterators at the end of containers. +struct End__; +typedef Tag End_; + +// Internally used tag for creating iterators inside of containers. +struct Position__; +typedef Tag Position_; + +struct ArrayGaps_; +typedef Tag ArrayGaps; + +template class Gaps; + +template +inline void _reinitArrayGaps(Gaps & gaps); + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +struct ArrayGaps_; +typedef Tag ArrayGaps; + +/*! + * @class ArrayGaps + * @headerfile + * @extends Gaps + * @brief Stores length of gap- and non-gap runs in an array. + * + * @signature template + * class Gaps + * + * @tparam TSequence The type of the underling sequence. + */ + +/*! + * @fn ArrayGaps::Gaps + * @headerfile + * @brief Constructor. + * + * @signature Gaps::Gaps([other]); + * @signature Gaps::Gaps(seq); + * + * @param[in] other Other Gaps object to copy from. + * @param[in] seq Sequence concept to construct the gaps for. + */ + +template +class Gaps +{ +public: + // ----------------------------------------------------------------------- + // Internal Typedefs + // ----------------------------------------------------------------------- + + typedef typename Size::Type TSize_; + typedef typename Size::Type TSequenceSize_; + typedef typename Position::Type TPosition_; + typedef typename Position::Type TSequencePosition_; + typedef typename Value::Type TValue_; + + typedef String TArray_; + typedef typename Position::Type TArrayPos_; + + // ----------------------------------------------------------------------- + // Member Variables + // ----------------------------------------------------------------------- + + // Holder of the underlying sequence. + Holder _source; + + // The array with the alternating gap/source char counts. + TArray_ _array; + + // Begin and end position in the source. + TSequencePosition_ _sourceBeginPos, _sourceEndPos; + // Begin and end position in the view. + TPosition_ _clippingBeginPos, _clippingEndPos; + // TODO(holtgrew): The following is a possible optimization. + // // Index of clipping begin and end in the _array seq/gap char count array. + // // This identifies a slice of the view. + // TArrayPos_ _clippingBeginIdx, _clippingEndIdx; + // // Offset within the slice. + // TSequenceSize_ _clippingBeginOffset, _clippingEndOffset; + + // ----------------------------------------------------------------------- + // Constructors + // ----------------------------------------------------------------------- + + Gaps() : _sourceBeginPos(0), _sourceEndPos(0), _clippingBeginPos(0), _clippingEndPos(0)//, + // _clippingBeginIdx(0), _clippingEndIdx(0), _clippingBeginOffset(0), _clippingEndOffset(0) + {} + + explicit + Gaps(TSequence & seq) : + _source(seq), _sourceBeginPos(0), _sourceEndPos(length(seq)), + _clippingBeginPos(0), _clippingEndPos(length(seq))//, + // _clippingBeginIdx(0), _clippingEndIdx(0), _clippingBeginOffset(0), + // _clippingEndOffset(0) + { + // Initialize array gaps object for ungapped sequence. + _reinitArrayGaps(*this); + } + + Gaps(Gaps const & other) : + _source(other._source), _array(other._array), _sourceBeginPos(other._sourceBeginPos), + _sourceEndPos(other._sourceEndPos), _clippingBeginPos(other._clippingBeginPos), + _clippingEndPos(other._clippingEndPos) + {} + + // ----------------------------------------------------------------------- + // Array Subscript Operator + // ----------------------------------------------------------------------- + + inline Gaps & + operator=(Gaps const & other) + { + setValue(_source, source(other)); + _array = other._array; + _sourceBeginPos = other._sourceBeginPos; + _sourceEndPos = other._sourceEndPos; + _clippingBeginPos = other._clippingBeginPos; + _clippingEndPos = other._clippingEndPos; + return *this; + } + + // ----------------------------------------------------------------------- + // Array Subscript Operator + // ----------------------------------------------------------------------- + + inline typename Reference::Type + operator[](TPosition_ const clippedViewPos) + { + return value(*this, clippedViewPos); + } + + inline typename Reference::Type + operator[](TPosition_ const clippedViewPos) const + { + return value(*this, clippedViewPos); + } +}; + +// ---------------------------------------------------------------------------- +// Function swap() +// ---------------------------------------------------------------------------- + +template +void swap(Gaps & lhs, Gaps & rhs) +{ + swap(lhs._source, rhs._source); + swap(lhs._array, rhs._array); + + std::swap(lhs._sourceBeginPos, rhs._sourceBeginPos); + std::swap(lhs._sourceEndPos, rhs._sourceEndPos); + std::swap(lhs._clippingBeginPos, rhs._clippingBeginPos); + std::swap(lhs._clippingEndPos, rhs._clippingEndPos); +} + +// ============================================================================ +// Metafunctions +// ============================================================================ + + + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function detach() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Remove? Only used by module blast. + +template +void detach(Gaps & gaps) +{ + detach(gaps._source); +} + +// ---------------------------------------------------------------------------- +// Function _setLength() +// ---------------------------------------------------------------------------- + +// Set the length, only use if TSequence is Nothing. + +template +inline void _setLength(Gaps & gaps, TSize newLen) +{ + // Reset array. + resize(gaps._array, 3); + gaps._array[0] = 0; + gaps._array[1] = newLen; + gaps._array[2] = 0; + // Reset clipping information. + gaps._clippingBeginPos = 0; + gaps._clippingEndPos = newLen; + gaps._sourceBeginPos = 0; + gaps._sourceEndPos = gaps._clippingEndPos; + // gaps._clippingBeginIdx = 1; + // gaps._clippingBeginOffset = 0; + // gaps._clippingEndIdx = 1; + // gaps._clippingEndOffset = value(gaps._source)[1]; +} + +// ---------------------------------------------------------------------------- +// Helper Function _reinitArrayGaps() +// ---------------------------------------------------------------------------- + +// Reset the array gaps DS such that represents the ungapped sequence. + +template +inline void _reinitArrayGaps(Gaps & gaps) +{ + _setLength(gaps, length(value(gaps._source))); +} + +// ---------------------------------------------------------------------------- +// Function begin() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We'd rather have "TTag const &" here. +template +inline typename Iterator >::Type +begin(Gaps & gaps, Tag const /*tag*/) +{ + typedef typename Iterator >::Type TIter; + return TIter(gaps, Begin_()); +} + +// TODO(holtgrew): We'd rather have "TTag const &" here. +template +inline typename Iterator const>::Type +begin(Gaps const & gaps, Tag const /*tag*/) +{ + typedef typename Iterator const>::Type TIter; + return TIter(gaps, Begin_()); +} + +// ---------------------------------------------------------------------------- +// Function end() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We'd rather have "TTag const &" here. +template +inline typename Iterator >::Type +end(Gaps & gaps, Tag const /*tag*/) +{ + typedef typename Iterator >::Type TIter; + return TIter(gaps, End_()); +} + +// TODO(holtgrew): We'd rather have "TTag const &" here. +template +inline typename Iterator const>::Type +end(Gaps const & gaps, Tag const /*tag*/) +{ + typedef typename Iterator const>::Type TIter; + return TIter(gaps, End_()); +} + +// ---------------------------------------------------------------------------- +// Function iter() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We'd rather have "TTag const &" here. +template +inline typename Iterator >::Type +iter(Gaps & gaps, TPosition pos, Tag const /*tag*/) +{ + typedef typename Iterator >::Type TIter; + return TIter(gaps, pos, Position_()); +} + +// TODO(holtgrew): We'd rather have "TTag const &" here. +template +inline typename Iterator const>::Type +iter(Gaps const & gaps, TPosition pos, Tag const /*tag*/) +{ + typedef typename Iterator const>::Type TIter; + return TIter(gaps, pos, Position_()); +} + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +template +inline typename Size >::Type +length(Gaps const & gaps) +{ + SEQAN_ASSERT_GEQ(gaps._clippingEndPos, gaps._clippingBeginPos); + return gaps._clippingEndPos - gaps._clippingBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function unclippedLength() +// ---------------------------------------------------------------------------- + +template +inline typename Size >::Type +unclippedLength(Gaps const & gaps) +{ + typedef typename Size >::Type TSize; + + TSize result = 0; + for (unsigned i = 0; i < length(gaps._array); ++i) + result += gaps._array[i]; + + return result; +} + +// ---------------------------------------------------------------------------- +// Function createSource() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Remove? Switch to Hosted Type Interface? + +template +inline void createSource(Gaps & gaps) +{ + create(gaps._source); +} + +// ---------------------------------------------------------------------------- +// Function source() +// ---------------------------------------------------------------------------- + +template +inline typename Source const>::Type & +source(Gaps const & gaps) +{ + return value(gaps._source); +} + +template +inline typename Source >::Type & +source(Gaps & gaps) +{ + return value(gaps._source); +} + +// ---------------------------------------------------------------------------- +// Function setSource() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Test with clippings, also for AnchorGaps. + +template +inline void +setSource(Gaps & gaps, TSequence & source) +{ + setValue(gaps._source, source); + _reinitArrayGaps(gaps); +} + +template +inline void +setSource(Gaps & gaps, TSequence & source) +{ + setValue(gaps._source, source); + _reinitArrayGaps(gaps); +} + +// ---------------------------------------------------------------------------- +// Function assignSource() +// ---------------------------------------------------------------------------- + +template +inline void +assignSource(Gaps & gaps, TSequence2 const & source) +{ + value(gaps._source) = source; + _reinitArrayGaps(gaps); +} + +// ---------------------------------------------------------------------------- +// Function toSourcePosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position::Type +toSourcePosition(Gaps const & gaps, TPosition const clippedViewPos, LeftOfViewPos const & /*tag*/) +{ + typedef Gaps TGaps; + typedef typename Position::Type TGapsPos; + typedef typename TGaps::TArrayPos_ TArrayPos; + typedef typename Position::Type TSourcePos; + + // Translate from clipped view position to unclipped view position. + TGapsPos unclippedViewPos = clippedViewPos + clippedBeginPosition(gaps); + + // Get index i of the according bucket and offset within bucket. + TSourcePos result = 0; + TArrayPos i = 1; + TSourcePos const iEnd = length(gaps._array); + + if (unclippedViewPos < static_cast(gaps._array[0])) + return 0; + + TSourcePos counter = unclippedViewPos - gaps._array[0]; + for (; counter > TGapsPos(0) && i < iEnd; ++i) + { + if (counter < gaps._array[i]) + break; + + if (i % 2) // character bucket + result += gaps._array[i]; + counter -= gaps._array[i]; + } + if (i % 2) // character bucket. + { + if (i == length(gaps._array)) // We pointing behind the last bucket. + return --result; + result += counter; // If maps into char bucket. + if (counter == gaps._array[i]) + --result; + return result; + } + return --result; +} + +template +inline typename Position::Type +toSourcePosition(Gaps const & gaps, TPosition const clippedViewPos, RightOfViewPos const & /*tag*/) +{ + typedef Gaps TGaps; + typedef typename Position::Type TGapsPos; + typedef typename TGaps::TArrayPos_ TArrayPos; + typedef typename Position::Type TSourcePos; + + // Translate from clipped view position to unclipped view position. + TGapsPos unclippedViewPos = clippedViewPos + clippedBeginPosition(gaps); + + // Get index i of the according bucket and offset within bucket. + TSourcePos result = 0; + TArrayPos i = 0; + TSourcePos const iEnd = length(gaps._array); + + for (TSourcePos counter = unclippedViewPos; counter > TGapsPos(0) && i < iEnd;) + { + if (counter > gaps._array[i]) + { + if (i % 2) // character bucket + result += gaps._array[i]; + counter -= gaps._array[i]; + i += 1; + } + else if (counter <= gaps._array[i]) + { + if (i % 2) // character bucket + result += counter; + counter = 0; + } + } + + return result; +} + +// ---------------------------------------------------------------------------- +// Function toViewPosition() +// ---------------------------------------------------------------------------- + +// Parameter rightOfGaps moves to the right end of gaps if the character at sourcePosition is followed by a gap in the +// view. +template +inline typename Position >::Type +toViewPosition(Gaps const & gaps, TPosition sourcePosition, bool rightOfGaps = true) +{ + typedef Gaps TGaps; + typedef typename Position::Type TGapsPosition; + typedef typename TGaps::TArray_ TArray; + typedef typename TGaps::TArrayPos_ TArrayPos; + typedef typename Value::Type TArrayValue; + + if (sourcePosition == TPosition(0)) + return gaps._array[0] - clippedBeginPosition(gaps); + + // First, convert to unclipped source position. + TGapsPosition unclippedViewPosition = 0; + TArrayPos i = 0; + for (TArrayValue counter = sourcePosition; counter > TArrayValue(0); ++i) + { + if (i % 2 /*== 1*/) // sequence bucket + { + if (counter > gaps._array[i]) + { + unclippedViewPosition += gaps._array[i]; + counter -= gaps._array[i]; + } + else if (counter < gaps._array[i]) + { + unclippedViewPosition += counter; + counter = 0; + } + else // counter == gaps._array[i] + { + unclippedViewPosition += counter; + if (rightOfGaps && i + 2 < length(gaps._array)) + unclippedViewPosition += gaps._array[i + 1]; + counter = 0; + } + } + else // gaps bucket + { + unclippedViewPosition += gaps._array[i]; + } + } + + // Return after clipping. + return unclippedViewPosition - clippedBeginPosition(gaps); +} + +// ---------------------------------------------------------------------------- +// Function insertGaps() +// ---------------------------------------------------------------------------- + +template +inline void +insertGaps(Gaps & gaps, TPosition clippedViewPos, TCount count) +{ + typedef Gaps TGaps; + typedef typename Position::Type TGapsPosition; + typedef typename TGaps::TArray_ TArray; + typedef typename TGaps::TArrayPos_ TArrayPos; + typedef typename Position::Type TSeqPos; + + // Translate from clipped view position to unclipped view position. + TGapsPosition unclippedViewPos = clippedViewPos + clippedBeginPosition(gaps); + + // Get index i of the according bucket and offset within bucket. + TArrayPos i = 0; + TSeqPos offset = 0; + for (TSeqPos counter = unclippedViewPos; counter > 0;) + { + SEQAN_ASSERT_LT(i, length(gaps._array)); + if (counter > gaps._array[i]) + { + counter -= gaps._array[i]; + i += 1; + } + else + { + offset = counter; + counter = 0; + } + } + + SEQAN_ASSERT_GEQ(gaps._array[i], offset); + + // Insert gaps, simple and fast if we are in a gaps bucket, a bit harder + // otherwise. + if (i % 2) // character bucket + { + if (gaps._array[i] > offset) // In the middle of the bucket. + { + TArray arr; + resize(arr, 2, 0); + arr[0] = count; + arr[1] = gaps._array[i] - offset; + gaps._array[i] = offset; + insert(gaps._array, i + 1, arr); + } + else // At the end of the bucket. + { + if (i + 1 < length(gaps._array)) // Not at end of array. + { + gaps._array[i + 1] += count; + } + else // At end of array. + { + resize(gaps._array, length(gaps._array) + 2, 0); + gaps._array[i + 1] = count; + gaps._array[i + 2] = 0; + } + } + } + else // gap bucket + { + gaps._array[i] += count; + } + + // Adjust clipping information. + gaps._clippingEndPos += count; +} + +// ---------------------------------------------------------------------------- +// Function removeGaps() +// ---------------------------------------------------------------------------- + +template +inline typename Size >::Type +removeGaps(Gaps & gaps, TPosition clippedViewPos, TCount count) +{ + typedef Gaps TGaps; + typedef typename Position::Type TGapsPosition; + typedef typename TGaps::TArray_ TArray; + typedef typename TGaps::TArrayPos_ TArrayPos; + typedef typename Value::Type TArrayValue; + typedef typename Position::Type TSeqPos; + + // Translate from clipped view position to unclipped view position. + TGapsPosition pos = clippedViewPos + clippedBeginPosition(gaps); + + // Get index i of the according bucket and offset within bucket. + SEQAN_ASSERT_GEQ(length(gaps._array), 2u); + // Start at position 1 if there are no leading gaps. + TArrayPos i = (gaps._array[0] == 0); + TSeqPos offset = 0; + for (TSeqPos counter = pos; counter > 0;) + { + SEQAN_ASSERT_LT(i, length(gaps._array)); + if (counter > gaps._array[i]) + { + counter -= gaps._array[i]; + i += 1; + } + else + { + offset = counter; + counter = 0; + } + } + + // Advance into next bucket if at end of current. + if (offset > 0 && offset == gaps._array[i]) + { + i += 1; + offset = 0; + } + + // If we are inside a non-gap bucket then we cannot remove any gaps. + if (i % 2) + return 0; + + // Otherwise, we can remove gaps right of the current position but not + // more than there are. + TSeqPos toRemove = count; + if (toRemove > gaps._array[i] - offset) + toRemove = gaps._array[i] - offset; + gaps._array[i] -= toRemove; + // In some cases, we remove the whole gap and merge the character buckets. + if (gaps._array[i] == TArrayValue(0)) + { + // No merging for leading and trailing gap. + if (i != TArrayPos(0) && i != TArrayPos(length(gaps._array) - 1)) + { + gaps._array[i - 1] += gaps._array[i + 1]; + erase(gaps._array, i, i + 2); + } + } + + // Also update the right clipping position. + gaps._clippingEndPos -= toRemove; + + // Finally, return number of removed gaps. + return toRemove; +} + +// ---------------------------------------------------------------------------- +// Function clearGaps() +// ---------------------------------------------------------------------------- + +template +inline void +clearGaps(Gaps & gaps) +{ + _reinitArrayGaps(gaps); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +inline void +clear(Gaps & gaps) +{ + clear(gaps._source); + clear(gaps._array); + gaps._sourceBeginPos = 0; + gaps._sourceEndPos = 0; + gaps._clippingBeginPos = 0; + gaps._clippingEndPos = 0; + // cannot use clearGaps() here, since that calls value() on _source + // which instates the Holder to Owner; we want it to be empty +} + +// ---------------------------------------------------------------------------- +// Function isGap() +// ---------------------------------------------------------------------------- + +template +inline bool +isGap(Gaps const & gaps, TPosition clippedViewPos) +{ + typedef Gaps TGaps; + typedef typename Position::Type TGapsPosition; + typedef typename TGaps::TArrayPos_ TArrayPos; + typedef typename Position::Type TSeqPos; + + // Translate from clipped view position to unclipped view position. + TGapsPosition pos = clippedViewPos + clippedBeginPosition(gaps); + + // Get index i of the according bucket and offset within bucket. + SEQAN_ASSERT_GEQ(length(gaps._array), 2u); + // Start at position 1 if there are no leading gaps. + TArrayPos i = (gaps._array[0] == 0); + TSeqPos offset = 0; + for (TSeqPos counter = pos; counter > TSeqPos(0);) + { + SEQAN_ASSERT_LT(i, length(gaps._array)); + if (counter > gaps._array[i]) + { + counter -= gaps._array[i]; + i += 1; + } + else + { + offset = counter; + counter = 0; + } + } + + // Advance into next bucket if at end of current. + if (offset > TSeqPos(0) && offset == gaps._array[i]) + i += 1; + + return !(i % 2); +} + +// ---------------------------------------------------------------------------- +// Function clearClipping() +// ---------------------------------------------------------------------------- + +template +inline void +clearClipping(Gaps & gaps) +{ + typedef Gaps TGaps; + typedef typename TGaps::TArrayPos_ TArrayPos; + + gaps._sourceBeginPos = 0; + gaps._sourceEndPos = length(value(gaps._source)); + gaps._clippingBeginPos = 0; + gaps._clippingEndPos = 0; + for (TArrayPos i = 0; i < length(gaps._array); ++i) + gaps._clippingEndPos += gaps._array[i]; + + SEQAN_ASSERT_LEQ(static_cast(gaps._sourceEndPos), static_cast(gaps._clippingEndPos)); +} + +// ---------------------------------------------------------------------------- +// Function setClippedBeginPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setClippedBeginPosition(Gaps & gaps, TPosition unclippedViewPosition) +{ + gaps._sourceBeginPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); + gaps._clippingBeginPos = unclippedViewPosition; +} + +// ---------------------------------------------------------------------------- +// Function setClippedEndPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setClippedEndPosition(Gaps & gaps, TPosition unclippedViewPosition) +{ + gaps._sourceEndPos = toSourcePosition(gaps, unclippedViewPosition - clippedBeginPosition(gaps)); + //if (isGap(gaps, unclippedViewPosition - clippedBeginPosition(gaps))) + // gaps._sourceEndPos += 1; + gaps._clippingEndPos = unclippedViewPosition; +} + +// ---------------------------------------------------------------------------- +// Function clippedBeginPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position >::Type +clippedBeginPosition(Gaps const & gaps) +{ + return gaps._clippingBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function clippedEndPosition() +// ---------------------------------------------------------------------------- + +template +inline typename Position >::Type +clippedEndPosition(Gaps const & gaps) +{ + return gaps._clippingEndPos; +} + +// ---------------------------------------------------------------------------- +// Function setBeginPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setBeginPosition(Gaps & gaps, TPosition sourcePosition) +{ + setClippedBeginPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); +} + +// ---------------------------------------------------------------------------- +// Function setEndPosition() +// ---------------------------------------------------------------------------- + +template +inline void +setEndPosition(Gaps & gaps, TPosition sourcePosition) +{ + setClippedEndPosition(gaps, toViewPosition(gaps, sourcePosition) + clippedBeginPosition(gaps)); +} + +// ---------------------------------------------------------------------------- +// Function beginPosition() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We would rather like to have the const version only :( +template +inline typename Position::Type +beginPosition(Gaps const & gaps) +{ + return gaps._sourceBeginPos; +} + +template +inline typename Position::Type +beginPosition(Gaps & gaps) +{ + return gaps._sourceBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function endPosition() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We would rather like to have the const version only :( +template +inline typename Position::Type +endPosition(Gaps const & gaps) +{ + return gaps._sourceEndPos; +} + +template +inline typename Position::Type +endPosition(Gaps & gaps) +{ + return gaps._sourceEndPos; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ARRAY_H_ diff --git a/seqan/align/gaps_base.h b/seqan/align/gaps_base.h new file mode 100644 index 0000000..e187688 --- /dev/null +++ b/seqan/align/gaps_base.h @@ -0,0 +1,1234 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +// TODO(holtgrew): Switch to Host interface. + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +struct GapsIterator; + +/*! + * @defgroup GapsSpecTag Gaps Specialization Tags + * @brief Tags for specializing the Gaps class. + */ + +/*! + * @tag GapsSpecTag#ArrayGaps + * @headerfile + * @brief Tag for the Array Gaps specialization. + * + * @signature struct ArrayGaps_; + * @signature typedef Tag ArrayGaps; + */ + +struct ArrayGaps_; +typedef Tag ArrayGaps; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @defgroup GapDirectionTags Gap Direction Tags + * @brief Tags to select the direction to which side of a view position an operation should be projected. + */ + +/*! + * @tag GapDirectionTags#LeftOfViewPos + * @headerfile + * @brief Projects to the left side of the current view position. + * + * @signature struct LeftOfViewPos_; + * typedef Tag LeftOfViewPos; + */ + +struct LeftOfViewPos_; +typedef Tag LeftOfViewPos; + +/*! + * @tag GapDirectionTags#RightOfViewPos + * @headerfile + * @brief Projects to the right side of the current view position. + * + * @signature struct RightOfViewPos_; + * typedef Tag RightOfViewPos; + */ + +struct RightOfViewPos_; +typedef Tag RightOfViewPos; + +// ---------------------------------------------------------------------------- +// Class Gaps +// ---------------------------------------------------------------------------- + +/*! + * @class Gaps + * @implements ContainerConcept + * @headerfile + * @brief Store the gapped version of a sequence. + * + * @signature template + * class Gaps; + * + * @tparam TSequence The type of the underlying sequence. + * @tparam TSpec Tag for specialization. + * + * Gaps wrap a @link ContainerConcept Sequence @endlink and allows one to (1) insert gaps into the sequence and (2) select + * an infix of the gapped sequence (clipping). The gaps are not inserted into the underlying sequence (source) but + * stored separately. Using the clipping is optional and meant for selecting parts of the alignment as a part of the + * result of a local alignment algorithm. + * + * + * + * In the figure above, the source sequence has seven characters, the gapped sequence has four gaps and thus consists + * of eleven characters. The gapped sequence is clipped to start at position 0 in the gapped sequence and to end at + * position 8 in the gapped sequence (the positions given as half-open intervals [begin, end)). + * + * The figure shows the three coordinate systems that are used with Gaps objects. The source position is the position + * in the underlying sequence. The unclipped view position is the position in the gapped sequence without gaps. The + * view position is the position in the gapped sequence but including the clipping: All (clipped) view positions have + * the clipping begin position subtracted from them. + * + * @section Examples + * + * The following example shows the construction of the gaps object from the image above together with some calls to + * toViewPosition and toSourcePosition. + * + * @include demos/dox/align/gaps_example.cpp + * + * The output is as follows: + * + * @include demos/dox/align/gaps_example.cpp.stdout + */ + +template +class Gaps; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +template +struct Value > +{ + typedef typename Value::Type TAlphabet; + typedef typename GappedValueType::Type Type; +}; + +template +struct Value const> : Value > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Iterator +// ---------------------------------------------------------------------------- + +template +struct Iterator, TIteratorSpec> +{ + typedef Iter, GapsIterator > Type; +}; + +template +struct Iterator const, TIteratorSpec> +{ + typedef Iter const, GapsIterator > Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction GetValue +// ---------------------------------------------------------------------------- + +template +struct GetValue > : Value > +{}; + +template +struct GetValue const> : GetValue > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Position +// ---------------------------------------------------------------------------- + +template +struct Position > +{ + typedef typename Position::Type TSeqPos_; + typedef typename MakeSigned::Type Type; +}; + +template +struct Position const> : Position > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +template +struct Reference > +{ + typedef typename Iterator, Standard>::Type TIterator_; + typedef Proxy > Type; +}; + +template +struct Reference const> +{ + typedef typename Iterator const, Standard>::Type TIterator_; + typedef Proxy > Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Size +// ---------------------------------------------------------------------------- + +template +struct Size > +{ + typedef typename Size::Type Type; +}; + +template +struct Size const> : Size > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Source +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Switch to Hosted Type interface + +template +struct Source > +{ + typedef TSequence Type; +}; + +template +struct Source const> : Source > +{}; + +// TODO(holtgrew): Also prefix/suffix/infix? Should work! + +// ---------------------------------------------------------------------------- +// Metafunction IsSequence +// ---------------------------------------------------------------------------- + +template +struct IsSequence > +{ + typedef True Type; + static const bool VALUE = true; +}; + +template +struct IsSequence const> : IsSequence > +{}; + + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +template +inline typename Reference >::Type +value(Gaps & gaps, + TPosition const clippedViewPos) +{ + return typename Reference >::Type(begin(gaps, Standard()) + clippedViewPos); +} + +template +inline typename Reference const>::Type +value(Gaps const & gaps, + TPosition const clippedViewPos) +{ + return typename Reference const>::Type(begin(gaps, Standard()) + clippedViewPos); +} + +// ---------------------------------------------------------------------------- +// Function iter() +// ---------------------------------------------------------------------------- + +// From ContainerConcept, only overwriting documentation here. + +/*! + * @fn Gaps#iter + * @brief Return an iterator to a specific position in the current clipping. + * + * @signature TIterator iter(gaps, viewPos[, tag]); + * + * @param[in] gaps The Gaps object to get an iterator into. + * @param[in] viewPos View position to get an iterator to (Metafunction: @link ContainerConcept#Position @endlink). + * @param[in] tag An optional tag for selecting the iterator type. + * + * @return TIterator The resulting iterator. The type is Iterator::Type where TTag is + * the type of tag. + */ + +// TODO(holtgrew): Adding links to implemented sequence. This should be cleaned up once we have better documentation with concepts. +// ---------------------------------------------------------------------------- +// Function setSource() +// ---------------------------------------------------------------------------- + +// ---------------------------------------------------------------------------- +// Function createSource() +// ---------------------------------------------------------------------------- + +// ---------------------------------------------------------------------------- +// Function clearClipping() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#clearClipping + * @brief Clear clipping from Gaps objects. + * + * @signature void clearClipping(gaps); + * + * @param[in,out] gaps Object to clear clipping from. + */ + +// ---------------------------------------------------------------------------- +// Function clearGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#clearGaps + * @brief Clear gaps from Gaps objects. + * + * @signature void clearGaps(gaps); + * + * @param[in,out] gaps Object to clear gaps from. + */ + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +// From ContainerConcept, only overwriting documentation here. + +/*! + * @fn Gaps#length + * @brief Return number of gap and characters between the beginning and the end of the clipping. + * + * @signature TSize length(gaps); + * + * @param[in] gaps The @link Gaps @endlink object to query for its length. + * + * @return TSize The number of gaps and characters between the beginning and the end of the clipping (Metafunction: + * @link ContainerConcept#Size @endlink). + */ + +// ---------------------------------------------------------------------------- +// Function unclippedLength() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#unclippedLength + * @brief Return length of the gapped sequence without clipping. + * + * @signature TSize unclippedLength(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TSize The result (Metafunction: @link ContainerConcept#Size @endlink). + */ + +// ---------------------------------------------------------------------------- +// Function toViewPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#toViewPosition + * @brief Conversion from source (without gaps or clipping) to view position (including gaps and clipping). + * + * @signature TPos toViewPosition(gaps, sourcePos); + * + * @param[in] gaps The gaps object to use for translation. + * @param[in] sourcePos The source position (in the underlying sequence) to translate. + * + * @return TPos The resulting position in the view (Metafunction: @link ContainerConcept#Position @endlink). + */ + +// ---------------------------------------------------------------------------- +// Function toSourcePosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#toSourcePosition + * @brief Conversion from view position (including gaps and clipping) to source (without gaps or clipping). + * + * @signature TPos toSourcePosition(gaps, viewPos); + * + * @param[in] gaps The gaps object to use for translation. + * @param[in] sourcePos The view position (including gaps and clipping) to translate. + * + * @return TPos The resulting position in the underlying sequence (Metafunction: @link ContainerConcept#Position + * @endlink). + */ + +template +inline typename Position::Type +toSourcePosition(Gaps const & gaps, TPosition const clippedViewPos) +{ + return toSourcePosition(gaps, clippedViewPos, RightOfViewPos()); +} + +// ---------------------------------------------------------------------------- +// Function isGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#isGap + * @brief Query positions in a Gaps object for being a gap. + * + * @signature bool isGap(gaps, viewPos); + * + * @param[in] gaps The Gaps object to query. + * @param[in] viewPos The view position (including clipping and gaps). + * + * @return bool The query result. + */ + +template +bool isGap(Gaps const & gaps, TPos clippedViewPos) +{ + return isGap(iter(gaps, clippedViewPos, Standard())); +} + +// ---------------------------------------------------------------------------- +// Function isCharacter() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#isCharacer + * @brief Query positions in a Gaps object for being a character. + * + * @signature bool isGap(gaps, viewPos); + * + * @param[in] gaps The Gaps object to query. + * @param[in] viewPos The view position (including clipping and gaps). + * + * @return bool The query result. + */ + +template +bool isCharacter(Gaps const & gaps, TPos clippedViewPos) +{ + return isCharacter(iter(gaps, clippedViewPos, Standard())); +} + +// ---------------------------------------------------------------------------- +// Function insertGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#insertGaps + * @brief Insert gap characters. + * + * @signature void insertGaps(gaps, viewPos, count); + * + * @param[in,out] gaps The Gaps object to insert gaps into. + * @param[in] viewPos The view position (including clipping and gaps) to insert gaps at. + * @param[in] count The number of gaps to insert. + */ + +// ---------------------------------------------------------------------------- +// Function insertGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#insertGap + * @brief Insert one gap character. + * + * @signature void insertGap(gaps, viewPos); + * + * @param[in,out] gaps The Gaps object to insert gap into. + * @param[in] viewPos The view position (including clipping and gaps) to insert the gap at. + */ + +// Forward to removeGaps() which has to be implemented in each subclass. + +template +inline void +insertGap(Gaps & gaps, TPosition clippedViewPos) +{ + insertGaps(gaps, clippedViewPos, 1u); +} + +// ---------------------------------------------------------------------------- +// Function removeGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#removeGaps + * @brief Remove gaps from a Gaps object. + * + * @signature TSize removeGaps(gaps, viewPos, count); + * + * @param[in,out] gaps The gaps object to remove gap characters from. + * @param[in] viewPos The view positions to remove gap characters from. + * @param[in] count The number of gap characters to remove. + * + * @return TSize The number of gap characters removed (Metafunction: @link ContainerConcept#Size @endlink). + */ + +// ---------------------------------------------------------------------------- +// Function removeGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#removeGap + * @brief Remove one gap from a Gaps object. + * + * @signature TSize removeGap(gaps, viewPos); + * + * @param[in,out] gaps The gaps object to remove one gap character from. + * @param[in] viewPos The view positions to remove one gap character from. + * + * @return TSize The number of gap characters removed (Metafunction: @link ContainerConcept#Size @endlink). + */ + +// Forward to removeGaps() which has to be implemented in each subclass. + +template +inline typename Size >::Type +removeGap(Gaps & gaps, TPosition clippedViewPos) +{ + return removeGaps(gaps, clippedViewPos, 1u); +} + +// ---------------------------------------------------------------------------- +// Function countGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#countGaps + * @brief The number of gaps following a position. + * + * @signature TSize countGaps(gaps, viewPos[, dir]); + * + * @param[in] gaps The Gaps object to query. + * @param[in] viewPos View position (including clipping and gaps) to query at. + * @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink. + * Defaults to @link GapDirectionTags#RightOfViewPos @endlink. + * + * @return TSize The number of gap characters at viewPos (Metafunction: @link ContainerConcept#Size + * @endlink). + * + * If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be + * included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected. + */ + +template +typename Size >::Type +countGaps(Gaps const & gaps, TPos const clippedViewPos, TDirSpec const & /*tag*/) +{ + return countGaps(iter(gaps, clippedViewPos, Standard()), TDirSpec()); +} + +template +typename Size >::Type +countGaps(Gaps const & gaps, TPos const clippedViewPos) +{ + return countGaps(gaps, clippedViewPos, RightOfViewPos()); +} + +// ---------------------------------------------------------------------------- +// Function countLeadingGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#countLeadingGaps + * @brief The number of leading gaps. + * + * @signature TSize countLeadingGaps(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TSize The number of leading gap characters (Metafunction: @link ContainerConcept#Size @endlink). + */ + +template +inline typename Size::Type +countLeadingGaps(TGaps const & gaps) +{ + return toViewPosition(gaps, 0); +} + +// ---------------------------------------------------------------------------- +// Function countTrailingGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#countTrailingGaps + * @brief The number of trailing gaps. + * + * @signature TSize countTrailingGaps(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TSize The number of trailing gap characters (Metafunction: @link ContainerConcept#Size @endlink). + */ + +template +inline typename Size::Type +countTrailingGaps(TGaps const & gaps) +{ + return length(gaps) - toViewPosition(gaps, length(source(gaps)) - 1) - 1; +} + +// ---------------------------------------------------------------------------- +// Function countGapOpens() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#countGapOpens + * @brief The number of gap openings. + * + * @signature TSize countGapOpens(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TSize The total number of gap openings (Metafunction: @link ContainerConcept#Size @endlink). + */ + +template +inline typename Size::Type +countGapOpens(TGaps const & gaps) +{ + typedef typename Iterator::Type TIter; + typedef typename Size::Type TCount; + + TCount count = 0; + + TIter it = begin(gaps, Standard()); + TIter itEnd = end(gaps, Standard()); + + while (it != itEnd) + { + count += isGap(it); + it += std::max(countGaps(it), (TCount)1); + } + + SEQAN_ASSERT(it == itEnd); + + return count; +} + +// ---------------------------------------------------------------------------- +// Function countGapExtensions() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#countGapExtensions + * @brief The number of gap extensions. + * + * @signature TSize countGapExtensions(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TSize The total number of gap extensions (Metafunction: @link ContainerConcept#Size @endlink). + */ + +template +inline typename Size::Type +countGapExtensions(TGaps const & gaps) +{ + typedef typename Iterator::Type TIter; + typedef typename Size::Type TCount; + + TCount count = 0; + + TIter it = begin(gaps, Standard()); + TIter itEnd = end(gaps, Standard()); + + while (it != itEnd) + { + count += countGaps(it); + it += std::max(countGaps(it), (TCount)1); + } + + SEQAN_ASSERT(it == itEnd); + + return count; +} + +// ---------------------------------------------------------------------------- +// Function countCharacters() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#countCharacters + * @brief The number of characters following a position. + * + * @signature TSize countCharacters(gaps, viewPos[, dir]); + * + * @param[in] gaps The Gaps object to query. + * @param[in] viewPos View position (including clipping and gaps) to query at. + * @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink. + * Defaults to @link GapDirectionTags#RightOfViewPos @endlink. + * + * @return TSize The number of non-gaps characters characters at viewPos (Metafunction: @link + * ContainerConcept#Size @endlink). + * + * If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be + * included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected. + */ + +template +typename Size >::Type +countCharacters(Gaps const & gaps, + TPos const clippedViewPos, + TDirSpec const & /*dir*/) +{ + return countCharacters(iter(gaps, clippedViewPos, Standard()), TDirSpec()); +} + +template +typename Size >::Type +countCharacters(Gaps const & gaps, TPos const clippedViewPos) +{ + return countCharacters(gaps, clippedViewPos, RightOfViewPos()); +} + +// ---------------------------------------------------------------------------- +// Function setClippedBeginPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#setClippedBeginPosition + * @brief Set the begin position of the clipping. + * + * @signature void setClippedBeginPosition(gaps, unclippedViewPos); + * + * @param[in,out] gaps The Gaps object to set the clipping begin position of. + * @param[in] unclippedViewPos View position (including gaps but excluding clipping) to set the clipping begin to. + */ + +// ---------------------------------------------------------------------------- +// Function setClippedEndPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#setClippedEndPosition + * @brief Set the end position of the clipping. + * + * @signature void setClippedEndPosition(gaps, unclippedViewPos); + * + * @param[in,out] gaps The Gaps object to set the clipping end position of. + * @param[in] unclippedViewPos View position (including gaps but excluding clipping) to set the clipping end to. + */ + +// ---------------------------------------------------------------------------- +// Function clippedBeginPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#clippedBeginPosition + * @brief Return begin position of the clipping. + * + * @signature TPos clippedBeginPosition(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TPos The begin position of the unclipped view (Metafunction: @link ContainerConcept#Position @endlink). + * + * @section Example + * + * In the following gaps configuration, the result of clippedBeginPosition(gaps) is 1. + * + * @code{.txt} + * clipping [ ) + * (half-open interval) + * + * gapped sequence: X--XXX-XX- + * + * source position: 0111234456 + * unclipped view position: 0123456789 + * clipped view position: 0123456 + * @endcode + */ + +// ---------------------------------------------------------------------------- +// Function clippedEndPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#clippedEndPosition + * @brief Return end position of the clipping. + * + * @signature TPos clippedEndPosition(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TPos The end position of the unclipped view (Metafunction: @link ContainerConcept#Position @endlink). + * + * @section Example + * + * In the following gaps configuration, the result of clippedEndPosition(gaps) is 7. + * + * @code{.txt} + * clipping [ ) + * (half-open interval) + * + * gapped sequence: X--XXX-XX- + * + * source position: 0111234456 + * unclipped view position: 0123456789 + * clipped view position: 0123456 + * @endcode + */ + +// ---------------------------------------------------------------------------- +// Function setBeginPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#setBeginPosition + * @brief Set the begin position of the clipped gapped sequence, given a source position. + * + * @signature void setBeginPosition(gaps, sourcePos); + * + * @param[in,out] gaps The Gaps object to set the begin position in. + * @param[in] sourcePos Position in the underlying sequence to set clipping to. + */ + +// ---------------------------------------------------------------------------- +// Function setEndPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#setEndPosition + * @brief Set the end position of the clipped gapped sequence, given a source position. + * + * @signature void setEndPosition(gaps, sourcePos); + * + * @param[in,out] gaps The Gaps object to set the end position in. + * @param[in] sourcePos Position in the underlying sequence to set clipping to. + */ + +// ---------------------------------------------------------------------------- +// Function beginPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#beginPosition + * @brief Return the clipping begin position as a source position. + * + * @signature TPos beginPosition(gaps); + * + * @param[in] gaps The Gaps object to query. + * + * @return TPos The clipping begin position in the source (Metafunction: @link ContainerConcept#Position @endlink). + * + * @section Example + * + * In the following gaps configuration, the result of beginPosition(gaps) is $1$. The clipping starts in a + * gap and the source position of the first non-gap character right of the clipping begin has source position 1. + * + * @code{.txt} + * clipping [ ) + * (half-open interval) + * + * gapped sequence: X--XXX-XX- + * + * source position: 0111234456 + * unclipped view position: 0123456789 + * clipped view position: 0123456 + * @endcode + */ + +// ---------------------------------------------------------------------------- +// Function endPosition() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#endPosition + * @brief Return the clipping end position as a source position. + * + * @signature TPos endPosition(gaps); + * + * @param[in] gaps The Gaps object to query for the end position as a source position. + * + * @return TPos The end position as a source position (Metafunction: @link ContainerConcept#Position @endlink). + * + * @section Example + * + * In the following gaps configuration, the result of endPositioN(gaps) is 4. + * + * @code{.txt} + * clipping [ ) + * (half-open interval) + * + * gapped sequence: X--XXX-XX- + * + * source position: 0111234456 + * unclipped view position: 0123456789 + * clipped view position: 0123456 + * @endcode + */ + +// ---------------------------------------------------------------------------- +// Function write() +// ---------------------------------------------------------------------------- + +template +inline void +write(TTarget & target, + Gaps const & source) +{ + // Print gaps row + typedef typename Iterator const>::Type TIter; + TIter begin_ = begin(source); + TIter end_ = end(source); + for (; begin_ != end_; ++begin_) { + if (isGap(begin_)) + writeValue(target, gapValue()); + else + writeValue(target, convert(getValue(begin_))); + } +} + +// ---------------------------------------------------------------------------- +// Function operator<<() [stream operator] +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Document appropriately. + +template +inline TTarget & +operator<<(TTarget & target, Gaps const & gaps) +{ + typename DirectionIterator::Type it = directionIterator(target, Output()); + write(it, gaps); + return target; +} + +// ---------------------------------------------------------------------------- +// Function _pumpTraceToGaps() +// ---------------------------------------------------------------------------- + +// Internal function for converting AlignTrace<> objects into alignments in two Gaps objects. Note that the traceback +// in the trace is stored in reverse, from back to front. We insert the gaps in descending order of their position. +// The reason is that Gaps<> objects store the gaps in ascending order of coordinates in String<> objects and inserting +// at the end is in O(1) while inserting in the front is O(n). + +template +void _pumpTraceToGaps(Gaps & gapsH, + Gaps & gapsV, + AlignTraceback const & trace) +{ + typedef Gaps TGapsH; + typedef typename Iterator::Type TGapsHIter; + + typedef Gaps TGapsV; + typedef typename Iterator::Type TGapsVIter; + + // TODO(holtgrew): I don't understand the following. Originally, this function used Align objects, but I did not understand it there either. + // TODO(rausch): Pump trace into align_ (note: this is relatively slow code here. it could be improved if specialized to the Align Specs). + clearGaps(gapsH); + clearClipping(gapsH); + clearGaps(gapsV); + clearClipping(gapsV); + + TSize i = length(trace.sizes); // Scan trace backwards. + TGapsHIter itH = begin(gapsH); + TGapsVIter itV = begin(gapsV); + while (i > 0) + { + --i; + TSize size = trace.sizes[i]; + switch ((int) trace.tvs[i]) + { + case 1: // Go horizontal. + insertGaps(itV, size); + break; + + case 2: // Go vertical. + insertGaps(itH, size); + break; + } + goFurther(itH, size); + goFurther(itV, size); + } +} + +// ---------------------------------------------------------------------------- +// Function source() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Document TSource via metafunctio. + +/*! + * @fn Gaps#source + * @brief Return underlying object. + * + * @signature TSource source(gaps); + * + * @param[in] gaps The Gaps object to return the underling sequence for. + * + * @return TSource Reference to the source of the Gaps. + */ + +// ---------------------------------------------------------------------------- +// Function sourceSegment() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Rename/remove? + +// We need some forwards for function sourceSegment(). + +template +inline typename Position >::Type clippedBeginPosition(Gaps const & gaps); +template +inline typename Position >::Type clippedEndPosition(Gaps const & gaps); +template +inline typename Position::Type +toSourcePosition(Gaps const & gaps, TPosition clippedViewPos); + +template +inline typename Infix::Type +sourceSegment(Gaps const & gaps) +{ + return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(gaps, clippedEndPosition(gaps))); +} + +template +inline typename Infix::Type +sourceSegment(Gaps & gaps) +{ + return infix(source(gaps), toSourcePosition(gaps, clippedBeginPosition(gaps)), toSourcePosition(gaps, clippedEndPosition(gaps))); +} + +// ---------------------------------------------------------------------------- +// Function assignSource() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#assignSource + * @brief Assign the source of a gaps object, copying data. + * + * @signature void assignSource(gaps, seq); + * + * @param[in,out] gaps The Gaps object to assign the source of. + * @param[in] seq The @link ContainerConcept sequence @endlink to assign to the underlying string. + */ + +// TOOD(holtgrew): Switch to Hosted Type? + +template +inline void +assignSource(Gaps & gaps, TValue const & value) +{ + assign(source(gaps), value); +} + +// ---------------------------------------------------------------------------- +// Function setSource() +// ---------------------------------------------------------------------------- + +// ---------------------------------------------------------------------------- +// Function copyGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#copyGaps + * @brief Copy gaps from one Gaps object to another (in the clipped view of both arguments). + * + * The user is responsible for ensuring that the gaps are over sequences of same length and appropriate clipping. + * + * @signature void copyGaps(dest, source); + * + * @param[in,out] dest The destination Gaps object (appropriate clipping, no gaps). + * @param[in] source The source Gaps object. + */ + +template +void copyGaps(Gaps & dest, Gaps const & source) +{ + typedef Gaps TLhs; + typedef typename Iterator::Type TLhsIter; + typedef Gaps const TRhs; + typedef typename Iterator::Type TRhsIter; + + TLhsIter lhsIt = begin(dest, Standard()); + //TLhsIter lhsItEnd = end(dest, Standard()); + TRhsIter rhsIt = begin(source, Standard()); + TRhsIter rhsItEnd = end(source, Standard()); + + for (unsigned num = 0; rhsIt != rhsItEnd; lhsIt += num, rhsIt += num) + { + if (isGap(rhsIt)) + { + num = countGaps(rhsIt); + insertGaps(lhsIt, num); + } + else + { + num = countCharacters(rhsIt); + } + + SEQAN_ASSERT_NOT((lhsIt == end(dest, Standard())) && num > 0); + } +} + +// ---------------------------------------------------------------------------- +// Function copyClipping() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#copyClipping + * @brief Copy clipping information from one Gaps object to another. + * + * @signature void copyClipping(dest, source); + * + * @param[in,out] dest The destination Gaps object. + * @param[in] source The source Gaps object. + */ + +template +void copyClipping(Gaps & dest, Gaps const & source) +{ + setClippedBeginPosition(dest, clippedBeginPosition(source)); + setClippedEndPosition(dest, clippedEndPosition(source)); +} + +// ---------------------------------------------------------------------------- +// Function clipSemiGlobal() +// ---------------------------------------------------------------------------- + +/*! + * @fn Gaps#clipSemiGlobal + * @brief Clip the Gaps objects to reflect a semi-global alignment. + * + * Leading and trailing gaps are clipped in the local Gaps object. The global Gaps object is updated accordingly. + * + * @signature void clipSemiGlobal(global, local); + * + * @param[in,out] global The global Gaps object. + * @param[in,out] local The local Gaps object. + */ + +template +inline void clipSemiGlobal(TGlobalGaps & global, TLocalGaps & local) +{ + typedef typename Size::Type TGapsSize; + + TGapsSize leadingGaps = countLeadingGaps(local); + TGapsSize trailingGaps = countTrailingGaps(local); + TGapsSize globalLenght = length(global); + TGapsSize localLength = length(local); + + setClippedBeginPosition(global, leadingGaps); + setClippedBeginPosition(local, leadingGaps); + setClippedEndPosition(global, globalLenght - trailingGaps); + setClippedEndPosition(local, localLength - trailingGaps); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +inline void clearGaps(Gaps & gaps); +template +inline void clearClipping(Gaps & gaps); + +template +inline void clear(Gaps & gaps) +{ + clearGaps(gaps); + clearClipping(gaps); +} + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool operator==(Gaps const & lhs, + Gaps const & rhs) +{ + typename Comparator >::Type lex(lhs, rhs); + return isEqual(lex); +} + +template +inline bool operator==(Gaps const & lhs, + TRightHandSide const & rhs) +{ + typename Comparator >::Type lex(lhs, rhs); + return isEqual(lex); +} + +// ---------------------------------------------------------------------------- +// Function operator!=() +// ---------------------------------------------------------------------------- + +template +inline bool operator!=(Gaps const & lhs, + Gaps const & rhs) +{ + return !(lhs == rhs); +} + + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_BASE_H_ diff --git a/seqan/align/gaps_iterator_anchor.h b/seqan/align/gaps_iterator_anchor.h new file mode 100644 index 0000000..775af98 --- /dev/null +++ b/seqan/align/gaps_iterator_anchor.h @@ -0,0 +1,781 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// Iterator for AnchorGaps objects. + +template //Gaps > +class Iter > > +{ +public: + typedef TGaps_ TGaps; + typedef typename Source::Type TSource; + typedef TGapAnchors_ TGapAnchors; + + // TODO(holtgrew): Why is the following commented out? +// typedef typename Value::Type TGapAnchor; + typedef typename Size::Type>::Type TGapAnchorSize_; + typedef GapAnchor::Type> TGapAnchor; + typedef typename MakeSigned::Type>::Type TGapPos; + typedef typename Iterator::Type TAnchorIter; + + TGaps * data_container; //the gaps object + TGapPos seqLength; + mutable TGapAnchor current; + mutable TGapAnchor prevAnchor; + mutable TGapAnchor nextAnchor; + mutable TGapAnchor viewBegin; + mutable TGapAnchor viewEnd; + mutable int anchorIdx; + +public: + Iter() + { + data_container = NULL; + seqLength = 0; + } +/* Iter(Iter const & other_): + data_container(other_.data_container), + seqLength(other_.seqLength), + current(other_.current), + prevAnchor(other_.prevAnchor), + nextAnchor(other_.nextAnchor), + anchorIdx(other_.anchorIdx) + { + } +*/ Iter(TGaps & container_): + data_container(&container_) + { + _assignSourceLength(seqLength, container_); + _goToGapAnchorIterator(*this, data_container->data_viewCutBegin + data_container->data_cutBegin); + viewBegin = current; + viewEnd.gapPos = _unclippedLength(*data_container) + data_container->data_cutBegin - data_container->data_viewCutEnd; + viewEnd.seqPos = positionGapToSeq(*data_container, viewEnd.gapPos); + } + Iter(TGaps & container_, TGapPos clippedViewPosition): + data_container(&container_) + { + _assignSourceLength(seqLength, container_); + _goToGapAnchorIterator(*this, clippedViewPosition + data_container->data_viewCutBegin + data_container->data_cutBegin); + viewBegin.gapPos = data_container->data_viewCutBegin + data_container->data_cutBegin; + viewEnd.gapPos = _unclippedLength(*data_container) + data_container->data_cutBegin - data_container->data_viewCutEnd; + viewBegin.seqPos = positionGapToSeq(*data_container, viewBegin.gapPos); + viewEnd.seqPos = positionGapToSeq(*data_container, viewEnd.gapPos); + } + ~Iter() + { + } + + Iter const & operator = (Iter const & other_) + { + data_container = other_.data_container; + seqLength = other_.seqLength; + current = other_.current; + prevAnchor = other_.prevAnchor; + nextAnchor = other_.nextAnchor; + anchorIdx = other_.anchorIdx; + viewBegin = other_.viewBegin; + viewEnd = other_.viewEnd; + return *this; + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function container() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Can go if data_container were _container, dupe in _base.h + +template +inline TGaps & +container(Iter > > & me) +{ + return *me.data_container; +} + +template +inline TGaps & +container(Iter > > const & me) +{ + return *me.data_container; +} + +// ---------------------------------------------------------------------------- +// Function source() +// ---------------------------------------------------------------------------- + +template +inline typename Source > > const>::Type +source(Iter > > & me) +{ + return begin(source(*me.data_container), Rooted()) + me.current.seqPos; +} + +template +inline typename Source > > >::Type +source(Iter > > const & me) +{ + return begin(source(*me.data_container), Rooted()) + me.current.seqPos; +} + +// ---------------------------------------------------------------------------- +// Function getValue() +// ---------------------------------------------------------------------------- + +template +inline typename GetValue< Iter > > >::Type +getValue(Iter > > & me) +{ + typedef typename Value > >::Type TValue; + if (isGap(me)) return gapValue(); + else if (isUnknown(me)) return unknownValue(); + else return getValue(source(me)); +} + +template +inline typename GetValue< Iter > > const>::Type +getValue(Iter > > const & me) +{ + typedef typename Value > const>::Type TValue; + if (isGap(me)) return gapValue(); + else if (isUnknown(me)) return unknownValue(); + else return getValue(source(me)); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +template +inline typename Reference< Iter > > >::Type +value(Iter > > & it) +{ + typedef typename Reference > > >::Type TProxy; + return TProxy(it); +} + +template +inline typename Reference< Iter > > const>::Type +value(Iter > > const & it) +{ + typedef typename Reference > > const>::Type TProxy; + return TProxy(it); +} + +// ---------------------------------------------------------------------------- +// Function isGap() +// ---------------------------------------------------------------------------- + +template +inline bool +isGap(Iter > > const & me) +{ + return me.current.seqPos == me.nextAnchor.seqPos; +} + +// ---------------------------------------------------------------------------- +// Function isUnknown() +// ---------------------------------------------------------------------------- + +template +inline bool +isUnknown(Iter > > const & me) +{ + int len; + _assignSourceLength(len, *me.data_container); + return me.current.seqPos < 0 || me.current.seqPos >= len; +} + +// ---------------------------------------------------------------------------- +// Function isClipped() +// ---------------------------------------------------------------------------- + +template +inline bool +isClipped(Iter > > const & me) +{ + return me.current.gapPos == me.nextAnchor.gapPos; +} + +// ---------------------------------------------------------------------------- +// Function countGaps() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +countGaps(Iter > > const & me, LeftOfViewPos const & /*dir*/) +{ + typedef Iter > > TIter; + typedef typename TIter::TGapAnchor TGapAnchor; + + if (isGap(me)) + { + if (me.prevAnchor.gapPos < me.viewBegin.gapPos) + return me.current.gapPos - me.viewBegin.gapPos; + return me.current.gapPos - me.prevAnchor.gapPos - (me.current.seqPos - me.prevAnchor.seqPos); + } + // In case we are at the beginning of a new anchor we need to get back the previous one. + if (me.prevAnchor.gapPos == me.current.gapPos) + { + TGapAnchor tmp; + _getAnchor(tmp, *me.data_container, me.anchorIdx - 1); + if (tmp.gapPos < me.viewBegin.gapPos) + tmp.gapPos = me.viewBegin.gapPos; + return me.current.gapPos - tmp.gapPos - (me.current.seqPos - tmp.seqPos); + } + return 0; +} + +template +inline typename Size::Type +countGaps(Iter > > const & me, RightOfViewPos const & /*dir*/) +{ + if (!isGap(me)) + return 0; + if (me.nextAnchor.gapPos > me.viewEnd.gapPos) + return me.viewEnd.gapPos - me.current.gapPos; + return me.nextAnchor.gapPos - me.current.gapPos; +} + +// ---------------------------------------------------------------------------- +// Function countCharacters() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +countCharacters(Iter > > const & me, LeftOfViewPos const & /*dir*/) +{ + if (!isGap(me)) + return me.current.seqPos - me.prevAnchor.seqPos; + // In case we are at the beginning of a new anchor we need to get back the previous one. + if (me.current.seqPos - me.prevAnchor.seqPos == me.current.gapPos - me.prevAnchor.gapPos) + return me.current.seqPos - me.prevAnchor.seqPos; + return 0; +} + +template +inline typename Size::Type +countCharacters(Iter > > const & me, RightOfViewPos const & /*dir*/) +{ + if (isGap(me)) + return 0; + if (me.nextAnchor.seqPos > me.viewEnd.seqPos) + return me.viewEnd.seqPos - me.current.seqPos; + return me.nextAnchor.seqPos - me.current.seqPos; +} + +// ---------------------------------------------------------------------------- +// Function blockLength() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +blockLength(Iter > > & me) +{ + if (isGap(me)) + return countGaps(me); + else + return countCharacters(me); +} + +// ---------------------------------------------------------------------------- +// Function atBegin() +// ---------------------------------------------------------------------------- + +template +inline bool +atBegin(Iter > > & me) +{ +// return me.current.seqPos == 0 && me.current.gapPos == 0; + return me.current <= me.viewBegin; +} + +template +inline bool +atBegin(Iter > > const & me) +{ +// return me.current.seqPos == 0 && me.current.gapPos == 0; + return me.current <= me.viewBegin; +} + +// ---------------------------------------------------------------------------- +// Function atEnd() +// ---------------------------------------------------------------------------- + +template +inline bool +atEnd(Iter > > & me) +{ +// return me.current == me.nextAnchor; + return me.current >= me.viewEnd; +} + +template +inline bool +atEnd(Iter > > const & me) +{ +// return me.current == me.nextAnchor; + return me.current >= me.viewEnd; +} + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool +operator == ( + Iter > > const & left, + Iter > > const & right) +{ + return left.current == right.current; +} + +// ---------------------------------------------------------------------------- +// Function operator!=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator != ( + Iter > > const & left, + Iter > > const & right) +{ + return left.current != right.current; +} + +// ---------------------------------------------------------------------------- +// Function operator<() +// ---------------------------------------------------------------------------- + +template +inline bool +operator < ( + Iter > > const & left, + Iter > > const & right) +{ + return left.current < right.current; +} + +// ---------------------------------------------------------------------------- +// Function operator<=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator<=( + Iter > > const & left, + Iter > > const & right) +{ + return !(left.current > right.current); +} + +// ---------------------------------------------------------------------------- +// Function operator>() +// ---------------------------------------------------------------------------- + +template +inline bool +operator > ( + Iter > > const & left, + Iter > > const & right) +{ + return left.current > right.current; +} + +// ---------------------------------------------------------------------------- +// Function operator>=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator>=(Iter > > const & lhs, + Iter > > const & rhs) +{ + return !(lhs < rhs); +} + +// ---------------------------------------------------------------------------- +// Function insertGaps() +// ---------------------------------------------------------------------------- + +template +inline void +insertGaps(Iter > > const & me, + TCount size) +{ + TGapAnchors & anchors = _dataAnchors(*me.data_container); + typedef typename Iterator::Type TIter; + + if (size <= 0) return; + + // insert a new anchor + if (!isGap(me)) + { + if (me.prevAnchor.gapPos == me.current.gapPos) + { + me.nextAnchor = me.prevAnchor; + _getAnchor(me.prevAnchor, *me.data_container, --me.anchorIdx); + } + else + { + me.nextAnchor = me.current; + insertValue(anchors, me.anchorIdx, me.nextAnchor, Generous()); + } + } + else + { + if (me.anchorIdx >= (int)length(anchors)) + { + // add gap after the sequence and in (or at the right boundary of) the view + if (me.current.gapPos <= me.viewEnd.gapPos) + { + container(me).data_cutEnd -= size; + me.viewEnd.gapPos += size; + } + return; + } + if (empty(anchors)) + appendValue(anchors, me.nextAnchor, Generous()); + } + if (me.anchorIdx < (int)length(anchors)) + { + if (me.anchorIdx >= 0) + { + me.nextAnchor.gapPos += size; + TIter it = begin(anchors, Standard()); + TIter itEnd = end(anchors, Standard()); + if (me.anchorIdx >= 0) + it += me.anchorIdx; + for (; it != itEnd; ++it) + (*it).gapPos += size; + } + else + // add gap before the sequence and in (or at the left boundary of) the view + if (me.current.gapPos >= me.viewBegin.gapPos) + { + container(me).data_cutBegin -= size; + me.viewBegin.gapPos -= size; + me.current.gapPos -= size; + return; + } + } + if (me.current.gapPos <= me.viewEnd.gapPos) + me.viewEnd.gapPos += size; + +/* + Iter > > it2 = begin(*me.data_container) + me.current.gapPos; + if (me.current != it2.current || me.prevAnchor != it2.prevAnchor || me.nextAnchor != it2.nextAnchor || me.anchorIdx != it2.anchorIdx) + std::cout<<"*"; +*/ +} + +// ---------------------------------------------------------------------------- +// Function removeGaps() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +removeGaps(Iter > > const & it, + TCount size_) +{ + TGapAnchors & anchors = _dataAnchors(*it.data_container); + typedef typename Iterator::Type TAnchorsIter; + + typedef Iter > > TIter; + typedef typename TIter::TGapAnchor TGapAnchor; + // typedef typename Value::Type TGapAnchor; + typedef typename Position::Type TPos; + + if (size_ <= 0 || !isGap(it)) + return 0; + TPos size = size_; + + // static_cast(Nothing()); + // static_cast(Nothing()); + if (it.current.gapPos + size > it.nextAnchor.gapPos) + size = it.nextAnchor.gapPos - it.current.gapPos; + + if (it.prevAnchor.gapPos + it.current.seqPos == it.current.gapPos + it.prevAnchor.seqPos && + it.current.gapPos + size == it.nextAnchor.gapPos) + { + // remove the gap + if (it.anchorIdx < (int)length(anchors)) + erase(anchors, it.anchorIdx); + _getAnchor(it.nextAnchor, *it.data_container, it.anchorIdx); + } + + // shift anchors + if (it.anchorIdx < (int)length(anchors)) + { + if (it.anchorIdx >= 0) + { + it.nextAnchor.gapPos -= size; + TAnchorsIter itA = begin(anchors, Standard()); + TAnchorsIter itAEnd = end(anchors, Standard()); + if (it.anchorIdx >= 0) + itA += it.anchorIdx; + for (; itA != itAEnd; ++itA) + (*itA).gapPos -= size; + } + else + // remove gap before the sequence and in (or at the left boundary of) the view + if (it.current.gapPos >= it.viewBegin.gapPos) + { + // assure that we don't remove more gaps than available + if (size > it.nextAnchor.gapPos - it.current.gapPos) + size = it.nextAnchor.gapPos - it.current.gapPos; + container(it).data_cutBegin += size; + it.viewBegin.gapPos += size; + it.current.gapPos += size; + return size; + } + } + else + { + if (it.current.gapPos <= it.viewEnd.gapPos) + container(it).data_cutEnd += size; + } + if (it.current.gapPos <= it.viewEnd.gapPos) + it.viewEnd.gapPos -= size; + + return size; +/* + Iter > > it2 = begin(*me.data_container) + me.current.gapPos; + if (me.current != it2.current || me.prevAnchor != it2.prevAnchor || me.nextAnchor != it2.nextAnchor || me.anchorIdx != it2.anchorIdx) + std::cout<<"*"; +*/ +} + +// ---------------------------------------------------------------------------- +// Helper Function _goNextGapAnchorIterator() +// ---------------------------------------------------------------------------- + +template +inline void +_goNextGapAnchorIterator(T & me) +{ + if (me.current.gapPos < me.nextAnchor.gapPos) + { + ++me.current.gapPos; + if (me.current.seqPos < me.nextAnchor.seqPos) + ++me.current.seqPos; + } + while (me.current.gapPos == me.nextAnchor.gapPos) + { + me.current = me.prevAnchor = me.nextAnchor; + _getAnchor(me.nextAnchor, *me.data_container, ++me.anchorIdx + 1); + } +} + +// ---------------------------------------------------------------------------- +// Helper Function _goPreviousGapAnchorIterator() +// ---------------------------------------------------------------------------- + +template +inline void +_goPreviousGapAnchorIterator(T & me) +{ + while (me.current.gapPos == me.prevAnchor.gapPos) + { + me.current = me.nextAnchor = me.prevAnchor; + _getAnchor(me.prevAnchor, *me.data_container, --me.anchorIdx); + } + --me.current.gapPos; + if (me.nextAnchor.seqPos - me.prevAnchor.seqPos > me.current.gapPos - me.prevAnchor.gapPos) + me.current.seqPos = me.prevAnchor.seqPos + (me.current.gapPos - me.prevAnchor.gapPos); + else + me.current.seqPos = me.nextAnchor.seqPos; +} + +// ---------------------------------------------------------------------------- +// Helper Function _goToGapAnchorIterator() +// ---------------------------------------------------------------------------- + +template +inline void +_goToGapAnchorIterator(T & me, TPos pos) +{ + typedef typename T::TGapAnchors TGapAnchors; + typedef typename Value::Type TGapAnchor; + typedef typename Position::Type TAnchorPos; + typedef typename MakeSigned::Type TAnchorSPos; + + if (isNegative(pos)) + me.anchorIdx = -1; + else + { + TGapAnchors const & anchors = _dataAnchors(*me.data_container); + if (!empty(anchors)) + { + me.anchorIdx = upperBoundGapAnchor(anchors, pos, SortGapPos()) - begin(anchors, Standard()); + if (me.anchorIdx < (int)length(anchors)) + if (anchors[me.anchorIdx].gapPos == (TAnchorPos)pos && anchors[me.anchorIdx].seqPos != (TAnchorPos)me.seqLength) + ++me.anchorIdx; + } + else + { + me.anchorIdx = ((TAnchorSPos)pos < me.seqLength)? 0: 1; + } + } + _getAnchor(me.prevAnchor, *me.data_container, me.anchorIdx); + _getAnchor(me.nextAnchor, *me.data_container, me.anchorIdx + 1); + + me.current.gapPos = pos; + if (me.nextAnchor.seqPos - me.prevAnchor.seqPos > (int)pos - me.prevAnchor.gapPos) + me.current.seqPos = me.prevAnchor.seqPos + ((int)pos - me.prevAnchor.gapPos); + else + me.current.seqPos = me.nextAnchor.seqPos; +} + +// ---------------------------------------------------------------------------- +// Function goNext() +// ---------------------------------------------------------------------------- + +template +inline void +goNext(Iter > > & me) +{ + _goNextGapAnchorIterator(me); +} + +// ---------------------------------------------------------------------------- +// Function goPrevious() +// ---------------------------------------------------------------------------- + +template +inline void +goPrevious(Iter > > & me) +{ + _goPreviousGapAnchorIterator(me); +} + +// ---------------------------------------------------------------------------- +// Function goFurther() +// ---------------------------------------------------------------------------- + +template +inline void +goFurther(Iter > > & me, TSize steps) +{ + _goToGapAnchorIterator(me, me.current.gapPos + steps); +} + +// ---------------------------------------------------------------------------- +// Function position() +// ---------------------------------------------------------------------------- + +// Returns clipped view position of gaps iterator. + +template +inline typename Position > > >::Type +position(Iter > > const & it) +{ + return it.current.gapPos - it.viewBegin.gapPos; +} + +// ---------------------------------------------------------------------------- +// Function difference() +// ---------------------------------------------------------------------------- + +template +inline typename Difference > > >::Type +difference(Iter > > const & lhs, + Iter > > const & rhs) +{ + return lhs.current.gapPos - rhs.current.gapPos; +} + +// ---------------------------------------------------------------------------- +// Function operator-() [difference] +// ---------------------------------------------------------------------------- + +template +inline typename Difference > > >::Type +operator-(Iter > > const & lhs, + Iter > > const & rhs) +{ + return difference(lhs, rhs); +} + +// ---------------------------------------------------------------------------- +// Function operator-() [copy movement] +// ---------------------------------------------------------------------------- + +template +inline Iter > > +operator-(Iter > > const & lhs, TDifference d) +{ + Iter > > result = lhs; + result -= d; + return result; +} + +// ---------------------------------------------------------------------------- +// Function operator+() [copy movement] +// ---------------------------------------------------------------------------- + +template +inline Iter > > +operator+(Iter > > const & lhs, TDifference d) +{ + Iter > > result = lhs; + result += d; + return result; +} + + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ANCHOR_H_ diff --git a/seqan/align/gaps_iterator_array.h b/seqan/align/gaps_iterator_array.h new file mode 100644 index 0000000..b32de15 --- /dev/null +++ b/seqan/align/gaps_iterator_array.h @@ -0,0 +1,783 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +template +class Iter > +{ +public: + // ----------------------------------------------------------------------- + // Internal Typedefs + // ----------------------------------------------------------------------- + + typedef typename TGaps::TArrayPos_ TArrayPos_; + typedef typename TGaps::TArray_ TArray_; + typedef typename Value::Type TArrayValue_; + typedef typename Position::Type TGapsPos_; + typedef typename Source::Type TSource_; + typedef typename Position::Type TSourcePos_; + + // ----------------------------------------------------------------------- + // Member Variables + // ----------------------------------------------------------------------- + + // The following index and position members must be mutable since the + // insertion and deletion of gaps does not modify the iterator conceptually. + + // Pointer to the iterated container / gaps object. + TGaps * _container; + // Index in the bucket array of the gaps object. + mutable TArrayPos_ _bucketIndex; + // Offset within the current bucket. + mutable TArrayValue_ _bucketOffset; + // Source position of the iterator. + mutable TSourcePos_ _sourcePosition; + // View position of the iterator. + mutable TGapsPos_ _unclippedViewPosition; + + // ----------------------------------------------------------------------- + // Constructors + // ----------------------------------------------------------------------- + + // Default constructor. + Iter() : _container(0), _bucketIndex(0), _bucketOffset(0), _sourcePosition(0), _unclippedViewPosition(0) + {} + + // Copy constructor, required since we specify the one with complemented const below. + Iter(Iter const & other) : + _container(other._container), _bucketIndex(other._bucketIndex), _bucketOffset(other._bucketOffset), + _sourcePosition(other._sourcePosition), _unclippedViewPosition(other._unclippedViewPosition) + {} + + // Copy construtor for iterator -> const iterator conversion. + // TODO(holtgrew): Think of something smarter, to restrict source types? + template + Iter(TOtherIter const & other) : + _container(other._container), _bucketIndex(other._bucketIndex), _bucketOffset(other._bucketOffset), + _sourcePosition(other._sourcePosition), _unclippedViewPosition(other._unclippedViewPosition) + {} + + // Create at begin of gaps. + Iter(TGaps & container_, Begin_ const &) : + _container(&container_), _bucketIndex(0), _bucketOffset(0), _sourcePosition(0), + _unclippedViewPosition(0) + { + if (_container->_array[0] == 0u) + _bucketIndex = 1; + // Go to beginning of clipping. + goFurther(*this, container_._clippingBeginPos); + } + + // Create at end of gaps. + Iter(TGaps & container_, End_ const &) : + _container(&container_), _bucketIndex(0), _bucketOffset(0), _sourcePosition(0), + _unclippedViewPosition(0) + { + if (_container->_array[0] == 0u) + _bucketIndex = 1; + // Go to end of clipping position. + goFurther(*this, container_._clippingEndPos); + } + + // Create with position. + // TODO(holtgrew): Chain constructor call to Begin_() here in C++11. + template + Iter(TGaps & container_, TPos pos, Position_ const &) : + _container(&container_), _bucketIndex(0), _bucketOffset(0), _sourcePosition(0), + _unclippedViewPosition(0) + { + if (_container->_array[0] == 0u) + _bucketIndex = 1; + // pos is an unclipped view position, make it clipped. + pos += container_._clippingBeginPos; + // Initialized for begin position. Now, advance. + goFurther(*this, pos); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function isGap() +// ---------------------------------------------------------------------------- + +template +inline bool +isGap(Iter > const & it) +{ + return !(it._bucketIndex % 2); +} + +// ---------------------------------------------------------------------------- +// Function value() +// ---------------------------------------------------------------------------- + +template +inline typename Reference > >::Type +value(Iter > & it) +{ + typedef typename Reference > >::Type TProxy; + return TProxy(it); +} + +template +inline typename Reference > const>::Type +value(Iter > const & it) +{ + typedef typename Reference > const>::Type TProxy; + return TProxy(it); +} + +// ---------------------------------------------------------------------------- +// Function getValue() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Ideally, we would only have one here. + +template +inline typename GetValue > >::Type +getValue(Iter > & it) +{ + typedef typename Value::Type TAlphabet; + if (isGap(it)) + return gapValue(); + else + return value(source(container(it)), it._sourcePosition); +} + +template +inline typename GetValue > const>::Type +getValue(Iter > const & it) +{ + typedef typename Value::Type TAlphabet; + if (isGap(it)) + return gapValue(); + else + return value(source(container(it)), it._sourcePosition); +} + +// ---------------------------------------------------------------------------- +// Function position() +// ---------------------------------------------------------------------------- + +// Returns clipped view position of gaps iterator. + +template +inline typename Position > >::Type +position(Iter > const & it) +{ + if (it._container == 0) + return 0; + + typedef Iter > TIter; + typedef typename Position::Type TPosition; + typedef typename TIter::TArrayPos_ TArrayPos; + + TPosition unclippedViewPosition = 0; + for (TArrayPos i = 0; i < it._bucketIndex; ++i) + unclippedViewPosition += it._container->_array[i]; + unclippedViewPosition += it._bucketOffset; + + // TODO(holtgrew): Simply return it._unclippedViewPosition? + SEQAN_ASSERT_EQ(it._unclippedViewPosition, unclippedViewPosition); + + return unclippedViewPosition - clippedBeginPosition(*it._container); +} + +// ---------------------------------------------------------------------------- +// Function countGaps() +// ---------------------------------------------------------------------------- + +// Count left. +template +inline typename Size::Type +countGaps(Iter > const & it, LeftOfViewPos const & /*tag*/) +{ + typedef typename Size::Type TSize; + TSize result = 0; + + // Get number of gaps left of current position ignoring any clipping. + if (isGap(it) && it._bucketOffset) + result = it._bucketOffset; + else if (!isGap(it) && !it._bucketOffset && it._bucketIndex) + result = it._container->_array[it._bucketIndex - 1]; + + // Limit to the clipping begin position. + if (it._unclippedViewPosition - result < (TSize)it._container->_clippingBeginPos) + result = it._unclippedViewPosition - it._container->_clippingBeginPos; + + return result; +} + +// Count right. +template +inline typename Size::Type +countGaps(Iter > const & it, RightOfViewPos const & /*tag*/) +{ + if (!isGap(it) || atEnd(it)) + return 0; // Not on a gap or at end, no gap here. + + typedef typename Size::Type TSize; + TSize result = it._container->_array[it._bucketIndex] - it._bucketOffset; + // Check whether gaps reach behind the clipping and trim gaps for counting. + if ((TSize)(it._unclippedViewPosition + result) > (TSize)it._container->_clippingEndPos) + result = it._container->_clippingEndPos - it._unclippedViewPosition; + return result; +} + +// ---------------------------------------------------------------------------- +// Function countCharacters() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +countCharacters(Iter > const & it, LeftOfViewPos const & /*dir*/) +{ + typedef typename Size::Type TSize; + TSize result = 0; + + // Get number of characters left of current position ignoring any clipping. + if (!isGap(it) && it._bucketOffset) + result = it._bucketOffset; + else if (isGap(it) && !it._bucketOffset && it._bucketIndex) + result = it._container->_array[it._bucketIndex - 1]; + + // Limit to the clipping begin position. + if (it._unclippedViewPosition - result < (TSize)it._container->_clippingBeginPos) + result = it._unclippedViewPosition - it._container->_clippingBeginPos; + + return result; +} + +template +inline typename Size::Type +countCharacters(Iter > const & it, RightOfViewPos const & /*dir*/) +{ + if (isGap(it) || atEnd(it)) + return 0; // On a gap or at end, no characters here. + + typedef typename Size::Type TSize; + TSize result = it._container->_array[it._bucketIndex] - it._bucketOffset; + // Check whether gaps reach behind the clipping and trim gaps for counting. + if ((TSize)(it._unclippedViewPosition + result) > (TSize)it._container->_clippingEndPos) + result = it._container->_clippingEndPos - it._unclippedViewPosition; + return result; +} + +// ---------------------------------------------------------------------------- +// Function goPrevious() +// ---------------------------------------------------------------------------- + +template +inline bool +goPrevious(Iter > & it) +{ + typedef typename Position::Type TGapsPos; + + if (atBegin(it)) // Handle case of being at the beginning of the gaps. + return false; + + if (it._bucketOffset > TGapsPos(0)) + { + // Not at the beginning of a bucket. + it._bucketOffset -= 1; + } + else + { + // At the beginning of a bucket. + it._bucketIndex -= 1; + SEQAN_ASSERT_GT(it._container->_array[it._bucketIndex], 0u); + it._bucketOffset = it._container->_array[it._bucketIndex] - 1; + } + + // Adjust source position. + if (!isGap(it)) + it._sourcePosition -= 1; + // Adjust clipped view position. + it._unclippedViewPosition -= 1; + + return true; +} + +// ---------------------------------------------------------------------------- +// Function goNext() +// ---------------------------------------------------------------------------- + +template +inline bool +goNext(Iter > & it) +{ + if (atEnd(it)) // Handle case of being at the end of the gaps. + return false; + + // Adjust source position. + if (!isGap(it)) + it._sourcePosition += 1; + // Adjust clipped view position. + it._unclippedViewPosition += 1; + + if (it._bucketOffset + 1 != it._container->_array[it._bucketIndex]) + { + // Not on last entry of a bucket. + it._bucketOffset += 1; + } + else + { + // On last entry of a bucket. If we are not in the last bucket then go + // to next bucket. Otherwise, go over the bucket, marks iterator-at-end. + if (it._bucketIndex + 1 != length(it._container->_array)) + { + // Go to next. + it._bucketIndex += 1; + if (it._bucketIndex > length(it._container->_array)) + SEQAN_ASSERT_GT(it._container->_array[it._bucketIndex], 0u); + it._bucketOffset = 0; + } + else + { + // Go to end of bucket. + it._bucketOffset += 1; + SEQAN_ASSERT_EQ(it._bucketIndex + 1, length(it._container->_array)); + SEQAN_ASSERT_EQ(it._bucketOffset, back(it._container->_array)); + } + } + + return true; +} + + +// ---------------------------------------------------------------------------- +// Function goNext() +// ---------------------------------------------------------------------------- + +template +inline void +goFurther(Iter > & it, + TDifference delta) +{ + // TODO(holtgrew): Handle going backwards more efficiently. + if (delta == TDifference(0)) + return; + if (isNegative(delta)) + { + typedef typename MakeSigned::Type TSignedDifference; + for (; -static_cast(delta); ++delta) + goPrevious(it); + return; + } + + // Do nothing if we want are already at the end. + if (atEnd(it)) + return; + + // Case: Going forward. + + // Get shortcut to new unclipped view position that we want to go to and + // limit this to the clipping end pos of the gaps object. + unsigned posEnd = it._unclippedViewPosition + delta; + if (posEnd > static_cast(it._container->_clippingEndPos)) + posEnd = it._container->_clippingEndPos; + + // The variable counter is the number of view positions to go forward. + for (unsigned counter = posEnd - it._unclippedViewPosition; counter > 0u;) + { + // Number of elements in bucket and number of remaining (behind offset in bucket). + unsigned count = it._container->_array[it._bucketIndex]; + unsigned shift = count - it._bucketOffset; + + if (shift < counter) + { + it._unclippedViewPosition += shift; + if (it._bucketIndex % 2) + it._sourcePosition += shift; + it._bucketOffset = 0; + it._bucketIndex += 1; + counter -= shift; + } + else if (shift == counter) + { + it._unclippedViewPosition += shift; + if (it._bucketIndex % 2) + it._sourcePosition += shift; + + // On last entry of a bucket. If we are not in the last bucket then go to next bucket. + // Otherwise, go over the bucket, marks iterator-at-end. + if (it._bucketIndex + 1 != length(it._container->_array)) + { + // Go to next. + it._bucketIndex += 1; + if (it._bucketIndex > length(it._container->_array)) + SEQAN_ASSERT_GT(it._container->_array[it._bucketIndex], 0u); + it._bucketOffset = 0; + } + else + { + // Go to end of bucket. + it._bucketOffset += shift; + SEQAN_ASSERT_EQ(it._bucketIndex + 1, length(it._container->_array)); + SEQAN_ASSERT_EQ(it._bucketOffset, back(it._container->_array)); + } + counter = 0; + } + else // shift > counter + { + it._unclippedViewPosition += counter; + if (it._bucketIndex % 2) + it._sourcePosition += counter; + it._bucketOffset += counter; + counter = 0; + } + } +} + +// ---------------------------------------------------------------------------- +// Function atBegin() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Non-const version is superfluous :( +template +inline bool +atBegin(Iter > const & it) +{ + return it._unclippedViewPosition == it._container->_clippingBeginPos; +} + +template +inline bool +atBegin(Iter > & it) +{ + return it._unclippedViewPosition == it._container->_clippingBeginPos; +} + +// ---------------------------------------------------------------------------- +// Function atEnd() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Non-const version is superfluous :( +template +inline bool +atEnd(Iter > const & it) +{ + return it._unclippedViewPosition == it._container->_clippingEndPos; +} + +template +inline bool +atEnd(Iter > & it) +{ + return it._unclippedViewPosition == it._container->_clippingEndPos; +} + +// ---------------------------------------------------------------------------- +// Function insertGaps() +// ---------------------------------------------------------------------------- + +template +inline void +insertGaps(Iter > const & it, + TCount count) +{ + if (count == TCount(0)) + return; // Do nothing! + + typedef typename TGaps::TArray_ TArray; + typedef typename Position::Type TArrayPos; + + // Get shortcut to gaps. + TGaps & gaps = *it._container; + TArrayPos idx = it._bucketIndex; + + // Handle case of being at the start of a character bucket. + if (idx % 2 && it._bucketOffset == 0) + { + idx -= 1; + it._bucketIndex -= 1; + it._bucketOffset = gaps._array[idx]; + } + + // Insert gaps, simple and fast if we are in a gaps bucket, a bit harder + // otherwise. + if (idx % 2) // character bucket + { + if (gaps._array[idx] > it._bucketOffset) // In the middle of the bucket. + { + TArray arr; + resize(arr, 2, 0); + arr[0] = count; + arr[1] = gaps._array[idx] - it._bucketOffset; + gaps._array[idx] = it._bucketOffset; + insert(gaps._array, idx + 1, arr); + + // Update iterator. + it._bucketIndex += 1; + it._bucketOffset = 0; + } + else // At the end of the bucket. + { + if (idx + 1 < length(gaps._array)) // Not at end of array. + { + gaps._array[idx + 1] += count; + } + else // At end of array. + { + resize(gaps._array, length(gaps._array) + 2, 0); + gaps._array[idx + 1] = count; + gaps._array[idx + 2] = 0; + } + } + } + else // gap bucket + { + gaps._array[idx] += count; + } + + // Adjust clipping information. + gaps._clippingEndPos += count; +} + +// ---------------------------------------------------------------------------- +// Function removeGaps() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +removeGaps(Iter > const & it, TCount count) +{ + typedef typename TGaps::TArray_ TArray; + typedef typename Position::Type TArrayPos; + typedef typename Value::Type TArrayValue; + typedef typename Source::Type TSource; + typedef typename Position::Type TSeqPos; + + if (count == TCount(0)) + return 0; // Do nothing! + + // Get shortcuts. + TGaps & gaps = *it._container; + TArrayPos idx = it._bucketIndex; + TSeqPos offset = it._bucketOffset; + + // If we are inside a non-gap bucket then we cannot remove any gaps. + if (idx % 2) + return 0; + + // Otherwise, we can remove gaps right of the current position but not + // more than there are. + TSeqPos toRemove = count; + if (toRemove > gaps._array[idx] - offset) + toRemove = gaps._array[idx] - offset; + gaps._array[idx] -= toRemove; + // TODO(holtgrew): We have to decrement idx and adjust offset in case of merging! + // In some cases, we remove the whole gap and merge the character buckets. + if (gaps._array[idx] == TArrayValue(0)) + { + // No merging for leading and trailing gap. + if (idx == TArrayPos(0) || idx == TArrayPos(length(gaps._array) - 1)) + { + gaps._array[idx - 1] += gaps._array[idx + 1]; + erase(gaps._array, idx, idx + 2); + } + } + + // Also update the right clipping position. + gaps._clippingEndPos -= toRemove; + + // Finally, return number of removed gaps. + return toRemove; +} + +// ---------------------------------------------------------------------------- +// Function operator<() +// ---------------------------------------------------------------------------- + +template +inline bool +operator<(Iter > const & lhs, + Iter > const & rhs) +{ + return lhs._bucketIndex < rhs._bucketIndex || + (lhs._bucketIndex == rhs._bucketIndex && lhs._bucketOffset < rhs._bucketOffset); +} + +// ---------------------------------------------------------------------------- +// Function operator>() +// ---------------------------------------------------------------------------- + +template +inline bool +operator>(Iter > const & lhs, + Iter > const & rhs) +{ + return lhs._bucketIndex > rhs._bucketIndex || + (lhs._bucketIndex == rhs._bucketIndex && lhs._bucketOffset > rhs._bucketOffset); +} + +// ---------------------------------------------------------------------------- +// Function operator<=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator<=(Iter > const & lhs, + Iter > const & rhs) +{ + return !(lhs > rhs); +} + +// ---------------------------------------------------------------------------- +// Function operator>=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator>=(Iter > const & lhs, + Iter > const & rhs) +{ + return !(lhs < rhs); +} + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool +operator==(Iter > const & _lhs, + Iter > const & _rhs) +{ + return _lhs._container == _rhs._container && + _lhs._bucketIndex == _rhs._bucketIndex && + _lhs._bucketOffset == _rhs._bucketOffset; +} + +// ---------------------------------------------------------------------------- +// Function operator!=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator!=(Iter > const & _lhs, + Iter > const & _rhs) +{ + return _lhs._container != _rhs._container || + _lhs._bucketIndex != _rhs._bucketIndex || + _lhs._bucketOffset != _rhs._bucketOffset; +} + +// ---------------------------------------------------------------------------- +// Function difference() +// ---------------------------------------------------------------------------- + +template +inline typename Difference > >::Type +difference(Iter > const & lhs, + Iter > const & rhs) +{ + // TODO(holtgrew): Implementation could be more efficient. + // We only need to solve the case lhs < rhs. + if (lhs > rhs) + return -difference(rhs, lhs); + if (lhs == rhs) + return 0; + SEQAN_ASSERT(lhs < rhs); // Makes code below simpler. + + typedef Iter > TIter; + typedef typename Difference::Type TDifference; + TDifference d = 0; + for (TIter it = lhs; it != rhs; ++it) + ++d; + + return -d; +} + +// ---------------------------------------------------------------------------- +// Function operator-() [difference] +// ---------------------------------------------------------------------------- + +template +inline typename Difference > >::Type +operator-(Iter > const & lhs, + Iter > const & rhs) +{ + return difference(lhs, rhs); +} + +// ---------------------------------------------------------------------------- +// Function operator-() [copy movement] +// ---------------------------------------------------------------------------- + +template +inline Iter > +operator-(Iter > const & lhs, TDifference d) +{ + Iter > result = lhs; + result -= d; + return result; +} + +// ---------------------------------------------------------------------------- +// Function operator+() [copy movement] +// ---------------------------------------------------------------------------- + +template +inline Iter > +operator+(Iter > const & lhs, TDifference d) +{ + Iter > result = lhs; + result += d; + return result; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_ARRAY_H_ diff --git a/seqan/align/gaps_iterator_base.h b/seqan/align/gaps_iterator_base.h new file mode 100644 index 0000000..097943d --- /dev/null +++ b/seqan/align/gaps_iterator_base.h @@ -0,0 +1,525 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== + +// TODO(holtgrew): Switch to Host interface. + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// Internally used tag for creating iterators at the begin of containers. +struct Begin__; +typedef Tag Begin_; + +// Internally used tag for creating iterators at the end of containers. +struct End__; +typedef Tag End_; + +// Internally used tag for creating iterators inside of containers. +struct Position__; +typedef Tag Position_; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class GapsIterator + * @implements RandomAccessIteratorConcept + * + * @brief Iterator class for @link Gaps @endlink. + * + * @signature template + * class Iter >; + * + * @tparam TGaps The @link Gaps @endlink object for the iterator. + * @tparam TSpec The specializing tag. + */ + +template +struct GapsIterator; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Position +// ---------------------------------------------------------------------------- + +template +struct Position > > : + Position +{}; + +template +struct Position > const> : + Position > > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Difference +// ---------------------------------------------------------------------------- + +template +struct Difference > > : + Difference +{}; + +template +struct Difference > const> : + Difference > > +{}; + +// ---------------------------------------------------------------------------- +// Metafunction Source +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Should this be Host? or SourceIterator? + +template +struct Source > > +{ + typedef typename Source::Type TSource_; + typedef typename Iterator::Type Type; +}; + +template +struct Source > const> +{ + typedef typename Source::Type TSource_; + typedef typename Iterator::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +template +struct Value > > +{ + typedef typename Source > >::Type TSource_; + typedef typename Value::Type TSourceValue_; + //typedef TSourceValue_ Type; + // TODO(holtgrew): We really want gapped values here but there are issues... + typedef typename GappedValueType::Type Type; +}; + +template +struct Value > const> : + Value > > {}; + +// ---------------------------------------------------------------------------- +// Metafunction GetValue +// ---------------------------------------------------------------------------- + +template +struct GetValue > > : + Value > > +{ +}; + +template +struct GetValue > const> : + Value > const> +{ +}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +template +struct Reference > > +{ + typedef Iter > TIterator_; + typedef Proxy > Type; +}; + +template +struct Reference > const> +{ + typedef Iter const > TIterator_; + typedef Proxy > Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function operator++ +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Could be general forward + +template +inline Iter > & +operator++(Iter > & it) +{ + goNext(it); + return it; +} + +template +inline Iter > +operator++(Iter > & it, int) +{ + Iter > ret = it; + goNext(it); + return ret; +} + +// ---------------------------------------------------------------------------- +// Function operator-- +// ---------------------------------------------------------------------------- + +template +inline Iter > & +operator--(Iter > & it) +{ + goPrevious(it); + return it; +} + +template +inline Iter > +operator--(Iter > & it, int) +{ + Iter > ret = it; + goPrevious(it); + return ret; +} + +// ---------------------------------------------------------------------------- +// Function insertGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#insertGap + * @brief Insert gap at the current position. + * + * @signature void insertGap(it); + * + * @param[in,out] it The iterator to insert gaps at. + */ + +// Forward to insertGaps() which has to be implemented by the specific gap +// iterator. + +template +inline void +insertGap(Iter > & it) +{ + insertGaps(it, 1); +} + +// ---------------------------------------------------------------------------- +// Function isCharacter() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#isCharacter + * @brief Query an iterator for being at a character + * + * @signature bool isCharacter(it); + * + * @param[in] it Iterator to query for pointing at a character. + * + * @return bool true if it is at a character and false otherwise. + */ + +template +bool isCharacter(Iter > const & it) +{ + return !isGap(it); +} + +// ---------------------------------------------------------------------------- +// Function countCharacters() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#countCharacters + * @brief Count characters at iterator. + * + * @signature TSize countCharacters(it[, dir]); + * + * @param[in] it Iterator for counting characters at. + * @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink. + * Defaults to @link GapDirectionTags#RightOfViewPos @endlink. + * + * @return TSize Number of characters. + * + * If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be + * included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected. + */ + +template +inline typename Size::Type +countCharacters(Iter > const & it) +{ + return countCharacters(it, RightOfViewPos()); +} + +// ---------------------------------------------------------------------------- +// Function isGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#isGap + * @brief Query an iterator for being at a gap + * + * @signature bool isGap(it); + * + * @param[in] it Iterator to query for pointing at a gap. + * + * @return bool true if it is at a gap and false otherwise. + */ + +// ---------------------------------------------------------------------------- +// Function countGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#countGaps + * @brief Count gaps at iterator. + * + * @signature TSize countGaps(it[, dir]); + * + * @param[in] it Iterator for counting gaps at. + * @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink. + * Defaults to @link GapDirectionTags#RightOfViewPos @endlink. + * + * @return TSize Number of gaps. + * + * If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be + * included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected. + */ + +template +inline typename Size::Type +countGaps(Iter > const & it) +{ + return countGaps(it, RightOfViewPos()); +} + +// ---------------------------------------------------------------------------- +// Function insertGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#insertGaps + * @brief Insert gaps at the current position. + * + * @signature void insertGaps(it, num); + * + * @param[in,out] it Remove gap at the given position (if any). + * @param[in] num Number of gaps to insert. + */ + +// ---------------------------------------------------------------------------- +// Function removeGap() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#removeGap + * @brief Insert gap at the current position. + * + * @signature TSize removeGap(it); + * + * @param[in,out] it Remove gap at the given position (if any). + * + * @return TSize Number of removed gaps. + */ + +// Forward to removeGaps() which has to be implemented by the specific gap +// iterator. + +template +inline typename Size::Type +removeGap(Iter > & it) +{ + return removeGaps(it, 1); +} + +// ---------------------------------------------------------------------------- +// Function removeGaps() +// ---------------------------------------------------------------------------- + +/*! + * @fn GapsIterator#removeGaps + * @brief Remove gaps from the current position. + * + * @signature TSize removeGaps(it, num); + * + * @param[in,out] it Remove gap at the given position (if any). + * @param[in] num Number of gaps to remove. + * + * @return TSize Number of removed gaps. + */ + +// ---------------------------------------------------------------------------- +// Function assignValue() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Const consistency problems. + +template +inline void +assignValue(Iter > & me, + TValue const & val) +{ + if (!isGap(me)) + { + assignValue(source(me), val); + } + // TODO(holtgrew): Else, inserting gaps is problematic... +} + +template +inline void +assignValue(Iter > const & me, + TValue const & val) +{ + if (!isGap(me)) + { + assignValue(source(me), val); + } +} + +// ---------------------------------------------------------------------------- +// Function container() +// ---------------------------------------------------------------------------- + +template +inline TGaps & +container(Iter > & me) +{ + return *me._container; +} + +template +inline TGaps & +container(Iter > const & me) +{ + return *me._container; +} + +// ---------------------------------------------------------------------------- +// Function source +// ---------------------------------------------------------------------------- + +// Returns host iterator. + +// TODO(holtgrew): Non-const version is superfluous. +template +inline typename Source > >::Type /*returns copy*/ +source(Iter > & it) +{ + return iter(container(it), toSourcePosition(container(it), position(it))); +} + +template +inline typename Source > const>::Type /*returns copy*/ +source(Iter > const & it) +{ + return iter(container(source(it)), toSourcePosition(container(it), position(it))); +} + +// TODO(holtgrew): setSource? setContainer? + +// ---------------------------------------------------------------------------- +// Function operator+= +// ---------------------------------------------------------------------------- + +template +inline Iter > & +operator+=(Iter > & it, TDiff diff) +{ + goFurther(it, diff); + return it; +} + +// ---------------------------------------------------------------------------- +// Function operator-= +// ---------------------------------------------------------------------------- + +template +inline Iter > & +operator-=(Iter > & it, TDiff diff) +{ + goFurther(it, -(int64_t)(diff)); + return it; +} + +// ---------------------------------------------------------------------------- +// Function goFurther +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Implementation could be faster. +template +inline void +goFurther(Iter > & it, + TDifference steps) +{ + typedef typename MakeSigned::Type TSignedDifference; + if (steps > TDifference(0)) + for (; steps; --steps) + goNext(it); + else + for (; -static_cast(steps); ++steps) + goPrevious(it); +} + +// ---------------------------------------------------------------------------- +// Function isClipped() +// ---------------------------------------------------------------------------- + +template +inline bool +isClipped(Iter > const &) +{ + return false; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_ diff --git a/seqan/align/global_alignment_banded.h b/seqan/align/global_alignment_banded.h new file mode 100644 index 0000000..eab33c6 --- /dev/null +++ b/seqan/align/global_alignment_banded.h @@ -0,0 +1,786 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Global alignment interface for the banded Needleman-Wunsch and Gotoh +// algorithms. +// +// We define the interface functions pretty explicitely (versus just TAlign, +// TFragments etc.) so the candidates the compiler gives when resolution to +// the globalFunction() fails is actually meaningful. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +class Score; +template +class Graph; +template +struct Alignment; +template +class Fragment; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [banded, Align] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef Align TAlign; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String trace; + + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), + scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); + + _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, LinearGaps()); + else + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, AffineGaps()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [banded, Gaps] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String trace; + + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), TGapModel()); + _adaptTraceSegmentsTo(gapsH, gapsV, trace); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [banded, Graph >] +// ---------------------------------------------------------------------------- + +// Full interface. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef Graph > TGraph; + typedef typename Position::Type TPosition; + typedef typename Size::Type TSize; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String trace; + + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), + value(stringSet(alignmentGraph), 1), scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), TGapModel()); + + _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0), + positionToId(stringSet(alignmentGraph), 1), trace); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [banded, String >] +// ---------------------------------------------------------------------------- + +// Full interface. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef String, TStringSpec> TFragments; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String trace; + + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), TGapModel()); + + _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [banded, 2 Strings] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + DPScoutState_ dpScoutState; + String > traceSegments; // Dummy segments. + return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), TGapModel()); +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [banded, StringSet] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + SEQAN_ASSERT_EQ(length(strings), 2u); + + DPScoutState_ dpScoutState; + String > traceSegments; // Dummy segments. + return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), TGapModel()); +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + + AlignConfig<> alignConfig; + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + + AlignConfig<> alignConfig; + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, lowerDiag, upperDiag); +} + + +// ============================================================================ +// Many-vs-Many align interfaces. +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [banded, SIMD version, 2x StringSet] +// ---------------------------------------------------------------------------- + +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + SEQAN_ASSERT_EQ(length(stringsH), length(stringsV)); + return _alignWrapper(stringsH, stringsV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); +} + +// Interface without AlignConfig<>. +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [banded, SIMD version, String vs StringSet] +// ---------------------------------------------------------------------------- + +template +String globalAlignmentScore(TStringH const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int lowerDiag, + int upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(stringH, stringsV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); +} + +// Interface without AlignConfig<>. +template +String globalAlignmentScore(TString const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +String globalAlignmentScore(TString const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, + int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +String globalAlignmentScore(TString const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [banded, SIMD version, GapsH, GapsV] +// ---------------------------------------------------------------------------- + +template +inline auto +globalAlignment(StringSet & gapSeqSetH, + StringSet & gapSeqSetV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + int const lowerDiag, + int const upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [banded, SIMD version, StringSet] +// ---------------------------------------------------------------------------- + +template +String globalAlignment(StringSet > & alignSet, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int const lowerDiag, + int const upperDiag, + TAlgoTag const & algoTag) +{ + typedef Align TAlign; + typedef typename Row::Type TGapSequence; + + StringSet > gapSetH; + StringSet > gapSetV; + reserve(gapSetH, length(alignSet)); + reserve(gapSetV, length(alignSet)); + + for (auto & align : alignSet) + { + appendValue(gapSetH, row(align, 0)); + appendValue(gapSetV, row(align, 1)); + } + + return globalAlignment(gapSetH, gapSetV, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without AlignConfig<>. +template +String globalAlignment(StringSet > & align, + Score const & scoringScheme, + int lowerDiag, int upperDiag, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, algoTag); +} + +// Interface without algorithm tag. +template +String globalAlignment(StringSet > & align, + Score const & scoringScheme, + AlignConfig const & alignConfig, + int lowerDiag, int upperDiag) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); + else + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +String globalAlignment(StringSet > & align, + Score const & scoringScheme, + int lowerDiag, int upperDiag) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig, lowerDiag, upperDiag); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_BANDED_H_ diff --git a/seqan/align/global_alignment_hirschberg_impl.h b/seqan/align/global_alignment_hirschberg_impl.h new file mode 100644 index 0000000..0497f7d --- /dev/null +++ b/seqan/align/global_alignment_hirschberg_impl.h @@ -0,0 +1,694 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#include + +// TODO(holtgrew): Get rid of this? +//#define SEQAN_HIRSCHBERG_DEBUG_CUT + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +struct Hirschberg_; +typedef Tag Hirschberg; + +// ---------------------------------------------------------------------------- +// Helper Class HirschbergSet_ +// ---------------------------------------------------------------------------- + +// State for the implementation of Hirschberg's algorithm. + +class HirschbergSet_ +{ +public: + unsigned x1; + unsigned x2; + unsigned y1; + unsigned y2; + int score; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _begin1() +// ---------------------------------------------------------------------------- + +inline unsigned & +_begin1(HirschbergSet_ & me) { + return me.x1; +} + + +inline unsigned const & +_begin1(HirschbergSet_ const & me) { + return me.x1; +} + +// ---------------------------------------------------------------------------- +// Function _setBegin1() +// ---------------------------------------------------------------------------- + +inline void +_setBegin1(HirschbergSet_ & me, unsigned const & new_begin) { + me.x1 = new_begin; +} + +// ---------------------------------------------------------------------------- +// Function _end1() +// ---------------------------------------------------------------------------- + +inline unsigned & +_end1(HirschbergSet_ & me) { + return me.x2; +} + +inline unsigned const & +_end1(HirschbergSet_ const & me) { + return me.x2; +} + +// ---------------------------------------------------------------------------- +// Function _setEnd1() +// ---------------------------------------------------------------------------- + +inline void +_setEnd1(HirschbergSet_ & me, unsigned const & new_end) { + me.x2 = new_end; +} + +// ---------------------------------------------------------------------------- +// Function _begin2() +// ---------------------------------------------------------------------------- + +inline unsigned & +_begin2(HirschbergSet_ & me) { + return me.y1; +} + +inline unsigned const & +_begin2(HirschbergSet_ const & me) { + return me.y1; +} + +// ---------------------------------------------------------------------------- +// Function _setBegin2() +// ---------------------------------------------------------------------------- + +inline void +_setBegin2(HirschbergSet_ & me, unsigned const & new_begin) { + me.y1 = new_begin; +} + +// ---------------------------------------------------------------------------- +// Function _end2() +// ---------------------------------------------------------------------------- + +inline unsigned & +_end2(HirschbergSet_ & me) { + return me.y2; +} + +inline unsigned const & +_end2(HirschbergSet_ const & me) { + return me.y2; +} + +// ---------------------------------------------------------------------------- +// Function _setEnd2() +// ---------------------------------------------------------------------------- + +inline void +_setEnd2(HirschbergSet_ & me, unsigned const & new_end) { + me.y2 = new_end; +} + +// ---------------------------------------------------------------------------- +// Function _score() +// ---------------------------------------------------------------------------- + +inline int & +_score(HirschbergSet_ & me) { + return me.score; +} + +// ---------------------------------------------------------------------------- +// Function _score() +// ---------------------------------------------------------------------------- + +inline int const & +_score(HirschbergSet_ const & me) +{ + return me.score; +} + +// ---------------------------------------------------------------------------- +// Function _setScore() +// ---------------------------------------------------------------------------- + +inline void +_setScore(HirschbergSet_ & me,int new_score) { + me.score = new_score; +} + +// ---------------------------------------------------------------------------- +// Function _setBegin2() +// ---------------------------------------------------------------------------- + +// ////////////////////////////////////////////////////////////////////////////////////////////// +// Debug Methods +// functions are only used for debugging or verbose output, therefore they +// are only active in SEQAN_DEBUG +// ////////////////////////////////////////////////////////////////////////////////////////////// +#ifdef SEQAN_DEBUG + +inline +void +print(HirschbergSet_ const & me) +{ + std::cout << me.x1 << " " << me.x2 << "\t" << me.y1 << " " << me.y2 << std::endl; +} +#endif + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +inline bool +operator==(HirschbergSet_ const & lhs, + HirschbergSet_ const & rhs) +{ + return ((_begin1(lhs) == _begin1(rhs)) && (_end1(lhs) == _end1(rhs)) && + (_begin2(lhs) == _begin2(rhs)) && (_end2(lhs) == _end2(rhs))); +} + +// ---------------------------------------------------------------------------- +// Function _writeDebugMatrix() +// ---------------------------------------------------------------------------- + +#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT + template + void _writeDebugMatrix(TSource s1,TSource s2) + { + int l1 = length(s1); + int l2 = length(s2); + + int i,j,sg,sd; + + String > fMatrix,rMatrix,tMatrix; + + resize(fMatrix,l1 + 1); + resize(rMatrix,l1 + 1); + resize(tMatrix,l1 + 1); + + for(i = 0;i <= l1;++i) + { + resize(fMatrix[i],l2 + 1); + resize(rMatrix[i],l2 + 1); + resize(tMatrix[i],l2 + 1); + } + + for(i = 0;i <= l1;++i) + fMatrix[i][0] = i * (-1); + + for(i = l1;i >= 0;--i) + rMatrix[i][l2] = (l1 - i) * (-1); + + // calculate forward matrix + for(j = 1;j <= l2;++j) + { + fMatrix[0][j] = j*(-1); + for(i = 1;i <= l1;++i) + { + sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]); + sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 ); + + fMatrix[i][j] = ((sg > sd) ? sg : sd); + } + } + + // calculate reverse matrix + for(j = l2 - 1;j >= 0;--j) + { + rMatrix[l1][j] = (l2 - j)*(-1); + for(i = l1 - 1;i >= 0;--i) + { + sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]); + sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 ); + + rMatrix[i][j] = ((sg > sd) ? sg : sd); + } + } + + // print fMatrix + std::cout << ";-;"; + for(i = 0;i < l1;++i) + std::cout << s1[i] << ";"; + + std::cout << std::endl << "-;"; + for(j = 0;j <= l2;++j) + { + if(j != 0) std::cout << s2[j-1] << ";"; + for(i = 0;i <= l1;++i) + { + std::cout << fMatrix[i][j] << ";"; + } + std::cout << std::endl; + } + // print rMatrix + std::cout << ";"; + for(i = 0;i < l1;++i) + std::cout << s1[i] << ";"; + std::cout << "-;" << std::endl; + + for(j = 0;j <= l2;++j) + { + if(j != l2) std::cout << s2[j] << ";"; + else std::cout << "-;"; + for(i = 0;i <= l1;++i) + { + std::cout << rMatrix[i][j] << ";"; + } + std::cout << std::endl; + } + + // fill and print target matrix + std::cout << ";-;"; + for(i = 0;i < l1;++i) + std::cout << s1[i] << ";"; + + std::cout << std::endl << "-;"; + for(j = 0;j <= l2;++j) + { + if(j != 0) std::cout << s2[j-1] << ";"; + for(i = 0;i <= l1;++i) + { + tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j]; + std::cout << tMatrix[i][j] << ";"; + } + std::cout << std::endl; + } + } + +#endif + +// debug flag .. define to see where Hirschberg cuts the sequences +//#define SEQAN_HIRSCHBERG_DEBUG_CUT + +// ---------------------------------------------------------------------------- +// Function globalAlignment() +// ---------------------------------------------------------------------------- + +template +TScoreValue +_globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & score_, + Hirschberg const & /*algorithmTag*/) +{ + TSequenceH const & s1 = source(gapsH); + TSequenceV const & s2 = source(gapsV); + + TScoreValue total_score = 0; + + typedef typename Value::Type TValueV; + + typedef typename Size::Type TStringSize; + + typedef typename Iterator::Type TSequenceHIter; + typedef typename Iterator::Type TSequenceVIter; + + typedef typename Iterator >::Type TGapsHIter; + typedef typename Iterator >::Type TGapsVIter; + + TGapsHIter target_0 = begin(gapsH); + TGapsVIter target_1 = begin(gapsV); + + typedef typename Iterator >::Type TMatrixIterator; + + TValueV v; + + TStringSize len1 = length(s1); + TStringSize len2 = length(s2); + + // string to store the score values for the currently active cell + String c_score; + resize(c_score,len2 + 1); + // string to strore the backpointers + String pointer; + resize(pointer,len2 + 1); + + // scoring-scheme specific score values + TScoreValue score_match = scoreMatch(score_); + TScoreValue score_mismatch = scoreMismatch(score_); + TScoreValue score_gap = scoreGapExtend(score_); + + TScoreValue border,s,sg,sd,sg1,sg2; + int dp; + + std::stack to_process; + HirschbergSet_ target; + + unsigned i,j; + + HirschbergSet_ hs_complete{0, static_cast(len1), 0, static_cast(len2), 0}; + to_process.push(hs_complete); + + while(!to_process.empty()) + { + target = to_process.top(); + to_process.pop(); + + if(_begin2(target) == _end2(target)) + { + for(i = 0;i < (_end1(target) - _begin1(target));++i) + { + insertGap(target_1); + ++target_0; + ++target_1; + } + } + if(_begin1(target) == _end1(target)) + { + for(i = 0;i < (_end2(target) - _begin2(target));++i) + { + insertGap(target_0); + ++target_0; + ++target_1; + } + } + else if(_begin1(target) + 1 == _end1(target) || _begin2(target) + 1 == _end2(target)) + { + /* ALIGN */ +#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT + std::cout << "align s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl; + std::cout << "align " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl << std::endl; +#endif + + TStringSize len_1 = _end1(target) - _begin1(target); + TStringSize len_2 = _end2(target) - _begin2(target); + + Matrix matrix_; + + setDimension(matrix_, 2); + setLength(matrix_, 0, len_1 + 1); + setLength(matrix_, 1, len_2 + 1); + resize(matrix_); + + /* init matrix */ + TSequenceHIter x_begin = iter(s1, _begin1(target), Standard()) - 1; + TSequenceHIter x_end = iter(s1, _end1(target), Standard()) - 1; + TSequenceVIter y_begin = iter(s2, _begin2(target), Standard()) - 1; + TSequenceVIter y_end = iter(s2, _end2(target), Standard()) - 1; + + TSequenceHIter x = x_end; + TSequenceVIter y; + + TMatrixIterator col_ = end(matrix_) - 1; + TMatrixIterator finger1; + TMatrixIterator finger2; + + + TScoreValue h = 0; + TScoreValue border_ = score_gap; + TScoreValue v = border_; + + + //------------------------------------------------------------------------- + // init + + finger1 = col_; + *finger1 = 0; + for (x = x_end; x != x_begin; --x) + { + goPrevious(finger1, 0); + *finger1 = border_; + border_ += score_gap; + } + + //------------------------------------------------------------------------- + //fill matrix + border_ = 0; + for (y = y_end; y != y_begin; --y) + { + TValueV cy = *y; + h = border_; + border_ += score_gap; + v = border_; + + finger2 = col_; + goPrevious(col_, 1); + finger1 = col_; + + *finger1 = v; + + for (x = x_end; x != x_begin; --x) + { + goPrevious(finger1, 0); + goPrevious(finger2, 0); + if (*x == cy) + { + v = h + score_match; + h = *finger2; + } + else + { + TScoreValue s1 = h + score_mismatch; + h = *finger2; + TScoreValue s2 = score_gap + ((h > v) ? h : v); + v = (s1 > s2) ? s1 : s2; + } + *finger1 = v; + } + } + total_score += value(matrix_, 0,0); +#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT + std::cout << "alignment score is " << total_score << std::endl << std::endl; +#endif + + /* TRACE BACK */ + finger1 = begin(matrix_); + x = iter(s1,_begin1(target)); + y = iter(s2,_begin2(target)); + x_end = iter(s1,_end1(target)); + y_end = iter(s2,_end2(target)); + + while ((x != x_end) && (y != y_end)) + { + bool gv; + bool gh; + + if (*x == *y) + { + gv = gh = true; + } + else + { + TMatrixIterator it_ = finger1; + + goNext(it_, 0); + TScoreValue v = *it_; + + goNext(it_, 1); + TScoreValue d = *it_; + + it_ = finger1; + goNext(it_, 1); + TScoreValue h = *it_; + + gv = (v >= h) | (d >= h); + gh = (h >= v) | (d >= v); + } + + if (gv) + { + ++x; + goNext(finger1, 0); + } + else + { + insertGap(target_0); + } + + if (gh) + { + ++y; + goNext(finger1, 1); + } + else + { + insertGap(target_1); + } + + ++target_0; + ++target_1; + } + + // if x or y did not reached there end position, fill the rest with gaps + while(x != x_end) + { + insertGap(target_1); + ++target_0; + ++target_1; + ++x; + } + + while(y != y_end) + { + insertGap(target_0); + ++target_0; + ++target_1; + ++y; + } + /* END ALIGN */ + } + else + { + /* + Calculate cut using the algorithm as proposed in the lecture of Clemens Gröpl + using a backpointer to remember the position where the optimal alignment passes + the mid column + */ + unsigned mid = static_cast(floor( static_cast((_begin1(target) + _end1(target))/2) )); + +#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT + std::cout << "calculate cut for s1 " << _begin1(target) << " to " << _end1(target) << " and s2 " << _begin2(target) << " to " << _end2(target) << std::endl; + std::cout << "calculate cut for " << infix(s1,_begin1(target),_end1(target)) << " and " << infix(s2,_begin2(target),_end2(target)) << std::endl; + std::cout << "cut is in row " << mid << " symbol is " << getValue(s1,mid-1) << std::endl << std::endl; + + + _writeDebugMatrix(infix(s1,_begin1(target),_end1(target)),infix(s2,_begin2(target),_end2(target))); +#endif + + border = 0; + for(i = _begin2(target);i <= _end2(target);++i) + { + c_score[i] = border; + border += score_gap; + pointer[i] = i; + } + + // iterate over s1 until the mid column is reached + border = score_gap; + for(i = _begin1(target) + 1;i <= mid;++i) + { + s = c_score[_begin2(target)]; + c_score[_begin2(target)] = border; + border += score_gap; + v = getValue(s1,i-1); + for(j = _begin2(target) + 1;j <= _end2(target);++j) + { + sg = score_gap + ((c_score[j] > c_score[j - 1]) ? c_score[j] : c_score[j - 1]); + sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch); + + s = c_score[j]; + c_score[j] = (sg > sd) ? sg : sd; + } + } + + // from here, rememeber the cell of mid-column, where optimal alignment passed + for(i = mid + 1;i <= _end1(target);++i) + { + s = c_score[_begin2(target)]; + c_score[_begin2(target)] = border; + border += score_gap; + v = getValue(s1,i-1); + + dp = _begin2(target); + + for(j = _begin2(target) + 1;j <= _end2(target);++j) + { + sg1 = score_gap + c_score[j]; + sg2 = score_gap + c_score[j - 1]; + + sd = s + ((v == getValue(s2,j-1)) ? score_match : score_mismatch); + + s = c_score[j]; + sg = pointer[j]; + if(sd >= _max(sg1,sg2)) + { + c_score[j] = sd; + pointer[j] = dp; + } + else + { + if(sg2 > sg1) + { + c_score[j] = sg2; + pointer[j] = pointer[j-1]; + } + else + { + // gap introduced from left + // no update for the pointer + c_score[j] = sg1; + } + } + dp = sg; + } + } + +#ifdef SEQAN_HIRSCHBERG_DEBUG_CUT + std::cout << "hirschberg calculates cut in column " << mid << " and row " << pointer[_end2(target)] << std::endl; + std::cout << "requested position in c_score and pointer is " << _end2(target) << std::endl; + std::cout << "alignment score is " << c_score[_end2(target)] << std::endl << std::endl; +#endif + to_process.push(HirschbergSet_{mid, _end1(target), pointer[_end2(target)], _end2(target), 0}); + to_process.push(HirschbergSet_{_begin1(target), mid, _begin2(target), pointer[_end2(target)], 0}); + } + /* END CUT */ + } + return total_score; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_HIRSCHBERG_IMPL_H_ diff --git a/seqan/align/global_alignment_myers_hirschberg_impl.h b/seqan/align/global_alignment_myers_hirschberg_impl.h new file mode 100644 index 0000000..24e67ec --- /dev/null +++ b/seqan/align/global_alignment_myers_hirschberg_impl.h @@ -0,0 +1,762 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _writeDebugMatrix() +// ---------------------------------------------------------------------------- + +#ifdef MYERS_HIRSCHBERG_VERBOSE + template + void _writeDebugMatrix(TSource s1,TSource s2) + { +//IOREV _notio_ not relevant for iorev + int l1 = length(s1); + int l2 = length(s2); + + int i,j,sg,sd; + + String > fMatrix,rMatrix,tMatrix; + + resize(fMatrix,l1 + 1); + resize(rMatrix,l1 + 1); + resize(tMatrix,l1 + 1); + + for(i = 0;i <= l1;++i) + { + resize(fMatrix[i],l2 + 1); + resize(rMatrix[i],l2 + 1); + resize(tMatrix[i],l2 + 1); + } + + for(i = 0;i <= l1;++i) + fMatrix[i][0] = i * (-1); + + for(i = l1;i >= 0;--i) + rMatrix[i][l2] = (l1 - i) * (-1); + + // calculate forward matrix + for(j = 1;j <= l2;++j) + { + fMatrix[0][j] = j*(-1); + for(i = 1;i <= l1;++i) + { + sg = -1 + ((fMatrix[i-1][j] > fMatrix[i][j-1]) ? fMatrix[i-1][j] : fMatrix[i][j-1]); + sd = fMatrix[i-1][j-1] + ((s1[i - 1] == s2[j-1]) ? 0 : -1 ); + + fMatrix[i][j] = ((sg > sd) ? sg : sd); + } + } + + // calculate reverse matrix + for(j = l2 - 1;j >= 0;--j) + { + rMatrix[l1][j] = (l2 - j)*(-1); + for(i = l1 - 1;i >= 0;--i) + { + sg = -1 + ((rMatrix[i+1][j] > rMatrix[i][j+1]) ? rMatrix[i+1][j] : rMatrix[i][j+1]); + sd = rMatrix[i+1][j+1] + ((s1[i] == s2[j]) ? 0 : -1 ); + + rMatrix[i][j] = ((sg > sd) ? sg : sd); + } + } + + // print fMatrix + std::cout << ";-;"; + for(i = 0;i < l1;++i) + std::cout << s1[i] << ";"; + + std::cout << std::endl << "-;"; + for(j = 0;j <= l2;++j) + { + if(j != 0) std::cout << s2[j-1] << ";"; + for(i = 0;i <= l1;++i) + { + std::cout << fMatrix[i][j] << ";"; + } + std::cout << std::endl; + } + // print rMatrix + std::cout << ";"; + for(i = 0;i < l1;++i) + std::cout << s1[i] << ";"; + std::cout << "-;" << std::endl; + + for(j = 0;j <= l2;++j) + { + if(j != l2) std::cout << s2[j] << ";"; + else std::cout << "-;"; + for(i = 0;i <= l1;++i) + { + std::cout << rMatrix[i][j] << ";"; + } + std::cout << std::endl; + } + + // fill and print target matrix + std::cout << ";-;"; + for(i = 0;i < l1;++i) + std::cout << s1[i] << ";"; + + std::cout << std::endl << "-;"; + for(j = 0;j <= l2;++j) + { + if(j != 0) std::cout << s2[j-1] << ";"; + for(i = 0;i <= l1;++i) + { + tMatrix[i][j] = fMatrix[i][j] + rMatrix[i][j]; + std::cout << tMatrix[i][j] << ";"; + } + std::cout << std::endl; + } + } +#endif + +// ---------------------------------------------------------------------------- +// Function _printBinary() +// ---------------------------------------------------------------------------- + +// Debug integer types in binary format. +template +inline void +_printBinary(TStream & stream, T const n) +{ + std::bitset::VALUE> bits(n); + stream << bits; + stream << '\n'; +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() +// ---------------------------------------------------------------------------- + +// When using different alphabets, we will internally use the pattern alphabet +// for the comparison. This means that the text character is converted to the +// pattern alphabet. Here, the "pattern" is the shorter source sequence. + +template +int +_globalAlignment(Gaps & gapsH, + Gaps & gapsV, + MyersHirschberg const & algorithmTag) +{ + // Switch horizontal and vertical gap roles, gapsV should be the shorter one + // to fit into less words. + if (length(source(gapsH)) < length(source(gapsV))) + return _globalAlignment(gapsV, gapsH, algorithmTag); + + clearGaps(gapsH); + clearGaps(gapsV); + clearClipping(gapsH); + clearClipping(gapsV); + + typedef int TScoreValue; + + // use size of unsigned int as blocksize for bit-vectors + const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; + + // saves the score value that will be returned + TScoreValue score,total_score = 0; + + typedef typename Value::Type TPatternAlphabet; + typedef typename Size::Type TStringSize; + + typedef typename Iterator::Type TSequenceHIterator; + typedef typename Iterator::Type TSequenceVIterator; + typedef Gaps TGapsH; + typedef Gaps TGapsV; + typedef typename Iterator::Type TGapsHIterator; + typedef typename Iterator::Type TGapsVIterator; + + typedef typename Iterator, Rooted>::Type TMatrixIterator; + + TGapsHIterator target_0 = begin(gapsH); + TGapsVIterator target_1 = begin(gapsV); + + TSequenceH const & x = source(gapsH); + TSequenceV const & y = source(gapsV); + + TStringSize len_x = length(x); + TStringSize len_y = length(y); + + // string to store the score values for the currently active cell + String c_score; + resize(c_score, len_x + 1, 0); + + // scoring-scheme specific score values + TScoreValue score_match = 0; + TScoreValue score_mismatch = -1; + TScoreValue score_gap = -1; + + // additional vars + unsigned i; + + // stack with parts of matrix that have to be processed + std::stack to_process; + HirschbergSet_ target; + + // myers specific vars and preprocessing + unsigned int patternAlphabetSize = ValueSize::VALUE; + unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE; // maximal count of blocks + + String VP; + String VN; + String forwardBitMask; + String reverseBitMask; + + resize(VP, blockCount, maxValue()); + resize(VN, blockCount, 0); + + // first bitMask will be constructed from the shorter sequence + resize(forwardBitMask, patternAlphabetSize * blockCount, 0); + resize(reverseBitMask, patternAlphabetSize * blockCount, 0); + + // encoding the letters as bit-vectors + for (unsigned int j = 0; j < len_y; j++){ + forwardBitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = forwardBitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE); + reverseBitMask[blockCount * ordValue(getValue(y,len_y - j - 1)) + j/BLOCK_SIZE] = reverseBitMask[blockCount * ordValue(getValue(y,len_y - j - 1)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE); + } + + HirschbergSet_ hs_complete{0, static_cast(len_x), 0, static_cast(len_y), 1}; + to_process.push(hs_complete); + + while(!to_process.empty()) + { + target = to_process.top(); + to_process.pop(); + /* if score is zero, the whole part of the sequence can be simply skipped */ + if(_score(target) == 0) + { + /* coukd work faster */ + for(i = 0;i < (_end1(target) - _begin1(target));++i) + { + ++target_0; + ++target_1; + } + +#ifdef MYERS_HIRSCHBERG_VERBOSE + printf("skipped %i to %i in first sequence\n",_begin1(target),_end1(target)); +#endif + } + else if(_begin1(target) == _end1(target)) + { + +#ifdef MYERS_HIRSCHBERG_VERBOSE + std::cout << "align y " << _begin2(target) << " to " << _end2(target) << std::endl; + std::cout << "align " << infix(y,_begin2(target),_end2(target)) << std::endl << std::endl; +#endif + for(i = 0;i < (_end2(target) - _begin2(target));++i) + { + insertGap(target_0); + ++target_0; + ++target_1; + } + } + else if(_begin2(target) + 1 == _end2(target)) + { + /* ALIGN */ +#ifdef MYERS_HIRSCHBERG_VERBOSE + std::cout << "align x " << _begin1(target) << " to " << _end1(target) << " and y " << _begin2(target) << " to " << _end2(target) << std::endl; + std::cout << "align " << infix(x,_begin1(target),_end1(target)) << " and " << infix(y,_begin2(target),_end2(target)) << std::endl << std::endl; +#endif + + TStringSize len_1 = _end1(target) - _begin1(target); + TStringSize len_2 = _end2(target) - _begin2(target); + + Matrix matrix_; + + setDimension(matrix_, 2); + setLength(matrix_, 0, len_1 + 1); + setLength(matrix_, 1, len_2 + 1); + resize(matrix_); + + /* init matrix */ + TSequenceHIterator xs_begin = iter(x,_begin1(target)) - 1; + TSequenceHIterator xs_end = iter(x,_end1(target)) - 1; + TSequenceVIterator ys_begin = iter(y,_begin2(target)) - 1; + TSequenceVIterator ys_end = iter(y,_end2(target)) - 1; + + TSequenceHIterator xs = xs_end; + TSequenceVIterator ys; + + TMatrixIterator col_ = end(matrix_) - 1; + TMatrixIterator finger1; + TMatrixIterator finger2; + + + TScoreValue h = 0; + TScoreValue border_ = score_gap; + TScoreValue v = border_; + + + //------------------------------------------------------------------------- + // init + + finger1 = col_; + *finger1 = 0; + for (xs = xs_end; xs != xs_begin; --xs) + { + goPrevious(finger1, 0); + *finger1 = border_; + border_ += score_gap; + } + + //------------------------------------------------------------------------- + //fill matrix + + border_ = 0; + for (ys = ys_end; ys != ys_begin; --ys) + { + TPatternAlphabet cy = *ys; + h = border_; + border_ += score_gap; + v = border_; + + finger2 = col_; + goPrevious(col_, 1); + finger1 = col_; + + *finger1 = v; + + for (xs = xs_end; xs != xs_begin; --xs) + { + goPrevious(finger1, 0); + goPrevious(finger2, 0); + if (*xs == cy) + { + v = h + score_match; + h = *finger2; + } + else + { + TScoreValue s1 = h + score_mismatch; + h = *finger2; + TScoreValue s2 = score_gap + ((h > v) ? h : v); + v = (s1 > s2) ? s1 : s2; + } + *finger1 = v; + } + } + + // if computed the whole matrix last value of v = alignment score + if(target == hs_complete) total_score = v; + + /* TRACE BACK */ + finger1 = begin(matrix_); + xs = iter(x,_begin1(target)); + ys = iter(y,_begin2(target)); + xs_end = iter(x,_end1(target)); + ys_end = iter(y,_end2(target)); + + while ((xs != xs_end) && (ys != ys_end)) + { + bool gv; + bool gh; + + if (*xs == *ys) + { + gv = gh = true; + } + else + { + TMatrixIterator it_ = finger1; + + goNext(it_, 0); + TScoreValue v = *it_; + + goNext(it_, 1); + TScoreValue d = *it_; + + it_ = finger1; + goNext(it_, 1); + TScoreValue h = *it_; + + gv = (v >= h) | (d >= h); + gh = (h >= v) | (d >= v); + } + + if (gv) + { + ++xs; + goNext(finger1, 0); + } + else + { + insertGap(target_0); + } + + if (gh) + { + ++ys; + goNext(finger1, 1); + } + else + { + insertGap(target_1); + } + + ++target_0; + ++target_1; + } + + // if x or y did not reached there end position, fill the rest with gaps + while(xs != xs_end) + { + insertGap(target_1); + ++target_0; + ++target_1; + ++xs; + } + + while(ys != ys_end) + { + insertGap(target_0); + ++target_0; + ++target_1; + ++ys; + } + /* END ALIGN */ + + +#ifdef MYERS_HIRSCHBERG_VERBOSE + std::cout << std::endl << align_ << std::endl << std::endl; +#endif + + } + else + { + /* + --------------------------------------------------------------- + Calculate cut position using extended Myers-Bitvector-Algorithm + --------------------------------------------------------------- + */ + + /* declare variables */ + unsigned int X, D0, HN, HP; + + /* compute cut position */ + unsigned mid = static_cast(floor( static_cast((_begin2(target) + _end2(target))/2) )); + + /* debug infos */ +#ifdef MYERS_HIRSCHBERG_VERBOSE + std::cout << "calculate cut for x " << _begin1(target) << " to " << _end1(target) << " and y " << _begin2(target) << " to " << _end2(target) << std::endl; + std::cout << "calculate cut for " << infix(x,_begin1(target),_end1(target)) << " and " << infix(y,_begin2(target),_end2(target)) << std::endl; + std::cout << "cut is in row " << mid << " symbol is " << getValue(x,mid-1) << std::endl << std::endl; + + std::cout << std::endl; + _writeDebugMatrix(infix(x,_begin1(target),_end1(target)),infix(y,_begin2(target),_end2(target))); + std::cout << std::endl; +#endif + /* compute blocks and score masks */ + unsigned fStartBlock = _begin2(target) / BLOCK_SIZE; + unsigned fEndBlock = (mid - 1) / BLOCK_SIZE; + unsigned fSpannedBlocks = (fEndBlock - fStartBlock) + 1; + + unsigned int fScoreMask = 1 << ((mid - 1) % BLOCK_SIZE); + + unsigned int fOffSet = _begin2(target) % BLOCK_SIZE; + unsigned int fSilencer = ~0; + fSilencer <<= fOffSet; + + /* reset v-bitvectors */ + std::fill(begin(VP, Standard()) + fStartBlock, begin(VP, Standard()) + fEndBlock + 1, maxValue()); + std::fill(begin(VN, Standard()) + fStartBlock, begin(VN, Standard()) + fEndBlock + 1, 0); + + /* determine start-position and start-score */ + auto pos = _begin1(target); + score = (mid - _begin2(target)) * score_gap; + c_score[pos] = score; + + /* compute with myers - forward - begin */ + if(fSpannedBlocks == 1) + { + while (pos < _end1(target)) { + X = (fSilencer & forwardBitMask[(blockCount * ordValue(static_cast(getValue(x,pos)))) + fStartBlock]) | VN[fStartBlock]; + + D0 = ((VP[fStartBlock] + (X & VP[fStartBlock])) ^ VP[fStartBlock]) | X; + HN = VP[fStartBlock] & D0; + HP = VN[fStartBlock] | ~(VP[fStartBlock] | D0); + + X = (HP << 1) | (1 << fOffSet); + VN[fStartBlock] = X & D0; + VP[fStartBlock] = (HN << 1) | ~(X | D0); + + if (HP & fScoreMask) + score--; + else if (HN & fScoreMask) + score++; + + c_score[pos + 1] = score; + + ++pos; + } + } /* end - short patten */ + else + { + unsigned shift, currentBlock; + unsigned int temp, carryD0, carryHP, carryHN; + + while (pos < _end1(target)) + { + carryD0 = carryHP = carryHN = 0; + shift = blockCount * ordValue(static_cast(getValue(x,pos))); + + // computing first the top most block + X = (fSilencer & forwardBitMask[shift + fStartBlock]) | VN[fStartBlock]; + + temp = VP[fStartBlock] + (X & VP[fStartBlock]); + carryD0 = temp < VP[fStartBlock]; + + D0 = (temp ^ VP[fStartBlock]) | X; + HN = VP[fStartBlock] & D0; + HP = VN[fStartBlock] | ~(VP[fStartBlock] | D0); + + X = (HP << 1) | (1 << fOffSet); + carryHP = HP >> (BLOCK_SIZE - 1); + + VN[fStartBlock] = X & D0; + + temp = (HN << 1); + carryHN = HN >> (BLOCK_SIZE - 1); + + VP[fStartBlock] = temp | ~(X | D0); + + // compute the remaining blocks + for (currentBlock = fStartBlock + 1; currentBlock <= fEndBlock; currentBlock++) { + X = forwardBitMask[shift + currentBlock] | VN[currentBlock]; + + temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0; + + carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]); + + D0 = (temp ^ VP[currentBlock]) | X; + HN = VP[currentBlock] & D0; + HP = VN[currentBlock] | ~(VP[currentBlock] | D0); + + X = (HP << 1) | carryHP; + carryHP = HP >> (BLOCK_SIZE-1); + + VN[currentBlock] = X & D0; + + temp = (HN << 1) | carryHN; + carryHN = HN >> (BLOCK_SIZE - 1); + + VP[currentBlock] = temp | ~(X | D0); + } + + /* update score */ + if (HP & fScoreMask) + score--; + else if (HN & fScoreMask) + score++; + + c_score[pos + 1] = score; + + ++pos; + } + + } /* end - long patten */ + /* compute with myers - forward - end */ + + /* compute blocks and score masks */ + unsigned rStartBlock = (len_y - _end2(target)) / BLOCK_SIZE; + unsigned rEndBlock = (len_y - mid - 1) / BLOCK_SIZE; + unsigned rSpannedBlocks = (rEndBlock - rStartBlock) + 1; + + unsigned int rScoreMask = 1 << ((len_y - mid - 1) % BLOCK_SIZE); + unsigned int rOffSet = (len_y - _end2(target)) % BLOCK_SIZE; + unsigned int rSilencer = ~0; + rSilencer <<= rOffSet; + + /* reset v-bitvectors */ + std::fill(begin(VP, Standard()) + rStartBlock, begin(VP, Standard()) + rEndBlock + 1, maxValue()); + std::fill(begin(VN, Standard()) + rStartBlock, begin(VN, Standard()) + rEndBlock + 1, 0); + + /* determine start-position and start-score */ + pos = _end1(target); + score = (_end2(target) - mid) * score_gap; + + /* set start score */ + c_score[_end1(target)] += score; + + /* determine optimal cut position -- score extension */ + TScoreValue max = c_score[_end1(target)]; + TScoreValue rmax = score; + unsigned int pos_max = _end1(target); + + /* compute with myers - reverse - begin */ + if(rSpannedBlocks == 1) + { + while (pos-- > _begin1(target)) { + X = (rSilencer & reverseBitMask[(blockCount * ordValue(static_cast(getValue(x,pos)))) + rStartBlock]) | VN[rStartBlock]; + + D0 = ((VP[rStartBlock] + (X & VP[rStartBlock])) ^ VP[rStartBlock]) | X; + HN = VP[rStartBlock] & D0; + HP = VN[rStartBlock] | ~(VP[rStartBlock] | D0); + + X = (HP << 1) | (1 << rOffSet); + VN[rStartBlock] = X & D0; + VP[rStartBlock] = (HN << 1) | ~(X | D0); + + if (HP & rScoreMask) + --score; + else if (HN & rScoreMask) + ++score; + + c_score[pos] += score; + + /* check for optimality -- score extension */ + if(c_score[pos]> max) + { + pos_max = pos; + max = c_score[pos]; + rmax = score; + } + } + } /* end - short pattern */ + else + { + unsigned shift, currentBlock; + unsigned int temp, carryD0, carryHP, carryHN; + + while (pos-- > _begin1(target)) + { + carryD0 = carryHP = carryHN = 0; + shift = blockCount * ordValue(static_cast(getValue(x,pos))); + + // compute first the top most block + X = (rSilencer & reverseBitMask[shift + rStartBlock]) | VN[rStartBlock]; + + temp = VP[rStartBlock] + (X & VP[rStartBlock]); + carryD0 = temp < VP[rStartBlock]; + + D0 = (temp ^ VP[rStartBlock]) | X; + HN = VP[rStartBlock] & D0; + HP = VN[rStartBlock] | ~(VP[rStartBlock] | D0); + + X = (HP << 1) | (1 << rOffSet); + carryHP = HP >> (BLOCK_SIZE - 1); + + VN[rStartBlock] = X & D0; + + temp = (HN << 1); + carryHN = HN >> (BLOCK_SIZE - 1); + + VP[rStartBlock] = temp | ~(X | D0); + + // compute the remaining blocks + for (currentBlock = rStartBlock + 1; currentBlock <= rEndBlock; currentBlock++) { + X = reverseBitMask[shift + currentBlock] | VN[currentBlock]; + + temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0; + + carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]); + + D0 = (temp ^ VP[currentBlock]) | X; + HN = VP[currentBlock] & D0; + HP = VN[currentBlock] | ~(VP[currentBlock] | D0); + + X = (HP << 1) | carryHP; + carryHP = HP >> (BLOCK_SIZE-1); + + VN[currentBlock] = X & D0; + + temp = (HN << 1) | carryHN; + carryHN = HN >> (BLOCK_SIZE - 1); + + VP[currentBlock] = temp | ~(X | D0); + } + + if (HP & rScoreMask) + --score; + else if (HN & rScoreMask) + ++score; + + c_score[pos] += score; + + /* check for optimality -- score extension*/ + if(c_score[pos] > max) + { + pos_max = pos; + max = c_score[pos]; + rmax = score; + } + } + + } /* end - long pattern */ + /* compute with myers - reverse - end */ + + // if computed the whole matrix max = alignment score + if(target == hs_complete) + total_score = max; + +#ifdef MYERS_HIRSCHBERG_VERBOSE + printf("Optimal cut is at %i and %i with forward score %i and reverse score %i\n\n",mid,pos_max,(max - rmax),rmax); +#endif + /* push the two computed parts of the dp-matrix on process stack */ + to_process.push(HirschbergSet_{pos_max, _end1(target), mid, _end2(target), rmax}); + to_process.push(HirschbergSet_{_begin1(target), pos_max, _begin2(target), mid, max - rmax}); + + } + /* END CUT */ + } + + return total_score; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_HIRSCHBERG_IMPL_H_ diff --git a/seqan/align/global_alignment_myers_impl.h b/seqan/align/global_alignment_myers_impl.h new file mode 100644 index 0000000..8082f3b --- /dev/null +++ b/seqan/align/global_alignment_myers_impl.h @@ -0,0 +1,201 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +// TODO(holtgrew): Should be called _globalAlignmentScore()! + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// When using different alphabets, we will internally use the pattern alphabet +// for the comparison. This means that the text character is converted to the +// pattern alphabet. Here, the "pattern" is the shorter source sequence. + +template +int +_globalAlignmentScore(String const & seqH, + String const & seqV, + MyersBitVector const & algorithmTag) +{ + // Switch horizontal and vertical gap roles, gapsV should be the shorter one + // to fit into less words. + if (length(seqH) < length(seqV)) + return _globalAlignmentScore(seqV, seqH, algorithmTag); + + // Use size of unsigned int as blocksize for bit-vectors. + const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; + + typedef String const TSequenceH; + typedef String const TSequenceV; + + typedef typename Value::Type TPatternAlphabet; + typedef typename Size::Type TSourceSize; + + TSequenceH const & x = seqH; + TSequenceV const & y = seqV; + + TSourceSize len_x = length(x); + unsigned int pos = 0; + + // init variables + unsigned int len_y = length(y); + int score = (-1)*len_y; + unsigned int patternAlphabetSize = ValueSize::VALUE; + unsigned int blockCount = (len_y + BLOCK_SIZE - 1) / BLOCK_SIZE; + + unsigned int scoreMask = 1 << ((len_y % BLOCK_SIZE) - 1); // the mask with a bit set at the position of the last active cell + + String VP; + resize(VP, blockCount, maxValue()); + String VN; + resize(VN, blockCount, 0); + String bitMask; + resize(bitMask, patternAlphabetSize * blockCount, 0); + + // encoding the letters as bit-vectors + for (unsigned int j = 0; j < len_y; j++) + bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] = bitMask[blockCount * ordValue(getValue(y,j)) + j/BLOCK_SIZE] | 1 << (j%BLOCK_SIZE); + + // compute score + unsigned int X, D0, HN, HP; + if(blockCount == 1) + { + while (pos < len_x) { + X = bitMask[ordValue(static_cast(getValue(x,pos)))] | VN[0]; + + D0 = ((VP[0] + (X & VP[0])) ^ VP[0]) | X; + HN = VP[0] & D0; + HP = VN[0] | ~(VP[0] | D0); + + // customized to compute edit distance + X = (HP << 1) | 1; + VN[0] = X & D0; + VP[0] = (HN << 1) | ~(X | D0); + + if (HP & scoreMask) + score--; + else if (HN & scoreMask) + score++; + + ++pos; + } + } // end compute score - short pattern + else + { + unsigned int temp, shift, currentBlock; + unsigned int carryD0, carryHP, carryHN; + + while (pos < len_x) + { + // set vars + carryD0 = carryHP = carryHN = 0; + shift = blockCount * ordValue(static_cast(getValue(x,pos))); + + // computing first the top most block + X = bitMask[shift] | VN[0]; + + temp = VP[0] + (X & VP[0]); + carryD0 = temp < VP[0]; + + D0 = (temp ^ VP[0]) | X; + HN = VP[0] & D0; + HP = VN[0] | ~(VP[0] | D0); + + // customized to compute edit distance + X = (HP << 1) | 1; + carryHP = HP >> (BLOCK_SIZE - 1); + + VN[0] = X & D0; + + temp = (HN << 1); + carryHN = HN >> (BLOCK_SIZE - 1); + + VP[0] = temp | ~(X | D0); + + // computing the necessary blocks, carries between blocks following one another are stored + for (currentBlock = 1; currentBlock < blockCount; currentBlock++) { + X = bitMask[shift + currentBlock] | VN[currentBlock]; + + temp = VP[currentBlock] + (X & VP[currentBlock]) + carryD0; + + carryD0 = ((carryD0) ? temp <= VP[currentBlock] : temp < VP[currentBlock]); + + D0 = (temp ^ VP[currentBlock]) | X; + HN = VP[currentBlock] & D0; + HP = VN[currentBlock] | ~(VP[currentBlock] | D0); + + X = (HP << 1) | carryHP; + carryHP = HP >> (BLOCK_SIZE-1); + + VN[currentBlock] = X & D0; + + temp = (HN << 1) | carryHN; + carryHN = HN >> (BLOCK_SIZE - 1); + + VP[currentBlock] = temp | ~(X | D0); + } + + // update score with the HP and HN values of the last block the last block + if (HP & scoreMask) + score--; + else if (HN & scoreMask) + score++; + ++pos; + } + + } // end compute score - long pattern + + return score; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_MYERS_IMPL_H_ diff --git a/seqan/align/global_alignment_specialized.h b/seqan/align/global_alignment_specialized.h new file mode 100644 index 0000000..1fa2a4d --- /dev/null +++ b/seqan/align/global_alignment_specialized.h @@ -0,0 +1,201 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Test for globalAlignmentScore() implementations that use Hirschberg and +// MyersBitVector, MyersHirschberg. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [Hirschberg] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + Hirschberg const & /*algorithmTag*/) +{ + SEQAN_ASSERT_EQ(scoreGapOpen(scoringScheme), scoreGapExtend(scoringScheme)); + return _globalAlignment(gapsH, gapsV, scoringScheme, Hirschberg()); +} + +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + Hirschberg const & /*algorithmTag*/) +{ + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + + return globalAlignment(row(align, 0), row(align, 1), scoringScheme, Hirschberg()); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [Myers-Hirschberg] +// ---------------------------------------------------------------------------- + +template +int globalAlignment(Align & align, + MyersHirschberg const & algorithmTag) +{ + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + return _globalAlignment(row(align, 0), row(align, 1), algorithmTag); +} + +template +int globalAlignment(Gaps & gapsH, + Gaps & gapsV, + MyersHirschberg const & algorithmTag) +{ + return _globalAlignment(gapsH, gapsV, algorithmTag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [MyersBitVector] +// ---------------------------------------------------------------------------- + +template +int globalAlignment(Align & align, + MyersBitVector const & algorithmTag) +{ + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + return _globalAlignment(row(align, 0), row(align, 1), algorithmTag); +} + +template +int globalAlignment(Gaps & gapsH, + Gaps & gapsV, + MyersBitVector const & algorithmTag) +{ + return _globalAlignment(gapsH, gapsV, algorithmTag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [Hirschberg] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignmentScore(String const & seqH, + String const & seqV, + Score const & scoringScheme, + Hirschberg const & algorithmTag) +{ + Gaps const, ArrayGaps> gapsH(seqH); + Gaps const, ArrayGaps> gapsV(seqV); + return globalAlignment(gapsH, gapsV, scoringScheme, algorithmTag); +} + +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + Hirschberg const & algorithmTag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + return globalAlignmentScore(strings[0], strings[1], scoringScheme, algorithmTag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [Myers-Hirschberg] +// ---------------------------------------------------------------------------- + +template +int globalAlignmentScore(String const & seqH, + String const & seqV, + MyersHirschberg const & algorithmTag) +{ + Gaps const, ArrayGaps> gapsH(seqH); + Gaps const, ArrayGaps> gapsV(seqV); + return _globalAlignment(gapsH, gapsV, algorithmTag); +} + +template +int globalAlignmentScore(StringSet const & strings, + MyersHirschberg const & algorithmTag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + return globalAlignmentScore(strings[0], strings[1], algorithmTag); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [MyersBitVector] +// ---------------------------------------------------------------------------- + +template +int globalAlignmentScore(String const & seqH, + String const & seqV, + MyersBitVector const & algorithmTag) +{ + return _globalAlignmentScore(seqH, seqV, algorithmTag); +} + +template +int globalAlignmentScore(StringSet const & strings, + MyersBitVector const & algorithmTag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + return _globalAlignmentScore(strings[0], strings[1], algorithmTag); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_SPECIALIZED_H_ diff --git a/seqan/align/global_alignment_unbanded.h b/seqan/align/global_alignment_unbanded.h new file mode 100644 index 0000000..a58c539 --- /dev/null +++ b/seqan/align/global_alignment_unbanded.h @@ -0,0 +1,841 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Global alignment interface for the unbanded Needleman-Wunsch and Gotoh +// algorithms. +// +// We define the interface functions pretty explicitly (versus just TAlign, +// TFragments etc.) so the candidates the compiler gives when resolution to +// the globalFunction() fails is actually meaningful. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +class Score; +template +class Graph; +template +struct Alignment; +template +class Fragment; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function globalAlignment() +// ---------------------------------------------------------------------------- + +/*! + * @fn globalAlignment + * @headerfile + * @brief Computes the best global pairwise alignment. + * + * @signature TScoreVal globalAlignment(align, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]); + * @signature TScoreVal globalAlignment(gapsH, gapsV, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]); + * @signature TScoreVal globalAlignment(frags, strings, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]); + * @signature TScoreVal globalAlignment(alignGraph, scoringScheme, [alignConfig,] [lowerDiag, upperDiag,] [algorithmTag]); + * + * @param[in,out] align The @link Align @endlink object to use for storing the pairwise alignment. + * @param[in,out] gapsH The @link Gaps @endlink object for the first row (horizontal in the DP matrix). + * @param[in,out] gapsV The @link Gaps @endlink object for the second row (vertical in the DP matrix). + * @param[in,out] frags String of @link Fragment @endlink objects to store alignment in. + * @param[in] strings StringSet of length two with the strings to align. + * @param[in,out] alignGraph Alignment Graph for the resulting alignment. Must be initialized with two strings. + * @param[in] scoringScheme The @link Score scoring scheme @endlink to use for the alignment. Note that + * the user is responsible for ensuring that the scoring scheme is compatible with algorithmTag. + * @param[in] alignConfig @link AlignConfig @endlink instance to use for the alignment configuration. + * @param[in] lowerDiag Optional lower diagonal (int). + * @param[in] upperDiag Optional upper diagonal (int). + * @param[in] algorithmTag Tag to select the alignment algorithm (see @link AlignmentAlgorithmTags @endlink). + * + * @return TScoreVal Score value of the resulting alignment (Metafunction: @link Score#Value @endlink of + * the type of scoringScheme). + * + * There exist multiple overloads for this function with four configuration dimensions. + * + * First, you can select whether begin and end gaps are free in either sequence using alignConfig. + * + * Second, you can select the type of the target storing the alignment. This can be either an @link Align @endlink + * object, two @link Gaps @endlink objects, a @link AlignmentGraph @endlink, or a string of @link Fragment @endlink + * objects. @link Align @endlink objects provide an interface to tabular alignments with the restriction of all rows + * having the same type. Using two @link Gaps @endlink objects has the advantage that you an align sequences with + * different types, for example @link DnaString @endlink and @link Dna5String @endlink. @link AlignmentGraph Alignment + * Graphs @endlink provide a graph-based representation of segment-based colinear alignments. Using @link Fragment + * @endlink strings is useful for collecting many pairwise alignments, for example in the construction of @link + * AlignmentGraph Alignment Graphs @endlink for multiple-sequence alignments (MSA). + * + * Third, you can optionally give a band for the alignment using lowerDiag and upperDiag. The center + * diagonal has index 0, the ith diagonal below has index -i, the ith above has + * index i. + * + * Fourth, you can select the algorithm to use with algorithmTag. This can be one of @link + * AlignmentAlgorithmTags#NeedlemanWunsch @endlink and @link AlignmentAlgorithmTags#Gotoh @endlink. The + * Needleman-Wunsch algorithm supports scoring schemes with linear gap costs only while Gotoh's algorithm also allows + * affine gap costs. + * + * The available alignment algorithms all have some restrictions. Gotoh's algorithm can handle arbitrary substitution + * and affine gap scores. Needleman-Wunsch is limited to linear gap scores. The implementation of Hirschberg's + * algorithm is further limited that it does not support alignConfig objects or banding. The implementation of + * the Myers-Hirschberg algorithm further limits this to only support edit distance (as scores, matches are scored with + * 0, mismatches are scored with -1). + * + * The examples below show some common use cases. + * + * @section Examples + * + * Global alignment of two sequences using an @link Align @endlink object and + * the Needleman-Wunsch algorithm. + * + * @include demos/dox/align/global_alignment_unbanded.cpp + * + * The output is as follows: + * + * @include demos/dox/align/global_alignment_unbanded.cpp.stdout + * + * Global banded alignment of two sequences using two @link Gaps @endlink objects and the Gotoh algorithm. + * + * @include demos/dox/align/global_alignment_banded.cpp + * + * The output is as follows: + * + * @include demos/dox/align/global_alignment_banded.cpp.stdout + * + * https://seqan.readthedocs.io/en/develop/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.html + * + * @section References + * + *
    + *
  • Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence + * of two proteins. J Mol Biol 1970, 48(3): 443-53.
    • + *
  • Gotoh O: An improved algorithm for matching biological sequences. J Mol Biol 1982, 162(3):705-8
    • + *
+ * + * @see localAlignment + * @see globalAlignmentScore + * @see AlignmentAlgorithmTags + */ + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [unbanded, Align] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef Align TAlign; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String trace; + TScoreValue res; + DPScoutState_ dpScoutState; + res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), scoringScheme, + TAlignConfig2(), TGapModel()); + + _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(align, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignment(align, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(Align & align, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [unbanded, Gaps] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String traceSegments; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, source(gapsH), source(gapsV), scoringScheme, + TAlignConfig2(), TGapModel()); + _adaptTraceSegmentsTo(gapsH, gapsV, traceSegments); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [unbanded, Graph >] +// ---------------------------------------------------------------------------- + +// Full interface. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef Graph > TGraph; + typedef typename Position::Type TPosition; + typedef typename Size::Type TSize; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String traceSegments; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(stringSet(alignmentGraph), 0), + value(stringSet(alignmentGraph), 1), scoringScheme, TAlignConfig2(), + TGapModel()); + + _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0), + positionToId(stringSet(alignmentGraph), 1), traceSegments); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignment(alignmentGraph, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(Graph > & alignmentGraph, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignment(alignmentGraph, scoringScheme, alignConfig); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [unbanded, String >] +// ---------------------------------------------------------------------------- + +// Full interface. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef String, TStringSpec> TFragments; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + String traceSegments; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(traceSegments, dpScoutState, value(strings, 0), value(strings, 1), + scoringScheme, TAlignConfig2(), TGapModel()); + + _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), traceSegments); + return res; +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignment(fragmentString, strings, scoringScheme, alignConfig); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() +// ---------------------------------------------------------------------------- + +/*! + * @fn globalAlignmentScore + * @headerfile + * @brief Computes the best global pairwise alignment score. + * + * @signature TScoreVal globalAlignmentScore(seqH, seqV, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]); + * @signature TScoreVal globalAlignmentScore(strings, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]); + * @signature TScoreVal globalAlignmentScore(seqH, seqV, {MyersBitVector | MyersHirschberg}); + * @signature TScoreVal globalAlignmentScore(strings, {MyersBitVector | MyersHirschberg}); + * + * @param[in] seqH Horizontal gapped sequence in alignment matrix. Types: String + * @param[in] seqV Vertical gapped sequence in alignment matrix. Types: String + * @param[in] strings A @link StringSet @endlink containing two sequences. Type: StringSet. + * @param[in] alignConfig The @link AlignConfig @endlink to use for the alignment. Type: AlignConfig + * @param[in] scoringScheme The scoring scheme to use for the alignment. Note that the user is responsible for ensuring + * that the scoring scheme is compatible with algorithmTag. Type: @link Score @endlink. + * @param[in] lowerDiag Optional lower diagonal. Types: int + * @param[in] upperDiag Optional upper diagonal. Types: int + * @param[in] algorithmTag The Tag for picking the alignment algorithm. Types: @link PairwiseLocalAlignmentAlgorithms + * @endlink. + * + * @return TScoreVal Score value of the resulting alignment (Metafunction: @link Score#Value @endlink of + * the type of scoringScheme). + * + * This function does not perform the (linear time) traceback step after the (mostly quadratic time) dynamic programming + * step. Note that Myers' bit-vector algorithm does not compute an alignment (only in the Myers-Hirschberg variant) but + * scores can be computed using globalAlignmentScore. + * + * The same limitations to algorithms as in @link globalAlignment @endlink apply. Furthermore, the + * MyersBitVector and MyersHirschberg variants can only be used without any other parameter. + * + * @see https://seqan.readthedocs.io/en/develop/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.html + * @see globalAlignment + */ + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [unbanded, 2 Strings] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + DPScoutState_ dpScoutState; + String > traceSegments; // Dummy segments. + return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, TAlignConfig2(), TGapModel()); +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignmentScore(TSequenceH const & seqH, + TSequenceV const & seqV, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(seqH, seqV, scoringScheme, alignConfig); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [unbanded, StringSet] +// ---------------------------------------------------------------------------- + +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + SEQAN_ASSERT_EQ(length(strings), 2u); + + DPScoutState_ dpScoutState; + String > traceSegments; // Dummy segments. + return _setUpAndRunAlignment(traceSegments, dpScoutState, strings[0], strings[1], scoringScheme, TAlignConfig2(), + TGapModel()); +} + +// Interface without AlignConfig<>. +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + + AlignConfig<> alignConfig; + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +TScoreValue globalAlignmentScore(StringSet const & strings, + Score const & scoringScheme) +{ + SEQAN_ASSERT_EQ(length(strings), 2u); + + AlignConfig<> alignConfig; + return globalAlignmentScore(strings[0], strings[1], scoringScheme, alignConfig); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignmentScore() [unbanded, SIMD version, 2x StringSet] +// ---------------------------------------------------------------------------- + +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + SEQAN_ASSERT_EQ(length(stringsH), length(stringsV)); + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(stringsH, stringsV, scoringScheme, TAlignConfig2(), TGapModel()); +} + +// Interface without AlignConfig<>. +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +String globalAlignmentScore(StringSet const & stringsH, + StringSet const & stringsV, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringsH, stringsV, scoringScheme, alignConfig); +} + +// -------------------------------------------------------------------------------- +// Function globalAlignmentScore() [unbanded, SIMD version, String vs StringSet] +// -------------------------------------------------------------------------------- +template +String globalAlignmentScore(TString1 const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps, TracebackOff> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(stringH, stringsV, scoringScheme, TAlignConfig2(), TGapModel()); +} + +// Interface without AlignConfig<>. +template +String globalAlignmentScore(TString1 const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +String globalAlignmentScore(TString1 const & stringH, + StringSet const & stringsV, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +String globalAlignmentScore(TString1 const & stringH, + StringSet const & stringsV, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignmentScore(stringH, stringsV, scoringScheme, alignConfig); +} + +// ============================================================================ +// Many-vs-Many align interfaces. +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [unbanded, SIMD version, GapsH, GapsV] +// ---------------------------------------------------------------------------- + +template +inline auto +globalAlignment(StringSet, TSetSpecH> & gapSeqSetH, + StringSet, TSetSpecV> & gapSeqSetV, + Score const & scoringScheme, + AlignConfig const & /*alignConfig*/, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig TAlignConfig; + typedef typename SubstituteAlignConfig_::Type TFreeEndGaps; + typedef AlignConfig2, TFreeEndGaps> TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); +} + +// ---------------------------------------------------------------------------- +// Function globalAlignment() [unbanded, SIMD version, StringSet] +// ---------------------------------------------------------------------------- + +template +String globalAlignment(StringSet > & alignSet, + Score const & scoringScheme, + AlignConfig const & alignConfig, + TAlgoTag const & algoTag) +{ + typedef Align TAlign; + typedef typename Row::Type TGapSequence; + + StringSet > gapSetH; + StringSet > gapSetV; + reserve(gapSetH, length(alignSet)); + reserve(gapSetV, length(alignSet)); + + for (auto & align : alignSet) + { + appendValue(gapSetH, row(align, 0)); + appendValue(gapSetV, row(align, 1)); + } + + return globalAlignment(gapSetH, gapSetV, scoringScheme, alignConfig, algoTag); +} + +// Interface without AlignConfig<>. +template +String globalAlignment(StringSet > & align, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig, algoTag); +} + +// Interface without algorithm tag. +template +String globalAlignment(StringSet > & align, + Score const & scoringScheme, + AlignConfig const & alignConfig) +{ + if (scoreGapOpen(scoringScheme) == scoreGapExtend(scoringScheme)) + return globalAlignment(align, scoringScheme, alignConfig, NeedlemanWunsch()); + else + return globalAlignment(align, scoringScheme, alignConfig, Gotoh()); +} + +// Interface without AlignConfig<> and algorithm tag. +template +String globalAlignment(StringSet > & align, + Score const & scoringScheme) +{ + AlignConfig<> alignConfig; + return globalAlignment(align, scoringScheme, alignConfig); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GLOBAL_ALIGNMENT_UNBANDED_H_ diff --git a/seqan/align/local_alignment_banded.h b/seqan/align/local_alignment_banded.h new file mode 100644 index 0000000..8edcfd5 --- /dev/null +++ b/seqan/align/local_alignment_banded.h @@ -0,0 +1,298 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Interface functions for banded local alignment. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function localAlignment() [banded, Align] +// ---------------------------------------------------------------------------- + +template +TScoreValue localAlignment(Align & align, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TTag const & tag) +{ + typedef Align TAlign; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), + scoringScheme, TAlignConfig2(lowerDiag, upperDiag), tag); + + _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace); + return res; +} + +template +TScoreValue localAlignment(Align & align, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + SEQAN_ASSERT(length(rows(align)) == 2u); + if (_usesAffineGaps(scoringScheme, source(row(align, 0)), source(row(align, 1)))) + return localAlignment(align, scoringScheme, lowerDiag, upperDiag, AffineGaps()); + else + return localAlignment(align, scoringScheme, lowerDiag, upperDiag, LinearGaps()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [banded, Gaps] +// ---------------------------------------------------------------------------- + +template +TScoreValue localAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TTag const & tag) +{ + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), tag); + _adaptTraceSegmentsTo(gapsH, gapsV, trace); + return res; +} + +template +TScoreValue localAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + if (_usesAffineGaps(scoringScheme, source(gapsH), source(gapsV))) + return localAlignment(gapsH, gapsV, scoringScheme, lowerDiag, upperDiag, AffineGaps()); + else + return localAlignment(gapsH, gapsV, scoringScheme, lowerDiag, upperDiag, LinearGaps()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [banded, Graph >] +// ---------------------------------------------------------------------------- + +template +TScoreValue localAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TTag const & tag) +{ + typedef Graph > TGraph; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), + value(stringSet(alignmentGraph), 1), scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), tag); + + _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0), + positionToId(stringSet(alignmentGraph), 1), trace); + return res; +} + +template +TScoreValue localAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + SEQAN_ASSERT(length(stringSet(alignmentGraph)) == 2u); + + if (_usesAffineGaps(scoringScheme, stringSet(alignmentGraph)[0], stringSet(alignmentGraph)[1])) + return localAlignment(alignmentGraph, scoringScheme, lowerDiag, upperDiag, AffineGaps()); + else + return localAlignment(alignmentGraph, scoringScheme, lowerDiag, upperDiag, LinearGaps()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [banded, String >] +// ---------------------------------------------------------------------------- + +// Full interface. +template +TScoreValue localAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + int lowerDiag, + int upperDiag, + TTag const & tag) +{ + typedef String, TStringSpec> TFragments; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme, + TAlignConfig2(lowerDiag, upperDiag), tag); + _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace); + return res; +} + +template +TScoreValue localAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + int lowerDiag, + int upperDiag) +{ + SEQAN_ASSERT(length(strings) == 2u); + + if (_usesAffineGaps(scoringScheme, strings[0], strings[1])) + return localAlignment(fragmentString, strings, scoringScheme, lowerDiag, upperDiag, AffineGaps()); + else + return localAlignment(fragmentString, strings, scoringScheme, lowerDiag, upperDiag, LinearGaps()); +} + +// ============================================================================ +// Many-vs-Many align interfaces. +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function localAlignment() [banded, SIMD version, GapsH, GapsV] +// ---------------------------------------------------------------------------- + +template +inline auto +localAlignment(StringSet & gapSeqSetH, + StringSet & gapSeqSetV, + Score const & scoringScheme, + int const lowerDiag, + int const upperDiag, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [banded, SIMD version, StringSet] +// ---------------------------------------------------------------------------- + +template +inline String +localAlignment(StringSet, TSetSpec> & alignSet, + Score const & scoringScheme, + int const lowerDiag, + int const upperDiag, + TAlgoTag const & algoTag) +{ + typedef Align TAlign; + typedef typename Row::Type TGapSequence; + + StringSet > gapSetH; + StringSet > gapSetV; + reserve(gapSetH, length(alignSet)); + reserve(gapSetV, length(alignSet)); + + for (auto & align : alignSet) + { + appendValue(gapSetH, row(align, 0)); + appendValue(gapSetV, row(align, 1)); + } + + return localAlignment(gapSetH, gapSetV, scoringScheme, lowerDiag, upperDiag, algoTag); +} + +template +String localAlignment(StringSet > & align, + Score const & scoringScheme, + int lowerDiag, int upperDiag) +{ + if (_usesAffineGaps(scoringScheme, source(row(align[0], 0)), source(row(align[0], 1)))) + return localAlignment(align, scoringScheme, lowerDiag, upperDiag, AffineGaps()); + else + return localAlignment(align, scoringScheme, lowerDiag, upperDiag, LinearGaps()); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_H_ diff --git a/seqan/align/local_alignment_banded_waterman_eggert_impl.h b/seqan/align/local_alignment_banded_waterman_eggert_impl.h new file mode 100644 index 0000000..3f42d50 --- /dev/null +++ b/seqan/align/local_alignment_banded_waterman_eggert_impl.h @@ -0,0 +1,601 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Anne-Katrin Emde +// Author: Tobias Rausch +// Author: Birte Kehr +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// Legacy. +struct BandedWatermanEggert_; +typedef Tag BandedWatermanEggert; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _alignBandedSmithWaterman() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +_alignBandedSmithWaterman(LocalAlignmentFinder& finder, + TSequenceH const & seqH, + TSequenceV const & seqV, + TScore const& sc, + TScoreValue const cutoff, + TDiagonal const diagL, + TDiagonal const diagU) { + typedef typename Size::Type TSize; + typedef LocalAlignmentFinder TFinder; + + // Initialization + TSequenceH const& str1 = seqH; + TSequenceV const& str2 = seqV; + TSize len1 = length(str1); + TSize len2 = length(str2); + + TSize lo_row = (diagU <= 0) ? static_cast(-diagU) : 0; + TSize hi_row = len2;// + 1; + if (len1 - diagL < hi_row) hi_row = static_cast(len1 - diagL); + + TSize height = hi_row - lo_row + 1; + TSize diagonalWidth = (TSize) (diagU - diagL + 1); + + TSize actualCol, actualRow; + TScoreValue verti_val, hori_val; + + // Initialize iterators + typename TFinder::TMatrixIterator matIt = begin(finder.matrix); // Iterator in current row + goNext(matIt, 1); + typename TFinder::TMatrixIterator matIt2 = begin(finder.matrix); // Iterator in previous row (for diagonal and vertical value) + + for (TSize row = 1; row < height; ++row) { + actualRow = row + lo_row; + hori_val = 0; + + for (TSize col = 0; col < diagonalWidth; ++col, ++matIt) { + // handle begin and end triangle of band + if ((int)col + diagL + (int)actualRow < 0) {++matIt2; continue;} + actualCol = static_cast(col + diagL + actualRow); + if (actualCol > len1) {++matIt2; continue;} + + if (actualCol != 0) { + // Get the new maximum for diagonal + *matIt = *matIt2 + + score(const_cast(sc), sequenceEntryForScore(sc, str1, (int) actualCol - 1), + sequenceEntryForScore(sc, str2, (int) actualRow - 1)); + + ++matIt2; + + // Get the new maximum for vertical + if (col < diagonalWidth - 1) { + verti_val = *matIt2 + + scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, (int) actualCol - 1), + sequenceEntryForScore(sc, str2, (int) actualRow - 1)); + if (verti_val > *matIt) { + *matIt = verti_val; + } + } + + // Get the new maximum for horizontal + if (col > 0) { + hori_val = hori_val + + scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, (int) actualCol - 1), + sequenceEntryForScore(sc, str2, (int) actualRow - 1)); + if (hori_val > *matIt) { + *matIt = hori_val; + } + } + + // Check if new maximum is greater than 0 + if (0 > *matIt) { + *matIt = 0; + } + + // Record the new best score + if (*matIt >= cutoff) { + push(finder.pQ, ScoreAndID(*matIt, position(matIt))); + } + } else { + // First column (*matIt = 0) + ++matIt2; + } + hori_val = *matIt; + } + } + // // Debug code + // std::cerr << std::endl; + //for(TSize i= 0; i 0) std::cerr << " " << str2[i-1] << std::endl; + // else std::cerr << std::endl; + //} + // if(length(finder.pQ) > 0) std::cerr << "Max score: " << top(finder.pQ).value_ << std::endl; + + if(!empty(finder.pQ)) { + finder.bestEndPos = top(finder.pQ).id_; + return top(finder.pQ).value_; + } else { + return 0; + } +} + +// ---------------------------------------------------------------------------- +// Helper Function _alignBandedSmithWatermanDeclump() +// ---------------------------------------------------------------------------- + +template +inline void +_setForbiddenCell(String& forbidden, + TSize len1, + TSize len2, + TSize numRows) +{ + forbidden[(len1 - 1)*numRows + (len2 - 1)] = true; +} + + +template +inline void +_setForbiddenCell(Nothing&, + TSize, + TSize, + TSize) +{ +} + +// ---------------------------------------------------------------------------- +// Function _alignBandedSmithWatermanDeclump() +// ---------------------------------------------------------------------------- + +template +inline void +_alignBandedSmithWatermanDeclump(LocalAlignmentFinder& finder, + TSequenceH const & seqH, + TSequenceV const & seqV, + TScore const& sc, + TScoreValue const cutoff, + TDiagonal const diagL, + TDiagonal const diagU) +{ + typedef typename Size::Type TSize; + typedef LocalAlignmentFinder TFinder; + typedef unsigned char TTraceValue; + + // Traceback values + TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; + + TSequenceH const& str1 = seqH; + TSequenceV const& str2 = seqV; + TSize len1 = length(str1); + + TSize diagonalWidth = (TSize) (diagU - diagL + 1); + TSize lo_row = (diagU <= 0) ? static_cast(-diagU) : 0; + TSize hi_row = length(seqV);// + 1; + if (len1 - diagL < hi_row) hi_row = static_cast(len1 - diagL); + TSize height = hi_row - lo_row + 1; + + TSize actualRow, actualCol; + //TSize row, col; + + // Initialize iterators + typename TFinder::TMatrixIterator matIt = iter(finder.matrix, finder.bestBeginPos); + typename TFinder::TMatrixIterator matIt2; + + // Initialize column boundaries + TSize minCol = diagonalWidth, newMinCol = diagonalWidth; + TSize maxCol = 0, newMaxCol = 0; + TSize row = coordinate(matIt, 1); + TSize col = coordinate(matIt, 0); + TSize traceCol = col; + + matIt -= col; + + // Initialize position in trace + TSize tracePos = length(finder.trace.sizes); + while (tracePos > 0 && finder.trace.tvs[tracePos-1] != Diagonal) --tracePos; + if (tracePos == 0) return; + TSize traceSize = finder.trace.sizes[tracePos-1]; + TTraceValue traceValue = finder.trace.tvs[tracePos-1]; + + // iterate over rows + while((row < height) && ((maxCol > minCol) || (tracePos > 0))) { + actualRow = row + lo_row; + + // make sure that all matrix entries of trace are re-calculated and set to forbidden + while (traceSize == 0 && tracePos > 1) { + // determine next trace direction + --tracePos; + traceValue = finder.trace.tvs[tracePos-1]; + if (traceValue == Horizontal) { + traceCol += finder.trace.sizes[tracePos-1]; + } else { + traceSize = finder.trace.sizes[tracePos-1]; + } + } + if (tracePos > 0) { + // follow the trace in the current row + if (traceValue == Diagonal) { + --traceSize; + _setForbiddenCell(finder.forbidden, row+1, traceCol+1, diagonalWidth); + minCol = _min(minCol, traceCol); + maxCol = _max(maxCol, traceCol+1); + } else if (traceValue == Vertical) { + if (traceCol > 0) --traceCol; + --traceSize; + } + + if (traceCol >= maxCol) { + maxCol = traceCol + 1; + } + } + + // iterate over columns that have to be re-calculated + if (maxCol > minCol) { + col = minCol; + matIt += col; + matIt2 = matIt - diagonalWidth; + while (col < maxCol) { + actualCol = static_cast(col + diagL + actualRow); + if (actualCol > len1) break; + + TScoreValue newVal = 0; + + // diagonal + if (!value(finder.forbidden, position(matIt))) { + newVal = _max(newVal, *matIt2 + score(sc, sequenceEntryForScore(sc, str1, (int)actualCol-1), + sequenceEntryForScore(sc, str2, (int)actualRow-1))); + } + ++matIt2; + + // horizontal + if (col > 0) { + newVal = _max(newVal, *(matIt-1) + + scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, (int) actualCol-1), + sequenceEntryForScore(sc, str2, (int)actualRow-1))); + } + + // vertical + if (col+1 < maxCol) { + newVal = _max(newVal, *matIt2 + + scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, (int)actualCol-1), + sequenceEntryForScore(sc, str2, (int)actualRow-1))); + } + + if (newVal != *matIt) { + // matrix entry changed + *matIt = newVal; + maxCol = _min(_max(maxCol, col+2), diagonalWidth); + newMaxCol = _max(newMaxCol, col+1); + newMinCol = ((col != 0) ? _min(newMinCol, col-1) : 0); + + // Record the new best score + if (newVal >= cutoff) { + push(finder.pQ, ScoreAndID(newVal, position(matIt))); + } + } else { + // matrix entry did not change + if (col == minCol) { + ++minCol; + } + } + ++col; + ++matIt; + } + matIt += diagonalWidth - col; + } else { + matIt += diagonalWidth; + } + + minCol = _max((TSize)0, newMinCol); + maxCol = _min(diagonalWidth, newMaxCol); + newMinCol = diagonalWidth; + newMaxCol = 0; + + ++row; + } + // // Debug code + // std::cerr << std::endl; + // for (TSize i = 0; i < height; ++i) { + // for(TSize j = 0; j < diagonalWidth; ++j) { + // std::cerr << value(finder.matrix, j, i) << ','; + // } + //if (i > 0) std::cerr << " " << str2[i-1] << " "; + //else std::cerr << " "; + // for (TSize j= 0; j 0) std::cerr << " " << str2[i-1] << std::endl; + //else std::cerr << std::endl; + // } +} + +// ---------------------------------------------------------------------------- +// Function _alignBandedSmithWatermanTrace() +// ---------------------------------------------------------------------------- + +template +inline Pair > +_alignBandedSmithWatermanTrace(LocalAlignmentFinder & finder, + TSequenceH const & seqH, + TSequenceV const & seqV, + TId id1, + TId id2, + TScore& sc, + TDiagonal diagL, + TDiagonal diagU) +{ + typedef LocalAlignmentFinder TFinder; + typedef typename Size::Type TSize; + typedef unsigned char TTraceValue; + + clear(finder.trace.sizes); + clear(finder.trace.tvs); + + // Traceback values + TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2; TTraceValue Stop = 3; + + // Initialization + TSequenceH const& str1 = seqH; + TSequenceV const& str2 = seqV; + TSize len1 = length(str1); + TSize len2 = length(str2); + + TSize lo_row = (diagU <= 0) ? static_cast(-diagU) : 0; + //TSize diagonalWidth = static_cast(diagU - diagL + 1); + + // Start the trace from the cell with the max value + typename TFinder::TMatrixIterator matIt = iter(finder.matrix, finder.bestEndPos); + typename TFinder::TMatrixIterator matIt2 = iter(finder.matrix, finder.bestEndPos); + goPrevious(matIt2, 1); + + TSize row = coordinate(matIt, 1); + TSize col = coordinate(matIt, 0); + TSize endRow = row + lo_row; + TSize endCol = static_cast(col + diagL + endRow); + + TSize actualRow = row + lo_row; + TSize actualCol = static_cast(col + diagL + actualRow); + if ((actualCol == 0) || (actualRow == 0)) + return Pair >(); + + if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); + if (actualRow < len2) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len2 - actualRow, Vertical); + + TTraceValue traceValue = Stop; + TTraceValue nextTraceValue = Horizontal; + TSize segLen = 0; + + while (nextTraceValue != Stop) { + traceValue = nextTraceValue; + if (*matIt == 0) { + nextTraceValue = Stop; + } + else if (*matIt == *matIt2 + + score(const_cast(sc), sequenceEntryForScore(sc, str1, (int)actualCol-1), + sequenceEntryForScore(sc, str2, (int)actualRow-1))) + { + nextTraceValue = Diagonal; + --actualRow; --actualCol; + --row; + goPrevious(matIt, 1); + goPrevious(matIt2, 1); + } else if (*matIt == *(matIt2+1) + + scoreGapExtendVertical(sc, sequenceEntryForScore(sc, str1, (int)actualCol-1), + sequenceEntryForScore(sc, str2, (int)actualRow-1))) + { + nextTraceValue = Vertical; + --actualRow; + --row; ++col; + goPrevious(matIt, 1); goNext(matIt, 0); + goPrevious(matIt2, 1); goNext(matIt2, 0); + } else { + SEQAN_ASSERT_EQ(*matIt, *(matIt-1) + + scoreGapExtendHorizontal(sc, sequenceEntryForScore(sc, str1, (int) actualCol-1), + sequenceEntryForScore(sc, str2, (int) actualRow-1))); + nextTraceValue = Horizontal; + --actualCol; + --col; + goPrevious(matIt, 0); + goPrevious(matIt2, 0); + } + if (traceValue == nextTraceValue) { + ++segLen; + } else { + _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, segLen, traceValue); + segLen = 1; + } + } + + // Handle the remaining sequence + if (actualCol != 0) _alignTracePrint(finder.trace, seqH, seqV, (TId) id1, (TSize) 0, (TId) 0, (TSize) 0, (TSize) actualCol, Horizontal); + if (actualRow != 0) _alignTracePrint(finder.trace, seqH, seqV, (TId) 0, (TSize) 0, (TId) id2, (TSize) 0, (TSize) actualRow, Vertical); + + goNext(matIt, 1); // assumes that each trace ends with a diagonal + finder.bestBeginPos = position(matIt); + + return Pair >(Pair(actualCol, endCol), Pair(actualRow, endRow)); +} + +// ---------------------------------------------------------------------------- +// Function _initLocalAlignmentFinder() +// ---------------------------------------------------------------------------- + +template +void +_initLocalAlignmentFinder(TSequenceH const & seqH, + TSequenceV const & seqV, + LocalAlignmentFinder & finder, + BandedWatermanEggert const &, + TDiagonal const lowerDiag, + TDiagonal const upperDiag) { + typedef LocalAlignmentFinder TFinder; + typedef typename TFinder::TMatrix TMatrix; + typedef typename Size::Type TSize; + + TSize lo_row = (upperDiag <= 0) ? static_cast(-upperDiag) : 0; + TSize hi_row = length(seqV) + 1; + TSize len0 = length(seqH); + if (len0 - lowerDiag < hi_row) hi_row = static_cast(len0 - lowerDiag); + TSize height = hi_row - lo_row + 1; + SEQAN_ASSERT_GEQ(upperDiag, lowerDiag); + TSize diagonalWidth = (TSize) (upperDiag - lowerDiag + 1); + + setDimension(finder.matrix, 2); + setLength(finder.matrix, 0, diagonalWidth); + setLength(finder.matrix, 1, height); + resize(finder.matrix, 0); + + resize(finder.forbidden, height * diagonalWidth, false); + + finder.bestEndPos = minValue(); + finder.bestBeginPos = minValue(); +} + +// ---------------------------------------------------------------------------- +// Function _localAlignment() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +_localAlignment(LocalAlignmentFinder & finder, + Gaps & gapsH, + Gaps & gapsV, + Score const& sc, + TScoreValue cutoff, + TDiagonal diag1, + TDiagonal diag2, + BandedWatermanEggert const /*algorithmTag*/) +{ + clearGaps(gapsH); + clearClipping(gapsH); + clearGaps(gapsV); + clearClipping(gapsV); + + _initLocalAlignmentFinder(source(gapsH), source(gapsV), finder, BandedWatermanEggert(), diag1, diag2); + finder.needReinit = false; + + // Fill the matrix + TScoreValue maxScore = _alignBandedSmithWaterman(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); + if (maxScore < cutoff) return 0; + + // Follow the matrix back from max entry and create a trace path + Pair > alignmentPositions = _alignBandedSmithWatermanTrace(finder, source(gapsH), source(gapsV), 0u, 0u, sc, diag1, diag2); + + // Fill the gaps following the trace path. + _pumpTraceToGaps(gapsH, gapsV, finder.trace); + + // The following (using rightOfGaps = false) only works if the gap open cost is negative. In this case, we can + // assume that there are no leading or trailing gaps in either sequence. + // + // We need this assumption because the we get source positions through alignmentPositions and conversion from + // souce to view coordinates gives us the end of a gap if we are at the beginning. + // + // TODO(holtgrew): This should be done in a more robust way. It would probably be better if alignmentPositions gave us the lengths of the local alignments! + setClippedEndPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i2, false)); + setClippedEndPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i2, false)); + setClippedBeginPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i1)); + setClippedBeginPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i1)); + + pop(finder.pQ); + + return maxScore; +} + +// ---------------------------------------------------------------------------- +// Function _localAlignmentNext() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +_localAlignmentNext(LocalAlignmentFinder & finder, + Gaps & gapsH, + Gaps & gapsV, + TScore const& sc, + TScoreValue cutoff, + TDiagonal diag1, + TDiagonal diag2, + BandedWatermanEggert const & /*algorithmTag*/) { + // Declump the matrix and find new maximum score + _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); + typename LocalAlignmentFinder::TMatrixPosition nextBestEnd; + nextBestEnd = _getNextBestEndPosition(finder, cutoff); + if(nextBestEnd==0) + return 0; + TScoreValue maxScore = getValue(finder.matrix, nextBestEnd); + if(maxScore == 0) return 0; + + // Follow the trace matrix and create a trace path + Pair > alignmentPositions = _alignBandedSmithWatermanTrace(finder, source(gapsH), source(gapsV), 0u, 0u, sc, diag1, diag2); + + // Fill the gaps following the trace path. + _pumpTraceToGaps(gapsH, gapsV, finder.trace); + + // The following (using rightOfGaps = false) only works if the gap open cost is negative. In this case, we can + // assume that there are no leading or trailing gaps in either sequence. + // + // We need this assumption because the we get source positions through alignmentPositions and conversion from + // souce to view coordinates gives us the end of a gap if we are at the beginning. + // + // TODO(holtgrew): This should be done in a more robust way. It would probably be better if alignmentPositions gave us the lengths of the local alignments! + setClippedEndPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i2, false)); + setClippedEndPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i2, false)); + setClippedBeginPosition(gapsH, toViewPosition(gapsH, alignmentPositions.i1.i1)); + setClippedBeginPosition(gapsV, toViewPosition(gapsV, alignmentPositions.i2.i1)); + + return maxScore; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_BANDED_WATERMAN_EGGERT_IMPL_H_ diff --git a/seqan/align/local_alignment_enumeration.h b/seqan/align/local_alignment_enumeration.h new file mode 100644 index 0000000..0dd6946 --- /dev/null +++ b/seqan/align/local_alignment_enumeration.h @@ -0,0 +1,220 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class LocalAlignmentEnumerator +// ---------------------------------------------------------------------------- + +template +class LocalAlignmentEnumerator; + +/*! + * @class LocalAlignmentEnumerator + * @headerfile + * @brief Enumeration of local alignments. + * + * @signature template + * class LocalAlignmentEnumerator; + * + * @tparam TScore The type of the @link Score @endlink to use for the local alignment. + * @tparam TSpec The tag to use for specializing the enumerator. + * + * This is an abstract class that will only be instantiated through its subclasses. + * See the documentation of the specializations for examples. + * + * @section References + * + *
    + *
  • Waterman MS, Eggert M: A new algorithm for best subsequence alignments with application to tRNA-rRNA + * comparisons. J Mol Biol 1987, 197(4):723-728.
    • + *
+ */ + +/*! + * @class UnbandedLocalAlignmentEnumerator + * @extends LocalAlignmentEnumerator + * @headerfile + * @brief Unbanded enumeration of local alignments using the Waterman-Eggert algorithm. + * + * @signature template + * class LocalAlignmentEnumerator; + * + * @tparam TScore The @link Score @endlink type. + * + * @section Examples + * + * Enumerate all alignments into a @link Align @endlink object. + * + * @code{.cpp} + * SimpleScore scoringScheme(2, -1, -1, -2); + * LocalAlignmentEnumerator enumerator(scoringScheme, 5); + * + * Dna5String seqH = "CGAGAGAGACCGAGA"; + * Dna5String seqV = "TTCTGAGATCCGTTTTT"; + * + * Align align; + * resize(rows(align), 2);@s + * assignSource(row(align), 0, seqH); + * assignSource(row(align), 1, seqV); + * + * int i = 0; + * while (nextLocalAlignment(align, enumerator)) + * { + * std::cout << i << "-th alignment:\n"; + * std::cout << align << "\n\n"; + * std::cout << "score == " << getScore(enumerator) << "\n"; + * } + * @endcode + */ + +/*! + * @fn UnbandedLocalAlignmentEnumerator::LocalAlignmentEnumerator + * @brief Constructor. + * + * @signature LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme[, cutoff]); + * + * @param[in] scheme The @link Score @endlink object to use for the alignment score. + * @param[in] cutoff Alignments with scores < cutoff will be discarded (int, default 0). + */ + +/*! + * @class BandedLocalAlignmentEnumerator + * @extends LocalAlignmentEnumerator + * @headerfile + * @brief Banded enumeration of local alignments using the Waterman-Eggert algorithm. + * + * @signature template + * class LocalAlignmentEnumerator; + * + * @tparam TScore The @link Score @endlink type. + * + * @section Examples + * + * Enumerate all alignments in the band between -3 and 0 into an @link Align @endlink object. + * + * @code{.cpp} + * SimpleScore scoringScheme(2, -1, -1, -2); + * LocalAlignmentEnumerator enumerator(scoringScheme, -3, 0, 5); + * + * Dna5String seqH = "CGAGAGAGACCGAGA"; + * Dna5String seqV = "TTCTGAGATCCGTTTTT"; + * + * Align align; + * resize(rows(align), 2); + * assignSource(row(align), 0, seqH); + * assignSource(row(align), 1, seqV); + * + * int i = 0; + * while (nextLocalAlignment(align, enumerator)) + * { + * std::cout << i << "-th alignment:\n"; + * std::cout << align << "\n\n"; + * std::cout << "score == " << getScore(enumerator) << "\n"; + * } + * @endcode + */ + +/*! + * @fn BandedLocalAlignmentEnumerator::LocalAlignmentEnumerator + * @brief Constructor. + * + * @signature LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme, upperDiag, lowerDiag[, cutoff]); + * + * @param[in] scheme The @link Score @endlink object to use for the alignment score. + * @param[in] upperDiag An int with the upper diagonal. + * @param[in] lowerDiag An int with the lower diagonal. + * @param[in] cutoff Alignments with scores < cutoff will be discarded (int, default 0). + */ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function getScore() +// ---------------------------------------------------------------------------- + +/*! + * @fn LocalAlignmentEnumerator#getScore + * @headerfile + * @brief Get current alignment score. + * + * @signature TScoreVal getScore(enumerator); + * + * @param[in] enumerator The LocalAlignmentEnumerator to query. + * + * @return TScoreVal The current alignment score (@link Score#Value @endlink of TScore). + */ + +// ---------------------------------------------------------------------------- +// Function nextLocalAlignment() +// ---------------------------------------------------------------------------- + +/*! + * @fn LocalAlignmentEnumerator#nextLocalAlignment + * @headerfile + * @brief Compute next suboptimal local alignment. + * + * @signature bool nextLocalAlignment(align, enumerator); + * @signature bool nextLocalAlignment(gapsH, gapsV, enumerator); + * + * @param[in] align @link Align @endlink object to use for the alignment representation. + * @param[in] gapsH @link Gaps @endlink object to use for the first/horizontal sequence in the alignment matrix. + * @param[in] gapsV @link Gaps @endlink object to use for the second/vertical sequence in the alignment matrix. + * @param[in] enumerator The LocalAlignmentEnumerator to advance. + * + * @return bool true if another suboptimal alignment above the given threshold was found and false + * otherwise. + */ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_H_ diff --git a/seqan/align/local_alignment_enumeration_banded.h b/seqan/align/local_alignment_enumeration_banded.h new file mode 100644 index 0000000..4172d79 --- /dev/null +++ b/seqan/align/local_alignment_enumeration_banded.h @@ -0,0 +1,126 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Specialization Banded LocalAlignmentEnumerator +// ---------------------------------------------------------------------------- + +struct Banded_; +typedef Tag Banded; + +template +class LocalAlignmentEnumerator +{ +public: + typedef typename Value::Type TScoreValue_; + + TScore _score; + int _lowerDiag; + int _upperDiag; + TScoreValue_ _cutoff; + LocalAlignmentFinder _finder; + + LocalAlignmentEnumerator(TScore const & score, int lowerDiag, int upperDiag) : + _score(score), _lowerDiag(lowerDiag), _upperDiag(upperDiag), _cutoff(0) + {} + + LocalAlignmentEnumerator(TScore const & score, int lowerDiag, int upperDiag, int cutoff) : + _score(score), _lowerDiag(lowerDiag), _upperDiag(upperDiag), _cutoff(cutoff) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function getScore() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +getScore(LocalAlignmentEnumerator, Banded> const & enumerator) +{ + return getScore(enumerator._finder); +} + +// ---------------------------------------------------------------------------- +// Function nextLocalAlignment() +// ---------------------------------------------------------------------------- + +template +inline bool +nextLocalAlignment(Gaps & gapsH, + Gaps & gapsV, + LocalAlignmentEnumerator, Banded> & enumerator) +{ + if (enumerator._finder.needReinit) + return _localAlignment(enumerator._finder, gapsH, gapsV, enumerator._score, enumerator._cutoff, + enumerator._lowerDiag, enumerator._upperDiag, BandedWatermanEggert()); + else + return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, + enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, + BandedWatermanEggert()); +} + +template +inline bool +nextLocalAlignment(Align & align, + LocalAlignmentEnumerator, Banded> & enumerator) +{ + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + + return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_BANDED_H_ diff --git a/seqan/align/local_alignment_enumeration_unbanded.h b/seqan/align/local_alignment_enumeration_unbanded.h new file mode 100644 index 0000000..a5efcb8 --- /dev/null +++ b/seqan/align/local_alignment_enumeration_unbanded.h @@ -0,0 +1,122 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Specialization Unbanded LocalAlignmentEnumerator +// ---------------------------------------------------------------------------- + +struct Unbanded_; +typedef Tag Unbanded; + +template +class LocalAlignmentEnumerator +{ +public: + typedef typename Value::Type TScoreValue_; + + TScore _scoringScheme; + TScoreValue_ _cutoff; + LocalAlignmentFinder _finder; + + LocalAlignmentEnumerator(TScore const & score) : + _scoringScheme(score), _cutoff(0) + {} + + LocalAlignmentEnumerator(TScore const & score, int cutoff) : + _scoringScheme(score), _cutoff(cutoff) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function getScore() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +getScore(LocalAlignmentEnumerator, Unbanded> const & enumerator) +{ + // TODO(holtgrew): Const correctness! + return getScore(const_cast &>(enumerator._finder)); +} + +// ---------------------------------------------------------------------------- +// Function nextLocalAlignment() +// ---------------------------------------------------------------------------- + +template +inline bool +nextLocalAlignment(Gaps & gapsH, + Gaps & gapsV, + LocalAlignmentEnumerator, Unbanded> & enumerator) +{ + if (enumerator._finder.needReinit) + return _smithWaterman(gapsH, gapsV, enumerator._finder, enumerator._scoringScheme, enumerator._cutoff); + else + return _smithWatermanGetNext(gapsH, gapsV, enumerator._finder, enumerator._scoringScheme, enumerator._cutoff); +} + +template +inline bool +nextLocalAlignment(Align & align, + LocalAlignmentEnumerator, Unbanded> & enumerator) +{ + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + + return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_ENUMERATION_UNBANDED_H_ diff --git a/seqan/align/local_alignment_unbanded.h b/seqan/align/local_alignment_unbanded.h new file mode 100644 index 0000000..a6a920f --- /dev/null +++ b/seqan/align/local_alignment_unbanded.h @@ -0,0 +1,381 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Interface functions for unbanded local alignment. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function localAlignment() +// ---------------------------------------------------------------------------- + +/*! + * @fn localAlignment + * @headerfile + * @brief Computes the best pairwise local alignment using the Smith-Waterman algorithm. + * + * @signature TScoreVal localAlignment(align, scoringScheme, [lowerDiag, upperDiag]); + * @signature TScoreVal localAlignment(gapsH, gapsV, scoringScheme, [lowerDiag, upperDiag]); + * @signature TScoreVal localAlignment(fragmentString, scoringScheme, [lowerDiag, upperDiag]); + * + * @param[in,out] gapsH Horizontal gapped sequence in alignment matrix. Types: @link Gaps @endlink + * @param[in,out] gapsV Vertical gapped sequence in alignment matrix. Types: @link Gaps @endlink + * @param[in,out] align An @link Align @endlink object that stores the alignment. The + * number of rows must be 2 and the sequences must have already + * been set. align[0] is the horizontal one in the + * alignment matrix alignment, align[1] is the vertical + * one. + * @param[in,out] fragmentString + * String of @link Fragment @endlink objects. The sequence + * with id 0 is the horizontal one, the sequence + * with id 1 is the vertical one. + * @param[in] scoringScheme + * The @link Score scoring scheme @endlink to use for the alignment. + * @param[in] lowerDiag Optional lower diagonal (int). + * @param[in] upperDiag Optional upper diagonal (int). + * + * @return TScoreVal Score value of the resulting alignment (Metafunction @link Score#Value @endlink of the type of + * scoringScheme). + * + * The Waterman-Eggert algorithm (local alignment with declumping) is available through the @link + * LocalAlignmentEnumerator @endlink class. + * + * When using @link Gaps @endlink and @link Align @endlink objects, only parts (i.e. one infix) of each sequence will be + * aligned. This will be presented to the user by setting the clipping begin and end position of the gaps (the rows in + * the case of @link Align @endlink objects). When using @link Fragment @endlink strings, these parts of the sequences + * will not appear in any fragment. + * + * There exist multiple overloads for this function with two configuration dimensions. + * + * First, you can select the type of the target storing the alignment. This can be either an @link Align @endlink + * object, two @link Gaps @endlink objects, or a string of @link Fragment @endlink objects. @link Align @endlink objects + * provide an interface to tabular alignments with the restriction of all rows having the same type. Using two @link + * Gaps @endlink objects has the advantage that you an align sequences with different types, for example @link DnaString + * @endlink and @link Dna5String @endlink. Using @link Fragment @endlink strings is useful for collecting many pairwise + * alignments, for example in the construction of @link AlignmentGraph Alignment Graphs @endlink for multiple- sequence + * alignments (MSA). + * + * Second, you can optionally give a band for the alignment using lowerDiag and upperDiag. The center + * diagonal has index 0, the ith diagonal below has index -i, the ith above has + * index i. + * + * The examples below show some common use cases. + * + * @section Examples + * + * Local alignment of two sequences using an @link Align @endlink object. + * + * @code{.cpp} + * Dna5String seqH = "CGATT"; + * Dna5String seqV = "CGAAATT"; + * + * Align align; + * resize(rows(align), 2); + * assignSource(row(align, 0), seqH); + * assignSource(row(align, 0), seqV); + * Score scoringScheme(2, -1, -2); + * + * int result = localAlignment(align, scoringScheme); + * @endcode + * + * Local banded alignment of two sequences using two @link Gaps @endlink objects. + * + * @code{.cpp} + * Dna5String seqH = "CGATT"; + * Gaps gapsH(seqH); + * DnaString seqV = "CGAAATT"; + * Gaps > gapsV(seqV); + * + * Score scoringScheme(5, -3, -1, -5); + * + * int result = localAlignment(gapsH, gapsV, scoringScheme, -2, 2); + * @endcode + * + * https://seqan.readthedocs.io/en/develop/Tutorial/Algorithms/Alignment/PairwiseSequenceAlignment.html + * + * @section References + * + *
    + *
  • Smith TF, Waterman, MS: Identification of Common Molecular Subsequences. J Mol Biol 1981, 147(1):195-7.
    • + *
+ * + * @see globalAlignment + * @see LocalAlignmentEnumerator + * @see PairwiseLocalAlignmentAlgorithms + */ + +// ---------------------------------------------------------------------------- +// Function localAlignment() [unbanded, Align] +// ---------------------------------------------------------------------------- + +template +TScoreValue localAlignment(Align & align, + Score const & scoringScheme, + TTag const & tag) +{ + SEQAN_ASSERT_EQ(length(rows(align)), 2u); + typedef Align TAlign; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), + scoringScheme, TAlignConfig2(), tag); + + _adaptTraceSegmentsTo(row(align, 0), row(align, 1), trace); + return res; +} + + template + TScoreValue localAlignment(Align & align, + Score const & scoringScheme) + { + SEQAN_ASSERT(length(rows(align)) == 2u); + if (_usesAffineGaps(scoringScheme, source(row(align, 0)), source(row(align, 1)))) + return localAlignment(align, scoringScheme, AffineGaps()); + else + return localAlignment(align, scoringScheme, LinearGaps()); + } + +// ---------------------------------------------------------------------------- +// Function localAlignment() [unbanded, Gaps] +// ---------------------------------------------------------------------------- + + template + TScoreValue localAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme, + TTag const & tag) + { + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, + TAlignConfig2(), tag); + _adaptTraceSegmentsTo(gapsH, gapsV, trace); + return res; + } + + template +TScoreValue localAlignment(Gaps & gapsH, + Gaps & gapsV, + Score const & scoringScheme) +{ + if (_usesAffineGaps(scoringScheme, source(gapsH), source(gapsV))) + return localAlignment(gapsH, gapsV, scoringScheme, AffineGaps()); + else + return localAlignment(gapsH, gapsV, scoringScheme, LinearGaps()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [unbanded, Graph>] +// ---------------------------------------------------------------------------- + +// Full interface. + +template +TScoreValue localAlignment(Graph > & alignmentGraph, + Score const & scoringScheme, + TTag const & tag) +{ + typedef Graph > TGraph; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(stringSet(alignmentGraph), 0), + value(stringSet(alignmentGraph), 1), scoringScheme, TAlignConfig2(), tag); + + _adaptTraceSegmentsTo(alignmentGraph, positionToId(stringSet(alignmentGraph), 0), + positionToId(stringSet(alignmentGraph), 1), trace); + return res; +} + +template +TScoreValue localAlignment(Graph > & alignmentGraph, + Score const & scoringScheme) +{ + SEQAN_ASSERT(length(stringSet(alignmentGraph)) == 2u); + + if (_usesAffineGaps(scoringScheme, stringSet(alignmentGraph)[0], stringSet(alignmentGraph)[1])) + return localAlignment(alignmentGraph, scoringScheme, AffineGaps()); + else + return localAlignment(alignmentGraph, scoringScheme, LinearGaps()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [unbanded, String >] +// ---------------------------------------------------------------------------- + +// Full interface. + +template +TScoreValue localAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme, + TTag const & tag) +{ + typedef String, TStringSpec> TFragments; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + + String trace; + DPScoutState_ dpScoutState; + TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, value(strings, 0), value(strings, 1), scoringScheme, + TAlignConfig2(), tag); + + _adaptTraceSegmentsTo(fragmentString, positionToId(strings, 0), positionToId(strings, 1), trace); + return res; +} + +template +TScoreValue localAlignment(String, TStringSpec> & fragmentString, + StringSet const & strings, + Score const & scoringScheme) +{ + SEQAN_ASSERT(length(strings) == 2u); + + if (_usesAffineGaps(scoringScheme, strings[0], strings[1])) + return localAlignment(fragmentString, strings, scoringScheme, AffineGaps()); + else + return localAlignment(fragmentString, strings, scoringScheme, LinearGaps()); +} + +// ============================================================================ +// Many-vs-Many align interfaces. +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function localAlignment() [unbanded, SIMD version, GapsH, GapsV] +// ---------------------------------------------------------------------------- + +template +inline auto +localAlignment(StringSet & gapSeqSetH, + StringSet & gapSeqSetV, + Score const & scoringScheme, + TAlgoTag const & /*algoTag*/) +{ + typedef AlignConfig2, FreeEndGaps_<> > TAlignConfig2; + typedef typename SubstituteAlgoTag_::Type TGapModel; + + return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); +} + +// ---------------------------------------------------------------------------- +// Function localAlignment() [unbanded, SIMD version, StringSet] +// ---------------------------------------------------------------------------- + +template +inline String +localAlignment(StringSet > & alignSet, + Score const & scoringScheme, + TAlgoTag const & algoTag) +{ + typedef Align TAlign; + typedef typename Row::Type TGapSequence; + + StringSet > gapSetH; + StringSet > gapSetV; + reserve(gapSetH, length(alignSet)); + reserve(gapSetV, length(alignSet)); + + for (auto & align : alignSet) + { + appendValue(gapSetH, row(align, 0)); + appendValue(gapSetV, row(align, 1)); + } + + return localAlignment(gapSetH, gapSetV, scoringScheme, algoTag); +} + +template +String localAlignment(StringSet > & align, + Score const & scoringScheme) +{ + if (_usesAffineGaps(scoringScheme, source(row(align[0], 0)), source(row(align[0], 1)))) + return localAlignment(align, scoringScheme, AffineGaps()); + else + return localAlignment(align, scoringScheme, LinearGaps()); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_UNBANDED_H_ diff --git a/seqan/align/local_alignment_waterman_eggert_impl.h b/seqan/align/local_alignment_waterman_eggert_impl.h new file mode 100644 index 0000000..e78fc33 --- /dev/null +++ b/seqan/align/local_alignment_waterman_eggert_impl.h @@ -0,0 +1,751 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Anne-Katrin Emde +// ========================================================================== +// Implementation of the Waterman-Eggert algorithm, sometimes also called +// Smith-Waterman algorithm with declumping. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Helper Class ScoreAndID +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Why is Pair<> not enough? +// TODO(holtgrew): Rename to ScoreAndID_ (with trailing underscore) + +// Simple class that stores a value with an ID. +template +class ScoreAndID +{ +public: + TValue value_; + TID id_; + + ScoreAndID() : value_(MinValue::VALUE), id_(MaxValue::VALUE) + {} + + ScoreAndID(TValue score, TID id_pos) + { + value_ = score; + id_ = id_pos; + } + + inline bool operator>(ScoreAndID const & other) const + { + return value_ > other.value_; + } + + inline bool operator<(ScoreAndID const & other) const + { + return value_ < other.value_; + } +}; + +// ---------------------------------------------------------------------------- +// Class LocalAlignmentFinder +// ---------------------------------------------------------------------------- + +template +class LocalAlignmentFinder +{ +public: + typedef Matrix TMatrix; + typedef typename Position::Type TMatrixPosition; + typedef typename Size::Type TSize; + typedef ScoreAndID TPQEntry; + + typedef Iter TMatrixIterator; + typedef PriorityType TPriorityQ; + typedef String TBoolMatrix; + + //DP-matrix + TMatrix matrix; + //matrix that memorizes the cells from which not to go diagonal + TBoolMatrix forbidden; + //priority queue for quickly finding the maximum score in the DP-matrix + TPriorityQ pQ; + //position of maximum score (where traceback is started from) + TMatrixPosition bestEndPos; + //position where traceback ended and where declumping begins + TMatrixPosition bestBeginPos; + //traceback path that is set to forbidden while declumping + AlignTraceback trace; + + bool needReinit; //true: call "smithWaterman", false: call "smithWatermanGetNext" + + LocalAlignmentFinder() : bestEndPos(0), bestBeginPos(0), needReinit(true) + {} + + // TODO(holtgrew): Remove and replace all occurrences with default constructor. + template + LocalAlignmentFinder(TAlign const &) : bestEndPos(0), bestBeginPos(0), needReinit(true) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _initLocalAlignmentFinder() +// ---------------------------------------------------------------------------- + +template +void +_initLocalAlignmentFinder(TSequenceH const & seqH, + TSequenceV const & seqV, + LocalAlignmentFinder & finder, + TTag) { + typedef LocalAlignmentFinder TFinder; + typedef typename TFinder::TMatrix TMatrix; + typedef typename Size::Type TSize; + + TSize len0 = length(seqH); + TSize len1 = length(seqV); + + setDimension(finder.matrix, 2); + setLength(finder.matrix, 0, len0 + 1); + setLength(finder.matrix, 1, len1 + 1); + resize(finder.matrix); + + resize(finder.forbidden, (len0 + 1) * (len1 + 1), false); + + finder.bestEndPos = maxValue(); + finder.bestBeginPos = maxValue(); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +void clear(LocalAlignmentFinder & sw_finder) +{ + sw_finder.needReinit = true; +} + +// ---------------------------------------------------------------------------- +// Function getScore() +// ---------------------------------------------------------------------------- + +template +TScoreValue getScore(LocalAlignmentFinder const & sw) +{ + typedef LocalAlignmentFinder TFinder; + if(sw.bestEndPos != maxValue()) + return getValue(const_cast(sw.matrix), sw.bestEndPos); + return 0; +} + +// ---------------------------------------------------------------------------- +// Function _smithWatermanGetMatrix() +// ---------------------------------------------------------------------------- + +template +TScoreValue +_smithWatermanGetMatrix(LocalAlignmentFinder & sw, + TStringH const & strH, + TStringV const & strV, + Score const & score_, + TScoreValue cutoff) +{ + // typedefs + typedef Matrix TMatrix; + typedef typename Position::Type TMatrixPosition; + typedef Iter TMatrixIterator; + + typedef typename Iterator::Type TStringIteratorH; + //typedef typename Value::Type TValueH; + typedef typename Iterator::Type TStringIteratorV; + typedef typename Value::Type TValueV; + + //------------------------------------------------------------------------- + //define some variables + + +// TSize str1_length = length(strH); +// TSize str2_length = length(strV); + TStringIteratorH x_begin = begin(strH) - 1; + TStringIteratorH x_end = end(strH) - 1; + TStringIteratorV y_begin = begin(strV) - 1; + TStringIteratorV y_end = end(strV) - 1; + + TStringIteratorH x = x_end; + TStringIteratorV y; + + TScoreValue score_match = scoreMatch(score_); + TScoreValue score_mismatch = scoreMismatch(score_); + TScoreValue score_gap = scoreGapExtend(score_); + + TScoreValue h = 0; + TScoreValue v = 0; + + TMatrixIterator col_ = end(sw.matrix) - 1; + TMatrixIterator finger1; + TMatrixIterator finger2; + + //------------------------------------------------------------------------- + // init + + finger1 = col_; + *finger1 = 0; + //std::cout <<" "; + for (x = x_end; x != x_begin; --x) + { + goPrevious(finger1, 0); + *finger1 = 0; + } + + //------------------------------------------------------------------------- + //fill matrix + for (y = y_end; y != y_begin; --y) + { + TValueV cy = *y; + + h = 0; + v = 0; + + finger2 = col_; //points to last column + goPrevious(col_, 1); //points to this column + finger1 = col_; + + *finger1 = v; + + for (x = x_end; x != x_begin; --x) + { + goPrevious(finger1, 0); + goPrevious(finger2, 0); + + if (*x == cy) + { + v = h + score_match; + h = *finger2; + } + else + { + TScoreValue s1 = h + score_mismatch; + h = *finger2; + TScoreValue s2 = score_gap + ((h > v) ? h : v); + v = (s1 > s2) ? s1 : s2; + if (v < 0) v = 0; + + } + *finger1 = v; + if (v >= cutoff) + { + push(sw.pQ,ScoreAndID(v,position(finger1))); + } + } + } + + // check if any scores >= cutoff were found + if(!empty(sw.pQ)) + { + ScoreAndID best = top(sw.pQ); + v = getValue(sw.matrix,best.id_); + sw.bestEndPos = best.id_; + } + else + v=0; + + return v; +} + +// ---------------------------------------------------------------------------- +// Function _smithWatermanDeclump() +// ---------------------------------------------------------------------------- + +// declumping +template +void +_smithWatermanDeclump(LocalAlignmentFinder & sw , + Gaps & gapsH, + Gaps & gapsV, + Score const & score_) +{ +//------------------------------------------------------------------------- +//typedefs + //typedef typename LocalAlignmentFinder::TMatrixPosition TMatrixPosition; + typedef typename LocalAlignmentFinder::TMatrix TMatrix; + typedef Iter TMatrixIterator; + + typedef Gaps TGapsH; + typedef typename Iterator::Type TGapsHIter; + typedef typename Iterator::Type TSequenceHIter; + //typedef typename Value::Type TValueH; + + typedef Gaps TGapsV; + typedef typename Iterator::Type TGapsVIter; + typedef typename Iterator::Type TSequenceVIter; + typedef typename Value::Type TValueV; + +//------------------------------------------------------------------------- +//variables + // TRow row0 = row(align_,0); + // TRow row1 = row(align_,1); + + // beginPosition == # leading gaps + // endPosition == length of clipped region without trailing gaps + // clippedEndPosition == source position of clipping end. + + // TAlignIterator ali_it0_stop = iter(row0,beginPosition(row0)); + // TAlignIterator ali_it1_stop = iter(row1,beginPosition(row1)); + TGapsHIter ali_it0_stop = begin(gapsH); + TGapsVIter ali_it1_stop = begin(gapsV); + + // SEQAN_ASSERT( endPosition(row0)- beginPosition(row0) == endPosition(row1)- beginPosition(row1) ); + + // TAlignIterator ali_it0 = iter(row0,endPosition(row0)); + // TAlignIterator ali_it1 = iter(row1,endPosition(row1)); + TGapsHIter ali_it0 = end(gapsH); + TGapsVIter ali_it1 = end(gapsV); + + // TStringIterator x_begin = begin(source(row0))-1; + // TStringIterator y_begin = begin(source(row1))-1; + // TStringIterator x_end = iter(source(row0),clippedEndPosition(row0))-1; + // TStringIterator y_end = iter(source(row1),clippedEndPosition(row1))-1; + TSequenceHIter x_begin = begin(source(gapsH))-1; + TSequenceVIter y_begin = begin(source(gapsV))-1; + TSequenceHIter x_end = iter(source(gapsH), endPosition(gapsH) - 1); + TSequenceVIter y_end = iter(source(gapsV), endPosition(gapsV) - 1); + + // TStringIterator x = x_end; + // TStringIterator y = y_end; + // TStringIterator x_stop = x_end; + TSequenceHIter x = x_end; + TSequenceVIter y = y_end; + TSequenceHIter x_stop = x_end; + + + TScoreValue score_match = scoreMatch(score_); + TScoreValue score_mismatch = scoreMismatch(score_); + TScoreValue score_gap = scoreGapExtend(score_); + TScoreValue h,v; + + TMatrixIterator finger0 = iter(sw.matrix,sw.bestBeginPos); + TMatrixIterator end_col = finger0; + TMatrixIterator finger1 = finger0; + TMatrixIterator forbidden = finger0; + + bool different = true; + bool forbidden_reached = true; + bool end_reached = false; + bool skip_row = false; + + +/* int str0_length = length(source(row(align_,0)))+1; + int str1_length = length(source(row(align_,1)))+1; + for(int i = 0; i v) ? h : v); + v = (s1 > s2) ? s1 : s2; + if (v < 0) v = 0; + + } + + // value is the same as in the original matrix + if(*finger0==v) + { + //x_stop is as far as we have to go at least + if(x +typename Iterator, Standard >::Type +_smithWatermanTrace(Gaps & gapsH, + Gaps & gapsV, + typename LocalAlignmentFinder::TBoolMatrix & fb_matrix, + Iter< Matrix, PositionIterator > source_, + Score const & scoring_) { + //typedefs + typedef Iter, PositionIterator > TMatrixIterator; + typedef typename Position >::Type TPosition; + +// typedef Segment TTargetSourceSegment; + typedef typename Iterator::Type TSourceIteratorH; + typedef typename Iterator::Type TSourceIteratorV; + + typedef Gaps TGapsH; + typedef Gaps TGapsV; + typedef typename Iterator::Type TTargetIteratorH; + typedef typename Iterator::Type TTargetIteratorV; + + //------------------------------------------------------------------------- + //variables + TPosition pos_0 = coordinate(source_, 0); + TPosition pos_1 = coordinate(source_, 1); + + TSourceH strH = source(gapsH); + TSourceV strV = source(gapsV); + + TTargetIteratorH target_0 = iter(gapsH, pos_0); + TTargetIteratorV target_1 = iter(gapsV, pos_1); + + TSourceIteratorH it_0 = iter(strH, pos_0, Standard()); + TSourceIteratorH it_0_end = end(strH); + + TSourceIteratorV it_1 = iter(strV, pos_1, Standard()); + TSourceIteratorV it_1_end = end(strV); + + TScoreValue score_mismatch = scoreMismatch(scoring_); + TScoreValue score_gap = scoreGapExtend(scoring_); + + //------------------------------------------------------------------------- + //follow the trace until 0 is reached + while ((*source_!=0) && (it_0 != it_0_end) && (it_1 != it_1_end)) + { + bool gv; + bool gh; + bool forbidden = fb_matrix[position(source_)]; + + if (*it_0 == *it_1 && !forbidden) + { + gv = gh = true; + } + else + { + TMatrixIterator it_ = source_; + + goNext(it_, 0); + TScoreValue v = *it_ + score_gap; + + TScoreValue d; + if(forbidden) + d = 0; + else{ + goNext(it_, 1); + d = *it_ + score_mismatch; + } + + it_ = source_; + goNext(it_, 1); + TScoreValue h = *it_ + score_gap; + + gv = (v >= h) | (d >= h); + gh = (h > v) | (d >= v); + } + + if (gv) + { + ++it_0; + goNext(source_, 0); + } + else + { + insertGap(target_0); + } + + if (gh) + { + ++it_1; + goNext(source_, 1); + } + else + { + insertGap(target_1); + } + ++target_0; + ++target_1; + } + + // We have removed all gaps and clippings from gapsH and gapsV in the calling functions, so the following works. + // Note that we have to set the end position first. + // TODO(holtgrew): Use setBegin/EndPosition(). + setClippedEndPosition(gapsH, toViewPosition(gapsH, position(it_0, strH))); + setClippedEndPosition(gapsV, toViewPosition(gapsV, position(it_1, strV))); + setClippedBeginPosition(gapsH, toViewPosition(gapsH, pos_0)); + setClippedBeginPosition(gapsV, toViewPosition(gapsV, pos_1)); + + return source_; +} + +// ---------------------------------------------------------------------------- +// Function _getNextBestEndPosition() +// ---------------------------------------------------------------------------- + +// Adjust the priority queue of scores until the true maximum is found. +template +typename LocalAlignmentFinder::TMatrixPosition +_getNextBestEndPosition(LocalAlignmentFinder & sw , + TScoreValue cutoff) +{ + // get maximal score from priority queue + TScoreValue topScore = 0; + if (!empty(sw.pQ)) + topScore = getValue(sw.matrix, top(sw.pQ).id_); + + // check if matrix entry of topScore did not change while declumping + if (!empty(sw.pQ)) { + while (top(sw.pQ).value_ != topScore) { + if (topScore >= cutoff) { + ((sw.pQ).heap[0]).value_ = topScore; + adjustTop(sw.pQ); + } else { + pop(sw.pQ); + } + if (!empty(sw.pQ)) topScore = getValue(sw.matrix, top(sw.pQ).id_); + else break; + } + } + + // priority queue with top scores is empty + if(empty(sw.pQ)) {//||top(sw.pQ).value_::TMatrixPosition ret_pos = top(sw.pQ).id_; + sw.bestEndPos = ret_pos; + pop(sw.pQ); + + return ret_pos; +} + +// ---------------------------------------------------------------------------- +// Function _smithWaterman() +// ---------------------------------------------------------------------------- + +// Wrapper that computes the matrix and does the backtracking for the best alignment +template +TScoreValue +_smithWaterman(Gaps & gapsH, + Gaps & gapsV, + LocalAlignmentFinder & sw_finder, + Score const & score_, + TScoreValue cutoff) +{ + // TODO(holtgrew): This sourceSegment() stuff is confusing... Do we *really* need this? + // Clear gaps and clipping from result Gaps structures. + clearGaps(gapsH); + clearGaps(gapsV); + clearClipping(gapsH); + clearClipping(gapsV); + + _initLocalAlignmentFinder(sourceSegment(gapsH), sourceSegment(gapsV), sw_finder, WatermanEggert()); + + TScoreValue ret = _smithWatermanGetMatrix(sw_finder, sourceSegment(gapsH), sourceSegment(gapsV), score_,cutoff); + + if(ret==0) + return ret; + sw_finder.needReinit = false; + + typedef Iter::TMatrix,PositionIterator > TMatrixIterator; + TMatrixIterator best_begin; + + // TODO(holtgrew): What does the following comment mean? + // TODO: sw_finder statt kram + best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); + + sw_finder.bestBeginPos = position(best_begin); + + pop(sw_finder.pQ); + + return ret; +} + +// ---------------------------------------------------------------------------- +// Function _smithWatermanGetNext() +// ---------------------------------------------------------------------------- + +// Wrapper that declumps the matrix and traces back the next best alignment +template +TScoreValue +_smithWatermanGetNext(Gaps & gapsH, + Gaps & gapsV, + LocalAlignmentFinder & sw_finder , + Score const & score_, + TScoreValue cutoff) +{ + _smithWatermanDeclump(sw_finder, gapsH, gapsV, score_); + + clearGaps(gapsH); + clearGaps(gapsV); + clearClipping(gapsH); + clearClipping(gapsV); + + typename LocalAlignmentFinder::TMatrixPosition next_best_end; + next_best_end = _getNextBestEndPosition(sw_finder,cutoff); + if(next_best_end==0) + return 0; + typename LocalAlignmentFinder::TMatrixIterator next_best_begin; + next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); + sw_finder.bestBeginPos = position(next_best_begin); + + return getValue(sw_finder.matrix,next_best_end); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_LOCAL_ALIGNMENT_WATERMAN_EGGERT_IMPL_H_ diff --git a/seqan/align/matrix_base.h b/seqan/align/matrix_base.h new file mode 100644 index 0000000..e5ca253 --- /dev/null +++ b/seqan/align/matrix_base.h @@ -0,0 +1,1103 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Simple matrices; Used in many alignment algorithms. +// ========================================================================== + +#ifndef SEQAN_HEADER_MATRIX_BASE_H +#define SEQAN_HEADER_MATRIX_BASE_H + +namespace seqan +{ + +////////////////////////////////////////////////////////////////////////////// + +struct NDimensional; + + +template +class Matrix; + +////////////////////////////////////////////////////////////////////////////// +template struct SizeArr_; + +template +struct SizeArr_ > +{ + typedef Matrix TMatrix_; + typedef typename Size::Type TSize_; + typedef String Type; +}; + +////////////////////////////////////////////////////////////////////////////// + +template +struct Host > +{ + typedef typename StringSpecForValue_::Type TSpec_; + typedef String Type; +}; + +template +struct Host const> +{ + typedef typename StringSpecForValue_::Type TSpec_; + typedef String Type; +}; + +////////////////////////////////////////////////////////////////////////////// +////////////////////////////////////////////////////////////////////////////// + +// TODO(holtgrew): Add more comprehensive documentation! + +/*! + * @class Matrix + * @headerfile + * @brief A simple n-dimensional matrix type. + * + * @signature template + * class Matrix; + * + * @tparam TValue Type of matrix entries. + * @tparam DIMENSION Dimension of the matrix. Use 0 for n-dimensional, values > 0 for a matrix with + * DIMENSION dimensions. Defaults to 0. + */ + + +template +class Matrix +{ +//____________________________________________________________________________ + +public: + typedef typename Size::Type TSize; + typedef String TSizeArr; + typedef typename Host::Type THost; + + TSizeArr data_lengths; //Length of every dimension + TSizeArr data_factors; //used for positions of dimensions in host ("size of jumps" to get to next entry of specified dimension) + + Holder data_host; +//____________________________________________________________________________ + +public: + Matrix() + { + create(data_host); + } + Matrix(Matrix const & other_): + data_lengths(other_.data_lengths), + data_factors(other_.data_factors), + data_host(other_.data_host) + { + } + inline Matrix const & + operator = (Matrix const & other_) + { + data_lengths = other_.data_lengths; + data_factors = other_.data_factors; + data_host = other_.data_host; + + return *this; + } + ~Matrix() + { + } +//____________________________________________________________________________ + + +//____________________________________________________________________________ + + inline TValue & + operator () (TSize x1, TSize x2) + { + return value(*this, x1, x2); + } + inline TValue & + operator () (TSize x1, TSize x2, TSize x3) + { + return value(*this, x1, x2, x3); + } + inline TValue & + operator () (TSize x1, TSize x2, TSize x3, TSize x4) + { + return value(*this, x1, x2, x3, x4); + } + +//____________________________________________________________________________ +}; + + +template +class Matrix +{ +//____________________________________________________________________________ + +public: + typedef typename Size::Type TSize; + typedef String TSizeArr; + typedef typename Host::Type THost; + + TSizeArr data_lengths; + TSizeArr data_factors; + + Holder data_host; + + +//____________________________________________________________________________ + +public: + Matrix() + { + create(data_host); + + //setDimension to 2 + resize(data_lengths, 2, 0); + resize(data_factors, 2, 0); + data_factors[0] = 1; + } + Matrix(Matrix const & other_): + data_lengths(other_.data_lengths), + data_factors(other_.data_factors), + data_host(other_.data_host) + { + } + inline Matrix const & + operator = (Matrix const & other_) + { + data_lengths = other_.data_lengths; + data_factors = other_.data_factors; + data_host = other_.data_host; + + return *this; + } + + ~Matrix() + { + } +//____________________________________________________________________________ + + +//____________________________________________________________________________ + + inline TValue & + operator () (TSize x1, TSize x2) + { + return value(*this, x1, x2); + } + +//____________________________________________________________________________ +}; + +template +class Matrix +{ +//____________________________________________________________________________ + +public: + typedef typename Size::Type TSize; + typedef String TSizeArr; + typedef typename Host::Type THost; + + TSizeArr data_lengths; + TSizeArr data_factors; + + Holder data_host; + + +//____________________________________________________________________________ + +public: + Matrix() + { + create(data_host); + + //setDimension to 3 + resize(data_lengths, 3, 0); + resize(data_factors, 3); + data_factors[0] = 1; + } + Matrix(Matrix const & other_): + data_lengths(other_.data_lengths), + data_factors(other_.data_factors), + data_host(other_.data_host) + { + } + inline Matrix const & + operator = (Matrix const & other_) + { + data_lengths = other_.data_lengths; + data_factors = other_.data_factors; + data_host = other_.data_host; + + return *this; + } + + ~Matrix() + { + } +//____________________________________________________________________________ + + +//____________________________________________________________________________ + + inline TValue & + operator () (TSize x1, TSize x2, TSize x3) + { + return value(*this, x1, x2, x3); + } + +//____________________________________________________________________________ +}; + +template +inline typename SizeArr_ >::Type & +_dataLengths(Matrix & me) +{ + return me.data_lengths; +} + +template +inline typename SizeArr_ >::Type const & +_dataLengths(Matrix const & me) +{ + return me.data_lengths; +} + +template +inline typename SizeArr_ >::Type & +_dataFactors(Matrix & me) +{ + return me.data_factors; +} + +template +inline typename SizeArr_ >::Type const & +_dataFactors(Matrix const & me) +{ + return me.data_factors; +} + +//____________________________________________________________________________ + + +template +inline bool +dependent(Matrix & me) +{ + return dependent(me.data_host); +} + +//____________________________________________________________________________ + +template +inline Holder >::Type> & +_dataHost(Matrix & matrix) +{ + return matrix.data_host; +} + +template +inline Holder >::Type> const & +_dataHost(Matrix const & matrix) +{ + return matrix.data_host; +} + +//____________________________________________________________________________ + +template +inline void +assignHost(Matrix & me, THost const & value_) +{ + assignValue(me.data_host, value_); +} + +//____________________________________________________________________________ + +template +inline void +moveHost(Matrix & me, THost const & value_) +{ + moveValue(me.data_host, value_); +} +////////////////////////////////////////////////////////////////////////////// +////////////////////////////////////////////////////////////////////////////// + +template +struct Value< Matrix > +{ + typedef TValue Type; +}; + +////////////////////////////////////////////////////////////////////////////// + +template +struct Iterator< Matrix, TIteratorSpec > +{ + typedef Iter, PositionIterator> Type; +}; + +template +struct Iterator< Matrix const, TIteratorSpec > +{ + typedef Iter const, PositionIterator> Type; +}; + +////////////////////////////////////////////////////////////////////////////// +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Size const>::Type +dimension(Matrix const & me) +{ + return length(_dataLengths(me)); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +setDimension(Matrix & me, + unsigned int dim_) +{ + + SEQAN_ASSERT_GT(dim_, 0u); +//std::cout<<"\npress enter1\n"; +//std::cin.get(); + resize(_dataLengths(me), dim_, 0); + + resize(_dataFactors(me), dim_); + _dataFactors(me)[0] = 1; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Size >::Type +length(Matrix const & me, + unsigned int dim_) +{ + return me.data_lengths[dim_]; +} + +template +inline typename Size >::Type +length(Matrix const & me) +{ + return length(host(me)); +} + +template +inline bool empty(Matrix const & me) +{ + return empty(host(me)); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +setLength(Matrix & me, + unsigned int dim_, + TLength length_) +{ + SEQAN_ASSERT_GT(length_, static_cast(0)); + SEQAN_ASSERT_LT(dim_, dimension(me)); + + typedef typename SizeArr_ >::TSize_ TSize_; + + _dataLengths(me)[dim_] = static_cast(length_); +} + +////////////////////////////////////////////////////////////////////////////// + +/*! + * @fn Matrix#resize + * @brief Resize the matrix and fill it with a given value or zeroes. + * + * @signature void resize(matrix[, val]); + * + * @param[in,out] matrix The Matrix to fill. + * @param[in] val The optional value to fill the matrix with. + */ + + +template +inline void +resize(Matrix & me) +{ + typedef Matrix TMatrix; + typedef typename Size::Type TSize; + + unsigned int dimension_ = dimension(me); + + SEQAN_ASSERT_GT(dimension_, 0u); + + TSize factor_ = _dataFactors(me)[0] * length(me, 0); + for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i) + { + _dataFactors(me)[i] = factor_; + factor_ *= length(me, i); + } + + if (factor_ > 0) + { + resize(host(me), factor_); + } +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline void +resize(Matrix & me, TFillValue myValue) //resize the matrix and fill with value +{ + typedef Matrix TMatrix; + typedef typename Size::Type TSize; + + unsigned int dimension_ = dimension(me); + + SEQAN_ASSERT_GT(dimension_, 0u); + + TSize factor_ = _dataFactors(me)[0] * length(me, 0); + for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i) + { + _dataFactors(me)[i] = factor_; + factor_ *= length(me, i); + } + + if (factor_ > 0) + resize(host(me), factor_, myValue); +} + + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Position >::Type +nextPosition(Matrix & me, + TPosition position_, + unsigned int dimension_) +{ + return position_ + _dataFactors(me)[dimension_]; +} + +template +inline typename Position >::Type +nextPosition(Matrix const & me, + TPosition position_, + unsigned int dimension_) +{ + return position_ + _dataFactors(me)[dimension_]; +} + +template +inline typename Position >::Type +previousPosition(Matrix & me, + TPosition position_, + unsigned int dimension_) +{ + return position_ - _dataFactors(me)[dimension_]; +} + +template +inline typename Position >::Type +previousPosition(Matrix const & me, + TPosition position_, + unsigned int dimension_) +{ + return position_ - _dataFactors(me)[dimension_]; +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Size< Matrix >::Type +coordinate(Matrix const & me, + TPosition position_, + unsigned int dimension_) +{ + SEQAN_ASSERT_LT(dimension_, dimension(me)); + + if (dimension_ < dimension(me) - 1) + { + return (position_ / _dataFactors(me)[dimension_]) % _dataFactors(me)[dimension_ + 1]; + } + else + { + return position_ / _dataFactors(me)[dimension_]; + } +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Iterator, Tag const>::Type +begin(Matrix & me, + Tag const) +{ + return typename Iterator, Tag const >::Type(me, 0); +} +template +inline typename Iterator const, Tag const>::Type +begin(Matrix const & me, + Tag const) +{ + return typename Iterator const, Tag const >::Type(me, 0); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Iterator, Tag const >::Type +end(Matrix & me, + Tag const) +{ + return typename Iterator, Tag const >::Type(me, length(host(me))); +} +template +inline typename Iterator const, Tag const >::Type +end(Matrix const & me, + Tag const) +{ + return typename Iterator, Tag const >::Type(me, length(host(me))); +} + +////////////////////////////////////////////////////////////////////////////// + +template +inline typename Reference >::Type +value(Matrix & me, + TPosition position_) +{ + return value(host(me), position_); +} + +template +inline typename Reference const>::Type +value(Matrix const & me, + TPosition position_) +{ + return value(host(me), position_); +} + +//____________________________________________________________________________ + +//two dimensional value access +template +inline typename Reference >::Type +value(Matrix & me, + TOrdinate1 i1, + TOrdinate2 i2) +{ + return value(host(me), i1 + i2 * _dataFactors(me)[1]); +} + +template +inline typename Reference const>::Type +value(Matrix const & me, + TOrdinate1 i1, + TOrdinate2 i2) +{ + return value(host(me), i1 + i2 * _dataFactors(me)[1]); +} + +//____________________________________________________________________________ + +//3 dimensional value access + +template +inline typename Reference >::Type +value(Matrix & me, + TOrdinate1 i1, + TOrdinate2 i2, + TOrdinate3 i3) +{ + return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2]); +} + +//____________________________________________________________________________ + +//4 dimensional value access + +template +inline typename Reference >::Type +value(Matrix & me, + TOrdinate1 i1, + TOrdinate2 i2, + TOrdinate3 i3, + TOrdinate4 i4) +{ + return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2] + i4 * _dataFactors(me)[3]); +} + +////////////////////////////////////////////////////////////////////////////// +////////////////////////////////////////////////////////////////////////////// +// Iterator: goNext +////////////////////////////////////////////////////////////////////////////// + +template +inline void +goNext(Iter, PositionIterator> & me, + unsigned int dimension_) +{ + setPosition(me, nextPosition(container(me), position(me), dimension_)); +} + +template +inline void +goNext(Iter const, PositionIterator> & me, + unsigned int dimension_) +{ + setPosition(me, nextPosition(container(me), position(me), dimension_)); +} + +template +inline void +goNext(Iter, PositionIterator> & me) +{ + goNext(me, 0); +} + +template +inline void +goNext(Iter const, PositionIterator> & me) +{ + goNext(me, 0); +} + +////////////////////////////////////////////////////////////////////////////// +// Iterator: goPrevious +////////////////////////////////////////////////////////////////////////////// + +template +inline void +goPrevious(Iter< Matrix, PositionIterator > & me, + unsigned int dimension_) +{ + setPosition(me, previousPosition(container(me), position(me), dimension_)); +} + +template +inline void +goPrevious(Iter< Matrix const, PositionIterator > & me, + unsigned int dimension_) +{ + setPosition(me, previousPosition(container(me), position(me), dimension_)); +} + +template +inline void +goPrevious(Iter< Matrix, PositionIterator > & me) +{ + goPrevious(me, 0); +} + +template +inline void +goPrevious(Iter< Matrix const, PositionIterator > & me) +{ + goPrevious(me, 0); +} + +////////////////////////////////////////////////////////////////////////////// +// goTo +////////////////////////////////////////////////////////////////////////////// + +template +inline void +goTo(Iter, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1) +{ + setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1]); +} + + +template +inline void +goTo(Iter const, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1) +{ + setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1]); +} + + +template +inline void +goTo(Iter, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1, TPosition2 pos2) +{ + setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1] + pos2 * _dataFactors(container(me))[2]); +} + + +template +inline void +goTo(Iter const, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1, TPosition2 pos2) +{ + setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1] + pos2 * _dataFactors(container(me))[2]); +} + +////////////////////////////////////////////////////////////////////////////// +// Iterator: coordinate + +template +inline typename Size< Matrix >::Type +coordinate(Iter, PositionIterator > & me, + unsigned int dimension_) +{ + return coordinate(container(me), position(me), dimension_); +} + +template +inline typename Size< Matrix >::Type +coordinate(Iter const, PositionIterator > & me, + unsigned int dimension_) +{ + return coordinate(container(me), position(me), dimension_); +} + +/*! + * @fn Matrix::operator+ + * @brief Sum operator for the Matrix type. + * + * @signature TMatrix Matrix::operator+(lhs, rhs); + * + * @param[in] lhs First summand. + * @param[in] rhs Second summand. + * + * @return TMatrix The resulting matrix of same type as lhs and rhs. + */ + +template +Matrix +operator + (Matrix const & matrix1,Matrix const & matrix2) +{ + //the two matrices must have same dimension + SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2)); + + Matrix result; + //copy the first matrix + setDimension(result,length(_dataLengths(matrix1))); + _dataLengths(result) = _dataLengths(matrix1); + resize(result); + + //add the matrices + for(unsigned int i = 0;i< length(host(result));++i) + { + value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i); + } + //Return matrix sum + return result; +} + +template +Matrix +operator - (Matrix const & matrix1,Matrix const & matrix2) +{ + //the two matrices must have same dimension + SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2)); + + Matrix result; + //resize the matrix + setDimension(result,length(_dataLengths(matrix1))); + _dataLengths(result) = _dataLengths(matrix1); + resize(result); + + //subtract the matrices + for(unsigned int i = 0;i< length(host(result));++i) + { + value(host(result), i)=value(host(matrix1), i)-value(host(matrix2), i); + } + //Return matrix difference + return result; +} + +template +Matrix +operator * (Matrix const & matrix1, Matrix const & matrix2) +{ + SEQAN_ASSERT_EQ(length(matrix1,1), length(matrix2,0)); + + unsigned int nrow1=length(matrix1,0); + unsigned int ncol2=length(matrix2,1); + Matrix result; + //resize the matrix + setLength(result, 0, nrow1); + setLength(result, 1, ncol2); + resize(result,(TValue) 0); + + //Matrix product + for(unsigned int row = 0; row < nrow1; row++) + { + for(unsigned int col = 0; col < ncol2; col++) + { + for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++) + { + value(result,row,col)+= value(host(matrix1), row + colRes * matrix1.data_factors[1])*value(host(matrix2), colRes + col * matrix2.data_factors[1]); + } + } + } + //return the matrix product + return result; +} + + +template +Matrix +operator * (TValue const & scalar, Matrix const & matrix) +{ + Matrix result; + result= matrix; + //scalar multiplication + for(unsigned int i = 0;i< length(host(result));++i) + { + value(host(result), i)*=scalar; + } + //return the matrix product + return result; +} + +template +Matrix +operator * (Matrix const & matrix, TValue const & scalar) +{ + Matrix result; + result= matrix; + //scalar multiplication + for(unsigned int i = 0;i< length(host(result));++i) + { + value(host(result), i)*=scalar; + } + //return the matrix product + return result; +} + + +template +bool +operator == (Matrix const & matrix1, Matrix const & matrix2) +{ + bool result; + result= (matrix1.data_lengths==matrix2.data_lengths)&&(matrix1.data_factors==matrix2.data_factors)&&(value(matrix1.data_host)==value(matrix2.data_host))&&(DIMENSION1==DIMENSION2); + return result; +} + +/* +template +Matrix +matricialSum(Matrix &matrix1,Matrix &matrix2) +{ + //the two matrices must have same dimension + if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1)) + { + fprintf(stderr,"Error: The two matrices have different dimensions"); + } + + + unsigned int nrow=length(matrix1,0); + unsigned int ncol=length(matrix1,1); + + Matrix result; + //resize the matrix + setLength(result, 0, nrow); + setLength(result, 1, ncol); + resize(result); + + //add the matrices + for(unsigned int i = 0;i< nrow*ncol;++i) + { + value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i); + } + //Return matrix difference + return result; + +} +*/ +////////////////////////////////////////////////////////////////////////////// +// _matricialDifference +////////////////////////////////////////////////////////////////////////////// + +/* +template +inline Matrix +matricialDifference(Matrix & matrix1, Matrix & matrix2) +{ + //the two matrices must have same dimension + if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1)) + { + fprintf(stderr,"Error: The two matrices have different dimensions"); + } + + unsigned int nrow=length(matrix1,0); + unsigned int ncol=length(matrix1,1); + + Matrix result; + //resize the matrix + //setDimension(result, 2); + setLength(result, 0, nrow); + setLength(result, 1, ncol); + resize(result); + + //Substract the matrices + for(unsigned int i1 = 0;i1< nrow;++i1) + { + for(unsigned int i2 = 0;i2 +inline Matrix +matricialProduct(Matrix &matrix1, + Matrix &matrix2) +{ + //SEQAN_ASSERT_LT(dimension_, dimension(me)); + if(length(matrix1,1) != length(matrix2,0)) + { + fprintf(stderr,"Error: Number of columns of matrix1 is unequal to number of rows of matrix2"); + } + + unsigned int nrow1=length(matrix1,0); + unsigned int ncol2=length(matrix2,1); + Matrix result; + //resize the matrix + setLength(result, 0, nrow1); + setLength(result, 1, ncol2); + resize(result,(TValue) 0); + + //Matrix product + for(unsigned int row = 0; row < nrow1; row++) + { + for(unsigned int col = 0; col < ncol2; col++) + { + for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++) + { + value(result,row,col)+=value(matrix1, row,colRes)*value(matrix2,colRes,col); + } + } + } + //return the matrix product + return result; +} +*/ + +/*! + * @fn Matrix#transpose + * @brief Tranpose a 2D Matrix. + * + * @signature TMatrix transpose(matrix); + * + * @param[in] matrix The matrix to tranpose. + * @return TMatrix The resulting tranposed matrix. + */ + +template +Matrix +transpose(Matrix const & matrix) +{ + + unsigned int nrow=length(matrix,0); + unsigned int ncol=length(matrix,1); + + Matrix result; + //resize the matrix + setLength(result, 0, ncol); + setLength(result, 1, nrow); + resize(result); + + + for(unsigned int i1 = 0;i1< nrow;++i1) + { + for(unsigned int i2 = 0;i2 +std::ostream& operator<<(std::ostream &out, const Matrix &matrix) +{ + for(unsigned int i1 = 0;i1< matrix.data_lengths[0];++i1) + { + for(unsigned int i2 = 0;i2<(matrix.data_lengths[1]-1);++i2) + { + out< +// void read(FILE *file, Matrix & matrix) +// { +// //unsigned int column_size=3; +// unsigned int column_size=pow(4,5); +// //read the transition matrix +// setLength(matrix, 0, column_size); +// setLength(matrix, 1, column_size); +// resize(matrix,0.0); +// for(unsigned int row=0; row +// ========================================================================== +// Extras for the align module +// ========================================================================== + +#ifndef SEQAN_ALIGN_EXTEND_H +#define SEQAN_ALIGN_EXTEND_H + +#include +#include +#include + +#include +#include +#include + +#endif diff --git a/seqan/align_extend/align_extend.h b/seqan/align_extend/align_extend.h new file mode 100644 index 0000000..f5459fb --- /dev/null +++ b/seqan/align_extend/align_extend.h @@ -0,0 +1,647 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Hannes Hauswedell +// ========================================================================== +// This file contains routines to extend an existing Align object +// ========================================================================== + +#ifndef INCLUDE_ALIGN_ALIGN_EXTEND_H +#define INCLUDE_ALIGN_ALIGN_EXTEND_H + +namespace seqan { + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class AliExtContext_ +// ---------------------------------------------------------------------------- + +// Context with memory holding objects for alignment extension +// This can be reused to prevent repeated memory allocations +template +struct AliExtContext_ +{ + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + + TGaps0 leftRow0, centerRow0, rightRow0; + TGaps1 leftRow1, centerRow1, rightRow1; + + TDPContext dpContext; + + String > traceSegment; +}; + +template +inline void +clear(AliExtContext_ & prov) +{ + // gaps don't need to be cleared, because they are always + // re-assigned before use; dpContext, too! + + // trace segment always needs to be cleared + clear(prov.traceSegment); + // dpContext doesn't need to be cleared +} + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _reverseTrace() +// ---------------------------------------------------------------------------- + +// Reverse a trace string and adapt internal position. +template +void _reversePartialTrace(String, TSpec> & trace, + TPos2 const lengthH, + TPos2 const lengthV) +{ + typedef String, TSpec> TTrace; + typedef typename Iterator::Type TTraceIter; + + if (empty(trace)) + return; + + for (TTraceIter it = begin(trace, Rooted()); !atEnd(it); goNext(it)) + { + it->_horizontalBeginPos = lengthH - _getEndHorizontal(*it); + it->_verticalBeginPos = lengthV - _getEndVertical(*it); + } + reverse(trace); +} + +// ---------------------------------------------------------------------------- +// Function _setUpAndRunAlignImpl() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +_setUpAndRunAlignImpl(TAliExtContext_ & alignContext, + TString0 const & str0, + TString1 const & str1, + Score const & scoreScheme, + int const /*lowerDiag*/, + int const /*upperDiag*/, + TScoreValue const /*xDrop*/, + TTracebackConfig const & /*gapOrientation*/, + False const & /*TBoolBanded*/, + False const & /*TBoolXDrop*/) +{ + typedef FreeEndGaps_ TFreeEndGaps; + typedef AlignConfig2, DPBandConfig, TFreeEndGaps, + TracebackOn > > TAlignConfig; + + DPScoutState_ scoutState; + return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme, + TAlignConfig()); +} + +template +inline TScoreValue +_setUpAndRunAlignImpl(TAliExtContext_ & alignContext, + TString0 const & str0, + TString1 const & str1, + Score const & scoreScheme, + int const lowerDiag, + int const upperDiag, + TScoreValue const /*xDrop*/, + TTracebackConfig const & /*gapOrientation*/, + True const & /*TBoolBanded*/, + False const & /*TBoolXDrop*/) +{ + typedef FreeEndGaps_ TFreeEndGaps; + typedef AlignConfig2, DPBandConfig, TFreeEndGaps, + TracebackOn > > TAlignConfig; + + DPScoutState_ scoutState; + return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme, + TAlignConfig(lowerDiag, upperDiag)); +} + +template +inline TScoreValue +_setUpAndRunAlignImpl(TAliExtContext_ & alignContext, + TString0 const & str0, + TString1 const & str1, + Score const & scoreScheme, + int const /*lowerDiag*/, + int const /*upperDiag*/, + TScoreValue const xDrop, + TTracebackConfig const & /*gapOrientation*/, + False const & /*TBoolBanded*/, + True const & /*TBoolXDrop*/) +{ + typedef FreeEndGaps_ TFreeEndGaps; + typedef AlignConfig2 >, DPBandConfig, TFreeEndGaps, + TracebackOn > > TAlignConfig; + + DPScoutState_ > > scoutState(xDrop); + return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme, + TAlignConfig()); +} + +template +inline TScoreValue +_setUpAndRunAlignImpl(TAliExtContext_ & alignContext, + TString0 const & str0, + TString1 const & str1, + Score const & scoreScheme, + int const lowerDiag, + int const upperDiag, + TScoreValue const xDrop, + TTracebackConfig const & /*gapOrientation*/, + True const & /*TBoolBanded*/, + True const & /*TBoolXDrop*/) +{ + typedef FreeEndGaps_ TFreeEndGaps; + typedef AlignConfig2 >, DPBandConfig, TFreeEndGaps, + TracebackOn > > TAlignConfig; + + DPScoutState_ > > scoutState(xDrop); + return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme, + TAlignConfig(lowerDiag, upperDiag)); +} + +// ---------------------------------------------------------------------------- +// Function _extendAlignmentImpl() +// ---------------------------------------------------------------------------- + +template +inline TScoreValue +_extendAlignmentImpl(Gaps & row0, + Gaps & row1, + TScoreValue const & origScore, + TString0 const & hSeq, + TString1 const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + TScoreValue const & xDrop, + Score const & scoreScheme, + TBoolBanded const & /**/, + TBoolXDrop const & /**/, + TAliExtContext_ & alignContext) +{ + typedef typename Infix::Type TInf0; + typedef typename Infix::Type TInf1; + + TPos const hBeginPos = positions[0]; + TPos const vBeginPos = positions[1]; + TPos const hEndPos = positions[2]; + TPos const vEndPos = positions[3]; + + SEQAN_ASSERT_EQ(infix(source(row0), beginPosition(row0), endPosition(row0)), + infix(hSeq, hBeginPos, hEndPos)); + SEQAN_ASSERT_EQ(infix(source(row1), beginPosition(row1), endPosition(row1)), + infix(vSeq, vBeginPos, vEndPos)); + + bool extendLeft = ((direction & EXTEND_LEFT) && (hBeginPos > 0u) && (vBeginPos > 0u)); + bool extendRight = ((direction & EXTEND_RIGHT) && (hEndPos < length(hSeq)) && (vEndPos < length(vSeq))); + + clear(alignContext); + alignContext.centerRow0 = row0; + alignContext.centerRow1 = row1; + + TScoreValue leftScore = 0; + TScoreValue centerScore = origScore; + TScoreValue rightScore = 0; + + TPos newAlignLen = length(row0); + + // centerScore was set to "compute yourself" by interface function without score parameter + if (centerScore == minValue()) + { + centerScore = 0; + + for (TPos i = 0; i < length(row0); ++i) + { + if ( ( isGap(row0, i)) || ( isGap(row1, i)) ) + { + if (( i==0 ) || + (isGap(row0, i-1) != isGap(row0, i)) || + (isGap(row1, i-1) != isGap(row1, i)) ) + { + centerScore += scoreGapOpen(scoreScheme); + } + else + { + centerScore += scoreGapExtend(scoreScheme); + } + } + else + { + centerScore += score(scoreScheme, row0[i], row1[i]); + } + } + } + + // "reset" original alignment to full length on sequences and no gaps + assignSource(row0, infix(hSeq, 0, length(hSeq))); + assignSource(row1, infix(vSeq, 0, length(vSeq))); + + // left + if (extendLeft) + { + TInf0 inf0 = infix(hSeq, 0, hBeginPos); + TInf1 inf1 = infix(vSeq, 0, vBeginPos); + + // reverse input + ModifiedString const r_inf0(inf0); + ModifiedString const r_inf1(inf1); + + leftScore = _setUpAndRunAlignImpl(alignContext, r_inf0, r_inf1, scoreScheme, lowerDiag, upperDiag, xDrop, + TracebackConfig_(), TBoolBanded(), TBoolXDrop()); + // un-reverve + _reversePartialTrace(alignContext.traceSegment, length(inf0), length(inf1)); + + setSource(alignContext.leftRow0, inf0); + setSource(alignContext.leftRow1, inf1); + + _adaptTraceSegmentsTo(alignContext.leftRow0, alignContext.leftRow1, alignContext.traceSegment); + + if (length(alignContext.leftRow0) > 0) + { + integrateGaps(row0, alignContext.leftRow0); + integrateGaps(row1, alignContext.leftRow1); + setClippedBeginPosition(row0, clippedBeginPosition(alignContext.leftRow0)); + setClippedBeginPosition(row1, clippedBeginPosition(alignContext.leftRow1)); + + newAlignLen += length(alignContext.leftRow0); + } + else + { + extendLeft = false; + } + } + + // center + if (extendLeft) + { + integrateGaps(row0, alignContext.centerRow0, length(alignContext.leftRow0)); + integrateGaps(row1, alignContext.centerRow1, length(alignContext.leftRow1)); + } + else + { + integrateGaps(row0, alignContext.centerRow0, hBeginPos); + integrateGaps(row1, alignContext.centerRow1, vBeginPos); + TPos leadGaps0 = countGaps(begin(alignContext.centerRow0)); + TPos leadGaps1 = countGaps(begin(alignContext.centerRow1)); + + TPos sourceBeginPos0 = toSourcePosition(alignContext.centerRow0, leadGaps0) + hBeginPos - + beginPosition(alignContext.centerRow0); + TPos sourceBeginPos1 = toSourcePosition(alignContext.centerRow1, leadGaps1) + vBeginPos - + beginPosition(alignContext.centerRow1); + + setClippedBeginPosition(row0, toViewPosition(row0, sourceBeginPos0) - leadGaps0); + setClippedBeginPosition(row1, toViewPosition(row1, sourceBeginPos1) - leadGaps1); + } + + // right + if (extendRight) + { + TInf0 inf0 = infix(hSeq, hEndPos, length(hSeq)); + TInf1 inf1 = infix(vSeq, vEndPos, length(vSeq)); + + clear(alignContext.traceSegment); + rightScore = _setUpAndRunAlignImpl(alignContext, inf0, inf1, scoreScheme, lowerDiag, upperDiag, xDrop, + TracebackConfig_(), TBoolBanded(), TBoolXDrop()); + + setSource(alignContext.rightRow0, inf0); + setSource(alignContext.rightRow1, inf1); + _adaptTraceSegmentsTo(alignContext.rightRow0, alignContext.rightRow1, alignContext.traceSegment); + + if (length(alignContext.rightRow0) > 0) + { + integrateGaps(row0, alignContext.rightRow0); + integrateGaps(row1, alignContext.rightRow1); + + newAlignLen += length(alignContext.rightRow0); + } + } + + setClippedEndPosition(row0, clippedBeginPosition(row0) + newAlignLen); + setClippedEndPosition(row1, clippedBeginPosition(row1) + newAlignLen); + + return leftScore + centerScore + rightScore; +} + +// get rows from align object +template +inline TScoreValue +_extendAlignmentImpl(Align & align, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + TScoreValue const & xDrop, + Score const & scoreScheme, + TBoolBanded const & /**/, + TBoolXDrop const & /**/, + TAliExtContext_ & alignContext) +{ + SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments."); + SEQAN_ASSERT_EQ_MSG(length(row(align, 0)), length(row(align, 1)), "Invalid alignment!"); + + return _extendAlignmentImpl(row(align, 0), row(align, 1), origScore, hSeq, vSeq, positions, direction, lowerDiag, + upperDiag, xDrop, scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext); +} + +// create AlignContext +template +inline TScoreValue +_extendAlignmentImpl(Align & align, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + TScoreValue const & xDrop, + Score const & scoreScheme, + TBoolBanded const & /**/, + TBoolXDrop const & /**/) +{ + if (scoreGapOpen(scoreScheme) == scoreGapExtend(scoreScheme)) + { + typedef DPContext TDPContext; + typedef AliExtContext_, + Gaps, + TDPContext> TAliExtContext_; + TAliExtContext_ alignContext; + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop, + scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext); + } + else + { + typedef DPContext TDPContext; + typedef AliExtContext_, + Gaps, + TDPContext> TAliExtContext_; + TAliExtContext_ alignContext; + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop, + scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext); + } +} + +// ---------------------------------------------------------------------------- +// Function extendAlignment() +// ---------------------------------------------------------------------------- + +/*! + * @fn extendAlignment + * @headerfile + * @brief X-Drop extension for alignment objects. + * @signature TScoreValue extendAlignment(align, [origScore,] hSeq, vSeq, positions, extensionDirection, + * [lowerDiag, upperDiag,] [xDrop,] scoreScheme); + * + * @param[in,out] align The @link Align @endlink object to work on. Must be an alignment over the + * @link InfixSegment infix @endlink of the const type of hSeq + * and vSeq. Also see section "Returned Alignment". + * @param[in] origScore Original score value of the alignment (optional; computed if not provided). + * @param[in] hSeq Full horizontal sequence. + * @param[in] vSeq Full vertical sequence. + * @param[in] positions A @link Tuple @endlink of length 4 with the begin and end position of the + * infixes in align. + * @param[in] extensionDirection + * The extension direction (@link ExtensionDirection @endlink). + * @param[in] lowerDiag Lower alignment diagonal to use (int). + * @param[in] upperDiag Upper alignment diagonal to use (int). + * @param[in] xDrop The X-drop value to use (integral value). It only limits computation of new + * columns in the DP-Matrix and has no influence on the diagonals (but can be combined with them). + * @param[in] scoringScheme + * The @link Score @endlink to use. + * + * @return TScoreValue + * The score of the new alignment. TScoreValue is the value type of + * scoringScheme. + * + * @section Returned Alignment + * + * The resulting alignment has the infixes extended to the whole underlying sequence. The alignment + * is clipped to give the parts of the aligned sequences. + * + * @section Example + * + * @include demos/dox/align_extend/extend_alignment.cpp + * + * The output is as follows: + * + * @include demos/dox/align_extend/extend_alignment.cpp.stdout + * + * @section Remarks + * + * It is necessary to explicitly pass hSeq, vSeq and the positions, because the + * original hSeq and vSeq (that Align was created on), might have been infixes, + * (especially if they are members of a ConcatDirect set) in which cases their + * actual begin and end positions cannot be inferred from the Align object's + * rows' source(). + */ + +// NO BAND, NO XDROP +template +inline TScoreValue +extendAlignment(Align & align, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, minValue(), hSeq, vSeq, positions, direction, 0, 0, 0, scoreScheme, + False(), False()); +} + +template +inline TScoreValue +extendAlignment(Align & align, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, 0, 0, 0, scoreScheme, False(), + False()); +} + +// BAND, NO XDROP +template +inline TScoreValue +extendAlignment(Align & align, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, minValue(), hSeq, vSeq, positions, direction, lowerDiag, upperDiag, + 0, scoreScheme, True(), False()); +} + +template +inline TScoreValue +extendAlignment(Align & align, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, 0, + scoreScheme, True(), False()); +} + +// NO BAND, XDROP +template +inline TScoreValue +extendAlignment(Align & align, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + TScoreValue const & xDrop, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, minValue(), hSeq, vSeq, positions, direction, 0, 0, xDrop, + scoreScheme, False(), True()); +} + +template +inline TScoreValue +extendAlignment(Align & align, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + TScoreValue const & xDrop, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, 0, 0, xDrop, scoreScheme, False(), + True()); +} + +// BAND, XDROP +template +inline TScoreValue +extendAlignment(Align & align, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + TScoreValue const & xDrop, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, minValue(), hSeq, vSeq, positions, direction, lowerDiag, upperDiag, + xDrop, scoreScheme, True(), True()); +} + +template +inline TScoreValue +extendAlignment(Align & align, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + TScoreValue const & xDrop, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop, + scoreScheme, True(), True()); +} + +template +inline TScoreValue +extendAlignment(Align & align, + TAliExtContext & alignContext, + TScoreValue const & origScore, + TString const & hSeq, + TString const & vSeq, + Tuple const & positions, + ExtensionDirection const & direction, + int const lowerDiag, + int const upperDiag, + TScoreValue const & xDrop, + Score const & scoreScheme) +{ + return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop, + scoreScheme, True(), True(), alignContext); +} + +} + +#endif // INCLUDE_ALIGN_ALIGN_EXTEND_H diff --git a/seqan/align_extend/align_extend_base.h b/seqan/align_extend/align_extend_base.h new file mode 100644 index 0000000..336daed --- /dev/null +++ b/seqan/align_extend/align_extend_base.h @@ -0,0 +1,201 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Hannes Hauswedell +// ========================================================================== +// This file contains routines to extend an existing Align object +// ========================================================================== + + +#ifndef INCLUDE_ALIGN_ALIGN_EXTEND_BASE_H +#define INCLUDE_ALIGN_ALIGN_EXTEND_BASE_H + +namespace seqan { + + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +template +struct AlignExtend_ +{ +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + + +// overrides for AligExtend general case +template +struct SetupAlignmentProfile_, TAlignConfig, TGapCosts, + TTraceSwitch> +{ + typedef DPProfile_, TGapCosts, TracebackOn<> > Type; +}; + +template +struct TraceTail_ > : False +{}; + +template +struct TraceHead_ > : True +{}; + +template +struct IsFreeEndGap_, DPLastRow> : True +{}; + +template +struct IsFreeEndGap_, DPLastColumn> : True +{}; + + + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [FullColumn] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_, TGapCosts, + TTraceback>, + MetaColumnDescriptor > +{ + + typedef typename If, RecursionDirectionZero, + RecursionDirectionHorizontal + >::Type TRecursionTypeFirstCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionAll + >::Type TRecursionTypeInnerCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionAll + >::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [PartialColumnTop] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_, TGapCosts, + TTraceback>, + MetaColumnDescriptor > +{ + + typedef typename If, RecursionDirectionZero, + RecursionDirectionHorizontal + >::Type TRecursionTypeFirstCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionAll + >::Type TRecursionTypeInnerCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionLowerDiagonal + >::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [PartialColumnMiddle] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_, TGapCosts, + TTraceback>, + MetaColumnDescriptor > +{ + typedef typename If, RecursionDirectionZero, + RecursionDirectionUpperDiagonal + >::Type TRecursionTypeFirstCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionAll + >::Type TRecursionTypeInnerCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionLowerDiagonal + >::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +// ---------------------------------------------------------------------------- +// Class DPMetaColumn_ [PartialColumnBottom] +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_, TGapCosts, + TTraceback>, + MetaColumnDescriptor > +{ + typedef typename If, RecursionDirectionZero, + RecursionDirectionUpperDiagonal + >::Type TRecursionTypeFirstCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionAll + >::Type TRecursionTypeInnerCell_; + typedef typename If, RecursionDirectionVertical, + RecursionDirectionAll + >::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +} +#endif diff --git a/seqan/align_extend/dp_scout_xdrop.h b/seqan/align_extend/dp_scout_xdrop.h new file mode 100644 index 0000000..8331f22 --- /dev/null +++ b/seqan/align_extend/dp_scout_xdrop.h @@ -0,0 +1,206 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Hannes Hauswedell +// ========================================================================== +// This file contains routines to extend an existing Align object +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_DP_SCOUT_EXTEND_H_ +#define INCLUDE_SEQAN_ALIGN_DP_SCOUT_EXTEND_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag XDropScout. +// ---------------------------------------------------------------------------- + +template +struct XDrop_ +{ +}; + +// ---------------------------------------------------------------------------- +// Class DPScoutState_ +// ---------------------------------------------------------------------------- + +template +class DPScoutState_ > > +{ +public: + TScoreValue const terminationThreshold; + TScoreValue columnMax; + + DPScoutState_() : + terminationThreshold(MaxValue::VALUE), + columnMax(MinValue::VALUE) + { + } + + DPScoutState_(TScoreValue const & _terminationThreshold) : + terminationThreshold(_terminationThreshold), + columnMax(MinValue::VALUE) + { + } +}; + + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// overrides for AligExtend XDrop case +template +struct HasTerminationCriterium_ > > : True {}; + +template +struct ScoutSpecForAlignmentAlgorithm_ >, DPScoutState_ > +{ + typedef Terminator_ > Type; +}; + +template +struct ScoutSpecForAlignmentAlgorithm_ > const, DPScoutState_ > +{ + typedef Terminator_ > Type; +}; + +template +struct ScoutStateSpecForScout_< + DPScout_< + TDPCell, Terminator_::Type> > > > +{ + typedef Terminator_::Type> > Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _scoutBestScore() [DPScout_] +// ---------------------------------------------------------------------------- + +// NOTE: The original code here used Value::Type instead of TDPCellValue but this caused ambiguous call +// errors in MSVC. + +template +inline void +_scoutBestScore(DPScout_ > > & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn const & /**/, + False const & /*IsLastRow*/) +{ + typedef typename Value::Type TScoreValue; + typedef XDrop_ TXDrop; + typedef DPScout_ > TDPScout; + typedef typename TDPScout::TParent TParent; + + // global maximum + _scoutBestScore(static_cast( dpScout ), activeCell, navigator); + + // column maximum + dpScout.state->columnMax = _max(dpScout.state->columnMax, _scoreOfCell(activeCell)); +} + +template +inline void +_scoutBestScore(DPScout_ > > & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn const & /**/, + True const & /*IsLastRow*/) +{ + typedef typename Value::Type TScoreValue; + + _scoutBestScore(dpScout, activeCell, navigator, TIsLastColumn(), False()); + + // check termination condition + if (_scoreOfCell(dpScout._maxScore) - dpScout.state->columnMax >= dpScout.state->terminationThreshold) + terminateScout(dpScout); + else // reset columMax at end of column + dpScout.state->columnMax = MinValue::VALUE; +} + +// ---------------------------------------------------------------------------- +// Function _scoutBestScore() [DPScout_] +// ---------------------------------------------------------------------------- + +// Computes the score and tracks it if enabled. +template +inline void +_computeCell(TDPScout & scout, + TTraceMatrixNavigator & traceMatrixNavigator, + DPCell_ & activeCell, + DPCell_ const & previousDiagonal, + DPCell_ const & previousHorizontal, + DPCell_ const & previousVertical, + TSequenceHValue const & seqHVal, + TSequenceVValue const & seqVVal, + TScoringScheme const & scoringScheme, + TColumnDescriptor const &, + TCellDescriptor const &, // One of FirstCell, InnerCell or LastCell. + DPProfile_ >, TGapCosts, + TTraceback> const &) +{ + typedef DPProfile_ >, TGapCosts, TTraceback> TDPProfile; + typedef DPMetaColumn_ TMetaColumn; + + assignValue(traceMatrixNavigator, _computeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, + seqHVal, seqVVal, scoringScheme, + typename RecursionDirection_::Type(), + TDPProfile())); + if (TrackingEnabled_::VALUE) + { + typedef typename IsSameType< typename TColumnDescriptor::TColumnProperty, DPFinalColumn>::Type TIsLastColumn; + + // the following is the only change to the regular _computeCell: + // for the evaluation of the termination criterium we treat + // all lastCells as lastRows + typedef typename IsSameType::Type TIsLastRow; + _scoutBestScore(scout, activeCell, traceMatrixNavigator, TIsLastColumn(), TIsLastRow()); + } +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_ALIGN_DP_SCOUT_EXTEND_H_ diff --git a/seqan/align_profile.h b/seqan/align_profile.h new file mode 100644 index 0000000..f9436f8 --- /dev/null +++ b/seqan/align_profile.h @@ -0,0 +1,57 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for module align_profile. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ALIGN_PROFILE_H_ +#define INCLUDE_SEQAN_ALIGN_PROFILE_H_ + +// =========================================================================== +// Prerequisites +// =========================================================================== + +#include +#include +#include +#include +#include + +// =========================================================================== +// Module Contents +// =========================================================================== + +#include +#include + +#endif // INCLUDE_SEQAN_ALIGN_PROFILE_H_ diff --git a/seqan/align_profile/add_to_profile.h b/seqan/align_profile/add_to_profile.h new file mode 100644 index 0000000..76f035d --- /dev/null +++ b/seqan/align_profile/add_to_profile.h @@ -0,0 +1,165 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Algorithm for profile-to-sequence alignment that then adds the resulting +// sequence alignment to the profile. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_PROFILE_ADD_TO_PROFILE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_PROFILE_ADD_TO_PROFILE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function addToProfile() +// ---------------------------------------------------------------------------- + +/*! + * @fn addToProfile + * @headerfile + * @brief Sequence-to-profile alignment with sequence integration. + * + * seq will be aligned to profile using @link globalAlignment @endlink. To compute a banded alignment + * lDiag and uDiag have to be given. + * The resulting alignment will then be integrated into profile by incrementing the count values of + * the profile entries that correspond to the seq row of the alignment. + * + * @signature void addToProfile(profile, seq[, lDiag, uDiag]); + * + * @param[in,out] profile The profile to add seq to. A @link String @endlink over @link ProfileChar @endlink. + * @param[in] seq @link String @endlink to align to profile. + * @param[in] lDiag Lower diagonal for alignment (@link SignedIntegerConcept @endlink). + * @param[in] uDiag Upper diagonal for alignment (@link SignedIntegerConcept @endlink). + */ + +// TODO(holtgrew): Add example? + +template +void addToProfile(String > & profile, + String /*const*/ & seq, + int lDiag = minValue(), + int uDiag = maxValue()) // non-const because of holder issues +{ + typedef ProfileChar TProfileChar; + + typedef String TProfileString; + typedef String TSequence; + + // Define gaps and scoring scheme. + Gaps gapsH(profile); + Gaps gapsV(seq); + seqan::Score sScheme(profile); + + // Perform the global alignment. + if (lDiag == minValue() || uDiag == maxValue()) + globalAlignment(gapsH, gapsV, sScheme, Gotoh()); + else + globalAlignment(gapsH, gapsV, sScheme, lDiag, uDiag, Gotoh()); + + // Construct a new profile from the alignment into buffer and finally swap out the new profile. + TProfileString buffer; + reserve(buffer, length(gapsH)); + typename Iterator, Standard>::Type + itH = begin(gapsH, Standard()), + itHEnd = end(gapsH, Standard()); + typename Iterator, Standard>::Type itV = begin(gapsV, Standard()); + + // std::cout << "--- BEFORE ----\n"; + // std::cout << "HORIZONTAL\n"; + // for (; itH != itHEnd; ++itH) + // { + // if (isGap(itH)) + // { + // std::cerr << "-\n"; + // } + // else + // { + // TProfileChar c = (TProfileChar)*itH; + // std::cout << "(" << c.count[0] << ", " << c.count[1] << ", " << c.count[2] << ", " << c.count[3] << ", " << c.count[4] << ")\n"; + // } + //} + //std::cout << "VERTICAL\n"; + //std::cout << gapsV << "\n"; + + itH = begin(gapsH, Standard()); + SEQAN_ASSERT_EQ(length(gapsH), length(gapsV)); + for (; itH != itHEnd; ++itH, ++itV) + { + if (isGap(itH)) + { + SEQAN_ASSERT_NOT_MSG(isGap(itV), "Must not generate gaps columns!"); + appendValue(buffer, TProfileChar()); + back(buffer).count[valueSize()] += 1; + back(buffer).count[ordValue(TChar(*itV))] += 1; + } + else + { + TProfileChar c = *itH; + appendValue(buffer, c); + if (isGap(itV)) + back(buffer).count[valueSize()] += 1; + else + back(buffer).count[ordValue(TChar(*itV))] += 1; + } + } + + //std::cout << "--- AFTER ----\n"; + //std::cout << "HORIZONTAL\n"; + //for (typename Iterator::Type it = begin(buffer, Standard()); it != end(buffer, Standard()); ++it) + //{ + // std::cout << "(" << it->count[0] << ", " << it->count[1] << ", " << it->count[2] << ", " + // << it->count[3] << ", " << it->count[4] << ")\n"; + //} + + swap(buffer, profile); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_PROFILE_ADD_TO_PROFILE_H_ diff --git a/seqan/align_profile/score_profile_seq.h b/seqan/align_profile/score_profile_seq.h new file mode 100644 index 0000000..86b9a26 --- /dev/null +++ b/seqan/align_profile/score_profile_seq.h @@ -0,0 +1,536 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_PROFILE_SPROFILE_SEQ_H_ +#define SEQAN_INCLUDE_PROFILE_SPROFILE_SEQ_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ProfileSeqScore + +struct ProfileSeqScore_; +typedef Tag ProfileSeqScore; + +template +class Score; + +template +inline void +assignProfile(Score & me, TString const & profile); + +// ProfileSeqFracScore + +struct ProfileSeqFracScore_; +typedef Tag ProfileSeqFracScore; + +template +class Score; + +template +inline void +assignProfile(Score & me, TString const & profile); + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class ProfileSeq Score +// ---------------------------------------------------------------------------- + +struct ProfileSeqScore_; +typedef Tag ProfileSeqScore; + +/*! + * @class ProfileSeqScore ProfileSeq Score + * @extends Score + * @headerfile + * @brief Score for sequence-to-profile alignments. + * + * Using this class, you can align sequences to profiles. The profile is assumed to be in the horizontal direction + * (first row), the sequence in the vertical direction (second row). + * + * Scoring works as follows. + * + * The integer SEQAN_CONSENSUS_UNITY and fractions thereof are used to express scores. Gap opens in the + * profile are scored proportional to the number of gaps in the profile with two times unity, gap extends with one times + * unity at the position. + * + * Gap opens in the sequence are scored with two times unity, gap extends in the sequence with unity. Alignments of + * profile characters to sequence characters are scored with the fraction of profile characters that match the sequence + * characters times unity. + * + * @signature template + * class Score; + * + * @tparam TValue The integer type to use for representing scores. + * + * @section Examples + * + * The following example uses the ProfileSeq Score to align a sequence against a profile. + * Note that we print the gap state for each position since profiles cannot be printed to one stdout character. + * + * @include demos/dox/align_profile/profile_seq_score.cpp + * + * The output is as follows: + * + * @code{.output} + * score value = -2097152 + * gaps in profile/sequence + * pos G S + * 0 0 0 + * 1 1 0 + * 2 0 0 + * 3 1 0 + * 4 0 0 + * 5 0 0 + * @endcode + */ + +/*! + * @fn ProfileSeqScore::Score + * @brief Constructor + * + * @signature Score::Score(); + * @signature Score::Score(profile); + * + * @param[in] profile The profile to copy from (@link AllocString @endlink of @link ProfileChar @endlink objects). + * + * When providing profile, the function @link ProfileSeqScore#assignProfile @endlink is automatically used to + * assign the profile to this class. + */ + +template +class Score +{ + public: + // A table of position x (ord value) giving the counts of the characters at the given positions. + String consensusSet; + + Score() {} + + // Construct given a profile string. + template + explicit + Score(TProfile const & profile) + { + assignProfile(*this, profile); + } +}; + +// ---------------------------------------------------------------------------- +// Class ProfileSeqFrac Score +// ---------------------------------------------------------------------------- + +struct ProfileSeqFracScore_; +typedef Tag ProfileSeqFracScore; + +/*! + * @class ProfileSeqFracScore ProfileSeqFrac Score + * @extends Score + * @headerfile + * @brief Score for sequence-to-profile alignments. + * + * Using this class, you can align sequences to profiles. The profile is assumed to be in the horizontal direction + * (first row), the sequence in the vertical direction (second row). + * + * Scoring works as follows. + * + * The integer SEQAN_CONSENSUS_UNITY and fractions thereof are used to express scores. Gap opens in the + * profile are scored proportional to the number of gaps in the profile two times unity, gap extends are scored + * proportional to the number of gaps in the profile at the position. Gap opens in the sequence are scored with two + * times unity, gap extends with one times unity. + * + * @signature template + * class Score; + * + * @tparam TValue The integer type to use for representing scores. + * + * @section Examples + * + * The following example uses the ProfileSeqFrac Score to align a sequence against a profile. Note that we print the + * gap state for each position since profiles cannot be printed to one stdout character. + * + * @include demos/dox/align_profile/profile_seq_frac_score.cpp + * + * The output is as follows: + * + * @code + * score value = -2097152 + * gaps in profile/sequence + * pos G S + * 0 0 0 + * 1 1 0 + * 2 0 0 + * 3 1 0 + * 4 0 0 + * 5 0 0 + * @endcode + */ + +/*! + * @fn ProfileSeqFracScore::Score + * @brief Constructor + * + * @signature Score::Score(); + * @signature Score::Score(profile); + * + * @param[in] profile The profile to copy from (@link AllocString @endlink of @link ProfileChar @endlink objects). + * + * When providing profile, the function @link ProfileSeqFracScore#assignProfile @endlink is automatically used to + * assign the profile to this class. + */ + + +template +class Score +{ + public: + // Total number of profile characters in each column + String sum; + + Score() {} + + // Construct given a profile string. + template + explicit + Score(TProfile const & profile) + { + assignProfile(*this, profile); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// -------------------------------------------------------------------------- +// Metafunction SequenceEntryForScore [ProfileSeq Score] +// -------------------------------------------------------------------------- + +// Returns the type that holds a sequence entry. This is used for abstracting away the access to sequence characters. + +template +struct SequenceEntryForScore, TSequence> +{ + typedef ConsensusScoreSequenceEntry Type; +}; + +template +struct SequenceEntryForScore const, TSequence> : + SequenceEntryForScore, TSequence> +{}; + +// -------------------------------------------------------------------------- +// Metafunction SequenceEntryForScore [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +// Returns the type that holds a sequence entry. This is used for abstracting away the access to sequence characters. + +template +struct SequenceEntryForScore, TSequence> +{ + typedef ConsensusScoreSequenceEntry Type; +}; + +template +struct SequenceEntryForScore const, TSequence> : + SequenceEntryForScore, TSequence> +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// -------------------------------------------------------------------------- +// Function sequenceEntryForScore() [ProfileSeq Score] +// -------------------------------------------------------------------------- + +template +inline ConsensusScoreSequenceEntry +sequenceEntryForScore(Score const & /*sScheme*/, + TSequence const & seq, TPosition pos) +{ + return ConsensusScoreSequenceEntry(seq, pos); +} + +// -------------------------------------------------------------------------- +// Function assignProfile() [ProfileSeq Score] +// -------------------------------------------------------------------------- + +/*! + * @fn ProfileSeqScore#assignProfile + * @brief Assign profile to ProfileSeqScore. + * + * @signature void assignProfile(score, profile); + * + * @param[out] score The ProfileSeqScore object to assign the profile for. + * @param[in] profile The profile to assign to the score. @link AllocString @endlink of @link ProfileChar @endlink. + */ + +template +inline void +assignProfile(Score & me, + TString const & profile) +{ + typedef typename Size::Type TSize; + TSize alphSize = ValueSize::Type>::VALUE; + resize(me.consensusSet, alphSize * length(profile)); + + typedef typename Iterator::Type TIter; + typedef typename Iterator, Standard>::Type TConsSetIter; + TConsSetIter itConsSet = begin(me.consensusSet, Standard()); + TIter it = begin(profile, Standard()); + TIter itEnd = end(profile, Standard()); + TSize maxCount = 0; + for (;it!=itEnd;++it) + { + maxCount = 0; + for (TSize i = 0; i maxCount) + maxCount = (*it).count[i]; + for (TSize i = 0; i +inline TValue +scoreGapExtendHorizontal( + Score const & me, + ConsensusScoreSequenceEntry const & entry1, + ConsensusScoreSequenceEntry const & entry2) +{ + typedef typename Value::Type TValue1; + if ((int)position(entry2) < 0) + return -SEQAN_CONSENSUS_UNITY; + else + return me.consensusSet[position(entry1) * (ValueSize::VALUE) + (ValueSize::VALUE - 1)]; +} + +// -------------------------------------------------------------------------- +// Function scoreGapOpenHorizontal() [ProfileSeq Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapOpenHorizontal( + Score const & me, + ConsensusScoreSequenceEntry const & entry1, + ConsensusScoreSequenceEntry const & entry2) +{ + typedef typename Value::Type TValue1; + if ((int)position(entry2) < 0) + return -2 * SEQAN_CONSENSUS_UNITY; + else + return 2 * me.consensusSet[position(entry1) * (ValueSize::VALUE) + (ValueSize::VALUE - 1)]; +} + +// -------------------------------------------------------------------------- +// Function scoreGapExtendVertical() [ProfileSeq Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapOpenVertical( + Score const &, + ConsensusScoreSequenceEntry const & /*entry1*/, + ConsensusScoreSequenceEntry const & /*entry2*/) +{ + return -2 * SEQAN_CONSENSUS_UNITY; +} + +// -------------------------------------------------------------------------- +// Function scoreGapOpenVertical() [ProfileSeq Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapExtendVertical( + Score const &, + ConsensusScoreSequenceEntry const & /*entry1*/, + ConsensusScoreSequenceEntry const & /*entry2*/) +{ + return -SEQAN_CONSENSUS_UNITY; +} + +// -------------------------------------------------------------------------- +// Function score() [ProfileSeq Score] +// -------------------------------------------------------------------------- + +template +inline TValue +score(Score const & me, + ConsensusScoreSequenceEntry const & entry1, + ConsensusScoreSequenceEntry const & entry2) +{ + typedef typename Value::Type TValue1; + return me.consensusSet[position(entry1) * (ValueSize::VALUE) + ordValue(value(entry2))]; +} + +// -------------------------------------------------------------------------- +// Function sequenceEntryForScore() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +template +inline ConsensusScoreSequenceEntry +sequenceEntryForScore(Score const & /*sScheme*/, + TSequence const & seq, TPosition pos) +{ + return ConsensusScoreSequenceEntry(seq, pos); +} + +// -------------------------------------------------------------------------- +// Function assignProfile() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +/*! + * @fn ProfileSeqFracScore#assignProfile + * @brief Assign profile to ProfileSeqFrac Score. + * + * @signature void assignProfile(score, profile); + * + * @param[out] score The ProfileSeqScore object to assign the profile for. + * @param[in] profile The profile to assign to the score. @link AllocString @endlink of @link ProfileChar @endlink. + */ + +template +inline void +assignProfile(Score & me, + TString const & profile) +{ + typedef typename Size::Type TSize; + resize(me.sum, length(profile)); + typedef typename Iterator::Type TIter; + typedef typename Iterator, Standard>::Type TSumIter; + TSumIter itSum = begin(me.sum, Standard()); + TIter it = begin(profile, Standard()); + TIter itEnd = end(profile, Standard()); + for (; it!=itEnd; ++it, ++itSum) + { + *itSum = 0; + for (TSize i = 0; i < (TSize) ValueSize::Type>::VALUE; ++i) + *itSum += (*it).count[i]; + } +} + +// -------------------------------------------------------------------------- +// Function scoreGapExtendHorizontal() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapExtendHorizontal( + Score const & me, + ConsensusScoreSequenceEntry const & entry1, + ConsensusScoreSequenceEntry const & entry2) +{ + if (((int)position(entry2) < 0) || (!me.sum[position(entry1)])) + return -SEQAN_CONSENSUS_UNITY; + else + return ((TValue) (( (int)value(entry1).count[ValueSize::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]); +} + +// -------------------------------------------------------------------------- +// Function scoreGapOpenHorizontal() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapOpenHorizontal( + Score const & me, + ConsensusScoreSequenceEntry const & entry1, + ConsensusScoreSequenceEntry const & entry2) +{ + if (((int)position(entry2) < 0) || (!me.sum[position(entry1)])) + return -SEQAN_CONSENSUS_UNITY; + else + return ((TValue) (((int)value(entry1).count[ValueSize::Type>::VALUE - 1] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]); +} + +// -------------------------------------------------------------------------- +// Function scoreGapExtendVertical() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapOpenVertical( + Score const &, + ConsensusScoreSequenceEntry const & /*entry1*/, + ConsensusScoreSequenceEntry const & /*entry2*/) +{ + return -SEQAN_CONSENSUS_UNITY; +} + +// -------------------------------------------------------------------------- +// Function scoreGapOpenVertical() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +template +inline TValue +scoreGapExtendVertical( + Score const &, + ConsensusScoreSequenceEntry const & /*entry1*/, + ConsensusScoreSequenceEntry const & /*entry2*/) +{ + return -SEQAN_CONSENSUS_UNITY; +} + +// -------------------------------------------------------------------------- +// Function score() [ProfileSeqFrac Score] +// -------------------------------------------------------------------------- + +template +inline TValue +score(Score const & me, + ConsensusScoreSequenceEntry const & entry1, + ConsensusScoreSequenceEntry const & entry2) +{ + if (!me.sum[position(entry1)]) + return -SEQAN_CONSENSUS_UNITY; + else + return ((TValue) (((int)value(entry1).count[ordValue(value(entry2))] - me.sum[position(entry1)]) * SEQAN_CONSENSUS_UNITY) / me.sum[position(entry1)]); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_PROFILE_SPROFILE_SEQ_H_ diff --git a/seqan/align_split.h b/seqan/align_split.h new file mode 100644 index 0000000..b08ac58 --- /dev/null +++ b/seqan/align_split.h @@ -0,0 +1,55 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for module align_split. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_H_ + +// =========================================================================== +// Prerequisites. +// =========================================================================== + +#include +#include +#include + +// =========================================================================== +// Split Alignment Impelmentation. +// =========================================================================== + +#include +#include + +#endif // SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_H_ diff --git a/seqan/align_split/align_split_interface.h b/seqan/align_split/align_split_interface.h new file mode 100644 index 0000000..658536a --- /dev/null +++ b/seqan/align_split/align_split_interface.h @@ -0,0 +1,751 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Split alignment implementation. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_ALIGN_SPLIT_INTERFACE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_ALIGN_SPLIT_INTERFACE_H_ + +#include "dp_scout_split.h" + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// Tag for the split alignment algorithm in DPProfile_. + +template +struct SplitAlignment_ {}; + +// Tag for the split alignment algorithm. + +struct SplitAlignmentAlgo_; +typedef Tag SplitAlignmentAlgo; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction ScoutSpecForAlignmentAlgorithm_ +// ---------------------------------------------------------------------------- + +// For the split alignment, we will use our SplitAlignmentScout specialization of DPScout. + +template +struct ScoutSpecForAlignmentAlgorithm_, DPScoutState_ > +{ + typedef SplitAlignmentScout Type; +}; + +template +struct ScoutSpecForAlignmentAlgorithm_ const, DPScoutState_ > +{ + typedef SplitAlignmentScout Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IsSplitAlignment_ +// ---------------------------------------------------------------------------- + +// Convenience function used in the DP configuration below. + +template +struct IsSplitAlignment_ : False {}; + +template +struct IsSplitAlignment_ >: + True {}; + +template +struct IsSplitAlignment_ const>: + True {}; + +template +struct IsSplitAlignment_ >: + IsSplitAlignment_ {}; + +template +struct IsSplitAlignment_ const>: + IsSplitAlignment_ {}; + +// ---------------------------------------------------------------------------- +// Metafunction IsFreeEndGap_ +// ---------------------------------------------------------------------------- + +// We want the same free endgaps configuration as for global alignments. + +template +struct IsFreeEndGap_, TRow> : + IsFreeEndGap_, TRow> +{}; + +template +struct IsFreeEndGap_ const, TRow> : + IsFreeEndGap_ const, TRow> +{}; + +// ---------------------------------------------------------------------------- +// Metafunction IsGlobalAlignment_ +// ---------------------------------------------------------------------------- + +// We use similar functionality as the global alignment. + +template +struct IsGlobalAlignment_ > : + True +{}; + +template +struct IsGlobalAlignment_ const> : + True +{}; + +// ---------------------------------------------------------------------------- +// Metafunction TraceTail_ +// ---------------------------------------------------------------------------- + +template +struct TraceTail_ > : + False +{}; + +// ---------------------------------------------------------------------------- +// Metafunction LastColumnEnabled_ +// ---------------------------------------------------------------------------- + +template +struct LastColumnEnabled_, TColumnDescriptor> +{ + typedef typename If, + typename IsFreeEndGap_, DPLastColumn>::Type, + False>::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction LastRowEnabled_ +// ---------------------------------------------------------------------------- + +template +struct LastRowEnabled_, LastCell, TColumnDescriptor> +{ + typedef typename If, + IsSameType >, + typename IsFreeEndGap_, DPLastRow>::Type, + False>::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction DPMetaColumn_ +// ---------------------------------------------------------------------------- + +template +struct DPMetaColumn_, TGapCosts, TTraceFlag>, MetaColumnDescriptor > +{ + typedef DPProfile_, TGapCosts, TTraceFlag> TDPProfile; + typedef typename IsLocalAlignment_::Type TIsLocal; + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> Horizontal | Zero, All, All + // If FinalColumn -> Horizontal | Zero, All, All + + typedef typename If, + IsFreeEndGap_ >, RecursionDirectionZero, RecursionDirectionHorizontal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + + +template +struct DPMetaColumn_, TGapCosts, TTraceFlag>, MetaColumnDescriptor > +{ + typedef DPProfile_, TGapCosts, TTraceFlag> TDPProfile; + typedef typename IsLocalAlignment_::Type TIsLocal; + + // How does the recursion directions look like? + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> Horizontal | Zero, All, LowerBand + // If FinalColumn -> Horizontal | Zero, All, LowerBand + + typedef typename If, + IsFreeEndGap_ >, RecursionDirectionZero, RecursionDirectionHorizontal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionLowerDiagonal>::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +template +struct DPMetaColumn_, TGapCosts, TTraceFlag>, MetaColumnDescriptor > +{ + typedef DPProfile_, TGapCosts, TTraceFlag> TDPProfile; + typedef typename IsLocalAlignment_::Type TIsLocal; + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> UpperDiagonal, All, LowerDiagonal + // If FinalColumn -> UpperDiagonal, All, LowerDiagonal + + typedef typename If, RecursionDirectionZero, RecursionDirectionUpperDiagonal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionLowerDiagonal>::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +template +struct DPMetaColumn_, TGapCosts, TTraceFlag>, MetaColumnDescriptor > +{ + typedef DPProfile_, TGapCosts, TTraceFlag> TDPProfile; + typedef typename IsLocalAlignment_::Type TIsLocal; + + // If InitialColumn -> Zero, Vertical | Zero, Vertical | Zero // Within the algorithm we need to define the first row as only one cell if it is no initial column + // If InnerColumn -> UpperDiagonal, All, All + // If FinalColumn -> UpperDiagonal, All, All + + typedef typename If, RecursionDirectionZero, RecursionDirectionUpperDiagonal>::Type TRecursionTypeFirstCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeInnerCell_; + typedef typename If, + typename If, RecursionDirectionZero, RecursionDirectionVertical>::Type, + RecursionDirectionAll>::Type TRecursionTypeLastCell_; + + typedef DPMetaCell_ TFirstCell_; + typedef DPMetaCell_ TInnerCell_; + typedef DPMetaCell_ TLastCell_; +}; + +// ---------------------------------------------------------------------------- +// Metafunction SetupAlignmentProfile_ +// ---------------------------------------------------------------------------- + +template +struct SetupAlignmentProfile_ +{ + typedef DPProfile_, TGapCosts, TTraceSwitch> Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _reverseTrace() +// ---------------------------------------------------------------------------- + +// Reverse a trace string and adapt internal position. +template +void _reverseTrace(String, TSpec> & trace, + size_t const lengthH, + size_t const lengthV) +{ + typedef String, TSpec> TTrace; + typedef typename Iterator::Type TTraceIter; + + if (empty(trace)) + return; + + for (TTraceIter it = begin(trace, Rooted()); !atEnd(it); goNext(it)) + { + it->_horizontalBeginPos = lengthH - _getEndHorizontal(*it); + it->_verticalBeginPos = lengthV - _getEndVertical(*it); + } + reverse(trace); +} + +// ---------------------------------------------------------------------------- +// Function _computeSplitTrace() +// ---------------------------------------------------------------------------- + +template +void _computeSplitTrace(TTarget & target, + TSeqH const & seqH, + TSeqV const & seqV, + TDPContext const & dpContext, + TMatPos const matPos, + AlignConfig2, TFreeEndGaps, TTraceConfig> const & config) +{ + typedef typename SetupAlignmentProfile_::Type TDPProfile; + + typedef typename GetDPTraceMatrix::Type TDPTraceMatrixHost; + typedef typename Value::Type TTraceValue; + + typedef DPMatrix_ TDPTraceMatrix; + typedef DPMatrixNavigator_, NavigateColumnWise> TDPTraceMatrixNavigator; + + TDPTraceMatrix matrix; + setLength(matrix, +DPMatrixDimension_::HORIZONTAL, length(seqH) + 1 - std::max(0, lowerDiagonal(config._band))); + + if (IsSameType::VALUE) + { + setLength(matrix, +DPMatrixDimension_::VERTICAL, length(seqV) + 1); + } + else + { + int bandSize = _min(static_cast(length(seqH)), upperDiagonal(config._band)) - + _max(lowerDiagonal(config._band), -static_cast(length(seqV))) + 1; + setLength(matrix, +DPMatrixDimension_::VERTICAL, _min(static_cast(length(seqV)) + 1, bandSize)); + } + + setHost(matrix, getDpTraceMatrix(dpContext)); + resize(matrix); + SEQAN_ASSERT_EQ(length(getDpTraceMatrix(dpContext)), length(matrix)); + TDPTraceMatrixNavigator navi; + _init(navi, matrix, config._band); + _computeTraceback(target, navi, matPos, seqH, seqV, config._band, TDPProfile()); +} + +// ---------------------------------------------------------------------------- +// Function _splitAlignmentImpl() +// ---------------------------------------------------------------------------- + +// We call the long sequence contig and the shorter one read but could be changed roles. +template +auto _splitAlignmentImpl(Gaps & gapsContigL, + Gaps & gapsReadL, + Gaps & gapsContigR, + Gaps & gapsReadR, + Score const & scoringScheme, + TAlignConfigL const & alignConfigL, + TAlignConfigR const & alignConfigR, + TGapModel const & /*gapModel*/) +{ + typedef Gaps TGaps; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + typedef TraceSegment_ TTraceSegment; + + // Compute trace and split score sequence for the left alignment. + // We actually need to first compute the scores, than trace from the choosen split position. + DPContext dpContextL; + DPScoutState_ scoutStateL; + resize(scoutStateL.splitScore, length(source(gapsContigL)) + 1, minValue() / 2); + resize(scoutStateL.splitPos, length(scoutStateL.splitScore)); + + String traceL; + _setUpAndRunAlignment(dpContextL, traceL, scoutStateL, source(gapsContigL), source(gapsReadL), scoringScheme, alignConfigL); + + // Get reversed versions of the right contig and read sequence. + ModifiedString revContigR(source(gapsContigR)); + ModifiedString revReadR(source(gapsReadR)); + + // Compute trace and split score sequence for the right alignment. + DPContext dpContextR; + DPScoutState_ scoutStateR; + resize(scoutStateR.splitScore, length(source(gapsContigR)) + 1, minValue() / 2); + resize(scoutStateR.splitPos, length(scoutStateR.splitScore)); + + String traceR; + _setUpAndRunAlignment(dpContextR, traceR, scoutStateR, revContigR, revReadR, scoringScheme, alignConfigR); + + // Reverse trace so it fits to the forward right sequences. Also reverse the trace such that we can directly apply + // it for the right alignment. + reverse(scoutStateR.splitScore); + reverse(scoutStateR.splitPos); + + SEQAN_ASSERT_EQ(length(scoutStateL.splitScore), length(scoutStateR.splitScore)); + + // We will split the left and right alignments into two parts such that the alignment score is optimal. We compute + // the leftmost best position for a split (equivalent to the best prefix of the first left alignment). Note that + // placing the breakpoint at the leftmost position is coherent with the SNPdb semantics but there are other data + // bases that use rightmost placement. + + // TODO(holtgrew): Make selecting the left/right split position from interface possible? Maybe not necessary. + + auto itBegin = makeZipIterator(begin(scoutStateL.splitScore), begin(scoutStateR.splitScore)); + auto res = std::max_element(itBegin, makeZipIterator(end(scoutStateL.splitScore), end(scoutStateR.splitScore)), + [] (auto const & lhs, auto const & rhs) + { + return std::get<0>(lhs) + std::get<1>(lhs) < std::get<0>(rhs) + std::get<1>(rhs); + }); + auto bestPrefixLength = res - itBegin; + + // std::cerr << "bestPrefixLength = " << bestPrefixLength << "\n"; + + // std::cerr << "split store left "; + // for (unsigned i = 0; i < length(scoutStateL.splitScore); ++i) + // fprintf(stderr, " %3d", scoutStateL.splitScore[i]); + // std::cerr << "\n"; + // std::cerr << "split store right"; + // for (unsigned i = 0; i < length(scoutStateR.splitScore); ++i) + // fprintf(stderr, " %3d", scoutStateR.splitScore[i]); + // std::cerr << "\n"; + + // Recompute the best trace starting from the recorded split position for left ... + clear(traceL); + _computeSplitTrace(traceL, source(gapsContigL), source(gapsReadL), dpContextL, + scoutStateL.splitPos[bestPrefixLength], alignConfigL); + _adaptTraceSegmentsTo(gapsContigL, gapsReadL, traceL); + // ... and right anchor. + clear(traceR); + _computeSplitTrace(traceR, source(gapsContigR), source(gapsReadR), dpContextR, + scoutStateR.splitPos[bestPrefixLength], alignConfigR); + + _reverseTrace(traceR, length(source(gapsContigR)), length(source(gapsReadR))); + _adaptTraceSegmentsTo(gapsContigR, gapsReadR, traceR); + + // We have to correct the clipping position for the left alignment because of the to-right projection. The + // insertion itself is not part of the alignment. + TPosition cePosL = toViewPosition(gapsContigL, bestPrefixLength); + if (bestPrefixLength > 0) + cePosL = toViewPosition(gapsContigL, bestPrefixLength - 1) + 1; + setClippedEndPosition(gapsContigL, cePosL); + setClippedEndPosition(gapsReadL, cePosL); + + return std::make_pair(std::get<0>(*res), std::get<1>(*res)); +} + +template +auto _splitAlignmentImpl(Gaps & gapsContigL, + Gaps & gapsReadL, + Gaps & gapsContigR, + Gaps & gapsReadR, + Score const & scoringScheme, + AlignConfig const &, + int lowerDiagonal, + int upperDiagonal, + TGapModel const & /*gapModel*/) +{ + typedef typename SubstituteAlignConfig_ >::Type TFreeEndGaps; + // Check whether we need to run the banded versions. + if (lowerDiagonal != minValue() && upperDiagonal != maxValue()) + { + typedef AlignConfig2, TFreeEndGaps, + TracebackOn > > TAlignConfigL; + typedef AlignConfig2, TFreeEndGaps, + TracebackOn > > TAlignConfigR; + return _splitAlignmentImpl(gapsContigL, gapsReadL, gapsContigR, gapsReadR, scoringScheme, + TAlignConfigL(lowerDiagonal, upperDiagonal), + TAlignConfigR(lowerDiagonal, upperDiagonal), + TGapModel()); + } + else + { + typedef AlignConfig2, TFreeEndGaps, + TracebackOn > > TAlignConfigL; + typedef AlignConfig2, TFreeEndGaps, + TracebackOn > > TAlignConfigR; + return _splitAlignmentImpl(gapsContigL, gapsReadL, gapsContigR, gapsReadR, scoringScheme, TAlignConfigL(), + TAlignConfigR(), TGapModel()); + } +} + +template +auto _splitAlignmentImpl(Gaps & gapsContigL, + Gaps & gapsReadL, + Gaps & gapsContigR, + Gaps & gapsReadR, + Score const & scoringScheme, + AlignConfig const & config, + int lowerDiagonal = minValue(), + int upperDiagonal = maxValue()) +{ + if (_usesAffineGaps(scoringScheme, source(gapsContigL), source(gapsReadL))) + return _splitAlignmentImpl(gapsContigL, gapsReadL, gapsContigR, gapsReadR, + scoringScheme, config, lowerDiagonal, upperDiagonal, AffineGaps()); + else + return _splitAlignmentImpl(gapsContigL, gapsReadL, gapsContigR, gapsReadR, + scoringScheme, config, lowerDiagonal, upperDiagonal, LinearGaps()); +} + +// ---------------------------------------------------------------------------- +// Function splitAlignment() +// ---------------------------------------------------------------------------- + +/*! + * @fn splitAlignment + * @headerfile + * @brief Compute split alignments. + * + * @signature TScoreValue splitAlignment(alignL, alignR, scoringScheme[, config][, lowerDiag, upperDiag]); + * @signature TScoreValue splitAlignment(gapsHL, gapsVL, gapsHR, gapsVR, scoringScheme[, config][, lowerDiag, upperDiag]); + * + * @param[in,out] alignL @link Align @endlink object with two rows for the left alignment. + * @param[in,out] alignR @link Align @endlink object with two rows for the right alignment. + * @param[in,out] gapsHL @link Gaps @endlink object with the horizontal/contig row for the left alignment. + * @param[in,out] gapsVL @link Gaps @endlink object with the vertical/read row for the left alignment. + * @param[in,out] gapsHR @link Gaps @endlink object with the horizontal/contig row for the right alignment. + * @param[in,out] gapsVR @link Gaps @endlink object with the vertical/read row for the right alignment. + * @param[in] scoringScheme The scoring scheme to use for the alignment. + * @param[in] config A configuration object of type @link AlignConfig @endlink, to specify free-end-gaps. + * @param[in] lowerDiag The lower diagonal.You have to specify the upper and lower diagonals for the left + * alignment. For the right alignment, the corresponding diagonals are chosen for the + * lower right part of the DP matrix, int. + * @param[in] upperDiag The lower diagonal. Also see remark for lowerDiag, int. + * + * @return TScoreValue The sum of the alignment scores of both alignments (Metafunction: @link Score#Value @endlink + * of the type of scoringScheme). + * + * There are two variants of the split alignment problem. In the first variant, we want to align two sequences where the + * first (say the reference) one is shorter than the second (say a read) and the read contains an insertion with respect + * to the reference. We now want to align the read agains the reference such that the left part of the read aligns well + * against the left part of the reference and the right part of the read aligns well against the right part of the + * reference. The center gap in the reference is free. + * + * For example: + * + * @code{.console} + * reference AGCATGTTAGATAAGATAGC-----------TGTGCTAGTAGGCAGTCAGCGCCAT + * |||||||||||||||||||| ||||||||||||||||||||||||| + * read AGCATGTTAGATAAGATAGCCCCCCCCCCCCTGTGCTAGTAGGCAGTCAGCGCCAT + * @endcode + * + * The second variant is to align two sequences A and B against a reference such that the left part of A aligns well to + * the left part of the reference and the right part of B aligns well to the right part of the reference. Together, + * both reads span the whole reference and overlap with an insertion in the reference. + * + * @code{.console} + * reference AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT + * |||||||||||||||||| | || + * AGCATGTTAGATAAGATATCCGTCC + * read 1 + * ||| ||||||||||||||||||||||| + * CCGCTATGCTAGTAGGCAGTCAGCGCCAT + * read 2 + * @endcode + * + * The resulting alignment of the left/right parts is depicted below. The square brackets indicate clipping positions. + * + * @code{.console} + * reference AGCATGTTAGATAAGATA [GCTGTGCTAGTAGGCAGTCAGCGCCAT + * |||||||||||||||||| [ | || + * AGCATGTTAGATAAGATA [TCCGTCC + * read 1 + * reference AGCATGTTAGATAAGATA] GTGCTAGTAGGCAGTCAGCGCCAT + * ] ||||||||||||||||||||||| + * CCGCT] ATGCTAGTAGGCAGTCAGCGCCAT + * read 2 + * @endcode + * + * In the first case, we want to find the one breakpoint in the reference and the two breakpoints in the reads and the + * alignment of the left and right well-aligning read parts. In the second case, we want to find the one breakpoint in + * the reference and the breakpoint/clipping position in each read. + * + * The splitAlignment() function takes as the input two alignments. The sequence in each alignment's first row + * is the reference and the sequence of the second row is the read. The sequence has to be the same sequence whereas + * the reads might differ. If the reads are the same then this is the same as the first case and if the reads differ + * then this is the second case. + * + * The result is two alignments of the left and right contig path clipped appropriately. The resulting score is the sum + * of the scores of both alignments. + * + * @section Remarks + * + * The DP algorithm is chosen automatically depending on whether the gap open and extension costs are equal. + * + * @section Example + * + * The following example demonstrates the usage of splitAlignment in the first case. The second case + * works accordingly. + * + * @include demos/dox/align_split/split_alignment.cpp + * + * The output is as follows. + * + * @include demos/dox/align_split/split_alignment.cpp.stdout + */ + +// Variant: unbanded, with Align objects. + +template +int splitAlignment(Align & alignL, + Align & alignR, + Score const & scoringScheme, + AlignConfig const & config) +{ + SEQAN_ASSERT_EQ_MSG(source(row(alignL, 0)), source(row(alignR, 0)), + "Contig must be the same for left and right split alignment."); + + auto tmp = _splitAlignmentImpl(row(alignL, 0), row(alignL, 1), row(alignR, 0), row(alignR, 1), scoringScheme, config); + return std::get<0>(tmp) + std::get<1>(tmp); +} + +template +int splitAlignment(Align & alignL, + Align & alignR, + Score const & scoringScheme) +{ + return splitAlignment(alignL, alignR, scoringScheme, AlignConfig()); +} + +// Variant: unbanded, with Gaps objects. + +template +int splitAlignment(Gaps & gapsHL, + Gaps & gapsVL, + Gaps & gapsHR, + Gaps & gapsVR, + Score const & scoringScheme, + AlignConfig const & config) +{ + SEQAN_ASSERT_EQ_MSG(source(gapsHL), source(gapsHR), + "Contig must be the same for left and right split alignment."); + + auto tmp = _splitAlignmentImpl(gapsHL, gapsVL, gapsHR, gapsVR, scoringScheme, config); + return std::get<0>(tmp) + std::get<1>(tmp); +} + +template +int splitAlignment(Gaps & gapsHL, + Gaps & gapsVL, + Gaps & gapsHR, + Gaps & gapsVR, + Score const & scoringScheme) +{ + return splitAlignment(gapsHL, gapsVL, gapsHR, gapsVR, scoringScheme, AlignConfig()); +} + +// Variant: banded, with Align objects. +template +int splitAlignment(Align & alignL, + Align & alignR, + Score const & scoringScheme, + AlignConfig const & config, + int const lowerDiagonal, + int const upperDiagonal) +{ + SEQAN_ASSERT_EQ_MSG(source(row(alignL, 0)), source(row(alignR, 0)), + "Contig must be the same for left and right split alignment."); + + auto tmp = _splitAlignmentImpl(row(alignL, 0), row(alignL, 1), row(alignR, 0), row(alignR, 1), + scoringScheme, config, lowerDiagonal, upperDiagonal); + return std::get<0>(tmp) + std::get<1>(tmp); +} + +template +int splitAlignment(Align & alignL, + Align & alignR, + Score const & scoringScheme, + int const lowerDiagonal, + int const upperDiagonal) +{ + return splitAlignment(alignL, alignR, scoringScheme, AlignConfig(), + lowerDiagonal, upperDiagonal); +} + +// Variant: banded, with Gaps objects. +template +int splitAlignment(Gaps & gapsHL, + Gaps & gapsVL, + Gaps & gapsHR, + Gaps & gapsVR, + Score const & scoringScheme, + AlignConfig const & config, + int const lowerDiagonal, + int const upperDiagonal) +{ + SEQAN_ASSERT_EQ_MSG(source(gapsHL), source(gapsHR), + "Contig must be the same for left and right split alignment."); + + auto tmp = _splitAlignmentImpl(gapsHL, gapsVL, gapsHR, gapsVR, scoringScheme, config, lowerDiagonal, upperDiagonal); + return std::get<0>(tmp) + std::get<1>(tmp); +} + +template +int splitAlignment(Gaps & gapsHL, + Gaps & gapsVL, + Gaps & gapsHR, + Gaps & gapsVR, + Score const & scoringScheme, + int const lowerDiagonal, + int const upperDiagonal) +{ + return splitAlignment(gapsHL, gapsVL, gapsHR, gapsVR, scoringScheme, AlignConfig(), + lowerDiagonal, upperDiagonal); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_ALIGN_SPLIT_INTERFACE_H_ diff --git a/seqan/align_split/dp_scout_split.h b/seqan/align_split/dp_scout_split.h new file mode 100644 index 0000000..b107e43 --- /dev/null +++ b/seqan/align_split/dp_scout_split.h @@ -0,0 +1,137 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// DPScout_ specialization for the split alignment implementation. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag SplitAlignmentScout. +// ---------------------------------------------------------------------------- + +struct SplitAlignmentScout_; +typedef Tag SplitAlignmentScout; + +// ---------------------------------------------------------------------------- +// Class DPScoutState_ +// ---------------------------------------------------------------------------- + +template <> +class DPScoutState_ +{ +public: + // The best score for each column. Initialized with 0.5*minValue(). + seqan::String splitScore; + seqan::String splitPos; + + DPScoutState_() + {} +}; + +// ---------------------------------------------------------------------------- +// Class DPScout_ +// ---------------------------------------------------------------------------- + +template +class DPScout_ : public DPScout_ +{ +public: + typedef DPScout_ TParent; + + DPScoutState_ * state; + + DPScout_() : TParent(), state(0) + {} + + DPScout_(DPScoutState_ & state) : TParent(), state(&state) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _scoutBestScore() [DPScout_] +// ---------------------------------------------------------------------------- + +template +inline void +_scoutBestScore(DPScout_ & dpScout, + TDPCell const & activeCell, + TTraceMatrixNavigator const & navigator, + TIsLastColumn /*isLastColumn*/, + TIsLastRow /*isLastRow*/ ) +{ + //typedef typename Value::Type TScoreValue; + // Note that the underlying matrix has the coordinates flipped. We use posH/posV as we would in pairwise alignments + // and thus this is the reverse from the matrix representation. + unsigned posH = coordinate(navigator, +DPMatrixDimension_::HORIZONTAL); + // unsigned posV = coordinate(navigator, +DPMatrixDimension_::VERTICAL); + + int & i = dpScout.state->splitScore[posH]; + if (i < _scoreOfCell(activeCell)) + { + i = _scoreOfCell(activeCell); + dpScout.state->splitPos[posH] = position(navigator); + } + + // TODO(rrahn): Do we need the optimal end-point? + // We track only the last row for the best traceback score. + if (TIsLastColumn::VALUE || TIsLastRow::VALUE) + { + typedef DPScout_ TDPScout; + typedef typename TDPScout::TParent TParent; + _scoutBestScore(static_cast(dpScout), activeCell, navigator); + } +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_ diff --git a/seqan/alignment_free.h b/seqan/alignment_free.h new file mode 100644 index 0000000..8a68853 --- /dev/null +++ b/seqan/alignment_free.h @@ -0,0 +1,63 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// Facade header for module alignment_free. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_H_ + +// =========================================================================== +// Prerequisites. +// =========================================================================== + +#include +#include +#include +#include +#include + +// =========================================================================== +// Module's headers. +// =========================================================================== + +#include +#include +#include +#include +#include +#include + +#include + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_H_ diff --git a/seqan/alignment_free/af_d2.h b/seqan/alignment_free/af_d2.h new file mode 100644 index 0000000..7e5bcbe --- /dev/null +++ b/seqan/alignment_free/af_d2.h @@ -0,0 +1,124 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// This header contains the implementation of the D2 score for alignment free +// sequence comparison (inner product of kmer counts). +// +// These functions can be called with alignmentFreeComparison(). +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_ + +namespace seqan { + +/* + * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h) + */ +template +void _alignmentFreeComparison(Matrix & scoreMatrix, + TStringSet const & sequenceSet, + AFScore const & score) +{ + //typedef typename Value::Type TString; + //typedef typename Value::Type TAlphabet; + typedef typename Iterator::Type TIteratorSet; + typedef typename Iterator > >::Type TIteratorSetInt; + //typedef Matrix TMatrix; + + unsigned seqNumber = length(sequenceSet); + + // Resize the scoreMatrix + setLength(scoreMatrix, 0, seqNumber); + setLength(scoreMatrix, 1, seqNumber); + resize(scoreMatrix, (TValue) 0); + + StringSet > kmerCounts; + resize(kmerCounts, seqNumber); + + // Count all kmers + TIteratorSetInt itKmerCounts = begin(kmerCounts); + TIteratorSet itSeqSet = begin(sequenceSet); + + for (; itSeqSet < end(sequenceSet); ++itSeqSet) + { + countKmers(value(itKmerCounts), value(itSeqSet), score.kmerSize); + ++itKmerCounts; + } + if(score.verbose) + { + std::cout << "\ncounted words"; + } + + // Calculate all pairwise scores and store them in scoreMatrix + for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex) + { + if(score.verbose) + { + std::cout << "\nSequence number " << rowIndex; + } + for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex) + { + _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], kmerCounts[colIndex], score); + value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetric entries + } + } + +} + +/* + * Calculate pairwise score given the counts of all kmers + */ +template +void +_alignmentFreeCompareCounts(TValue & result, + String const & kmerCounts1, + String const & kmerCounts2, + AFScore const & /*score*/) +{ + typedef typename Iterator const>::Type TIteratorInt; + + TIteratorInt it1 = begin(kmerCounts1); + TIteratorInt it2 = begin(kmerCounts2); + + result = 0; + for (; it1 < end(kmerCounts1); ++it1) + { + result += value(it1) * value(it2); + ++it2; + } +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2_H_ diff --git a/seqan/alignment_free/af_d2star.h b/seqan/alignment_free/af_d2star.h new file mode 100644 index 0000000..c6bf16f --- /dev/null +++ b/seqan/alignment_free/af_d2star.h @@ -0,0 +1,224 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// This header contains the implementation of the D2star score for alignment +// free sequence comparison. +// +// See: Reinert et al. J Comput Biol. 2009 Dec;16(12):1615-34. +// +// These functions can be called with alignmentFreeComparison(). +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2STAR_ORIGINAL_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2STAR_ORIGINAL_H_ + +namespace seqan { + +/* + * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h) + */ +template +void _alignmentFreeComparison(Matrix & scoreMatrix, + TStringSet const & sequenceSet, + AFScore const & score) +{ + + //typedef typename Iterator::Type TIteratorSet; + //typedef typename Iterator > >::Type TIteratorSetDouble; + + //typedef Matrix TMatrix; + + unsigned seqNumber = length(sequenceSet); + + // Resize the scoreMatrix + setLength(scoreMatrix, 0, seqNumber); + setLength(scoreMatrix, 1, seqNumber); + resize(scoreMatrix, (TValue) 0); + StringSet > standardisedKmerCounts; + resize(standardisedKmerCounts, seqNumber); + + // Calculate all pairwise scores and store them in scoreMatrix + for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex) + { + if(score.verbose) + { + std::cout << "\nSequence number " << rowIndex; + } + for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex) + { + _d2star(value(scoreMatrix, rowIndex, colIndex), sequenceSet[rowIndex], sequenceSet[colIndex], score); + value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetric entries + } + } +} + +/* + * _d2star calculates the pairwise score of two sequences according to the paper referenced above. + */ +template +void _d2star(TValue & result, + TSequence const & sequence1, + TSequence const & sequence2, + AFScore const & score) +{ + typedef typename Value::Type TAlphabet; + typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + + TValue missing = -pow(10.0, 10); + TSequence seq1seq2; + append(seq1seq2, sequence1); + append(seq1seq2, sequence2); + result = 0.0; + + // Note that there is some code below that looks like copy-and-paste. However, pulling this out into another + // function is the only way to get rid of the duplicate lines since we use different types. After some discussion, + // weese, goeke and holtgrew agreed that it is probably easier to read and maintain this way than to spread the code + // over to one more function. + if (score.bgModelOrder == 0) + { + // -------------------------------------------------------------------- + // Order 0 Background Model + // -------------------------------------------------------------------- + + String kmerCounts1; + String kmerCounts2; + String backgroundCounts; + String backgroundFrequencies; + resize(backgroundFrequencies, 4, 0); + countKmers(kmerCounts1, sequence1, score.kmerSize); + countKmers(kmerCounts2, sequence2, score.kmerSize); + countKmers(backgroundCounts, seq1seq2, 1); + int sumBG = 0; + for (unsigned i = 0; i < length(backgroundCounts); ++i) + { + sumBG += backgroundCounts[i]; + } + for (unsigned i = 0; i < length(backgroundCounts); ++i) + { + backgroundFrequencies[i] = backgroundCounts[i] / ((double)sumBG); + } + unsigned nvals = length(kmerCounts1); // Number of kmers + int len1 = 0; + int len2 = 0; + + for (unsigned l = 0; l < nvals; l++) + { + len1 += kmerCounts1[l]; + len2 += kmerCounts2[l]; + } + + String probabilities; // String of TValue to store the word probabilities p_w + resize(probabilities, nvals, missing); + + for (unsigned i = 0; i < nvals; ++i) + { + TValue p_w = 1; // Probability of kmer + + String w; + unhash(w, i, score.kmerSize); + calculateProbability(p_w, w, backgroundFrequencies); + TValue variance1 = 0.0; + TValue variance2 = 0.0; + + variance1 = pow(len1 * p_w, 0.5); + variance2 = pow(len2 * p_w, 0.5); + + // Test if variance is larer than 0 and smaller than inf before dividing + if ((variance1 > missing) && (variance1 < pow(10.0, 10))) + { + if (p_w > 0) + { + TValue stCount1 = (kmerCounts1[i] - p_w * len1) / variance1; + TValue stCount2 = (kmerCounts2[i] - p_w * len2) / variance2; + result += stCount1 * stCount2; + } + } + } + } + else + { + // -------------------------------------------------------------------- + // Higher Order Background Model + // -------------------------------------------------------------------- + + String kmerCounts1; + String kmerCounts2; + StringSet > bgSequences; + stringToStringSet(bgSequences, seq1seq2); // Create unmasked sequences + MarkovModel backgroundModel(score.bgModelOrder); + buildMarkovModel(backgroundModel, bgSequences); + countKmers(kmerCounts1, sequence1, score.kmerSize); + countKmers(kmerCounts2, sequence2, score.kmerSize); + + unsigned nvals = length(kmerCounts1); // Number of kmers + int len1 = 0; + int len2 = 0; + + for (unsigned l = 0; l < nvals; l++) + { + len1 += kmerCounts1[l]; + len2 += kmerCounts2[l]; + } + String probabilities; + resize(probabilities, nvals, missing); + for (unsigned i = 0; i < nvals; ++i) + { + TValue p_w = 1.0; // Probability of kmer + TValue variance = 0.0; + String w; + unhash(w, i, score.kmerSize); + p_w = emittedProbability(backgroundModel, w); + variance = ((TValue) pow(((TValue) len1 * len2), 0.5)) * p_w; + TValue variance1 = 0.0; + TValue variance2 = 0.0; + + variance1 = pow(len1 * p_w, 0.5); + variance2 = pow(len2 * p_w, 0.5); + + // Calculate standardised kmer Count + if ((variance > pow(10.0, -10)) && (variance < pow(10.0, 10))) + { + if (p_w > 0) + { + TValue stCount1 = (kmerCounts1[i] - p_w * len1) / variance1; + TValue stCount2 = (kmerCounts2[i] - p_w * len2) / variance2; + result += stCount1 * stCount2; + } + } + } + } +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2STAR_ORIGINAL_H_ diff --git a/seqan/alignment_free/af_d2z.h b/seqan/alignment_free/af_d2z.h new file mode 100644 index 0000000..6325af2 --- /dev/null +++ b/seqan/alignment_free/af_d2z.h @@ -0,0 +1,631 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// This header contains the implementation of the D2z score for +// alignment free sequence comparison. +// +// See Kantorovitz et al. Bioinformatics 2007, Volume23, Issue13, +// Pp. i249-i255. +// +// These functions can be called with alignmentFreeComparison(). +// ========================================================================== + +// TODO(goeke): const could be added below for the input variables but the function value() in matrix_base (align) is not defined for const. Similarly, the function emittedProbabilty is not defined for const in statistics_markov_model.h + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2Z_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2Z_H_ + +namespace seqan { + +/* + * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h) + */ +template +void _alignmentFreeComparison(Matrix & scoreMatrix, + TStringSet const & sequenceSet, + AFScore const & score) +{ + typedef typename Value::Type TString; + typedef typename Value::Type TAlphabet; + typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + typedef typename Iterator::Type TIteratorSet; + typedef typename Iterator > >::Type TIteratorSetUnsigned; + typedef typename Iterator > >::Type TIteratorSetDouble; + typedef typename Iterator > >::Type TIteratorMarkovModel; + + unsigned seqNumber = length(sequenceSet); + + // Resize scoreMatrix + setLength(scoreMatrix, 0, seqNumber); + setLength(scoreMatrix, 1, seqNumber); + resize(scoreMatrix, (TValue) 0); + + StringSet > kmerCounts; + resize(kmerCounts, seqNumber); + + // Note that there is some code below that looks like copy-and-paste. However, pulling this out into another + // function is the only way to get rid of the duplicate lines since we use different types. After some discussion, + // weese, goeke and holtgrew agreed that it is probably easier to read and maintain this way than to spread the code + // over to one more function. + if (score.bgModelOrder == 0) + { + // -------------------------------------------------------------------- + // Order 0 Background Model + // -------------------------------------------------------------------- + + StringSet > backgroundFrequencies; + resize(backgroundFrequencies, seqNumber); + + // Count all kmers and all background nucleotide frequencies and store them in stringSets + TIteratorSetUnsigned itKmerCounts = begin(kmerCounts); + TIteratorSetDouble itBackgroundFrequencies = begin(backgroundFrequencies); + + TIteratorSet itSeqSet = begin(sequenceSet); + for (; itSeqSet < end(sequenceSet); ++itSeqSet) + { + countKmers(*itKmerCounts, *itBackgroundFrequencies, *itSeqSet, score.kmerSize); + ++itKmerCounts; + ++itBackgroundFrequencies; + } + if(score.verbose) + { + std::cout << "\ncounted words"; + } + // Calculate all pairwise scores and store them in scoreMatrix + for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex) + { + if(score.verbose) + { + std::cout << "\nSequence number " << rowIndex; + } + for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex) + { + _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], + backgroundFrequencies[rowIndex], kmerCounts[colIndex], + backgroundFrequencies[colIndex], score); + value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetric entries + } + } + } + else + { + // -------------------------------------------------------------------- + // Higher Order Background Model + // -------------------------------------------------------------------- + + String > backgroundModels; + resize(backgroundModels, seqNumber, MarkovModel(score.bgModelOrder)); + TIteratorMarkovModel itMM = begin(backgroundModels); + TIteratorSet itSeqSet = begin(sequenceSet); + // Count all kmers and all background nucleotide frequencies and store them in StringSets + TIteratorSetUnsigned itKmerCounts = begin(kmerCounts); + + for (; itSeqSet < end(sequenceSet); ++itSeqSet) + { + countKmers(*itKmerCounts, *itMM, *itSeqSet, score.kmerSize); + ++itKmerCounts; + if (itMM < end(backgroundModels)) + { + itMM->_computeAuxiliaryMatrices(); + ++itMM; + } + + } + if(score.verbose) + { + std::cout << "\ncounted words"; + } + // Calculate all pairwise scores and store them in scoreMatrix + for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex) + { + if(score.verbose) + { + std::cout << "\nSequence number " << rowIndex; + } + for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex) + { + _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], + backgroundModels[rowIndex], kmerCounts[colIndex], + backgroundModels[colIndex], score); + value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetric entries + } + } + } +} + +/* + * computeExpectationD2 calculates the expected value of the D2 score given a Bernoulli model, + * see paper referenced above + */ +template +double computeExpectationD2(int const len1, int const len2, unsigned const k, TValue const * q1, TValue const * q2) +{ + TValue p2 = 0; + for (int i = 0; i < 4; i++) + p2 += q1[i] * q2[i]; + + int nbar1 = len1 - k + 1; + int nbar2 = len2 - k + 1; + + TValue retval = nbar1; + retval *= nbar2; + retval *= pow((double)p2, (int)k); + return retval; +} + +/* + * computeExpectationD2 calculates the expected value of the D2 score given a Markov model, + * see paper referenced above + */ +template +double computeExpectationD2(int const slen1, + int const slen2, + unsigned const k, + MarkovModel /*const*/ & bkg1, + MarkovModel /*const*/ & bkg2, + TValue & indicatorexpectation) +{ + unsigned mo = bkg1.order; + if (mo >= k) + { + // Error: Can't suppport markov order greater or equal to word length + exit(1); + } + + long emo = 1 << (2 * mo); // This is equal to pow(4, mo) + long ekmo = 1 << (2 * (k - mo)); // This is equal to pow(4, k - mo) + + TValue mean = 0; + for (long i = 0; i < emo; i++) + { + TValue term = value(bkg1.stationaryDistribution, i) * value(bkg2.stationaryDistribution, i); + TValue subterm = 0; + + for (long j = 0; j < ekmo; j++) + { + TValue subprob1 = _computeWordProbGivenPrefix(i, j, bkg1, k, mo); + TValue subprob2 = _computeWordProbGivenPrefix(i, j, bkg2, k, mo); + subterm += subprob1 * subprob2; + } + mean += term * subterm; + } + + indicatorexpectation = mean; // This is E[Y_ij], see paper referenced above. + int nbar1 = slen1 - k + 1; // Number of kmers in sequence1 + int nbar2 = slen2 - k + 1; // Number of kmers in sequence2 + return mean * ((TValue) nbar1 * nbar2); +} + +/* + * computeVarianceD2 calculates the variance of the D2 score given a Bernoulli model, + * see paper referenced above + */ +template +double computeVarianceD2(int len1, int len2, unsigned k, TValue * q1, TValue * q2) +{ + int nbar1 = len1 - k + 1; // Number of kmers in sequence 1 + int nbar2 = len2 - k + 1; // Number of kmers in sequence 2 + + int qbar1 = len1 - 2 * k + 2; // Number of overlapping kmers in sequence 1 + int qbar2 = len2 - 2 * k + 2; + + TValue p2 = 0, p31 = 0, p32 = 0; + for (int i = 0; i < 4; i++) + { + p2 += q1[i] * q2[i]; + p31 += q1[i] * q2[i] * q1[i]; + p32 += q1[i] * q2[i] * q2[i]; + } + + TValue variance = 0; + // 'Crabgrass' with l = 0 (= complete overlap), see paper referenced above + TValue power1 = pow((double)p32, (int)k) - pow((double)p2, 2 * (int)k); + power1 *= TValue(nbar1) * TValue(qbar2) * TValue(qbar2 - 1); + TValue power2 = pow((double)p31, (int)k) - pow((double)p2, 2 * (int)k); + power2 *= TValue(nbar2) * TValue(qbar1) * TValue(qbar1 - 1); + variance += power1 + power2; + + // 'Crabgrasses' with l > 0, see paper referenced above + for (unsigned l = 1; l <= k - 1; l++) + variance += 2 * TValue(nbar1 - l) * TValue(qbar2) * TValue(qbar2 - 1) * (pow((double)p2, (int)(2 * l)) * pow((double)p32, (int)(k - l)) - pow((double)p2, (int)(2 * k))) + 2 * TValue(nbar2 - l) * TValue(qbar1) * TValue(qbar1 - 1) * (pow((double)p2, (int)(2 * l)) * pow((double)p31, (int)(k - l)) - pow((double)p2, (int)(2 * k))); + + // Accordion main diagonal, see paper referenced above + variance += TValue(nbar1) * TValue(nbar2) * (pow((double)p2, (int)(k)) - pow((double)p2, (int)(2 * k))); + for (unsigned l = 1; l <= k - 1; l++) + variance += 2 * TValue(nbar1 - l) * TValue(nbar2 - l) * (pow((double)p2, (int)(k + l)) - pow((double)p2, (int)(2 * k))); + + return variance; +} + + +/* + * computeVarianceD2 calculates the variance of the D2 score given a Markov model, + * see paper referenced above + */ +template +double computeVarianceD2(int const slen1, + int const slen2, + unsigned const k, + MarkovModel /*const*/ & bkg1, + MarkovModel /*const*/ & bkg2, + TValue indicatorexpectation) +{ + unsigned mo = bkg1.order; + if (mo >= k) + { + // Error: Can't support markov order greater or equal to word length + exit(1); + } + + long emo = 1 << (2 * mo); // Equivalent to pow(4, mo); + long ekmo = 1 << (2 * (k - mo)); // Equivalent to pow(4, k - mo); + + int q1 = slen1 - 2 * k + 2; + int q2 = slen2 - 2 * k + 2; + int nbar1 = slen1 - k + 1; + int nbar2 = slen2 - k + 1; + + // Create matrix for Sbctilde + Matrix Sbctilde1; + setLength(Sbctilde1, 0, emo); + setLength(Sbctilde1, 1, emo); + resize(Sbctilde1); + + Matrix Sbctilde2; + setLength(Sbctilde2, 0, emo); + setLength(Sbctilde2, 1, emo); + resize(Sbctilde2); + + for (long i = 0; i < emo; i++) + { + for (long j = 0; j < emo; j++) + { + value(Sbctilde1, i, j) = (q1 * (q1 + 1) / 2) * value(bkg1.stationaryDistribution, j) - (q1 - 1) * value(bkg1._qppp, i, j) - value(bkg1._qppqpp, i, j); + value(Sbctilde2, i, j) = (q2 * (q2 + 1) / 2) * value(bkg2.stationaryDistribution, j) - (q2 - 1) * value(bkg2._qppp, i, j) - value(bkg2._qppqpp, i, j); + } + } + + // Compute sums of word probabilities and star probabilities of x-mers (x between mo + 1 and k) conditional on last or first (resp) mo-word, see paper referenced above + Matrix sump; // sump[x][wk] is the total word probability of every x-word ending with wk (which is of length mo) + setLength(sump, 0, k + 1); + setLength(sump, 1, emo); + resize(sump, 0.0); + + Matrix sumpstar; + setLength(sumpstar, 0, k + 1); + setLength(sumpstar, 1, emo); + resize(sumpstar, 0.0); + + + for (unsigned x = 0; x <= k; x++) + { + if (x <= mo) + { + + continue; + } + + for (long wk = 0; wk < emo; wk++) + { + TValue sum = 0; + long exmo = 1 << (2 * (x - mo)); // Equivalent to pow(4, x - mo); + for (long wpre = 0; wpre < exmo; wpre++) + { + sum += _computeWordProb((wpre << (2 * mo)) + wk, bkg1, x, mo) * _computeWordProb((wpre << (2 * mo)) + wk, bkg2, x, mo); + } + value(sump, x, wk) = sum; + } + + for (long u1 = 0; u1 < emo; u1++) + { + TValue sum = 0; + long exmo = 1 << (2 * (x - mo)); // Equivalent to pow(4, x - mo); + for (long usuf = 0; usuf < exmo; usuf++) + { + sum += _computeWordProbGivenPrefix(u1, usuf, bkg1, x, mo) * _computeWordProbGivenPrefix(u1, usuf, bkg2, x, mo); + } + value(sumpstar, x, u1) = sum; + } + } + + // Handle the non overlap terms first + TValue covnonoverlap = 0; + for (long wk = 0; wk < emo; wk++) + { + for (long u1 = 0; u1 < emo; u1++) + { + TValue term = value(Sbctilde1, wk, u1) * value(Sbctilde2, wk, u1) * value(sump, k, wk) * value(sumpstar, k, u1); + covnonoverlap += 4 * term; + } + } + TValue subtractFromNonOverlap = (TValue)q1 * (q1 - 1) * q2 * (q2 - 1); + subtractFromNonOverlap *= pow(indicatorexpectation, 2); + covnonoverlap -= subtractFromNonOverlap; + // Compute 'crabgrass' terms, see paper referenced above + TValue covcrabgrass = 0; + + // Case 1: overlap >= mo + for (unsigned m = 1; m <= k - mo; m++) + { + long ekm = 1 << (2 * (k - m)); // Equivalent to pow(4, k - m) + long moonesflag = (1 << (2 * mo)) - 1; + long kmmoonesflag = (1 << (2 * (k - m - mo))) - 1; + for (long v = 0; v < ekm; v++) + { + long vsuf = v & moonesflag; // Last morder chars of v + long vpre = v >> (2 * (k - m - mo)); // First morder chars of v, equivalent to v / pow(4, k - m - mo) + long vsuf2 = v & kmmoonesflag; // Remaining k-m-morder chars of v; equivalent to v % pow(4, k - m - mo) + // In the following, if m = k - mo, _computeWordProbGivenPrefix(.,.,.,k - m, mo) will return 1, as it should + // Overlap in A, separate in B + TValue term1 = value(Sbctilde2, vsuf, vpre); + term1 *= _computeWordProbGivenPrefix(vpre, vsuf2, bkg1, k - m, mo); + term1 *= pow(_computeWordProbGivenPrefix(vpre, vsuf2, bkg2, k - m, mo), 2); + term1 *= value(sump, m + mo, vpre); + term1 *= value(sumpstar, m + mo, vsuf); + // Overlap in B, separate in A + TValue term2 = value(Sbctilde1, vsuf, vpre); + term2 *= _computeWordProbGivenPrefix(vpre, vsuf2, bkg2, k - m, mo); + term2 *= pow(_computeWordProbGivenPrefix(vpre, vsuf2, bkg1, k - m, mo), 2); + term2 *= value(sump, m + mo, vpre); + term2 *= value(sumpstar, m + mo, vsuf); + + covcrabgrass += 4 * q1 * term1 + 4 * q2 * term2; + } + } + // Case 2: overlap < morder + for (unsigned m = k - mo + 1; m <= k - 1; m++) + { + int tlen = 2 * mo - (k - m); + long et = 1 << (2 * tlen); // Equivalent to pow(4, tlen); + long moonesflag = (1 << (2 * mo)) - 1; + long tmoonesflag = (1 << (2 * (tlen - mo))) - 1; + for (long t = 0; t < et; t++) + { + long tsuf = t & moonesflag; // Last morder chars of t; equivalent to t % emo; + long tpre = t >> (2 * (tlen - mo)); // First morder chars of t, equivalent to t / pow(4, tlen - mo) + long tsuf2 = t & tmoonesflag; // Remaining tlen-morder chars of t, equivalent to t % etmo; + // Overlap in A, separate in B + TValue term1 = value(Sbctilde2, tpre, tsuf); + term1 *= _computeWordProbGivenPrefix(tpre, tsuf2, bkg1, tlen, mo); + term1 *= value(sump, k, tpre); + term1 *= value(sumpstar, k, tsuf); + // Overlap in B, separate in A + TValue term2 = value(Sbctilde1, tpre, tsuf); + term2 *= _computeWordProbGivenPrefix(tpre, tsuf2, bkg2, tlen, mo); + term2 *= value(sump, k, tpre); + term2 *= value(sumpstar, k, tsuf); + + covcrabgrass += 4 * q1 * term1 + 4 * q2 * term2; + } + } + + // Case 3: m=0 (complete overlap) + long moonesflag = (1 << (2 * mo)) - 1; + for (long wpre = 0; wpre < emo; wpre++) + { + // First morder chars of w + TValue term1 = 0; + TValue term2 = 0; + for (long wsuf2 = 0; wsuf2 < ekmo; wsuf2++) + { + // Remaining k-morder chars of w + long wsuf = ((wpre << (2 * (k - mo))) + wsuf2) & moonesflag; // Last morder chars of w + term1 += 2 * nbar1 * value(Sbctilde2, wsuf, wpre) * _computeWordProbGivenPrefix(wpre, wsuf2, bkg1, k, mo) * pow(_computeWordProbGivenPrefix(wpre, wsuf2, bkg2, k, mo), 2); + term2 += 2 * nbar2 * value(Sbctilde1, wsuf, wpre) * _computeWordProbGivenPrefix(wpre, wsuf2, bkg2, k, mo) * pow(_computeWordProbGivenPrefix(wpre, wsuf2, bkg1, k, mo), 2); + } + covcrabgrass += (term1 + term2) * value(bkg1.stationaryDistribution, wpre) * value(bkg2.stationaryDistribution, wpre); + } + + // Ignored edge effects, see paper referened above + // Subtract expectations + TValue subtractfromcrabgrass = (((2 * q1 * k - nbar1) * (double)q2 * double(q2 - 1)) + ((2 * q2 * k - nbar2) * (double)q1 * double(q1 - 1))); + subtractfromcrabgrass *= pow(indicatorexpectation, 2); + covcrabgrass -= subtractfromcrabgrass; + + // Compute the accordion main diagonal terms + TValue covaccordiondiag = 0; + + for (unsigned m = 1; m <= k - 1; m++) + { + long tlen; + if (m <= mo - 1) + tlen = m + mo; + else + tlen = 2 * mo - 1; + long et = 1 << (2 * tlen); // Equivalent to pow(4, tlen) + long moonesflag = (1 << (2 * mo)) - 1; + long tmoonesflag = (1 << (2 * (tlen - mo))) - 1; + + TValue mterm = 0; + for (long t = 0; t < et; t++) + { + TValue term = 1; + long tpre = t >> (2 * (tlen - mo)); // First morder chars of t, equivalent to t / pow(4, tlen - mo) + long tsuf2 = t & tmoonesflag; // The remaining tlen - morder chars of t, equivalent to t % etmo; + term *= _computeWordProbGivenPrefix(tpre, tsuf2, bkg1, tlen, mo) * _computeWordProbGivenPrefix(tpre, tsuf2, bkg2, tlen, mo); + term *= value(sump, k, tpre); + if (m >= mo) + { + long tsuf = t & moonesflag; // Last morder chars of t, equivalent to t%emo; + term *= value(sumpstar, m + 1, tsuf); + } + mterm += term; + } + covaccordiondiag += 2 * (nbar1 - m) * (nbar2 - m) * mterm; + } + covaccordiondiag += nbar1 * nbar2 * indicatorexpectation; // Complete overlap term + covaccordiondiag -= (nbar1 * nbar2 * (2 * k - 1) - (nbar1 + nbar2) * k * (k - 1) + (k - 1) * k * (2 * k - 1) / 3) * pow(indicatorexpectation, 2); + TValue variance = covnonoverlap + covcrabgrass + covaccordiondiag; + return variance; + +} + +/* + * Calculate pairwise score given the counts of all kmers and the background Bernoulli models + */ +template +void _alignmentFreeCompareCounts(TValue & result, + String const & kmerCounts1, + TStringBG const & backgroundFrequencies1, + String const & kmerCounts2, + TStringBG const & backgroundFrequencies2, + AFScore const & score) +{ + typedef typename Value::Type TValueBG; + TValueBG sum = 0; + unsigned len1 = score.kmerSize - 1; + unsigned len2 = score.kmerSize - 1; + unsigned nvals = length(kmerCounts1); + + for (unsigned l = 0; l < nvals; l++) + { + len1 += kmerCounts1[l]; + len2 += kmerCounts2[l]; + + sum += kmerCounts1[l] * kmerCounts2[l]; + } + + TValueBG q1[4]; + TValueBG q2[4]; + for (int l = 0; l < 4; l++) + { + q1[l] = backgroundFrequencies1[l]; + q2[l] = backgroundFrequencies2[l]; + } + + // Compute expected value and variance (IID) + double E = computeExpectationD2(len1, len2, score.kmerSize, q1, q2); + double var = computeVarianceD2(len1, len2, score.kmerSize, q1, q2); + + if ((var <= 0)) + { + if(score.verbose) + { + std::cout << "Error: negative variance\n"; + } + result = 0; + return; + } + // Calculate z-score + result = (TValue) (sum - E) / pow(var, 0.5); +} + +/* + * Calculate pairwise score given the counts of all kmers and the background Markov models + */ +template +void _alignmentFreeCompareCounts(TValue & result, + String const & kmerCounts1, + MarkovModel /*const*/ & bgModel1, + String const & kmerCounts2, + MarkovModel /*const*/ & bgModel2, + AFScore const & score) +{ + unsigned nvals = length(kmerCounts1); + int sum = 0; + int sumCounts1 = score.kmerSize - 1; + int sumCounts2 = score.kmerSize - 1; + + for (unsigned l = 0; l < nvals; l++) + { + sumCounts1 += kmerCounts1[l]; + sumCounts2 += kmerCounts2[l]; + sum += value(kmerCounts1, l) * value(kmerCounts2, l); // Calculate the inner product + } + + TValue D2 = (TValue) sum; + + // Compute mean and variance + TValue indicatorexpectation = 0; + + double E = computeExpectationD2(sumCounts1, sumCounts2, score.kmerSize, bgModel1, bgModel2, indicatorexpectation); + double var = computeVarianceD2(sumCounts1, sumCounts2, score.kmerSize, bgModel1, bgModel2, indicatorexpectation); + + if (var <= 0) + { + result = 0; + return; + } + // Return z-score of D2 + result = (D2 - E) / pow(var, 0.5); +} + +/* + * Compute the word probability given a Markov model + * see paper referenced on top + */ +template +double _computeWordProb(long const word, MarkovModel /*const*/ & bkg, unsigned const k, int const mo) +{ + // mo needs to be passed, since that decides the prefix + // Similarly, this function needs to know the total length of the word k + long prefix = word >> (2 * (k - mo)); // Equivalent to word / pow(4, k - mo); gets the first mo chars of word + long suffix = word & ((1 << (2 * (k - mo))) - 1); // Get the last (k - mo) chars of word + return value(bkg.stationaryDistribution, prefix) * _computeWordProbGivenPrefix(prefix, suffix, bkg, k, mo); +} + +/* + * Compute the word probability given a Markov model + * see paper referenced on top + */ +template +double _computeWordProbGivenPrefix(long const prefix, long const suffix, MarkovModel /*const*/ & bkg, unsigned const k, unsigned const mo) +{ + // Computes p_ * (prefix suffix) + // Calculate only if k - mo >= 1; otherwise return 1 + if (k - mo <= 0) + return 1; + + TValue prob = 1; + long pre = prefix; + long jcopy = suffix; + + // Iterate through successive positions of the suffix + for (unsigned l = 0; l < k - mo; l++) + { + // Get the first char of jcopy, which is of length k - mo; equivalent to jcopy / pow(4, k - mo - 1) + long jcopyfirst = jcopy >> (2 * (k - mo - 1)); + long suf = ((pre & ((1 << (2 * (mo - 1))) - 1)) << 2) + jcopyfirst; + + // prob *=P[pre][suf]; P is the transition matrix + prob *= value(bkg.transition, pre, suf); + // Erase the first char of jcopy, and preserve its length at k - mo by shifting one char to the left; equivalent to (jcopy % pow(4, k - mo - 1)) * 4; + jcopy = (jcopy & ((1 << (2 * (k - mo - 1))) - 1)) << 2; + pre = suf; + } + return prob; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_D2Z_H_ diff --git a/seqan/alignment_free/af_n2.h b/seqan/alignment_free/af_n2.h new file mode 100644 index 0000000..ac2110a --- /dev/null +++ b/seqan/alignment_free/af_n2.h @@ -0,0 +1,641 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// This header contains the implementation of the N2 score for alignment free +// sequence comparison with word neighbourhood counts +// +// See: Goeke et al, to appear. +// +// These functions can be called with alignmentFreeComparison(). +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_N2_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_N2_H_ + +namespace seqan { + +/* + * This function returns a string with indices indicating which k-mer is the + * reverse complement k-mer: i=revComIndex[revComIndex[i]] + */ +inline void _initialiseRevComIndex(String & revComIndex, unsigned const k) +{ + unsigned myLength = (unsigned)pow(4.0, (int)k); + resize(revComIndex, myLength, 0); + Shape myShape; + resize(myShape, k); + for (unsigned i = 0; i < myLength; ++i) + { + String w; + unhash(w, i, k); + DnaStringReverseComplement wRC(w); + unsigned hashValue = hash(myShape, begin(wRC)); + revComIndex[i] = hashValue; + } + +} + +/* + * This function returns a stringSet with strings of indices indicating which + * k-mers belong to the word neighbourhood for every k-mer (all k-mers with + * one mismatch) + */ +inline void _initialiseKmerNeighbourhood(StringSet > & kmerNeighbourhood, + unsigned const k, bool const revCom, + String const & revComIndex) +{ + unsigned myLength = (unsigned)pow(4.0, (int)k); + Shape myShape; + resize(myShape, k); + resize(kmerNeighbourhood, myLength); + for (unsigned i = 0; i < myLength; ++i) + { + resize(kmerNeighbourhood[i], 1, i); + + String w; + unhash(w, i, k); + if ((revComIndex[i] != i) && (revCom == true)) + { + appendValue(kmerNeighbourhood[i], revComIndex[i]); + } + for (unsigned j = 0; j < k; ++j) + { + for (unsigned l = 0; l < 4; ++l) + { + String wTMP; + wTMP = w; + if (wTMP[j] != l) + { + wTMP[j] = l; + unsigned hashValue = hash(myShape, begin(wTMP)); + // Check for double word occurrences + bool duplicate = false; + if (revCom == true) + { + + for (unsigned n = 0; n < length(kmerNeighbourhood[i]); ++n) + { + if ((hashValue) == kmerNeighbourhood[i][n]) + { + duplicate = true; + break; + } + } + + } + + if (duplicate == false) + { + appendValue(kmerNeighbourhood[i], hashValue); + if (revCom == true) + { + if (revComIndex[hashValue] != hashValue) + { + appendValue(kmerNeighbourhood[i], revComIndex[hashValue]); + } + } + } + } + } + } + } +} + +/* + * _alignmentFreeComparison is called by alignmentFreeComparison() (see alignment_free_comparison.h) + */ +template +void _alignmentFreeComparison(Matrix & scoreMatrix, + TStringSet const & sequenceSet, + AFScore const & score) +{ + + + + typedef typename Value::Type TString; + typedef typename Value::Type TAlphabet; + typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + typedef typename Iterator::Type TIteratorSet; + typedef typename Iterator > >::Type TIteratorSetDouble; + + + // Initialise the reverse complement hash table + String revComIndex; + StringSet > kmerNeighbourhood; + _initialiseRevComIndex(revComIndex, score.kmerSize); + if (score.revCom == "both_strands") + { + _initialiseKmerNeighbourhood(kmerNeighbourhood, score.kmerSize, true, revComIndex); + } + else + { + _initialiseKmerNeighbourhood(kmerNeighbourhood, score.kmerSize, false, revComIndex); + } + + unsigned seqNumber = length(sequenceSet); + + setLength(scoreMatrix, 0, seqNumber); + setLength(scoreMatrix, 1, seqNumber); + resize(scoreMatrix, (TValue) 0); + + StringSet > standardisedKmerCounts; + resize(standardisedKmerCounts, seqNumber); + // Count all kmers and all background nucleotide frequencies and store them in StringSets + TIteratorSetDouble itStandardisedKmerCounts = begin(standardisedKmerCounts); + TIteratorSet itSeqSet = begin(sequenceSet); + for (; itSeqSet < end(sequenceSet); ++itSeqSet) + { + + _standardiseCounts(*itStandardisedKmerCounts, revComIndex, kmerNeighbourhood, *itSeqSet, score); + if(score.verbose) + { + std::cout << "\n" << position(itSeqSet); + } + ++itStandardisedKmerCounts; + } + + if (score.norm == true) // Normalise the score so that sequence-self-comparisons are always 1 + { + itStandardisedKmerCounts = begin(standardisedKmerCounts); + for (; itStandardisedKmerCounts < end(standardisedKmerCounts); ++itStandardisedKmerCounts) + { + TValue normValue = 0.0; + for (unsigned i = 0; i < length(value(itStandardisedKmerCounts)); ++i) + { + normValue += value(itStandardisedKmerCounts)[i] * value(itStandardisedKmerCounts)[i]; + } + for (unsigned i = 0; i < length(value(itStandardisedKmerCounts)); ++i) + { + value(itStandardisedKmerCounts)[i] /= sqrt(normValue); + } + + } + } + + if (!(score.outputFile == "")) + { + std::ofstream myfile; + myfile.open(toCString(score.outputFile)); + for (unsigned i = 0; i < length(standardisedKmerCounts[0]); ++i) + { + String w; + unhash(w, i, score.kmerSize); + myfile << "\t" << w; + } + myfile << "\n"; + for (unsigned seqIndex = 0; seqIndex < seqNumber; ++seqIndex) + { + myfile << "Seq" << seqIndex; + for (unsigned i = 0; i < length(standardisedKmerCounts[seqIndex]); ++i) + { + myfile << "\t" << standardisedKmerCounts[seqIndex][i]; + } + myfile << "\n"; + } + myfile.close(); + } + + if(score.verbose) + { + std::cout << "\ncounted words"; + } + + // Calculate all pairwise scores and store them in scoreMatrix + for (unsigned rowIndex = 0; rowIndex < seqNumber; ++rowIndex) + { + if(score.verbose) + { + std::cout << "\nSequence number " << rowIndex; + } + for (unsigned colIndex = rowIndex; colIndex < seqNumber; ++colIndex) + { + _alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), revComIndex, standardisedKmerCounts[rowIndex], standardisedKmerCounts[colIndex], score); + value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetric entries + } + } +} + +/* + * Calculate pairwise score given the counts of all kmers + */ +template +void +_alignmentFreeCompareCounts(TValue & result, + String const revComIndex, + TString const & kmerCounts1, + TString const & kmerCounts2, + AFScore const & score) +{ + typedef typename Iterator::Type TIteratorTString; + + TIteratorTString it1 = begin(kmerCounts1); + TIteratorTString it2 = begin(kmerCounts2); + result = 0.0; + TValue resultRC = 0.0; + for (; it1 < end(kmerCounts1); ++it1) + { + result += (TValue)(value(it1) * value(it2)); + // Computation of the reverse complement strand score + if ((score.revCom != "") && (score.revCom != "both_strands")) + { + unsigned hashValue = revComIndex[position(it1)]; + resultRC += (TValue)(value(it1) * kmerCounts2[hashValue]); + } + ++it2; + } + + if (score.revCom == "mean") + { + result = (TValue) (resultRC + result) / 2; + } + else if (score.revCom == "max") + { + result = std::max(resultRC, result); + } + else if (score.revCom == "min") + { + result = std::min(resultRC, result); + } +} + +/* + * count kmers and standardise count vectors for Dna5 and markov model background + */ +template +void _standardiseCounts(TString & standardisedCounts, + String const & revComIndex, + StringSet > const & kmerNeighbourhood, + TSequence const & sequence, + AFScore const & score) +{ + typedef typename Value::Type TAlphabet; + typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + typedef typename Value::Type TValue; + typedef typename Iterator, Rooted>::Type TIteratorUnsigned; + typedef typename Iterator::Type TIteratorTString; + + unsigned alphabetSize = ValueSize::VALUE; + + // Save all word covariances which are computed in covariance Matrix to avoid double computations + Matrix covarianceMatrix; + TValue missing = -pow(10.0, 10); + if (score.mismatches > 0) + { + setLength(covarianceMatrix, 0, pow((double)alphabetSize, (int)score.kmerSize)); + setLength(covarianceMatrix, 1, pow((double)alphabetSize, (int)score.kmerSize)); + resize(covarianceMatrix, missing); + } + + // Note that there is some code below that looks like copy-and-paste. However, pulling this out into another + // function is the only way to get rid of the duplicate lines since we use different types. After some discussion, + // weese, goeke and holtgrew agreed that it is probably easier to read and maintain this way than to spread the code + // over to one more function. + if (score.bgModelOrder == 0) + { + // ---------------------------------------------------------------------- + // Order 0 Background Model + // ---------------------------------------------------------------------- + + String kmerCounts; + String backgroundFrequencies; + countKmers(kmerCounts, backgroundFrequencies, sequence, score.kmerSize); + int nvals = length(kmerCounts); // Number of kmers + int len1 = 0; + for (int l = 0; l < nvals; l++) + { + len1 += kmerCounts[l]; + } + resize(standardisedCounts, nvals, (TValue) 0.0); + + // String of TValue to store the word probabilites p_w + String probabilities; + resize(probabilities, nvals, missing); + + TIteratorUnsigned itCounts; + TIteratorTString itStandardisedCounts; + + itCounts = begin(kmerCounts); + itStandardisedCounts = begin(standardisedCounts); + + for (; itCounts < end(kmerCounts); ++itCounts) + { + // Temporary counter for mismatch kmer counting + TValue counterTMP = 0; + TValue p_w = 1; // Probability of kmer + + String w; + unhash(w, (unsigned)position(itCounts), score.kmerSize); + calculateProbability(p_w, w, backgroundFrequencies); + TValue variance = 0; + if ((score.mismatches == 1)) // Mismatch score calculation + { + p_w = 0; + // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally + // Sum of all entries in the covariance matrix. only once computed + unsigned wordHash = position(itCounts); + unsigned wordRCHash = revComIndex[wordHash]; + + for (unsigned row = 0; row < length(kmerNeighbourhood[wordHash]); ++row) + { + unsigned wordRowHash = kmerNeighbourhood[wordHash][row]; + // The kmer itself is weighted normally + if (wordRowHash == wordHash) // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally + { + counterTMP += (TValue) kmerCounts[wordRowHash]; + } + else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash)) + { + counterTMP += ((TValue) kmerCounts[wordRowHash]); + } + else + { + counterTMP += ((TValue) kmerCounts[wordRowHash]) * score.mismatchWeight; + } + String wMM1; + unhash(wMM1, wordRowHash, score.kmerSize); + + for (unsigned col = row; col < length(kmerNeighbourhood[wordHash]); ++col) + { + unsigned wordColHash = kmerNeighbourhood[wordHash][col]; + if (value(covarianceMatrix, wordColHash, wordRowHash) == missing) + { + String wMM2; + + unhash(wMM2, wordColHash, score.kmerSize); + calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundFrequencies, (len1 + score.kmerSize - 1)); + value(covarianceMatrix, wordRowHash, wordColHash) = value(covarianceMatrix, wordColHash, wordRowHash); + } + if (row == col) // Variance of weighted variables + { + if ((wordRowHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash))) // The variance of the kmer is counted full + { + variance += value(covarianceMatrix, wordRowHash, wordColHash); + } + else + { + variance += pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash); // Calculate weighted variances + } + } + // The covariance of the kmer and the reverse complement is weighted full + else if ((score.revCom == "both_strands") && (((wordRowHash == wordHash) && (wordColHash == wordRCHash)) || ((wordRowHash == wordRCHash) && (wordColHash == wordHash)))) + { + variance += (2.0) * value(covarianceMatrix, wordRowHash, wordColHash); + } + else if ((wordRowHash == wordHash || wordColHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash || wordColHash == wordRCHash))) // The covariance is weighted half + { + variance += (2.0) * score.mismatchWeight * value(covarianceMatrix, wordRowHash, wordColHash); + } + else // The covariance is weighted^2 + { + variance += (2.0) * pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash); + } + } + if (probabilities[wordRowHash] == missing) + { + calculateProbability(probabilities[wordRowHash], wMM1, backgroundFrequencies); + } + if (wordRowHash == wordHash) //Weight the probabilities and expected values, normal weight for the kmer itself + { + p_w += probabilities[wordRowHash]; + } + else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash)) // Weight the probabiliets and expected values, normal weight for the reverse complement kmer itself + { + p_w += probabilities[wordRowHash]; + } + else + { + p_w += score.mismatchWeight * probabilities[wordRowHash]; + } + } + variance = pow(variance, 0.5); + } // End of mismatch calculation + else if (score.revCom == "both_strands") + { + TValue variance1; + TValue variance2; + TValue covariance; + String wRC; + unhash(wRC, (unsigned) revComIndex[(unsigned)position(itCounts)], score.kmerSize); + calculateVariance(variance1, w, backgroundFrequencies, (len1 + score.kmerSize - 1)); + calculateVariance(variance2, wRC, backgroundFrequencies, (len1 + score.kmerSize - 1)); + calculateCovariance(covariance, w, wRC, backgroundFrequencies, (len1 + score.kmerSize - 1)); + variance = pow((variance1 + variance2 + (2.0) * covariance), 0.5); + TValue p_wRC = 1; // Probability of the reverse complement kmer + calculateProbability(p_wRC, wRC, backgroundFrequencies); + p_w += p_wRC; + } + else + { + calculateVariance(variance, w, backgroundFrequencies, (len1 + score.kmerSize - 1)); + variance = pow(variance, 0.5); + } + if ((variance > pow(10.0, -10)) && (variance < pow(10.0, 10))) + { + if (p_w > 0) + { + if (score.mismatches > 0) + { + value(itStandardisedCounts) = ((TValue) ((TValue) counterTMP) - p_w * ((TValue)len1)) / variance; + } + else if (score.revCom == "both_strands") + { + value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts) + kmerCounts[revComIndex[(unsigned)position(itCounts)]]) - p_w * ((TValue)len1)) / variance; + } + else + { + value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts)) - p_w * ((TValue)len1)) / variance; + } + } + } + ++itStandardisedCounts; + } + } + else + { + // ---------------------------------------------------------------------- + // Higher Order Background Model + // ---------------------------------------------------------------------- + + String kmerCounts; + MarkovModel backgroundModel(score.bgModelOrder); + countKmers(kmerCounts, backgroundModel, sequence, score.kmerSize); + + int nvals = length(kmerCounts); // Number of kmers + int len1 = 0; + for (int l = 0; l < nvals; l++) + { + len1 += kmerCounts[l]; + } + resize(standardisedCounts, nvals, (TValue) 0.0); + String probabilities; + resize(probabilities, nvals, missing); + TIteratorUnsigned itCounts; + TIteratorTString itStandardisedCounts; + itCounts = begin(kmerCounts); + itStandardisedCounts = begin(standardisedCounts); + + for (; itCounts < end(kmerCounts); ++itCounts) + { + TValue p_w = 1; // Probability of kmer + TValue variance = 0; + String w; + unhash(w, (unsigned)position(itCounts), score.kmerSize); + p_w = emittedProbability(backgroundModel, w); + + TValue counterTMP = 0.0; + if ((score.mismatches == 1)) // Start of mismatch calculations + { + p_w = 0; + // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally + // Sum of all entries in the covariance matrix, computed and stored dynamically + unsigned wordHash = position(itCounts); + unsigned wordRCHash = revComIndex[wordHash]; + + for (unsigned row = 0; row < length(kmerNeighbourhood[wordHash]); ++row) + { + unsigned wordRowHash = kmerNeighbourhood[wordHash][row]; + // The kmer itself is weighted normally + if (wordRowHash == wordHash) // The first word in the kmerNeighbourhood is the kmer itself, it is weighted normally + { + counterTMP += (TValue) kmerCounts[wordRowHash]; + } + else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash)) + { + counterTMP += ((TValue) kmerCounts[wordRowHash]); + } + else + { + counterTMP += ((TValue) kmerCounts[wordRowHash]) * score.mismatchWeight; + } + String wMM1; + unhash(wMM1, wordRowHash, score.kmerSize); + for (unsigned col = row; col < length(kmerNeighbourhood[wordHash]); ++col) + { + unsigned wordColHash = kmerNeighbourhood[wordHash][col]; + if (value(covarianceMatrix, wordColHash, wordRowHash) == missing) + { + String wMM2; + unhash(wMM2, wordColHash, score.kmerSize); + calculateCovariance(value(covarianceMatrix, wordColHash, wordRowHash), wMM1, wMM2, backgroundModel, (len1 + score.kmerSize - 1)); + value(covarianceMatrix, wordRowHash, wordColHash) = value(covarianceMatrix, wordColHash, wordRowHash); + } + if (row == col) // Variance of weighted variables + { + if ((wordRowHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash))) // The variance of the kmer is counted full + { + variance += value(covarianceMatrix, wordRowHash, wordColHash); + } + else + { + variance += pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash); + } + } + // The covariance of the kmer and the reverse complement is weighted full + else if ((score.revCom == "both_strands") && (((wordRowHash == wordHash) && (wordColHash == wordRCHash)) || ((wordRowHash == wordRCHash) && (wordColHash == wordHash)))) + { + variance += (2.0) * value(covarianceMatrix, wordRowHash, wordColHash); + } + else if ((wordRowHash == wordHash || wordColHash == wordHash) || (score.revCom == "both_strands" && (wordRowHash == wordRCHash || wordColHash == wordRCHash))) // The covariance is weighted half + { + variance += (2.0) * score.mismatchWeight * value(covarianceMatrix, wordRowHash, wordColHash); + } + else // The covariance is weighted^2 + { + variance += (2.0) * pow(score.mismatchWeight, 2) * value(covarianceMatrix, wordRowHash, wordColHash); + } + } + if (probabilities[wordRowHash] == missing) + { + probabilities[wordRowHash] = emittedProbability(backgroundModel, wMM1); + } + if (wordRowHash == wordHash) //Weight the probabiliets and expected values, normal weight for the kmer itself + { + p_w += probabilities[wordRowHash]; + } + else if ((score.revCom == "both_strands") && (wordRowHash == wordRCHash)) // Weight the probabiliets and expected values, normal weight for the reverse complement kmer itself + { + p_w += probabilities[wordRowHash]; + } + else + { + p_w += score.mismatchWeight * probabilities[wordRowHash]; + } + } + variance = pow(variance, 0.5); // Calculate the standard deviation + } // End of mismatch calculations + else if (score.revCom == "both_strands") + { + TValue variance1; + TValue variance2; + TValue covariance; + String wRC; + unhash(wRC, (unsigned)revComIndex[(unsigned)position(itCounts)], score.kmerSize); + calculateVariance(variance1, w, backgroundModel, (len1 + score.kmerSize - 1)); + calculateVariance(variance2, wRC, backgroundModel, (len1 + score.kmerSize - 1)); + calculateCovariance(covariance, w, wRC, backgroundModel, (len1 + score.kmerSize - 1)); + variance = pow((variance1 + variance2 + (2.0) * covariance), 0.5); + TValue p_wRC = 1; // Probability of the reverse complement kmer + p_wRC = emittedProbability(backgroundModel, wRC); + p_w += p_wRC; + } + else + { + calculateVariance(variance, w, backgroundModel, (len1 + score.kmerSize - 1)); + variance = pow(variance, 0.5); + } + if ((variance > pow(10.0, -10)) && (variance < pow(10.0, 10))) + { + if (p_w > 0) + { + if (score.mismatches > 0) + { + value(itStandardisedCounts) = ((TValue) ((TValue) counterTMP) - p_w * ((TValue)len1)) / variance; + } + else if (score.revCom == "both_strands") + { + value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts) + kmerCounts[revComIndex[(unsigned)position(itCounts)]]) - p_w * ((TValue)len1)) / variance; + } + else + { + value(itStandardisedCounts) = ((TValue) ((TValue) value(itCounts)) - p_w * ((TValue)len1)) / ((TValue) variance); + } + } + ++itStandardisedCounts; + } + } + } +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_AF_N2_H_ diff --git a/seqan/alignment_free/alignment_free_base.h b/seqan/alignment_free/alignment_free_base.h new file mode 100644 index 0000000..c3a7471 --- /dev/null +++ b/seqan/alignment_free/alignment_free_base.h @@ -0,0 +1,340 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// Definition of all AFScore and the specialisations, D2, D2star, D2z +// and N2. +// ========================================================================== + +// TODO(holtgrew): Make struct a class here. + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_BASE_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_BASE_H_ + +namespace seqan { + +/*! + * @class AFScore + * @headerfile + * @brief Used to specify parameters and methods for alignment-free sequence comparison. + * + * @signature template + * struct AFScore; + * + * @tparam TSpec Tag for specialization. + * + * @see alignmentFreeComparison + */ + +template +struct AFScore; + +/*! + * @class D2AFScore D2 AFScore + * @extends AFScore + * @headerfile + * + * @brief D2 computes the inner product of the kmer count vectors. + * + * @signature template <> + * struct AFScore; + * + * To be used for alignment free comparison. + * + * @section References + * + * Lippert RA, et al. Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl + * Acad. Sci. USA 2002. + * + * @see alignmentFreeComparison + * + * @var unsigned D2AFScore::kmerSize; + * @brief Size of the kmers. + * + * @var bool D2AFScore::verbose; + * @brief true to enable verbose debug output. + * + * @fn D2AFScore::AFScore + * + * @brief Constructor + * + * @signature AFScore::AFScore(kmerSize, verbose); + * + * @param[in] verbose This option will report progress to standard output (boolunsigned). + * + * @see alignmentFreeComparison + */ + +struct D2_; // Inner product of k-mer counts, d2 score +typedef Tag const D2; + +template <> +struct AFScore +{ + unsigned kmerSize; + bool verbose; + AFScore(unsigned k, bool verbose_ = false) : kmerSize(k), verbose(verbose_) + {} +}; + +/*! + * @class D2StarAFScore D2Star AFSScore + * @extends AFScore + * @headerfile + * @brief D2Star computes the inner product of the standardised kmer count vectors. + * + * @signature template <> + * struct AFScore; + * + * D2Star can be used for alignment-free sequence comparison, this version calculates the background model on the + * concatenation of both sequences + * + * @section References + * + * Reinert, G.; Chew, D.; Sun, F., Waterman, M. S. Alignment-Free Sequence Comparison (I): Statistics and Power. J + * Comput Biol, 2009. + * + * @see alignmentFreeComparison + * + * @fn D2StarAFScore::AFScore + * @brief Constructor + * @signature AFScore::AFScore(kmerSize, bgModelOrder, verbose); + * + * @param[in] kmerSize Size of kmer, unsigned. + * @param[in] bgModelOrder Order of the background Markov model, unsigned. + * @param[in] verbose This option will report progress to standard output, bool. + * + * @var unsigned D2StarAFScore::kmerSize + * @brief Size of the kmers. + * + * @var CharString D2StarAFScore::outputFile + * @brief When specified, all kmerWeights will be written to this file, for every sequence, and for every sequence + * comparison. + * + * @var unsigned D2StarAFScore::bgModelOrder + * @brief Order of the background model. + */ + +struct D2Star_; // Reinert and Waterman, D2 with centralised and standardised counts +typedef Tag const D2Star; + +template <> +struct AFScore +{ + unsigned kmerSize; + unsigned bgModelOrder; + bool verbose; + + + AFScore(unsigned k, unsigned m, bool verbose_ = false) : + kmerSize(k), bgModelOrder(m), verbose(verbose_) + {} +}; + +/*! + * @class N2AFScore N2 AFScore + * @extends AFScore + * @headerfile + * @brief N2 computes the inner product of the standardised neighbourhood kmer count vectors. + * + * @signature template <> + * struct AFScore; + * + * N2 can be used for alignment-free sequence comparison. + * + * @section References + * + * Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron. + Estimation of Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts. Bioinformatics + (2012). + * + * @fn N2AFScore::AFScore + * + * @brief Constructor + * + * @signature AFScore::AFScore(kmerSize, bgModelOrder, outputFile, verbose); + * @signature AFScore::AFScore(kmerSize, bgModelOrder, revCom, outputFile, verbose); + * @signature AFScore::AFScore(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight, outputFile, verbose); + * + * @param[in] kmerSize Size of kmer, unsigned. + * @param[in] bgModelOrder Order of the background Markov model, unsigned. + * @param[in] outputFile When specified, all normalised and standardised kmer neighbourhood counts will be written + * to this file for every sequence, @link CharString @endlink. + * @param[in] revCom Scoring of reverse complements words [''/'max'/'min'/'mean'/'both_strands'/], + * @link CharString @endlink. + * @param[in] verbose This option will report progress to standard output, bool, defaults to + * false. + * @param[in] mismatches Includes words with one mismatch into the word neighbourhood, unsigned, 0 or 1. + * @param[in] mismatchWeight Weight of word counts with one mismatch, double. + * + * @see alignmentFreeComparison + * + * @var unsigned N2AFScore::kmerSize; + * @brief Size of the kmers. + * + * @var double N2AFScore::mismatchWeight; + * @brief Weight for approximate word matches + * + * @var CharString N2AFScore::revCom; + * @brief Scoring of reverse complements words, @link CharString @endlink [''/'max'/'min'/'mean'/'both_strands'/]. + * + * @var CharString N2AFScore::outputFile; + * @brief When specified, all kmerWeights for every sequence will be written to this file. + * + * @var unsigned N2AFScore::bgModelOrder; + * @brief Order of the background model + * + * @var unsigned N2AFScore::mismatches; + * @brief Approximate word matches [0(exact)/1(one mismatch)] + * + * @var bool N2AFScore::verbose; + * @brief true to enable verbose debug output. + */ + +struct N2_; // Reinert and Waterman, D2 with centralised and standardised counts +typedef Tag const N2; + +template <> +struct AFScore +{ + unsigned kmerSize; + unsigned bgModelOrder; + String revCom; // Count reverse complement words? + // revCom="";"mean","max","both_strands" + unsigned mismatches; // Currently 0 or 1 + double mismatchWeight; // Weight of words in the mismatch neighbourhood + bool verbose; + bool norm; // Normalize score? Needed to provide a proper similarity measure + String outputFile; // Output of all kmer weights for every sequence into this file + + // Constructor for the simple case with only exact word counts (N2*) + AFScore(unsigned k, unsigned m, String kmerWeightsFile = "", bool verbose_ = false) + { + kmerSize = k; + bgModelOrder = m; + outputFile = kmerWeightsFile; + verbose = verbose_; + revCom = ""; + mismatches = 0; + mismatchWeight = 1.0; + norm = true; + + }; + + // Constructor for the case with exact word counts and reverse complement (N2rc) + AFScore(unsigned k, unsigned m, String revCom_, String kmerWeightsFile = "", bool verbose_ = false) + { + kmerSize = k; + bgModelOrder = m; + revCom = revCom_; + outputFile = kmerWeightsFile; + verbose = verbose_; + mismatches = 0; + mismatchWeight = 1.0; + norm = true; + }; + + // Constructor for the case with mismatch-neighbourhood word counts and reverse complement (N2mmrc) + AFScore(unsigned k, + unsigned m, + String revCom_, + unsigned mm, double mmw, + String kmerWeightsFile = "", + bool verbose_ = false) + { + kmerSize = k; + bgModelOrder = m; + revCom = revCom_; + mismatches = mm; + mismatchWeight = mmw; + outputFile = kmerWeightsFile; + verbose = verbose_; + norm = true; + }; +}; + +/*! + * @class D2zAFScore D2zAFScore + * @extends AFScore + * @headerfile + * @brief D2z computes a z-score of the inner product of kmer count vectors + * + * @signature template <> + * struct AFScore; + * + * D2z can be used for alignment-free sequence comparison. The algorithm differs from the original implementation by + * the way masked sequences are handled + * + * @section References + * + * Kantorovitz, M. R.; Robinson, G. E., Sinha, S. A statistical method for alignment-free comparison of regulatory + * sequences. Bioinformatics, 2007. + * + * @fn D2zAFScore::AFScore + * + * @brief Constructor + * + * @signature AFScore::AFScore(kmerSize, bgModelOrder[, verbose]); + * + * @param[in] kmerSize Size of kmer, unsigned. + * @param[in] bgModelOrder Order of the background Markov model, unsigned. + * @param[in] verbose This option will report progress to standard output; bool, defaults to + * false. + * + * @var unsigned D2zAFScore::bgModelOrder; + * @brief Order of the background model + * + * @var unsigned D2zAFScore::kmerSize; + * @brief Size of the kmers + * + * @var bool D2zAFScore::verbose; + * @brief true to enable verbose debug output. +] */ + +struct D2z_; // Inner product of k-mer counts, d2 score with z-score +typedef Tag const D2z; + +template <> +struct AFScore +{ + unsigned kmerSize; + unsigned bgModelOrder; + bool verbose; + AFScore(unsigned k, unsigned m, bool verbose_ = false) : + kmerSize(k), bgModelOrder(m), verbose(verbose_) + {} +}; + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_BASE_H_ diff --git a/seqan/alignment_free/alignment_free_comparison.h b/seqan/alignment_free/alignment_free_comparison.h new file mode 100644 index 0000000..bf33fa0 --- /dev/null +++ b/seqan/alignment_free/alignment_free_comparison.h @@ -0,0 +1,106 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// This file contains the function that calls alignment free sequence +// comparisons algorithms (see AFScore): +// alignmentFreeComparison() +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_ALIGNMENT_FREE_COMPARISON_H_ + +namespace seqan { + +/*! + * @fn alignmentFreeComparison + * @headerfile + * @brief Computes the pairwise similarity scores for a set of sequences. + * + * @signature void alignmentFreeComparison(scoreMatrix, sequenceSet, score); + * + * @param[out] scoreMatrix A two-dimensional @link Matrix @endlink, used to store all pairwise scores. + * @param[in] sequenceSet @link StringSet @endlink containing all sequences for which pairwise scores will be + * computed. + * @param[in] score The @link AFScore @endlink object to be used for computing the alignment. + * + * @section Examples + * + * Calculate the alignment free sequence similarity of two masked DNA sequences. + * + * @code{.cpp} + * using namespace seqan; + * StringSet sequences; + * Dna5String seq1 = + * "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG" + * "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG" + * "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC" + * "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT" + * "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA" + * "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT" + * "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG"; + * Dna5String seq2 = + * "ACCGACGATTAGCTTTGTCCGAGTTACAACGGTTCAATAATACAAAGGATGGCATAAACCCATTTGTGTGAA" + * "AGTGCCCATCACATTATGATTCTGTCTACTATGGTTAATTCCCAATATACTCTCGAAAAGAGGGTATGCTCC" + * "CACGGCCATTTACGTCACTAAAAGATAAGATTGCTCAAANNNNNNNNNACTGCCAACTTGCTGGTAGCTTCA" + * "GGGGTTGTCCACAGCGGGGGGTCGTATGCCTTTGTGGTATACCTTACTAGCCGCGCCATGGTGCCTAAGAAT" + * "GAAGTAAAACAATTGATGTGAGACTCGACAGCCAGGCTTCGCGCTAAGGACGCAAAGAAATTCCCTACATCA" + * "GACGGCCGCGNNNAACGATGCTATCGGTTAGGACATTGTGCCCTAGTATGTACATGCCTAATACAATTGGAT" + * "CAAACGTTATTCCCACACACGGGTAGAAGAACNNNNATTACCCGTAGGCACTCCCCGATTCAAGTAGCCGCG"; + * + * clear(sequences); + * appendValue(sequences, seq1); + * appendValue(sequences, seq2); + * + * Matrix myMatrix; + * + * unsigned kmerSize = 5; + * unsigned bgModelOrder = 1; + * String revCom = "both_strands"; + * unsigned mismatches = 1; + * double mismatchWeight = 0.5; + * AFScore myScoreN2(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight); + * + * alignmentFreeComparison(myMatrix, sequences, myScoreN2); + * std::cout << myMatrix; + * @endcode + */ + +template +void alignmentFreeComparison(Matrix & scoreMatrix, TStringSet const & sequenceSet, TComparisonMethod const & comparisonMethod) +{ + _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_COMPARISON_H_ diff --git a/seqan/alignment_free/kmer_functions.h b/seqan/alignment_free/kmer_functions.h new file mode 100644 index 0000000..118c7d8 --- /dev/null +++ b/seqan/alignment_free/kmer_functions.h @@ -0,0 +1,965 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Jonathan Goeke +// ========================================================================== +// This file contains helper functions to count words in sequences and to +// calculate probabilities and variances of word occurrences. +// ========================================================================== + +// TODO (goeke) const could be added below for the input variables but the function value() in matrix_base (align) is not defined for const. Similarly, the function emittedProbabilty is not defined for const in statistics_markov_model.h + +#ifndef SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_KMER_FUNCTIONS_H_ +#define SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_KMER_FUNCTIONS_H_ + +namespace seqan { + +template +struct UnmaskedAlphabet_ +{ + typedef TAlphabet Type; +}; + +template <> +struct UnmaskedAlphabet_ +{ + typedef Dna Type; +}; + +template +struct UnmaskedAlphabet_ +{ + typedef const typename UnmaskedAlphabet_::Type Type; +}; + +/*! + * @fn countKmers + * @headerfile + * @brief Counts kmers in a sequence. Optionally, a background model is returned. + * + * @signature void countKmers(kmerCounts, sequence, k); + * @signature void countKmers(kmerCounts, bgFrequencies, sequence, k); + * @signature void countKmers(kmerCounts, bgModel, sequence, k); + * + * @param[out] kmerCounts @link String @endlink of unsigned with kmer counts for every k-mer. + * @param[out] bgFrequencies @link String @endlink of background frequencies (double) representing the model. + * @param[out] bgModel @link MarkovModel @endlink to use. + * @param[in] sequence @link String @endlink (sequence) where k-mers are counted. + * @param[in] k k-mer length (unsigned). + * + * k-mers overlapping masked (aka 'N') letters are not counted in case of Dna5Strings. A Bernoulli or Markov Model + * can be choosen as a background model. + * + * @section Examples + * + * Calculate the alignment free sequence similarity o two masked DNA sequences. + * + * @code{.cpp} + * using namespace seqan; + * // Masked sequence, we do not want to count words overlapping 'N' + * Dna5String sequenceDna5 = + * "TAGGTTTTCCGAAAAGGTAGCAACTTTACGTGATCAAACCTCTGACGGGGTTTTCCCCGTCGAAATTGGGTG" + * "TTTCTTGTCTTGTTCTCACTTGGGGCATCTCCGTCAAGCCAAGAAAGTGCTCCCTGGATTCTGTTGCTAACG" + * "AGTCTCCTCTGCATTCCTGCTTGACTGATTGGGCGGACGGGGTGTCCACCTGACGCTGAGTATCGCCGTCAC" + * "GGTGCCACATGTCTTATCTATTCAGGGATCAGAATTTATTCAGGAAATCAGGAGATGCTACACTTGGGTTAT" + * "CGAAGCTCCTTCCAAGGCGTAGCAAGGGCGACTGAGCGCGTAAGCTCTAGATCTCCTCGTGTTGCAACTACA" + * "CGCGCGGGTCACTCGAAACACATAGTATGAACTTAACGACTGCTCGTACTGAACAATGCTGAGGCAGAAGAT" + * "CGCAGACCAGGCATCCCACTGCTTGAAAAAACTATNNNNCTACCCGCCTTTTTATTATCTCATCAGATCAAG"; + * + * String kmerCounts; + * unsigned k = 2; // Count all 2-mers + * countKmers(kmerCounts, sequenceDna5, k); + * + * for(unsigned i = 0; i<16; ++i) // Print the 2-mer counts + * std::cout< nucleotideFrequencies; // Defines a Bernoulli model for DNA sequences. + * // Count all 2-mers and save the nucleotide frequencies + * countKmers(kmerCounts, nucleotideFrequencies, sequenceDna5, k); + * + * for(unsigned i = 0; i<4; ++i) // Print the nucleotide frequencies + * std::cout << nucleotideFrequencies[i] << "\n"; + * // => p(A) = 0.238; p(C) = 0.254; p(G) = 0.238; p(T) = 0.27; + * + * MarkovModel backgroundModel(1); // Markov model of order 1 + * // Count all 2-mers and return a Markov model + * countKmers(kmerCounts, backgroundModel, sequenceDna5, k); + * std::cout< +void countKmers(String & kmerCounts, TString const & sequence, unsigned const k) +{ + typedef typename Value::Type TAlphabet; + typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + typedef typename Iterator::Type TIterator; + typedef typename Position::Type TPosition; + typedef Shape TShape; + // Declare variables + TShape myShape; // Shape, length can be changed (kmer_length) + resize(myShape, k); + // Calculate the number of kmers, length of count vector + int kmerNumber = _intPow((unsigned)ValueSize::VALUE, weight(myShape)); + clear(kmerCounts); + resize(kmerCounts, kmerNumber, 0); + TIterator itSequence = begin(sequence); + int counterN = 0; + + // Check for any N that destroys the first kmers + unsigned j = k - 1; + for (TPosition i = position(itSequence); i <= j; ++i) + { + if (_repeatMaskValue(sequence[i])) + { + counterN = i + 1; + } + } + for (; itSequence <= (end(sequence) - k); ++itSequence) + { + // Check if there is a "N" at the end of the new kmer + if (_repeatMaskValue(value(itSequence + (k - 1)))) + counterN = k; // Do not consider any kmer covering this "N" + + // If there is no "N" overlapping with the current kmer, count it + if (counterN <= 0) + { + unsigned hashValue = hash(myShape, itSequence); + ++kmerCounts[hashValue]; + } + counterN--; + } +} + +/* + * Function to count kmers and background nucleotide frequencies, Ns are not considered + * (for zero order background model) + */ +template +void countKmers(String & kmerCounts, String & backgroundFrequencies, TString const & sequence, unsigned const k) +{ + typedef typename Value::Type TAlphabet; + typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + typedef typename Iterator::Type TIterator; + typedef typename Iterator >::Type TIteratorTStringBG; + typedef typename Position::Type TPosition; + typedef Shape TShape; + unsigned alphabetSize = ValueSize::VALUE; + + // Declare variables + TShape myShape; // Shape, length can be changed (kmer_length) + TShape myShapeBG; // Shape for background, set to markovlen+1, here zero order only + resize(myShape, k); + resize(myShapeBG, 1); // Markov model of zero order (count background frequencies) + + // Calculate number of kmers/ length of count vector, respectively background vector + unsigned kmerNumber = _intPow(alphabetSize, k); + unsigned kmerNumberBG = alphabetSize; // Zero order model for DNA sequences (Bernoulli model) + clear(kmerCounts); + resize(kmerCounts, kmerNumber, 0); + resize(backgroundFrequencies, kmerNumberBG, (TValueBG) 0); + TIterator itSequence = begin(sequence); + + int counterN = 0; // Counter that counts how many kmers are effected by a N + int counterNbg = 0; // Counter for background model (different shape size) + + // Check for any N that destroys the first kmers + unsigned j = k - 1; + for (TPosition i = position(itSequence); i <= j; ++i) + { + if (_repeatMaskValue(sequence[i])) + counterN = i + 1; + } + + int sumBG = 0; // Count the number of nucleotides for the nucleotide frequency calculation (Ns are not considered anymore). + for (; itSequence <= (end(sequence) - k); ++itSequence) + { + // Check if there is a "N" at the end of the new kmer + if (_repeatMaskValue(value(itSequence + (k - 1)))) + { + counterN = k; // Do not consider any kmer covering this "N" + } + // If there is no "N" overlapping with the current kmer, count it. + if (counterN <= 0) + { + unsigned hashValue = hash(myShape, itSequence); + ++kmerCounts[hashValue]; + } + // Check if there is a "N" at the end of the new background word, here single letters only. + if (_repeatMaskValue(value(itSequence))) + { + counterNbg = 1; + } + if (counterNbg <= 0) + { + unsigned hashValueBG = hash(myShapeBG, itSequence); + backgroundFrequencies[hashValueBG] += 1.0; + ++sumBG; + } + counterN--; + counterNbg--; + } + // The background counts are updated until the last base is covered. + for (; itSequence < end(sequence); ++itSequence) + { + if (_repeatMaskValue(value(itSequence))) + { + counterNbg = 1; + } + if (counterNbg <= 0) + { + unsigned hashValueBG = hash(myShapeBG, itSequence); + ++backgroundFrequencies[hashValueBG]; + ++sumBG; + } + counterNbg--; + } + // Normalise the background counts to obtain the nucleotide frequencies (Bernoulli model of DNA sequences). + TIteratorTStringBG itBackground = begin(backgroundFrequencies); + for (; itBackground < end(backgroundFrequencies); ++itBackground) + if (sumBG != 0) + value(itBackground) /= ((TValueBG) sumBG); +} + +/* + * Function to count kmers and build a background markov model with masked sequences + */ +template +void countKmers(String & kmerCounts, MarkovModel & backgroundModel, TString const & sequence, unsigned k) +{ + //typedef typename Value::Type TAlphabet; + //typedef typename UnmaskedAlphabet_::Type TUnmaskedAlphabet; + typedef typename Iterator::Type TIterator; + //typedef typename Iterator, Rooted>::Type TIteratorInt; + typedef typename Position::Type TPosition; + typedef Shape TShape; + + // Declare variables + TShape myShape; // Shape, length can be changed (kmer_length) + resize(myShape, k); + // Only consider kmers without N + int kmerNumber = _intPow((unsigned)ValueSize::VALUE, weight(myShape)); + clear(kmerCounts); + resize(kmerCounts, kmerNumber, 0); + + // Create sequence set for the markov model, if Ns occur, the sequence is split and Ns are removed + StringSet > seqSetMM; + + TIterator itSeq = begin(sequence); + + // Check for any N that destroys the first kmers + unsigned j = (k - 1); + for (TPosition i = position(itSeq); i <= j; ++i) + { + if (_repeatMaskValue(sequence[i])) + { + if ((i - position(itSeq)) > 0) + { + appendValue(seqSetMM, infix(sequence, position(itSeq), i)); + } + goFurther(itSeq, i + 1 - position(itSeq)); + j = i + k - 1; + } + } + + int counterN = 0; + TPosition startSplitSequence = position(itSeq); // The position of possible start of a sequence after NNs is stored to split sequences. + + for (; itSeq <= (end(sequence) - k); ++itSeq) + { + if (_repeatMaskValue(value(itSeq + (k - 1)))) + { + counterN = k; + + if (((position(itSeq) + k - 1) > startSplitSequence)) + appendValue(seqSetMM, infix(sequence, startSplitSequence, (position(itSeq) + k - 1))); + + startSplitSequence = (position(itSeq) + k); // Position after N, possible start + } + if (counterN <= 0) + { + unsigned hashValue = hash(myShape, itSeq); + ++kmerCounts[hashValue]; + } + + counterN--; + } + // Create a stringSet, needed to create the Markov model + if ((position(itSeq) + k - 1) > startSplitSequence) + { + appendValue(seqSetMM, infix(sequence, startSplitSequence, (position(itSeq) + k - 1))); + } + // Build background Markov model + buildMarkovModel(backgroundModel, seqSetMM); +} + +/*! + * @fn calculateProbability + * @headerfile + * @brief Calculates the probability of a sequence given a Bernoulli model. + * + * @signature void calculateProbability(probability, sequence, bgFrequencies); + * + * @param[out] probability Probability (double) of the sequence given the model. + * @param[in] sequence @link String @endlink, usually of Dna characters. + * @param[in] bgFrequencies @link String @endlink of background frequencies (double) representing the model. + * + * @section Examples + * + * Calculate the probability for the word CCCAAGTTT with p(A) = p(T) = 0.3 and p(C) = p(G) = 0.2. + * + * @code{.cpp} + * using namespace seqan; + * double p = 0.0; + * DnaString word = "CCCAAGTTT"; + * String model; + * resize(model, 4); + * model[0] = 0.3; // p(A) + * model[1] = 0.2; // p(C) + * model[2] = 0.2; // p(G) + * model[3] = 0.3; // p(T) + * calculateProbability(p, word, model); // p = 3.888e-06 + * @endcode + * + * @see calculateVariance + * @see alignmentFreeComparison + * @see calculateCovariance + * @see countKmers + */ + +template +void calculateProbability(TValue & probability, TString const & sequence, TStringBG const & backgroundFrequencies) +{ + typedef typename Iterator::Type TIteratorTString; + + TIteratorTString itSequence = begin(sequence); + probability = (TValue) 1; + for (; itSequence < end(sequence); ++itSequence) + probability *= backgroundFrequencies[ordValue(*itSequence)]; +} + +/*! + * @fn calculateVariance + * @headerfile + * @brief Calculates the variance for the number of word occurrences of a word in a sequence of length n given a + * background model. + * + * @signature void calculateVariance(variance, word, bgFrequencies, n); + * @signature void calculateVariance(variance, word, bgModel, n); + * + * @param[out] variance Variance of the number of occurrences of the word in a sequence of length n given the + * model; double. + * @param[in] word @link String @endlink, usually of Dna to compute variance for. + * @param[in] bgFrequencies @link String @endlink of bg frequencies representing the model. + * @param[in] bgModel @link MarkovModel @endlink to use. + * @param[in] n Length of the sequence where the occurrences of word are counted, int. + * + * Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background + * model (Markov model or Bernoulli model). The formula is obtained from (Robin et al., 2005). + * + * @section References + * + * Robin, S., Rodolphe, F., and Schbath, S. (2005). DNA, Words and Models. Cambridge University Press. See Jonathan + * Goeke et al (to appear) for details on the implementation. + * + * @section Examples + * + * Calculate the variance for the number of occurrences of CAAGTC in a sequence of length 10000bp with + * p(A) = p(T) = 0.3 and p(C) = p(G) = 0.2. + * + * @code{.cpp} + * using namespace seqan; + * double var = 0.0; + * int n = 10000; + * DnaString word = "CAAGTC"; + * String model; + * resize(model, 4); + * model[0] = 0.3; // p(A) + * model[1] = 0.2; // p(C) + * model[2] = 0.2; // p(G) + * model[3] = 0.3; // p(T) + * calculateVariance(var, word, model, n); // var = 2.16 + * @endcode + * + * Estimate a Markov model on a set of sequences and calculate the variance for the number of occurrences of the word + * CAAGTC in a sequence of length 10000bp. + * + * @code{.cpp} + * using namespace seqan; + * double var = 0.0; + * int n = 10000; + * DnaString word = "CAAGTC"; + * StringSet sequences; + * appendValue(sequences, "CAGAAAAAAACACTGATTAACAGGAATAAGCAGTTTACTTATTTTGGGCCTGGGACCCGTGTCTCTAATTTAATTAGGTGATCCCTGCGAAGTTTCTCCA"); + * MarkovModel model(0); // Bernoulli model + * model.build(sequences); + * calculateVariance(var, word, model, n); // var = 2.16 + * MarkovModel model1(1); // First order Markov model + * model1.build(sequences); + * calculateVariance(var, word, model1, n); // var = 1.69716 + * @endcode + * + * @see calculateProbability + * @see calculateCovariance + * @see MarkovModel + * @see alignmentFreeComparison + * @see calculatePeriodicity + * @see countKmers + * @see calculateOverlapIndicator + */ + +template +void calculateVariance(TValue & variance, TString const & word, TStringBG const & backgroundFrequencies, int const n) +{ + typedef typename Value::Type TAlphabet; + typedef typename Value::Type TValueBG; + typedef typename Iterator, Rooted>::Type TIteratorInt; + + int l = length(word); + TValueBG p_w; + calculateProbability(p_w, word, backgroundFrequencies); + + String periodicity; + calculatePeriodicity(periodicity, word, word); + variance = (TValue) (n - l + 1) * p_w; + for (TIteratorInt i = begin(periodicity); i < end(periodicity); ++i) + { + TValueBG p_clump; + TValueBG p_tmp; + calculateProbability(p_tmp, word, backgroundFrequencies); + String wordPrefix = prefix(word, value(i)); + calculateProbability(p_clump, wordPrefix, backgroundFrequencies); + p_clump *= p_tmp; + variance += (TValue) 2 * (n - l + 1 - value(i)) * p_clump; + } + variance += (TValue) p_w * p_w * (n - 2 * n * l + 3 * l * l - 4 * l + 1); +} + + +template +void calculateVariance(TValue & variance, String const & word, MarkovModel /*const*/ & bgModel, int const n) +{ + typedef typename Iterator, Rooted>::Type TIteratorInt; + + int l = length(word); + TValue p_w; + p_w = emittedProbability(bgModel, word); + String periodicity; + calculatePeriodicity(periodicity, word, word); + variance = (TValue) (n - l + 1) * p_w; + for (TIteratorInt i = begin(periodicity); i < end(periodicity); ++i) + { + TValue p_clump; + String clump = prefix(word, value(i)); + append(clump, word); + p_clump = emittedProbability(bgModel, clump); + variance += (TValue) 2 * (n - l + 1 - value(i)) * p_clump; + } + variance += (TValue) p_w * p_w * (n - 2 * n * l + 3 * l * l - 4 * l + 1); +} + +/*! + * @fn calculateCovariance + * @headerfile + * @brief Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a + * background model. + * + * @signature void calculateCovariance(covariance, word1, word2, bgFrequencies, n); + * @signature void calculateCovariance(covariance, word1, word2, bgModel, n); + * + * @param[out] covariance Variance of the number of occurrences of the word in a sequence of length n given the + * model, double. + * @param[in] word1 @link String @endlink, usually of Dna. + * @param[in] word2 @link String @endlink, usually of Dna. + * @param[in] bgFrequencies @link String @endlink of double with the background frequencies representing + * @param[in] bgModel @link MarkovModel @endlink to use. + * @param[in] n Length of the sequence where the occurrences of word are counted, int. + * + * Calculates the covariance for the number of word occurrences for two words in a sequence of length n given a + * background model (Markov model or Bernoulli model). The covariance is influenced by the property of words to overlap, + * for example, the words ATAT and TATA have a high covariance since they are likely to overlap. The formula is based on + * (Robin et al., 2005). + * + * @section References + * + * Robin, S., Rodolphe, F., and Schbath, S. (2005). DNA, Words and Models. Cambridge University Press. See Jonathan + * Goeke et al (to appear) for details on the implementation. + * + * @section Examples + * + * Calculate the covariance for the number of occurrences of ATATAT and TATATA in a sequence of length 10000bp with + * p(A) = p(T) = 0.3 and p(C) = p(G) = 0.2. + * + * @code{.cpp} + * using namespace seqan; + * double covar = 0.0; + * int n = 10000; + * DnaString word1 = "ATATAT"; + * DnaString word2 = "TATATA"; + * String model; + * resize(model, 4); + * model[0] = 0.3; // p(A) + * model[1] = 0.2; // p(C) + * model[2] = 0.2; // p(G) + * model[3] = 0.3; // p(T) + * calculateCovariance(covar, word1, word2, model, n); // covar = 4.74 + * @endcode + * + * Estimate a Markov model on a set of sequences and calculate the covariance for the number of occurrences of ATATAT + * and TATATA in a sequence of length 10000bp. + * + * @code{.cpp} + * using namespace seqan; + * double covar = 0.0; + * int n = 10000; + * DnaString word1 = "ATATAT"; + * DnaString word2 = "TATATA"; + * StringSet sequences; + * appendValue(sequences, "CAGCACTGATTAACAGGAATAAGCAGTTTACTTCTGTCAGAATATTGGGCATATATA" + * "CTGGGACCCGTGTAATACTCTAATTTAATTAGGTGATCCCTGCGAAGTCTCCA"); + * MarkovModel modelMM0(0); // Bernoulli model + * modelMM0.build(sequences); + * calculateCovariance(covar, word1, word2, modelMM0, n); // covar = 4.74 + * MarkovModel modelMM1(1); // First order Markov model + * modelMM1.build(sequences); + * calculateCovariance(covar, word1, word2, modelMM1, n); // covar = 13.1541 + * @endcode + * + * @see calculateProbability + * @see calculateVariance + * @see MarkovModel + * @see alignmentFreeComparison + * @see calculatePeriodicity + * @see countKmers + * @see calculateOverlapIndicator + */ + +template +void calculateCovariance(TValue & covariance, TString const & word1, TString const & word2, TStringBG const & backgroundFrequencies, int const n) +{ + if (word1 == word2) + { + calculateVariance(covariance, word1, backgroundFrequencies, n); + return; + } + typedef typename Value::Type TAlphabet; + typedef typename Value::Type TValueBG; + typedef typename Iterator, Rooted>::Type TIteratorInt; + + covariance = 0; + int l1 = length(word1); + TValueBG p_w1; + calculateProbability(p_w1, word1, backgroundFrequencies); + String periodicity1; + calculatePeriodicity(periodicity1, word1, word2); + for (TIteratorInt i = begin(periodicity1); i < end(periodicity1); ++i) + { + TValueBG p_clump; + TValueBG p_tmp; + calculateProbability(p_tmp, word2, backgroundFrequencies); + String wordPrefix = prefix(word1, value(i)); + calculateProbability(p_clump, wordPrefix, backgroundFrequencies); + p_clump *= p_tmp; + covariance += (TValue) (n - l1 + 1 - value(i)) * p_clump; + } + + int l2 = length(word2); + TValueBG p_w2; + calculateProbability(p_w2, word2, backgroundFrequencies); + String periodicity2; + calculatePeriodicity(periodicity2, word2, word1); + for (TIteratorInt i = begin(periodicity2); i < end(periodicity2); ++i) + { + TValueBG p_clump; + TValueBG p_tmp; + calculateProbability(p_tmp, word1, backgroundFrequencies); + String wordPrefix = prefix(word2, value(i)); + calculateProbability(p_clump, wordPrefix, backgroundFrequencies); + p_clump *= p_tmp; + covariance += (TValue) (n - l2 + 1 - value(i)) * p_clump; + } + covariance += (TValue) p_w1 * p_w2 * (n - 2 * n * l1 + 3 * l1 * l1 - 4 * l1 + 1); +} + +template +void calculateCovariance(TValue & covariance, String const & word1, String const & word2, MarkovModel /*const*/ & bgModel, int const n) +{ + if (word1 == word2) + { + calculateVariance(covariance, word1, bgModel, n); + return; + } + typedef typename Iterator, Rooted>::Type TIteratorInt; + + covariance = 0; + int l1 = length(word1); + TValue p_w1; + p_w1 = emittedProbability(bgModel, word1); + String periodicity1; + calculatePeriodicity(periodicity1, word1, word2); // word2 is right + for (TIteratorInt i = begin(periodicity1); i < end(periodicity1); ++i) + { + TValue p_clump; + String clump = prefix(word1, value(i)); + append(clump, word2); + + p_clump = emittedProbability(bgModel, clump); + + covariance += (TValue) (n - l1 + 1 - value(i)) * p_clump; + } + TValue p_w2; + p_w2 = emittedProbability(bgModel, word2); + String periodicity2; + calculatePeriodicity(periodicity2, word2, word1); + for (TIteratorInt i = begin(periodicity2); i < end(periodicity2); ++i) + { + TValue p_clump; + String clump = prefix(word2, value(i)); + append(clump, word1); + + p_clump = emittedProbability(bgModel, clump); + + covariance += (TValue) (n - l1 + 1 - value(i)) * p_clump; + } + covariance += (TValue) p_w1 * p_w2 * (n - 2 * n * l1 + 3 * l1 * l1 - 4 * l1 + 1); +} + +/*! + * @fn calculatePeriodicity + * @headerfile + * @brief Calculate word periodicity (indicator for overlaps) + * + * @signature void calculatePeriodicity(periodicity, word1, word2); + * + * @param[out] periodicity String of int values giving the periodicity (overlap indicator) of + * word1 and word2. + * @param[int] word1 String, usually of Dna characters. + * @param[int] word2 String, usually of Dna characters. + * + * Calculate word periodicity (indicator for overlaps) for two words. + * + * @section Examples + * + * Calculate the periodicity of two words (At which positions can they overlap?) + * + * @code{.cpp} + * using namespace seqan; + * DnaString word1 = "ATATA"; + * DnaString word2 = "TATAT"; + * String periodicity; + * calculatePeriodicity(periodicity, word1, word2); + * for(unsigned i = 0; i < length(periodicity); ++i) // Print the periodicity + * std::cout << periodicity[i] << "\t"; + * + * // periodocity[0] = 1: + * // i = 01234 + * // word1 = ATATA + * // word2 = -TATAT + * + * // periodocity[1] = 3: + * // i = 01234 + * // word1 = ATATA + * // word2 = ---TATAT + * @endcode + * + * @see calculateVariance + * @see calculateCovariance + * @see calculateOverlapIndicator + * @see alignmentFreeComparison + */ + +template +void calculatePeriodicity(String & periodicity, TString const & word1, TString const & word2) +{ + typedef typename Value::Type TAlphabet; + //typedef typename Iterator::Type TIterator; + typedef typename Size::Type TSize; + + TSize length1 = length(word1); + TSize length2 = length(word2); + for (TSize i = 1; i < length1; ++i) + { + String my_suffix = suffix(word1, i); // Overlap of suffix of word1 with prefix of word2 + TSize my_min = std::min(length2, (length1 - i)); + String my_prefix = prefix(word2, my_min); + if (my_suffix == my_prefix) + { + appendValue(periodicity, i); + } + } +} + +/*! + * @fn calculateOverlapIndicator + * @headerfile + * @brief Calculate word overlaps: epsilon(word1, word2) = 1 where word2[j] = word1[j+p] for + * all j = 1..(k-p). + * + * @signature void calculateOverlapIndicator(epsilon, word1, word2); + * + * @param[out] epsilon String of int giving the periodicity (overlap indicator) of word1 and word2. + * @param[in] word1 String (for example a DNA sequence). + * @param[in] word2 String (for example a DNA sequence). + * + * Calculate the indicator for overlaps of two words. The formula is based on (Robin et al., 2005) + * + * @section References + * + * Robin, S., Rodolphe, F., and Schbath, S. (2005). DNA, Words and Models. Cambridge University Press. See Jonathan + * Goeke et al (to appear) for details on the implementation. + * + * @section Examples + * + * Calculate the overlap indicator (epsilon) for two words + * + * @code{.cpp} + * using namespace seqan; + * DnaString word1 = "ATATA"; + * DnaString word2 = "TATAT"; + * String epsilon; + * calculateOverlapIndicator(epsilon, word1, word2); + * for(unsigned i = 0; i < length(epsilon); ++i) + * std::cout << epsilon[i] << "\t"; + * // epsilon = 01010: + * // word1 ATATA + * // word2 overlap 1: -TATAT + * // word2 overlap 2: ---TATAT + * @endcode + * + * @see calculateVariance + * @see calculateCovariance + * @see calculatePeriodicity + * @see alignmentFreeComparison + */ + +template +void calculateOverlapIndicator(String & epsilon, TString const & word1, TString const & word2) +{ + typedef typename Value::Type TAlphabet; + //typedef typename Iterator::Type TIterator; + typedef typename Size::Type TSize; + + TSize length1 = length(word1); + TSize length2 = length(word2); + clear(epsilon); + resize(epsilon, length1, 0); + for (TSize i = 0; i < length1; ++i) + { + String my_suffix = suffix(word1, length1 - i - 1); // Overlap of suffix of word1 with prefix of word2 + TSize my_min = std::min(length2, i + 1); + String my_prefix = prefix(word2, my_min); + if (my_suffix == my_prefix) + epsilon[i] = 1; + } +} + +/*! + * @fn stringToStringSet + * @headerfile + * @brief Transform a String into a StringSet containing this String. + * + * @signature void stringToStringSet(stringSet, string); + * @signature void stringToStringSet(dnaStringSet, dna5String); + * + * @param[out] stringSet @link StringSet @endlink to create with one sequence. + * @param[in] string @link String @endlink to create the string set of. + * @param[out] dnaStringSet @link StringSet @endlink of @link String Strings @endlink over the alphabet @link Dna @endlink. + * @param[in] dna5String @link String @endlink over the alphabet @link Dna5 @endlink to convert. + * + * @note The second variant removes all N characters from the @link Dna5String @endlink. + * + * @section Examples + * + * Transform a masked DNA sequence into a set of sequences with all masked parts removed. + * + * @code{.cpp} + * using namespace seqan; + * Dna5String sequenceDna5 = + * "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG"; + * StringSet sequencesDna; + * stringToStringSet(sequencesDna, sequenceDna5); + * // Print the masked sequence + * std::cout< +void +stringToStringSet(StringSet & stringSet, TString const & sequence) +{ + resize(stringSet, 1); + stringSet[0] = sequence; +} + +inline void +stringToStringSet(StringSet > & dnaStringSet, String const & sequence) +{ + typedef Iterator const, Rooted>::Type TIterator; + typedef Position::Type TPosition; + + TIterator itSeq = begin(sequence); + // Check for any N that destroys the first kmers + unsigned j = 0; + for (TPosition i = position(itSeq); i <= j; ++i) + { + if (sequence[i] == 'N') + { + if ((i - position(itSeq)) > 0) + appendValue(dnaStringSet, infix(sequence, position(itSeq), i)); + goFurther(itSeq, i + 1 - position(itSeq)); + j = i; + } + } + int counterN = 0; + TPosition startSplitSequence = position(itSeq); // The position of possible starts of a sequence after Ns is stored to split the sequence. + for (; itSeq <= (end(sequence) - 1); ++itSeq) + { + if (value(itSeq) == 'N') + { + counterN = 1; + if (((position(itSeq)) > startSplitSequence)) + { + appendValue(dnaStringSet, infix(sequence, startSplitSequence, position(itSeq))); + } + startSplitSequence = (position(itSeq) + 1); // Position after N, possible start + } + counterN--; + } + // Create the stringSet, the stringSet can be used to create a Markov model + if (position(itSeq) > startSplitSequence) + appendValue(dnaStringSet, infix(sequence, startSplitSequence, position(itSeq))); +} + +/*! + * @fn cutNs + * @headerfile + * @brief Cut out all masked sequences from a Dna5String. + * + * @signature void cutNs(sequenceCut, sequence); + * + * @param[out] sequenceCut Dna5String similar to sequence with all Ns cut out. + * @param[in] sequence Masked DNA sequence. + * + * This function concatenates the nonmasked parts of the sequence, thereby changing the word content. If you want to + * remove the masked parts of a sequence without concatenation, use stringToStringSet. + * + * @section Examples + * + * Transform a masked DNA sequence into an unmasked sequences with all masked parts cut out + * + * @code{.cpp} + * using namespace seqan; + * Dna5String sequenceMasked = + * "NNNNNNTTTCCGAAAAGGTANNNNNGCAACTTTANNNCGTGATCAAAGTTTTCCCCGTCGAAATTGGGNNTG"; + * Dna5String sequenceMaskedPartsRemoved; + * cutNs(sequenceMaskedPartsRemoved, sequenceMasked); + * // Print the masked sequence + * std::cout< & sequenceCut, String const & sequence) +{ + typedef Iterator const, Rooted>::Type TIterator; + typedef Position::Type TPosition; + + sequenceCut = ""; + TIterator itSeq = begin(sequence); + + // Check for any N that destroys the first kmers + unsigned j = 0; + for (TPosition i = position(itSeq); i <= j; ++i) + { + if (sequence[i] == 'N') + { + if ((i - position(itSeq)) > 0) + sequenceCut += infix(sequence, position(itSeq), i); + goFurther(itSeq, i + 1 - position(itSeq)); + j = i; + } + } + int counterN = 0; + TPosition startSplitSequence = position(itSeq); // The position of possible starts of a sequence after Ns is stored to split the sequence. + for (; itSeq <= (end(sequence) - 1); ++itSeq) + { + if (value(itSeq) == 'N') + { + counterN = 1; + if (((position(itSeq)) > startSplitSequence)) + sequenceCut += infix(sequence, startSplitSequence, position(itSeq)); + startSplitSequence = (position(itSeq) + 1); // Position after N, possible start + } + counterN--; + } + // Create the sequence with any N cut out. + if (position(itSeq) > startSplitSequence) + { + sequenceCut += infix(sequence, startSplitSequence, position(itSeq)); + } +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ALIGNMENT_FREE_KMER_FUNCTIONS_H_ diff --git a/seqan/arg_parse.h b/seqan/arg_parse.h new file mode 100644 index 0000000..06b2d8d --- /dev/null +++ b/seqan/arg_parse.h @@ -0,0 +1,79 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== +// Facade header for module arg_parse. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_H_ + +// =========================================================================== +// Prerequisites. +// =========================================================================== + +#include +//#include +#include +#include + +#include +#include +#ifndef STDLIB_VS +#include +#endif + +#include +#include +#include + +// =========================================================================== +// The ArgParse Headers. +// =========================================================================== + +#include +#include +#include +#include + +#include +#include + +#include + +#include +#include +#include + +#include + +#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_H_ diff --git a/seqan/arg_parse/arg_parse_argument.h b/seqan/arg_parse/arg_parse_argument.h new file mode 100644 index 0000000..95ebf88 --- /dev/null +++ b/seqan/arg_parse/arg_parse_argument.h @@ -0,0 +1,1164 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_ + +#include +#include + +#include +#include +#include + +namespace seqan { + +// ========================================================================== +// Forwards +// ========================================================================== + +// Required for _checkStringRestrictions(). +inline std::string getFileExtension(ArgParseArgument const & me, unsigned pos); + +// ========================================================================== +// Tags, Classes, Enums +// ========================================================================== + +// ---------------------------------------------------------------------------- +// Class ArgParseArgument +// ---------------------------------------------------------------------------- + +/*! + * @class ArgParseArgument + * @implements AssignableConcept + * @headerfile + * @brief Information for a specific command line argument. + * + * @signature class ArgParseArgument + */ + +/*! + * @enum ArgParseArgument::ArgumentType + * @headerfile + * @brief Define the type of an @link ArgParseArgument @endlink. + * + * @signature enum ArgParseArgument::ArgumentType; + * + * @section Examples + * + * In the following example, the types INPUT_FILE, OUTPUT_FILE, and DOUBLE are used. + * + * @include demos/dox/arg_parse/argument_parser.cpp + */ + +/*! + * @val ArgParseArgument::ArgumentType STRING + * @brief Argument is a string. + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::INTEGER; + * @brief Argument is a signed 32 bit integer. + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::INT64; + * @brief Argument is a signed 64 bit integer. + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::DOUBLE; + * @brief Argument is a floating point number stored as double. + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::INPUT_FILE; + * @brief Argument is an input file. + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::OUTPUT_FILE; + * @brief Argument is an output file. + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::INPUT_PREFIX; + * @brief Argument is a prefix to input file(s). + * + * @val ArgParseArgument::ArgumentType ArgParseArgument::OUTPUT_PREFIX; + * @brief Argument is a prefix to output file(s). + */ + +/*! + * @fn ArgParseArgument::ArgParseArgument + * @brief Constructor + * + * @signature ArgParseArgument::ArgParseArgument(argumentType[, argumentLabel[, isListArgument[, numberOfArgument]]]); + * + * @param[in] argumentType Type of the argument (ArgParseArgument::ArgumentType). + * @param[in] argumentLabel Label for the argument (char const *). + * @param[in] isListArgument Whether or not this argument can be given multiple times (bool). + * @param[in] numberOfArguments Number of times the argument must be given. E.g. set to 2 for the parser to always + * expect two values (int, default is 1). + */ + +class ArgParseArgument +{ +public: + enum ArgumentType + { + // argument is + BOOL, + STRING, // .. a string + INTEGER, // .. an integer + INT64, // .. a 64 bit integer + DOUBLE, // .. a float + INPUT_FILE, // .. an inputfile (implicitly also a string) + OUTPUT_FILE, // .. an outputfile (implicitly also a string) + INPUT_PREFIX, // .. an inputprefix (implicitly also a string) + ///@deprecated use INPUT_PREFIX instead + INPUTPREFIX = INPUT_PREFIX, + OUTPUT_PREFIX, // .. an outoutprefix (implicitly also a string) + INPUT_DIRECTORY, + OUTPUT_DIRECTORY + }; + + + // ---------------------------------------------------------------------------- + // Members to store type information + // ---------------------------------------------------------------------------- + ArgumentType _argumentType; + unsigned _numberOfValues; + std::string _argumentLabel; + bool _isListArgument; + + // ---------------------------------------------------------------------------- + // Members to store the values + // ---------------------------------------------------------------------------- + std::vector defaultValue; + std::vector value; + // Override for the file extension; only used for input/output file arguments. + std::vector _fileExtensions; + + // ---------------------------------------------------------------------------- + // Members for restrictions + // ---------------------------------------------------------------------------- + std::string minValue; + std::string maxValue; + std::vector validValues; + + // ---------------------------------------------------------------------------- + // Tags + // ---------------------------------------------------------------------------- + // Tags can be used to attach hints to the arguments (and options). Currently, + // this is used for tagging the "-file-ext" arguments as "file-ext-override" + // and "gkn-ignore" for ignoring in GKN. + std::vector tags; + + // ---------------------------------------------------------------------------- + // Members to help text + // ---------------------------------------------------------------------------- + std::string _helpText; // The help text shown on the command line + + // ---------------------------------------------------------------------------- + // Constructors + // ---------------------------------------------------------------------------- + + ArgParseArgument(ArgumentType argumentType, + std::string const & argumentLabel = "", + bool isListArgument = false, + unsigned numberOfValues = 1) : + _argumentType(argumentType), + _numberOfValues(numberOfValues), + _argumentLabel(argumentLabel), + _isListArgument(isListArgument), + minValue(""), + maxValue(""), + _helpText("") + { + if (argumentType == ArgParseArgument::BOOL) + { + copy(BooleanArgumentValues_<>::LIST_TRUE.begin(), BooleanArgumentValues_<>::LIST_TRUE.end(), + std::back_inserter(validValues)); + copy(BooleanArgumentValues_<>::LIST_FALSE.begin(), BooleanArgumentValues_<>::LIST_FALSE.end(), + std::back_inserter(validValues)); + } + } +}; + +// ========================================================================== +// Metafunctions +// ========================================================================== + +// ========================================================================== +// Functions +// ========================================================================== + +// ---------------------------------------------------------------------------- +// Helper Function _typeToString() +// ---------------------------------------------------------------------------- + +inline std::string _typeToString(ArgParseArgument const & me) +{ + switch (me._argumentType) + { + case ArgParseArgument::BOOL: + return "bool"; + + case ArgParseArgument::DOUBLE: + return "double"; + + case ArgParseArgument::INTEGER: + return "integer"; + + case ArgParseArgument::INT64: + return "int64"; + + case ArgParseArgument::STRING: + return "string"; + + case ArgParseArgument::INPUT_FILE: + return "input_file"; + + case ArgParseArgument::OUTPUT_FILE: + return "output_file"; + + case ArgParseArgument::INPUT_PREFIX: + return "input_prefix"; + + case ArgParseArgument::OUTPUT_PREFIX: + return "output_prefix"; + + case ArgParseArgument::INPUT_DIRECTORY: + return "input_directory"; + + case ArgParseArgument::OUTPUT_DIRECTORY: + return "output_directory"; + + default: + return "unknown"; + } +} + +// ---------------------------------------------------------------------------- +// Function isListArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isListArgument + * @headerfile + * + * @brief Returns whether the argument can be given more than one time. + * + * @signature bool isListArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it can be given multiple times, false otherwise. + */ + +inline bool isListArgument(ArgParseArgument const & me) +{ + return me._isListArgument; +} + +// ---------------------------------------------------------------------------- +// Function isBooleanArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isBooleanArgument + * @headerfile + * @brief Returns whether the argument is a bool. + * + * @signature bool isBooleanArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is a bool, false otherwise. + */ + +inline bool isBooleanArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::BOOL; +} + +// ---------------------------------------------------------------------------- +// Function isStringArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isStringArgument + * @headerfile + * + * @brief Returns whether the argument is a string. + * + * @signature bool isStringArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is a string, false otherwise. + */ + +inline bool isStringArgument(ArgParseArgument const & me) +{ + return (me._argumentType == ArgParseArgument::STRING) || + (me._argumentType == ArgParseArgument::INPUT_FILE) || + (me._argumentType == ArgParseArgument::OUTPUT_FILE) || + (me._argumentType == ArgParseArgument::INPUT_PREFIX) || + (me._argumentType == ArgParseArgument::OUTPUT_PREFIX) || + (me._argumentType == ArgParseArgument::INPUT_DIRECTORY) || + (me._argumentType == ArgParseArgument::OUTPUT_DIRECTORY); +} + +// ---------------------------------------------------------------------------- +// Function isIntegerArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isIntegerArgument + * @headerfile + * @brief Returns whether the argument is an integer. + * + * @signature bool isIntegerArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is an integer, false otherwise. + */ + +inline bool isIntegerArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::INTEGER; +} + +// ---------------------------------------------------------------------------- +// Function isInt64Argument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isInt64Argument + * @headerfile + * @brief Returns whether the argument is a 64 bit integer. + * + * @signature bool isInt64Argument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is a 64 bit integer, false otherwise. + */ + +inline bool isInt64Argument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::INT64; +} + +// ---------------------------------------------------------------------------- +// Function isDoubleArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isDoubleArgument + * @headerfile + * @brief Returns whether the argument is a double integer. + * + * @signature bool isDoubleArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is a double argument, false otherwise. + */ + +inline bool isDoubleArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::DOUBLE; +} + +// ---------------------------------------------------------------------------- +// Function isInputFileArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isInputFileArgument + * @headerfile + * @brief Returns whether the argument is a input file. + * + * @signature bool isInputFileArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is a input file argument, false otherwise. + */ + +inline bool isInputFileArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::INPUT_FILE || + me._argumentType == ArgParseArgument::INPUT_DIRECTORY; +} + +// ---------------------------------------------------------------------------- +// Function isOutputFileArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isOutputFileArgument + * @headerfile + * @brief Returns whether the argument is a output file. + * + * @signature bool isOutputFileArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is a output file argument, false otherwise. + */ + +inline bool isOutputFileArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::OUTPUT_FILE || + me._argumentType == ArgParseArgument::OUTPUT_DIRECTORY; +} + +// ---------------------------------------------------------------------------- +// Function isOutputPrefixArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isOutputPrefixArgument + * @headerfile + * @brief Returns whether the argument is an output prefix. + * + * @signature bool isOutputPrefixArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is an output prefix argument, false otherwise. + */ + +inline bool isOutputPrefixArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::OUTPUT_PREFIX; +} + +// ---------------------------------------------------------------------------- +// Function isOutputFileArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isInputPrefixArgument + * @headerfile + * @brief Returns whether the argument is an input prefix argument. + * + * @signature bool isInputPrefixArgument(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if it is an input prefix argument, false otherwise. + */ + +inline bool isInputPrefixArgument(ArgParseArgument const & me) +{ + return me._argumentType == ArgParseArgument::INPUT_PREFIX; +} + +// ---------------------------------------------------------------------------- +// Function getArgumentType() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#getArgumentType + * @headerfile + * @brief Return the ArgParseArgument::ArgumentType. + * + * @signature std::string getArgumentType(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return ArgumentType The argument type. + */ + +inline ArgParseArgument::ArgumentType getArgumentType(ArgParseArgument const & me) +{ + return me._argumentType; +} + +// ---------------------------------------------------------------------------- +// Function getArgumentTypeAsString() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#getArgumentTypeAsString + * @headerfile + * @brief Return argument type As a string. + * + * @signature std::string getArgumentTypeAsString(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return std::string The argument type as a STL string. + */ + +inline std::string getArgumentTypeAsString(ArgParseArgument const & me) +{ + return _typeToString(me._argumentType); +} + +// ---------------------------------------------------------------------------- +// Function getArgumentLabel() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#getArgumentLabel + * @headerfile + * @brief Return argument label. + * + * @signature std::string getArgumentLabel(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return std::string The argument label as a STL string. + */ + +inline std::string getArgumentLabel(ArgParseArgument const & me) +{ + return me._argumentLabel; +} + +// ---------------------------------------------------------------------------- +// Helper Function _intervalAssert() +// ---------------------------------------------------------------------------- + +// this methods ensures that the given arguments define a valid interval +// otherwise it will trigger a SEQAN_CHECK failure +template +inline void _intervalAssert(const std::string minValueAsString, const std::string maxValueAsString) +{ + if (minValueAsString != "" && maxValueAsString != "") + SEQAN_CHECK(_cast(minValueAsString) <= _cast(maxValueAsString), + "The interval [%s:%s] is invalid. Please specify a valid interval.", + minValueAsString.c_str(), + maxValueAsString.c_str()); +} + +// ---------------------------------------------------------------------------- +// Function setMinValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#setMinValue + * @headerfile + * @brief Set smallest allowed value for the argument. + * + * @signature void setMinValue(arg, minValue); + * + * @param[in,out] arg The ArgParseArgument to set the smallest value of. + * @param[in] minValue The smallest value to set (std::string). + */ + +inline void setMinValue(ArgParseArgument & me, const std::string minValue) +{ + if (isDoubleArgument(me)) + { + SEQAN_CHECK(_isCastable(minValue), "The maximal value for a double argument must be double."); + _intervalAssert(minValue, me.maxValue); + me.minValue = minValue; + } + else if (isIntegerArgument(me)) + { + SEQAN_CHECK(_isCastable(minValue), "The maximal value for an integer argument must be an integer"); + _intervalAssert(minValue, me.maxValue); + me.minValue = minValue; + } + else if (isInt64Argument(me)) + { + SEQAN_CHECK(_isCastable(minValue), "The maximal value for a 64 integer argument must be a 64 bit integer"); + _intervalAssert(minValue, me.maxValue); + me.minValue = minValue; + } + else + SEQAN_FAIL("min/max values are not applicable to non numeric arguments"); +} + +// ---------------------------------------------------------------------------- +// Function setMaxValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#setMaxValue + * @headerfile + * @brief Set smallest allowed value for the argument. + * + * @signature void setMaxValue(arg, maxValue); + * + * @param[in,out] arg The ArgParseArgument to set the smallest value of. + * @param[in] maxValue The largest value to set (std::string). + */ + +inline void setMaxValue(ArgParseArgument & me, const std::string maxValue) +{ + if (isDoubleArgument(me)) + { + SEQAN_CHECK(_isCastable(maxValue), "The maximal value for a double argument must be double."); + _intervalAssert(me.minValue, maxValue); + me.maxValue = maxValue; + } + else if (isIntegerArgument(me)) + { + SEQAN_CHECK(_isCastable(maxValue), "The maximal value for an integer argument must be an integer"); + _intervalAssert(me.minValue, maxValue); + me.maxValue = maxValue; + } + else if (isInt64Argument(me)) + { + SEQAN_CHECK(_isCastable(maxValue), "The maximal value for a 64 bit integer argument must be an 64 bit integer"); + _intervalAssert(me.minValue, maxValue); + me.maxValue = maxValue; + } + else + SEQAN_FAIL("min/max values are not applicable to non numeric arguments"); +} + +// ---------------------------------------------------------------------------- +// Function setValidValues() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#setValidValues + * @headerfile + * @brief Set list of valid values. + * + * @signature void setValidValues(arg, values); + * + * @param[in,out] arg The ArgParseArgument to set the valid values for. + * @param[in] values Either a std::string containing all valid entries, separated by spaces or a + * std::vector<std::string> with the valid entries. + * + * If the argument is of type string then the list of valid values is the case-sensitive list of string values + * allowed for this argument. If it is an input or output file then the list of valid values is a list of + * case-insentive file extensions identifying the allowed types. + * + * @section Examples + * + * An example of setting allowed values for a string option. + * + * @code{.cpp} + * seqan::ArgParseArgument stringArg(seqan::ArgParseArgument::STRING); + * setValidValues(stringArg, "one two three"); // one of {"one", "two", "three"} + * + * std::vector values; + * values.push_back("four"); + * values.push_back("five"); + * setValidValues(stringArg, values); // one of {"four", "five"} + * @endcode + * + * An example for an input file option. Note that by changing INPUT_FILE to OUTPUT_FILE below, + * the example would be the same for output files. + * + * @code{.cpp} + * seqan::ArgParseArgument fileArg(seqan::ArgParseArgument::INPUT_FILE); + * setValidValues(fileArg, "fq fastq"); // file must end in ".fq" or ".fastq" + * + * std::vector values; + * values.push_back("sam"); + * values.push_back("bam"); + * setValidValues(fileArg, values); // file must end in ".sam" or ".bam" + * @endcode + */ + +inline void setValidValues(ArgParseArgument & me, std::vector const & values) +{ + if (isDoubleArgument(me) || isIntegerArgument(me) || isBooleanArgument(me)) + SEQAN_FAIL("ArgParseArgument does not support setting valid values for numeric or boolean arguments."); + + me.validValues = values; +} + +inline void setValidValues(ArgParseArgument & me, std::string const & valuesString) +{ + if (isDoubleArgument(me) || isIntegerArgument(me) || isBooleanArgument(me)) + SEQAN_FAIL("ArgParseArgument does not support setting valid values for numeric or boolean arguments."); + + // convert array to String + std::vector values; + std::string current_argument; + + for (std::string::const_iterator ch = valuesString.begin(); ch != valuesString.end(); ++ch) + { + if (*ch == ' ') + { + appendValue(values, current_argument); + current_argument = ""; + } + else + { + append(current_argument, *ch); + } + } + if (current_argument != "") + appendValue(values, current_argument); + + setValidValues(me, values); +} + +// ---------------------------------------------------------------------------- +// Function setHelpText() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#setHelpText + * @headerfile + * @brief Set the help text for an ArgParseArgument. + * + * @signature void setHelpText(arg, text); + * + * @param[in,out] arg The ArgParseArgument to set the help text for. + * @param[in] text The text to display as the description of the argument (std::string). + */ + +inline void setHelpText(ArgParseArgument & me, std::string const & text) +{ + me._helpText = text; +} + +// ---------------------------------------------------------------------------- +// Helper Function _isInInterval() +// ---------------------------------------------------------------------------- + +// check if the given value is in the provided interval +template +inline bool _isInInterval(TString value, TString lowerIntervalBound, TString upperIntervalBound) +{ + bool isInInterval = true; + + if (lowerIntervalBound != "") + isInInterval &= (_cast(lowerIntervalBound) <= _cast(value)); + if (upperIntervalBound != "") + isInInterval &= (_cast(value) <= _cast(upperIntervalBound)); + + return isInInterval; +} + +// ---------------------------------------------------------------------------- +// Helper Function _checkNumericArgument() +// ---------------------------------------------------------------------------- + +// test if the values can be assigned to the option and is in the given boundaries +template +inline void _checkNumericArgument(ArgParseArgument const & me, std::string const & value) +{ + if (!_isCastable(value)) + { + std::stringstream what; + what << "the given value '" << value << "' cannot be casted to " << _typeToString(me); + SEQAN_THROW(ParseError(what.str())); + } + + if (!_isInInterval(value, me.minValue, me.maxValue)) + { + std::stringstream what; + what << "the given value '" << value << "' is not in the interval [" + << (me.minValue != "" ? me.minValue : "-inf") << ":" + << (me.maxValue != "" ? me.maxValue : "+inf") << "]"; + + SEQAN_THROW(ParseError(what.str())); + } +} + +// ---------------------------------------------------------------------------- +// Helper Function _compareExtension() +// ---------------------------------------------------------------------------- + +inline bool _compareExtension(std::string const & str, std::string const & ext) +{ + std::string str_ext = str.substr(str.size() - ext.size()); + for (size_t i = 0; i < str_ext.size() && i < ext.size(); ++i) + { + if (tolower(str_ext[i]) != tolower(ext[i])) + return false; + } + return true; +} + +// ---------------------------------------------------------------------------- +// Helper Function _checkStringRestrictions() +// ---------------------------------------------------------------------------- + +// The parameter i gives the index of the value in the argument. + +inline void _checkStringRestrictions(ArgParseArgument const & me, std::string const &value, + unsigned i) +{ + typedef std::vector::const_iterator TVectorIterator; + + // we only check valid values for files and string arguments, but not for prefix arguments + if (!empty(me.validValues) && !(isInputPrefixArgument(me) || isOutputPrefixArgument(me))) + { + // The file name "-" is reserved for stdin or stdout + if ((isInputFileArgument(me) || isOutputFileArgument(me)) && value == "-") + return; + + // Allow the filename to be a pipe (without checking its extension) + if (isInputFileArgument(me) && _isPipe(value.c_str())) + return; + + bool isContained = false; + for (TVectorIterator validValue = me.validValues.begin(); + validValue != me.validValues.end(); + ++validValue) + { + // if it is an input or output file, we only check the file endings + if (isInputFileArgument(me) || isOutputFileArgument(me)) + { + if (length(*validValue) > length(getFileExtension(me, i))) + continue; + else + isContained |= _compareExtension(getFileExtension(me, i), *validValue); + } + else + { + isContained |= (*validValue == value); + } + if (isContained) + break; + } + if (!isContained) + { + std::stringstream what; + if (isInputFileArgument(me) || isOutputFileArgument(me)) + what << "the given path '" << value << "' does not have one of the valid file extensions ["; + else + what << "the given value '" << value << "' is not in the list of allowed values ["; + for (TVectorIterator validValue = me.validValues.begin(); + validValue != me.validValues.end(); + ++validValue) + { + if (validValue != me.validValues.begin()) + what << ", "; + what << ((isInputFileArgument(me) || isOutputFileArgument(me)) ? "*" : "") << *validValue; + } + what << "]"; + if (i < me._fileExtensions.size()) + what << "; the file extension was overridden to be '" << getFileExtension(me, i) << "'"; + SEQAN_THROW(ParseError(what.str())); + } + } +} + +// ---------------------------------------------------------------------------- +// Helper Function _checkBooleanValidValues() +// ---------------------------------------------------------------------------- + +inline void _checkBooleanValidValues(ArgParseArgument const & me, std::string const & value) +{ + SEQAN_ASSERT(isBooleanArgument(me)); + + std::string value_up{value}; + std::transform(value.begin(), value.end(), value_up.begin(), ::toupper); // allow for lowercase letters + bool isContained = (std::find(me.validValues.begin(), me.validValues.end(), value_up) + != me.validValues.end()); + + if (!isContained) + { + std::stringstream what; + what << "the given value '" << value << "' is not in the list of allowed values ["; + + for (auto validValue = me.validValues.begin(); validValue != me.validValues.end(); ++validValue) + { + if (validValue != me.validValues.begin()) + what << ", "; + what << *validValue; + } + what << "]"; + SEQAN_THROW(ParseError(what.str())); + } +} + +// ---------------------------------------------------------------------------- +// Function _checkValue() +// ---------------------------------------------------------------------------- + +// Check value before or after assignment. +// +// The parameter i gives the index of the value to check for overriding the extension in case of file arguments. + +inline void _checkValue(ArgParseArgument const & me, std::string val, unsigned i = 0) +{ + // type checks + if (isIntegerArgument(me)) + _checkNumericArgument(me, val); + + if (isInt64Argument(me)) + _checkNumericArgument(me, val); + + if (isDoubleArgument(me)) + _checkNumericArgument(me, val); + + // check valid values + if (isBooleanArgument(me)) + _checkBooleanValidValues(me, val); + + if (isStringArgument(me)) + _checkStringRestrictions(me, val, i); +} + +inline void _checkValue(ArgParseArgument const & me) +{ + unsigned i = 0; + for (std::vector::const_iterator it = me.value.begin(); it != me.value.end(); ++it, ++i) + _checkValue(me, *it, i); +} + +// ---------------------------------------------------------------------------- +// Function _assignArgumentValue() +// ---------------------------------------------------------------------------- + +inline void _assignArgumentValue(ArgParseArgument & me, std::string const & value) +{ + // assignment + if (isListArgument(me)) // just append + { + appendValue(me.value, value, Exact()); + } + else + { + // check if we already set all expected arguments + if (length(me.value) == me._numberOfValues) + clear(me.value); + appendValue(me.value, value, Exact()); + } +} + +// ---------------------------------------------------------------------------- +// Function getArgumentValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#getArgumentValue + * @headerfile + * @brief Return the value of the argument. + * + * @signature std::string getArgumentValue(arg[, argNo]); + * + * @param[in,out] arg The ArgParseArgument to query. + * @param[in] argNo In case that the ArgParseArgument allowed multiple values, give the index of the argument + * that you want to retrieve (unsigned, starts at 0). + * + * @return std::string Const-reference to the argument value. + */ + +inline std::string const & getArgumentValue(ArgParseArgument const & me, unsigned argNo) +{ + SEQAN_CHECK(argNo < me.value.size() || argNo < me.defaultValue.size(), + "ArgParseArgument: No value set for index %d", argNo); + + if (argNo < me.value.size()) + return me.value[argNo]; + else + return me.defaultValue[argNo]; +} + +inline std::string const & getArgumentValue(ArgParseArgument const & me) +{ + return getArgumentValue(me, 0); +} + +// ---------------------------------------------------------------------------- +// Function getArgumentValues() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#getArgumentValues + * @headerfile + * @brief Return all values of the argument. + * + * @signature std::vector getArgumentValue(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return std::vector Const-reference to the argument values. + */ + +inline std::vector const & getArgumentValues(ArgParseArgument const & me) +{ + if (!me.value.empty()) + return me.value; + else + return me.defaultValue; +} + +// ---------------------------------------------------------------------------- +// Function hasArgumentValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#hasArgumentValue + * @headerfile + * @brief Return whether a value is available. + * + * @signature bool hasValue(arg[, pos]); + * + * @param[in] arg The ArgParseArgument to query. + * @param[in] pos The position of the argument in case of being a list (unsigned, 0-based, default is 0). + * + * @return bool true if pos is less than the size and the argument is non-empty. + */ + +inline bool hasValue(ArgParseArgument const & arg, unsigned position) +{ + return arg.value.size() > position || arg.defaultValue.size() > position; +} + +inline bool hasValue(ArgParseArgument const & arg) +{ + return hasValue(arg, 0); +} + +// ---------------------------------------------------------------------------- +// Function isSet() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#isSet + * @headerfile + * @brief Returns true if a value was assigned to the argument. + * + * @signature bool isSet(arg): + * + * @param[in] arg The ArgParseArgument to query. + * + * @return bool true if a value was assigned, false otherwise. + */ + +inline bool isSet(ArgParseArgument const & me) +{ + return !me.value.empty(); +} + +// ---------------------------------------------------------------------------- +// Function hasDefault() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#hasDefault + * @headerfile + * @brief Returns whether the argument has a default value. + * + * @signature bool hasDefault(arg); + * + * @param[in] arg The argument to query. + * + * @return bool true if the argument has a default value and false if not. + */ + +inline bool hasDefault(ArgParseArgument const & me) +{ + return !me.defaultValue.empty(); +} + +// ---------------------------------------------------------------------------- +// Function numberOfArguments +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#numberOfAllowedValues + * @headerfile + * @brief Returns the number of allowed values for this ArgParseArgument. + * + * @signature unsigned numberOfAllowedValues(arg); + * + * @param[in] arg The ArgParseArgument to query. + * + * @return unsigned The number of allowed values. + */ + +inline unsigned numberOfAllowedValues(ArgParseArgument const & me) +{ + return me._numberOfValues; +} + +// ---------------------------------------------------------------------------- +// Function getFileExtension() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseArgument#getFileExtension + * @headerfile + * @brief Returns the file extension for the given file argument. + * + * Only valid when argument is an INPUT_FILE or OUTPUT_FILE. + * + * Halts the program if not an input or output file argument. + * + * Can be overridden with special hidden options. + * For arguments, you can pass --arg-<num>-file-ext for argument num. + * For parameters, you can pass --<param-name>-file-ext for the option named param-name. + * + * @signature std::string getFileExtension(arg[, pos]); + * + * @param[in] arg The ArgParseArgument to query. + * @param[in] pos The position of the value to retrieve if multiple values (unsigned). + * + * @return std::string The file extension, empty if no extension or not set. + */ + +inline std::string getFileExtension(ArgParseArgument const & me, unsigned pos = 0) +{ + if (!isInputFileArgument(me) && !isOutputFileArgument(me)) + SEQAN_FAIL("Cannot get file extension from non-file argument/option."); + + // Short-circuit to override file extension if set. + if (pos < me._fileExtensions.size()) + { + std::string result = me._fileExtensions[pos]; + if (!result.empty() && result[0] != '.') + result.insert(0, "."); + return result; + } + + // Get argument value and break if empty. + std::string value = getArgumentValue(me, pos); + if (value.empty()) + return ""; + + // If there is a list of valid values then we look for each of these in the path. + if (!me.validValues.empty()) + { + for (unsigned i = 0; i < length(me.validValues); ++i) + { + unsigned len = std::min(me.validValues[i].size(), value.size()); + std::string tmp = value.substr(value.size() - len); + std::transform(tmp.begin(), tmp.end(), tmp.begin(), ::tolower); + if (tmp == me.validValues[i]) + return me.validValues[i]; + } + return ""; + } + + // Fall back to finding position of last dot. Return suffix if found and empty string if not. + size_t dotPos = value.find_last_of('.'); + if (dotPos == std::string::npos) + return ""; + return value.substr(dotPos + 1); +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_ARGUMENT_H_ diff --git a/seqan/arg_parse/arg_parse_ctd_support.h b/seqan/arg_parse/arg_parse_ctd_support.h new file mode 100644 index 0000000..532cddd --- /dev/null +++ b/seqan/arg_parse/arg_parse_ctd_support.h @@ -0,0 +1,594 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Bjoern Kahlert +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_ + +#include + +#include +#include +#include + +#include + +namespace seqan { + +// ---------------------------------------------------------------------------- +// Function _toText() +// ---------------------------------------------------------------------------- +// Removes formatting (\fI, \fB, and \fP). +template +TSequence _toText(TSequence const & input) +{ + TSequence buffer = xmlEscape(input); + TSequence result; + String openTags; + + typedef typename Iterator::Type TIterator; + TIterator endIt = end(input, Standard()); + for (TIterator it = begin(input, Standard()); it != endIt; goNext(it)) + { + if (*it == '\\') + { + // Handle escape sequence, we interpret only "\-", "\fI", and "\fB". + goNext(it); + SEQAN_ASSERT_NOT(it == endIt); + if (*it == '-') + { + appendValue(result, *it); + } + else if (*it == 'f') + { + goNext(it); + SEQAN_ASSERT_NOT(it == endIt); + if (*it == 'I') + { + appendValue(openTags, "i"); + } + else if (*it == 'B') + { + appendValue(openTags, "b"); + } + else if (*it == 'P') + { + SEQAN_ASSERT_NOT(empty(openTags)); + eraseBack(openTags); + } + else + { + append(result, "\\f"); + appendValue(result, *it); + } + } + else + { + appendValue(result, '\\'); + appendValue(result, *it); + } + } + else + { + appendValue(result, *it); + } + } + + return result; +} + +// ---------------------------------------------------------------------------- +// Function _join() +// ---------------------------------------------------------------------------- + +template +inline std::string +_join(std::vector const & v, std::string const & delimiter) +{ + typedef typename std::vector::const_iterator TStringSetIterator; + + std::stringstream joined; + for (TStringSetIterator it = v.begin(); it != v.end(); ++it) + { + if (it != v.begin()) + joined << delimiter; + joined << *it; + } + return joined.str(); +} + +// ---------------------------------------------------------------------------- +// Function _getPrefixedOptionName() +// ---------------------------------------------------------------------------- + +inline std::string +_getPrefixedOptionName(ArgParseOption const & opt) +{ + std::string optName = ""; + if (!empty(opt.longName)) + optName = "--" + opt.longName; + else + optName = "-" + opt.shortName; + + return optName; +} + +// ---------------------------------------------------------------------------- +// Function _getOptionName() +// ---------------------------------------------------------------------------- + +inline std::string +_getOptionName(ArgParseOption const & opt) +{ + if (!empty(opt.longName)) + return opt.longName; + else + return opt.shortName; +} + +// ---------------------------------------------------------------------------- +// Function _getRestrictions() +// ---------------------------------------------------------------------------- +inline void +_getRestrictions(std::vector & restrictions, ArgParseArgument const & opt) +{ + // we only extract non-file restrictions + if (isOutputFileArgument(opt) || isInputFileArgument(opt) || isInputPrefixArgument(opt) || isOutputPrefixArgument(opt)) + { + return; + } + else if (isBooleanArgument(opt)) + { + appendValue(restrictions, "true,false"); + return; + } + if (length(opt.validValues) != 0) + { + for (std::vector::const_iterator valid = opt.validValues.begin(); + valid != opt.validValues.end(); + ++valid) + { + appendValue(restrictions, *valid); + } + } + else + { + std::string minMaxRestriction = ""; + if (opt.minValue != "") + { + append(minMaxRestriction, opt.minValue); + append(minMaxRestriction, ":"); + } + if (opt.maxValue != "") + { + if (minMaxRestriction == "") + append(minMaxRestriction, ":"); + append(minMaxRestriction, opt.maxValue); + } + + if (minMaxRestriction != "") + appendValue(restrictions, minMaxRestriction); + } +} + +// ---------------------------------------------------------------------------- +// Function _addValidValuesRestrictions() +// ---------------------------------------------------------------------------- + +inline void +_getSupportedFormats(std::vector & supported_formats, ArgParseArgument const & opt) +{ + // we check only file arguments + if (!(isOutputFileArgument(opt) || isInputFileArgument(opt) || isInputPrefixArgument(opt) || isOutputPrefixArgument(opt))) + return; + + if (length(opt.validValues) != 0) + { + std::string filetype; + for (std::vector::const_iterator valid = opt.validValues.begin(); + valid != opt.validValues.end(); + ++valid) + { + SEQAN_ASSERT_NOT(empty(*valid)); + + filetype = "*"; + + // ensure . as separator between * and file-extension + if (value(*valid, 0) != '.') + appendValue(filetype, '.'); + + append(filetype, *valid); + appendValue(supported_formats, filetype); + } + } +} + +// ---------------------------------------------------------------------------- +// Function _includeInCTD() +// ---------------------------------------------------------------------------- + +/* + * returns true if this option should be included in the ctd + */ +inline bool +_includeInCTD(ArgParseOption const & opt) +{ + return !(opt.longName == "help" || opt.longName == "version" || opt.longName == "write-ctd" || opt.longName == "export-help" || (opt.shortName == "" && opt.longName == "")); +} + +// ---------------------------------------------------------------------------- +// Function _indent() +// ---------------------------------------------------------------------------- + +inline std::string _indent(const int currentIndent) +{ + std::string indent = ""; + for (int i = 0; i < currentIndent; ++i) + indent += "\t"; + return indent; +} + +// ---------------------------------------------------------------------------- +// Function _writeCLIElement() +// ---------------------------------------------------------------------------- +inline void _writeCLIElement(std::ostream & ctdfile, int currentIndent, std::string const & optionIdentifier, std::string const & ref_name, bool isList) +{ + ctdfile << _indent(currentIndent) + << "\n"; + + ctdfile << _indent(currentIndent + 1) << "\n"; + + ctdfile << _indent(currentIndent) << "\n"; +} + +// ---------------------------------------------------------------------------- +// Function _getManual() +// ---------------------------------------------------------------------------- +inline std::string _getManual(ArgumentParser const & me) +{ + std::stringstream manual; + for (unsigned i = 0; i < me._description.size(); ++i) + { + manual << _toText(me._description[i]) << std::endl; + } + return manual.str(); +} + +// ---------------------------------------------------------------------------- +// Function _toValidGKNTypeSpecifier() +// ---------------------------------------------------------------------------- +// TODO(dadi): similar to _typeToString() function. Differs only in the case of bool, integer, int64 and types +//. that has underscores in them. hyphens are used instead of underscores. e.g. input-file instead +// of input_file. This should be removed and _typeToString() should be used instead once GKN is +// modified to accept the results of _typeToString() functions directly. + +inline std::string _toValidGKNTypeSpecifier(ArgParseArgument const & me) +{ + switch (me._argumentType) + { + case ArgParseArgument::BOOL: + return "string"; + + case ArgParseArgument::INTEGER: + return "int"; + + case ArgParseArgument::INT64: + return "int"; + + case ArgParseArgument::INPUT_FILE: + return "input-file"; + + case ArgParseArgument::OUTPUT_FILE: + return "output-file"; + + case ArgParseArgument::INPUT_PREFIX: + return "input-prefix"; + + case ArgParseArgument::OUTPUT_PREFIX: + return "output-prefix"; + + case ArgParseArgument::INPUT_DIRECTORY: + return "input-prefix"; + + case ArgParseArgument::OUTPUT_DIRECTORY: + return "output-prefix"; + + default: + return _typeToString(me); + } +} + +// ---------------------------------------------------------------------------- +// Function writeCTD() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Change argument order. + +/*! + * @fn ArgumentParser#writeCTD + * @headerfile \ + * @brief Export the app's interface description to a .ctd file. + * + * @signature bool writeCTD(parser[, stream]); + * + * @param[in] parser The ArgumentParser to write the CTD file for. + * @param[out] stream A std::ostream to write to. If omitted an output file with the name form the + * "write-ctd" parameter of the parser is used. + * + * @return bool true on success, false on failure. + */ + +inline bool +writeCTD(ArgumentParser const & me, std::ostream & ctdfile) +{ + typedef ArgumentParser::TOptionMap::const_iterator TOptionMapIterator; + typedef ArgumentParser::TArgumentMapSize TArgumentMapSize; + + int currentIndent = 1; + + std::string toolname(toCString(xmlEscape(getAppName(me)))); + + // remove "_" in the tool name and make the following letter uppercase + std::string class_name; + bool upcase = true; + for (unsigned i = 0; i < toolname.size(); ++i) + { + if (toolname[i] == '_') + { + upcase = true; + continue; + } + class_name.push_back(toolname[i]); + if (upcase) + class_name[class_name.size() - 1] = toupper(toolname[i]); + upcase = false; + } + + ctdfile << "\n"; + ctdfile << "\n"; + ctdfile << _indent(currentIndent) << "" << toolname << "\n"; + ctdfile << _indent(currentIndent) << "" << xmlEscape(getShortDescription(me)) << "\n"; + ctdfile << _indent(currentIndent) << "" << xmlEscape(_getManual(me)) << "\n"; // TODO(aiche): as soon as we have a more sophisticated documentation embedded into the CmdParser, we should at this here + ctdfile << _indent(currentIndent++) << "\n"; + + // the unix way 1st the options + for (TOptionMapIterator optionMapIterator = me.optionMap.begin(); + optionMapIterator != me.optionMap.end(); + ++optionMapIterator) + { + ArgParseOption const & opt = *optionMapIterator; + + // exclude hidden + if (isHidden(opt)) + continue; + + std::string optionIdentifier = _getPrefixedOptionName(opt); + std::string refName = toolname + "." + _getOptionName(opt); + + if (_includeInCTD(opt)) + { + _writeCLIElement(ctdfile, currentIndent, optionIdentifier, refName, isListArgument(opt)); + } + } + + // add a warning to the CTD that arguments are hard to interpret by the users + if (me.argumentList.size() > 0u) + { + ctdfile << _indent(currentIndent) + << "\n"; + } + // then the arguments + for (TArgumentMapSize argIdx = 0; argIdx != me.argumentList.size(); ++argIdx) + { + // arguments do not have an option identifier + std::string optionIdentifier = ""; + std::stringstream refName; + refName << toolname << "." << "argument-" << argIdx; + _writeCLIElement(ctdfile, currentIndent, optionIdentifier, refName.str(), isListArgument(me.argumentList[argIdx])); + } + + ctdfile << _indent(--currentIndent) << "\n"; + ctdfile << _indent(currentIndent++) << "\n"; + ctdfile << _indent(currentIndent++) << "\n"; + + for (TOptionMapIterator optionMapIterator = me.optionMap.begin(); + optionMapIterator != me.optionMap.end(); + ++optionMapIterator) + { + ArgParseOption const & opt = *optionMapIterator; + + // exclude help, version, etc. + if (!_includeInCTD(opt)) + continue; + + // exclude hidden + if (isHidden(opt)) + continue; + + // prefer short name for options + std::string optionName = _getOptionName(opt); + + std::string type = _toValidGKNTypeSpecifier(opt); + + // set up restrictions + std::vector restrictions; + _getRestrictions(restrictions, opt); + + // set up supported formats + // add *.* to supported_formats if none is specified AND the type of the argument is a + // prefix type. This is important for KNIME nodes as they require similar file types + // to connect one node to the other. In this particular case any file is aproprate + // since we are talking about prefixes. + std::vector supported_formats; + _getSupportedFormats(supported_formats, opt); + if (empty(supported_formats) && (type=="input-prefix" || type=="output-prefix" )) + supported_formats.push_back("*.*"); + + ctdfile << _indent(currentIndent) + << " 0) + ctdfile << ","; + ctdfile << opt.tags[i]; + } + ctdfile << "\" "; + } + + if (isListArgument(opt)) + { + ctdfile << ">\n"; + for (size_t i = 0; i < length(opt.defaultValue); ++i) + { + ctdfile << _indent(currentIndent + 1) << "\n"; + } + ctdfile << _indent(currentIndent) << "\n"; + } + else + { + ctdfile << "/>\n"; + } + } + + for (TArgumentMapSize argIdx = 0; argIdx != me.argumentList.size(); ++argIdx) + { + ArgParseArgument arg = me.argumentList[argIdx]; + + // prefer short name for options + std::stringstream argumentNameStream; + argumentNameStream << "argument-" << argIdx; + std::string optionName = argumentNameStream.str(); + + std::string type = _toValidGKNTypeSpecifier(arg); + + // set up restrictions + std::vector restrictions; + _getRestrictions(restrictions, arg); + + // set up supported formats + // add *.* to supported_formats if none is specified AND the type of the argument is a + // prefix type. This is important for KNIME nodes as they require similar file types + // to connect one node to the other. In this particular case any file is aproprate + // since we are talking about prefixes. + std::vector supported_formats; + _getSupportedFormats(supported_formats, arg); + if (empty(supported_formats) && (type=="input-prefix" || type=="output-prefix" )) + supported_formats.push_back("*.*"); + + + ctdfile << _indent(currentIndent) + << " 0) + ctdfile << ","; + ctdfile << arg.tags[i]; + } + ctdfile << "\" "; + } + + ctdfile << "/>\n"; + } + + ctdfile << _indent(--currentIndent) << "\n"; + ctdfile << _indent(--currentIndent) << "\n"; + ctdfile << "" << std::endl; + + return true; +} + +inline bool +writeCTD(ArgumentParser const & me) +{ + // create file [appname].ctd in working directory + std::string ctdfilename; + getOptionValue(ctdfilename, me, "write-ctd"); + + std::ofstream ctdfile; + ctdfile.open(toCString(ctdfilename)); + + if (!ctdfile.is_open()) + { + std::cerr << getAppName(me) << ": Unable to create ctd file: " << ctdfilename << std::endl; + return false; + } + + writeCTD(me, ctdfile); + + ctdfile.close(); + return true; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_CTD_SUPPORT_H_ diff --git a/seqan/arg_parse/arg_parse_doc.h b/seqan/arg_parse/arg_parse_doc.h new file mode 100644 index 0000000..528ce81 --- /dev/null +++ b/seqan/arg_parse/arg_parse_doc.h @@ -0,0 +1,1056 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_ + +#include +#include + +namespace seqan { + +// ============================================================================ +// Functions +// ============================================================================ + +// -------------------------------------------------------------------------- +// Function getAppName() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getAppName + * @brief Return program name of ArgumentParser. + * + * @signature TCharStringRef getAppName(parser); + * + * @param[in] parser The ArgumentParser to get the app name for. + * + * @return TCharStringRef The app name, const-ref to @link CharString @endlink. + */ + +inline CharString const & getAppName(ArgumentParser const & parser) +{ + return getName(parser._toolDoc); +} + +// ---------------------------------------------------------------------------- +// Helper Function _parseAppName() +// ---------------------------------------------------------------------------- + +inline void _parseAppName(ArgumentParser & parser, std::string const & candidate) +{ + //IOREV _notio_ irrelevant for io-revision + int i = length(candidate) - 1; + + for (; i >= 0; --i) + if (candidate[i] == '\\' || candidate[i] == '/') + break; + + setName(parser._toolDoc, candidate.substr(i + 1)); +} + +// ---------------------------------------------------------------------------- +// Helper Function _addLine() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addLine + * @brief Adds a line of text to the help output of the ArgumentParser. + * + * The line of text will be added to the block of the options. + * + * @signature void addLine(parser, line); + * + * @param[in,out] parser The ArgumentParser to add the line to. + * @param[in] line The line of text to add, @link StringConcept @endlink of char. + */ + +template +inline void addLine(ArgumentParser & me, TString const & line) +{ + addOption(me, ArgParseOption("", "", line)); +} + +// ---------------------------------------------------------------------------- +// Function addSection() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addSection + * @brief Begins a new section of the option block of the ArgumentParser help output. + * + * @signature void addSection(parser, title); + * + * @param[in,out] parser The ArgumentParser to add the line to. + * @param[in] title The title to add, @link StringConcept @endlink of char. + * + * @code{.cpp} + * ArgumentParser parser; + * + * [...] // init parser + * + * addSection(parser, "In-/Output-Options"); + * addOption("i", ... ); + * addOption("o", ... ); + * + * addSection(parser, "Other Options"); + * addOption("x", ... ); + * @endcode + */ + +template +inline void addSection(ArgumentParser & me, TString const & line) +{ + addLine(me, ""); + addLine(me, line); +} + +// ---------------------------------------------------------------------------- +// Function addUsageLine() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addUseLine + * @brief Adds a line of text to the usage output of the ArgumentParser. + * + * @signature void addUsageLine(parser, line); + * + * @param[in,out] parser The ArgumentParser to add the line to. + * @param[in] line The line to add, a std::string. + */ + +inline void addUsageLine(ArgumentParser & me, std::string const & line) +{ + me._usageText.push_back(line); +} + +// ---------------------------------------------------------------------------- +// Helper Function _addUsage() +// ---------------------------------------------------------------------------- + +inline void _addUsage(ToolDoc & toolDoc, ArgumentParser const & me) +{ + for (unsigned i = 0; i < length(me._usageText); ++i) + { + std::string text = "\\fB"; + append(text, getAppName(me)); + append(text, "\\fP "); + append(text, me._usageText[i]); + addText(toolDoc, text, false); + } +} + +// ---------------------------------------------------------------------------- +// Function addDescription() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addDescription + * @brief Appends a description paragraph to the ArgumentParser documentation. + * + * @signature void addDescription(parser, description); + * + * @param[in,out] parser The ArgumentParser to add the line to. + * @param[in] description The description text, a std::string. + */ + +inline void addDescription(ArgumentParser & me, std::string const & description) +{ + me._description.push_back(description); +} + +// ---------------------------------------------------------------------------- +// Function setAppName() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setAppName + * @brief Sets application name of ArgumentParser. + * + * @signature void setAppName(parser, name); + * + * @param[in,out] parser The ArgumentParser to set the name of. + * @param[in] name The application name, std::string. + */ + +inline void setAppName(ArgumentParser & me, std::string const & name) +{ + setName(me._toolDoc, name); +} + +// ---------------------------------------------------------------------------- +// Function setShortDescription() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setShortDescription + * @brief Sets shortDescription of ArgumentParser. + * + * @signature void setShortDescription(parser, desc); + * + * @param[in,out] parser The ArgumentParser to set the short description of. + * @param[in] desc The short description, std::string. + */ + +inline void setShortDescription(ArgumentParser & me, std::string const & description) +{ + setShortDescription(me._toolDoc, description); +} + +// ---------------------------------------------------------------------------- +// Function getShortDescription() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getShortDescription + * @brief Returns the short description. + * + * @signature CharString getShortDescription(parser); + * + * @param[in,out] parser The ArgumentParser to get short description for. + * + * @return CharString A @link CharString @endlink with the short description. + */ + +inline CharString getShortDescription(ArgumentParser const & me) +{ + return getShortDescription(me._toolDoc); +} + +// ---------------------------------------------------------------------------- +// Function setUrl() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setUrl + * @brief Sets url of ArgumentParser. + * + * @signature void setUrl(parser, url); + * + * @param[in,out] parser The ArgumentParser to set the url of. + * @param[in] url The url string to set, @link CharString @endlink. + */ + +inline void setUrl(ArgumentParser & me, CharString const & urlString) +{ + setUrl(me._toolDoc, urlString); +} + +// -------------------------------------------------------------------------- +// Function getUrl() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getUrl + * @brief Returns the url string. + * + * @signature TCharStringRef getUrl(parser); + * + * @param[in,out] parser The ArgumentParser to get the url string from. + * + * @return TCharString A const-ref to a @link CharString @endlink with the url string. + */ + +inline CharString const & getUrl(ArgumentParser const & me) +{ + return getUrl(me._toolDoc); +} + +// ---------------------------------------------------------------------------- +// Function setVersion() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setVersion + * @brief Sets version of ArgumentParser. + * + * @signature void setVersion(parser, version); + * + * @param[in,out] parser The ArgumentParser to set the version of. + * @param[in] version The version string to set, std::string. + */ + +inline void setVersion(ArgumentParser & me, std::string const & versionString) +{ + setVersion(me._toolDoc, versionString); + if (!hasOption(me, "version")) + addOption(me, ArgParseOption("", "version", "Display version information.")); +} + +// -------------------------------------------------------------------------- +// Function getVersion() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getVersion + * @brief Returns the version string. + * + * @signature TCharStringRef getVersion(parser); + * + * @param[in,out] parser The ArgumentParser to get the version string from. + * + * @return TCharString A const-ref to a @link CharString @endlink with the version string. + */ + +inline CharString const & getVersion(ArgumentParser const & me) +{ + return getVersion(me._toolDoc); +} + +// ---------------------------------------------------------------------------- +// Function setShortCopyright() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setShortCopyright + * @brief Sets short copyright of ArgumentParser. + * + * @signature void setShortCopyright(parser, short copyright); + * + * @param[in,out] parser The ArgumentParser to set the short copyright of. + * @param[in] short copyright The short copyright string to set, std::string. + */ + +inline void setShortCopyright(ArgumentParser & me, CharString const & shortCopyrightString) +{ + setShortCopyright(me._toolDoc, shortCopyrightString); +} + +// -------------------------------------------------------------------------- +// Function getShortCopyright() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getShortCopyright + * @brief Returns the short copyright string. + * + * @signature TCharStringRef getShortCopyright(parser); + * + * @param[in,out] parser The ArgumentParser to get the short copyright string from. + * + * @return TCharString A const-ref to a @link CharString @endlink with the short copyright string. + */ + +inline CharString const & getShortCopyright(ArgumentParser const & me) +{ + return getShortCopyright(me._toolDoc); +} + +// ---------------------------------------------------------------------------- +// Function setLongCopyright() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setLongCopyright + * @brief Sets long copyright of ArgumentParser. + * + * @signature void setLongCopyright(parser, long copyright); + * + * @param[in,out] parser The ArgumentParser to set the long copyright of. + * @param[in] long copyright The long copyright string to set, std::string. + */ + +inline void setLongCopyright(ArgumentParser & me, CharString const & longCopyrightString) +{ + setLongCopyright(me._toolDoc, longCopyrightString); + if (!hasOption(me, "copyright")) + addOption(me, ArgParseOption("", "copyright", "Display long copyright information.")); +} + +// -------------------------------------------------------------------------- +// Function getLongCopyright() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getLongCopyright + * @brief Returns the long copyright string. + * + * @signature TCharStringRef getLongCopyright(parser); + * + * @param[in,out] parser The ArgumentParser to get the long copyright string from. + * + * @return TCharString A const-ref to a @link CharString @endlink with the long copyright string. + */ + +inline CharString const & getLongCopyright(ArgumentParser const & me) +{ + return getLongCopyright(me._toolDoc); +} + + +// ---------------------------------------------------------------------------- +// Function setCitation() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setCitation + * @brief Sets citation of ArgumentParser. + * + * @signature void setCitation(parser, citation); + * + * @param[in,out] parser The ArgumentParser to set the citation of. + * @param[in] citation The citation string to set, std::string. + */ + +inline void setCitation(ArgumentParser & me, CharString const & citationString) +{ + setCitation(me._toolDoc, citationString); +} + +// -------------------------------------------------------------------------- +// Function getCitation() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getCitation + * @brief Returns the citation string. + * + * @signature TCharStringRef getCitation(parser); + * + * @param[in,out] parser The ArgumentParser to get the citation string from. + * + * @return TCharString A const-ref to a @link CharString @endlink with the citation string. + */ + +inline CharString const & getCitation(ArgumentParser const & me) +{ + return getCitation(me._toolDoc); +} + +// -------------------------------------------------------------------------- +// Function setCategory() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setCategory + * @brief Sets category of ArgumentParser. + * + * @signature void setCategory(parser, category); + * + * @param[in,out] parser The ArgumentParser to set the category of. + * @param[in] category The category to set, std::string. + */ + +inline void setCategory(ArgumentParser & parser, CharString const & category) +{ + setCategory(parser._toolDoc, category); +} + +// -------------------------------------------------------------------------- +// Function getCategory() +// -------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getCategory + * @brief Returns the category. + * + * @signature TCharStringRef getCategory(parser); + * + * @param[in,out] parser The ArgumentParser to get the category from. + * + * @return TCharString A const-ref to a @link CharString @endlink with the category. + */ + +inline CharString const & getCategory(ArgumentParser const & parser) +{ + return getCategory(parser._toolDoc); +} + +// ---------------------------------------------------------------------------- +// Function setDate() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setDate + * @brief Sets date string of ArgumentParser. + * + * @signature void setDate(parser, date); + * + * @param[in,out] parser The ArgumentParser to set the date string of. + * @param[in] date The date string to set, std::string. + */ + +inline void setDate(ArgumentParser & me, std::string const & date) +{ + setDate(me._toolDoc, date); +} + +// ---------------------------------------------------------------------------- +// Function addTextSection() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addTextSection + * @brief Add a text section to the ArgumentParser. + * + * @signature void addTextSection(parser, title); + * + * @param[in,out] parser The ArgumentParser to add the text section title to. + * @param[in] title The section title to add, std::string. + */ + +inline void addTextSection(ArgumentParser & me, std::string const & title) +{ + addSection(me._toolDoc, title); +} + +// ---------------------------------------------------------------------------- +// Function addTextSubSection() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addTextSubSection + * @brief Add a text sub section to the ArgumentParser. + * + * @signature void addTextSubSection(parser, title); + * + * @param[in,out] parser The ArgumentParser add the subsection title to of. + * @param[in] title The sub section title to add, std::string. + */ + +inline void addTextSubSection(ArgumentParser & me, std::string const & title) +{ + addSubSection(me._toolDoc, title); +} + +// ---------------------------------------------------------------------------- +// Function addText() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addText + * @brief Add text to an ArgumentParser. + * + * @signature void addText(parser, text); + * + * @param[in,out] parser ArgumentParser to add text to. + * @param[in] text The std::string to add to the parser. + */ + +inline void addText(ArgumentParser & me, std::string const & text) +{ + addText(me._toolDoc, text); +} + +// ---------------------------------------------------------------------------- +// Function addListItem() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addListItem + * @brief Appends a list item to the ArgumentParser + * + * @signature void addListItem(parser, item, description); + * + * @param[in,out] parser The ArgumentParser to add the list item to. + * @param[in] item The item to add, std::string. + * @param[in] description The item to add, std::string. + */ + +inline void addListItem(ArgumentParser & me, std::string const & item, std::string const & description) +{ + addListItem(me._toolDoc, item, description); +} + +// ---------------------------------------------------------------------------- +// Function printShortHelp() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#printShortHelp + * @brief Prints a short help message for the parser to a stream. + * + * @signature void printShortHelp(parser, out); + * + * @param[in,out] parser The ArgumentParser to print help for. + * @param[in,out] out The std::ostream to print help to. + */ + +inline void printShortHelp(ArgumentParser const & me, std::ostream & stream) +{ + // TODO: maybe we can get this a bit prettier + ToolDoc shortDoc(me._toolDoc); + clearEntries(shortDoc); + + _addUsage(shortDoc, me); + + std::stringstream shortHelp; + shortHelp << "Try '" << getAppName(me) << " --help' for more information.\n"; + addText(shortDoc, shortHelp.str()); + + print(stream, shortDoc, "txt"); +} + +inline void printShortHelp(ArgumentParser const & me) +{ + printShortHelp(me, std::cerr); +} + +// ---------------------------------------------------------------------------- +// Function printVersion() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#printVersion + * @brief Prints the version information of the parser to a stream. + * + * @signature void printVersion(parser, stream); + * + * @param[in,out] parser The ArgumenParser to print for. + * @param[in,out] stream The std::ostream to print to. + */ + +inline void printVersion(ArgumentParser const & me, std::ostream & stream) +{ + stream << getAppName(me) << " version: " << getVersion(me) << std::endl; + stream << "SeqAn version: " << SEQAN_VERSION_MAJOR << '.' << SEQAN_VERSION_MINOR << '.' + << SEQAN_VERSION_PATCH; + if (SEQAN_VERSION_PRE_RELEASE != 0) + stream << "-pre" << SEQAN_VERSION_PRE_RELEASE; + stream << "\n"; +} + +inline void printVersion(ArgumentParser const & me) +{ + printVersion(me, std::cerr); +} + +// ---------------------------------------------------------------------------- +// Function printLongCopyright() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#printLongCopyright + * @brief Prints the long copyright information of the parser to a stream. + * + * @signature void printLongCopyright(parser, stream); + * + * @param[in,out] parser The ArgumenParser to print for. + * @param[in,out] stream The std::ostream to print to. + */ + +inline void printLongCopyright(ArgumentParser const & me, std::ostream & stream) +{ + stream << "=============================================================================" << std::endl + << "Copyright information for " << getAppName(me) << ":" << std::endl + << "-----------------------------------------------------------------------------" << std::endl + << me._toolDoc._longCopyright << std::endl << std::endl + << "=============================================================================" << std::endl + << "This program contains SeqAn code licensed under the following terms:" << std::endl + << "-----------------------------------------------------------------------------" << std::endl + << " Copyright (c) 2006-2015, Knut Reinert, FU Berlin" << std::endl + << " All rights reserved." << std::endl + << "" << std::endl + << " Redistribution and use in source and binary forms, with or without" << std::endl + << " modification, are permitted provided that the following conditions are met:" << std::endl + << "" << std::endl + << " * Redistributions of source code must retain the above copyright" << std::endl + << " notice, this list of conditions and the following disclaimer." << std::endl + << " * Redistributions in binary form must reproduce the above copyright" << std::endl + << " notice, this list of conditions and the following disclaimer in the" << std::endl + << " documentation and/or other materials provided with the distribution." << std::endl + << " * Neither the name of Knut Reinert or the FU Berlin nor the names of" << std::endl + << " its contributors may be used to endorse or promote products derived" << std::endl + << " from this software without specific prior written permission." << std::endl + << "" << std::endl + << " THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"" << std::endl + << " AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE" << std::endl + << " IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE" << std::endl + << " ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE" << std::endl + << " FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL" << std::endl + << " DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR" << std::endl + << " SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER" << std::endl + << " CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT" << std::endl + << " LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY" << std::endl + << " OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH" << std::endl + << " DAMAGE." << std::endl; +} + +inline void printLongCopyright(ArgumentParser const & me) +{ + printLongCopyright(me, std::cerr); +} + +// ---------------------------------------------------------------------------- +// Function _addNumericalRestriction() +// ---------------------------------------------------------------------------- + +inline void _addNumericalRestriction(std::string & text, ArgParseArgument const & arg) +{ + // expand min/max restrictions + if (!empty(arg.minValue) || !empty(arg.maxValue)) + { + append(text, " In range ["); + + if (!empty(arg.minValue)) + append(text, arg.minValue); + else + append(text, "-inf"); + + append(text, ".."); + + if (!empty(arg.maxValue)) + append(text, arg.maxValue); + else + append(text, "inf"); + + append(text, "]."); + } +} + +// ---------------------------------------------------------------------------- +// Function _expandList() +// ---------------------------------------------------------------------------- + +// expands the given vector as text in the form v1, v2, and v3, while respecting +// the size with respect to the used commas and "and"s +inline void _expandList(std::string & text, std::vector const & list) +{ + for (std::vector::size_type i = 0; i < list.size(); ++i) + { + if (i + 1 == list.size() && list.size() == 2u) + append(text, " and "); + else if (i + 1 == list.size() && list.size() > 2u) + append(text, ", and "); + else if (i != 0) + append(text, ", "); + + append(text, "\\fI"); + append(text, list[i]); + append(text, "\\fP"); + + } +} + +// ---------------------------------------------------------------------------- +// Function _addDefaultValues() +// ---------------------------------------------------------------------------- + +inline void _addDefaultValues(std::string & text, ArgParseArgument const & arg) +{ + if (!empty(arg.defaultValue)) + { + append(text, " Default: "); + _expandList(text, arg.defaultValue); + append(text, "."); + } +} + +inline void _addDefaultValues(std::string & text, ArgParseOption const & arg) +{ + if (!isFlagOption(arg)) + _addDefaultValues(text, static_cast(arg)); +} + +// ---------------------------------------------------------------------------- +// Function _seperateExtensionsForPrettyPrinting() +// ---------------------------------------------------------------------------- + +inline void _seperateExtensionsForPrettyPrinting(std::vector & file_ext, + std::vector & comp_ext, + std::vector const & validValues) +{ + // seperate file extensions and compression extensions + for (std::vector::size_type i = 0; i < validValues.size(); ++i) + { + std::regex rgx("^(\\.)?([A-z0-9]+)(\\.)?([A-z0-9]+)?"); + std::smatch result; + + std::regex_search(validValues[i], result, rgx); + + if (!result[4].str().empty()) + { + comp_ext.push_back(result[4].str()); + file_ext.push_back("." + result[2].str() + "[.*]"); + } + else + { + file_ext.push_back("." + result[2].str()); + } + } + + std::sort(file_ext.rbegin(), file_ext.rend()); // sort extensions in reverse order such that '.fa[.x]' + std::sort(comp_ext.rbegin(), comp_ext.rend()); // comes before '.fa' and will be chosen by std::unique() + + comp_ext.erase(std::unique(comp_ext.begin(), comp_ext.end()), comp_ext.end()); // remove duplicates + file_ext.erase(std::unique(file_ext.begin(), file_ext.end(), + [&](auto& lhs, auto& rhs) + { + return lhs.substr(0, lhs.find('[')) == rhs.substr(0, rhs.find('[')); + }), file_ext.end()); +} + +// ---------------------------------------------------------------------------- +// Function _addValidValuesRestrictions() +// ---------------------------------------------------------------------------- + +inline void _addValidValuesRestrictions(std::string & text, ArgParseArgument const & arg) +{ + if (!empty(arg.validValues)) + { + if (isInputFileArgument(arg) || isOutputFileArgument(arg)) + { + std::vector file_extensions; + std::vector compresssion_extensions; + + _seperateExtensionsForPrettyPrinting(file_extensions, compresssion_extensions, arg.validValues); + + append(text, " Valid filetype"); + + if (file_extensions.size() > 1) + append(text, "s are: "); + else + append(text, " is: "); + + _expandList(text, file_extensions); + + if (compresssion_extensions.size() != 0) + { + append(text, ", where * is any of the following extensions: "); + _expandList(text, compresssion_extensions); + append(text, " for transparent (de)compression"); + } + } + else + { + append(text, " One of "); + _expandList(text, arg.validValues); + } + + append(text, "."); + } +} + +inline void _addValidValuesRestrictions(std::string & text, ArgParseOption const & opt) +{ + if (!isFlagOption(opt)) + _addValidValuesRestrictions(text, static_cast(opt)); +} + +// ---------------------------------------------------------------------------- +// Function _addTypeAndListInfo() +// ---------------------------------------------------------------------------- + +inline void _addTypeAndListInfo(std::string & text, ArgParseArgument const & arg) +{ + std::string type = getArgumentTypeAsString(arg); + for (auto & c: type) + c = toupper(c); + + // Write arguments to term line -> only exception, boolean flags + if (!empty(type)) + { + append(text, " "); + + if (isListArgument(arg)) + append(text, "List of "); + + if (arg._numberOfValues != 1) + append(text, std::to_string(arg._numberOfValues) + " "); + + append(text, "\\fI"); + append(text, type); + append(text, "\\fP"); + + if (isListArgument(arg) || arg._numberOfValues != 1) + append(text, "'s"); + } +} + +// ---------------------------------------------------------------------------- +// Function printHelp() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Parameter order. + +/*! + * @fn ArgumentParser#printHelp + * @brief Prints the help message for the parser. + * + * @signature void printHelp(parser, out, format, showAdvancedOptions); + * + * @param[in,out] parser The ArgumentParser print the help for. + * @param[out] out The output stream to print to (std::ostream). + * @param[in] format The format to print, one of "html", "man", and "txt". + * @param[in] showAdvancedOptions Also show advanced options to user (default = false). + */ + +inline void printHelp(ArgumentParser const & me, + std::ostream & stream, + CharString const & format, + bool const showAdvancedOptions) +{ + ToolDoc toolDoc(me._toolDoc); + clearEntries(toolDoc); // We will append me._toolDoc later. + + // Build synopsis section. + addSection(toolDoc, "Synopsis"); + _addUsage(toolDoc, me); + + // Add description to tool documentation. + addSection(toolDoc, "Description"); + for (unsigned i = 0; i < me._description.size(); ++i) + addText(toolDoc, me._description[i]); + + // Add arguments to arguments section + if (length(me.argumentList) != 0) + addSection(toolDoc, "Required Arguments"); + + for (unsigned i = 0; i < length(me.argumentList); ++i) + { + ArgParseArgument const & arg = me.argumentList[i]; + + // Build list item term. + std::string term; + if (!empty(arg._argumentLabel)) + { + std::regex space(" "); + term = "\\fB"; + append(term, std::regex_replace(arg._argumentLabel, space,"_")); + append(term, "\\fP"); + } + else + { + term = "\\fBARGUMENT "; + append(term, std::to_string(i)); + append(term, "\\fP"); + } + + // expand type, list and numValues information + _addTypeAndListInfo(term, arg); + + std::string helpText = arg._helpText; + + // expand min/max restrictions + _addNumericalRestriction(helpText, arg); + + // expand validValues restrictions + _addValidValuesRestrictions(helpText, arg); + + // expand defaultValue + _addDefaultValues(helpText, arg); + + // Add list item. + addListItem(toolDoc, term, helpText); + } + + // Add options to options section. + if (length(me.optionMap) != 0) + addSection(toolDoc, "Options"); + + for (unsigned i = 0; i < length(me.optionMap); ++i) + { + ArgParseOption const & opt = me.optionMap[i]; + if (empty(opt.shortName) && empty(opt.longName)) // this is not an option but a text line + { + if (empty(opt._helpText)) // TODO(holtgrew): Should go away in future. + continue; // Skip empty lines. + + // Is command line parser section, maps to ToolDoc subsection. + for (unsigned j = i + 1; j < length(me.optionMap); ++j) + { + ArgParseOption const & nextopt = me.optionMap[j]; + if (empty(nextopt.shortName) && empty(nextopt.longName)) + break; + // has visible children + if (!isHidden(nextopt) && (!isAdvanced(nextopt) || showAdvancedOptions)) + { + std::string title = opt._helpText; + append(title, ":"); + addSubSection(toolDoc, title); + break; + } + } + } + else if (!isHidden(opt) && (!isAdvanced(opt) || showAdvancedOptions)) + { + // Build list item term. + std::string term; + if (!empty(opt.shortName)) + { + term = "\\fB-"; + append(term, opt.shortName); + append(term, "\\fP"); + } + if (!empty(opt.shortName) && !empty(opt.longName)) + append(term, ", "); + if (!empty(opt.longName)) + { + append(term, "\\fB--"); + append(term, opt.longName); + append(term, "\\fP"); + } + + // expand type, list and numValues information + if (!opt._isFlag) + _addTypeAndListInfo(term, opt); + + std::string helpText = opt._helpText; + + // expand min/max restrictions + _addNumericalRestriction(helpText, opt); + + // expand validValues restrictions + _addValidValuesRestrictions(helpText, opt); + + // expand defaultValue + _addDefaultValues(helpText, opt); + + // Add list item. + addListItem(toolDoc, term, helpText); + } + } + + append(toolDoc, me._toolDoc); + print(stream, toolDoc, format); +} + +inline void printHelp(ArgumentParser const & me, std::ostream & stream, CharString const & format) +{ + printHelp(me, stream, format, false); +} + +inline void printHelp(ArgumentParser const & me, std::ostream & stream) +{ + printHelp(me, stream, "txt", false); +} + +inline void printHelp(ArgumentParser const & me) +{ + printHelp(me, std::cerr, "txt", false); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_DOC_H_ diff --git a/seqan/arg_parse/arg_parse_exceptions.h b/seqan/arg_parse/arg_parse_exceptions.h new file mode 100644 index 0000000..5c6ffe1 --- /dev/null +++ b/seqan/arg_parse/arg_parse_exceptions.h @@ -0,0 +1,89 @@ +// ========================================================================== +// arg_parse_exceptions.h +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_ + +namespace seqan { + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class ParseError +// ---------------------------------------------------------------------------- + +// Defined in include/seqan/stream/tokenization.h +struct ParseError; + +// ---------------------------------------------------------------------------- +// Class InvalidOption +// ---------------------------------------------------------------------------- + +class InvalidOption : public ParseError +{ +public: + InvalidOption(std::string const & option) : + ParseError("illegal option -- " + option) + {} +}; + +// ---------------------------------------------------------------------------- +// Class MissingArgument +// ---------------------------------------------------------------------------- + +class MissingArgument : public ParseError +{ +public: + MissingArgument(std::string const & option) : + ParseError("option requires an argument -- " + option) + {} +}; + +// ---------------------------------------------------------------------------- +// Class NotEnoughArguments +// ---------------------------------------------------------------------------- + +class NotEnoughArguments : public ParseError +{ +public: + NotEnoughArguments(std::string const & option) : + ParseError("option requires more arguments -- " + option) + {} +}; + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_EXCEPTIONS_H_ diff --git a/seqan/arg_parse/arg_parse_option.h b/seqan/arg_parse/arg_parse_option.h new file mode 100644 index 0000000..7b6d8bd --- /dev/null +++ b/seqan/arg_parse/arg_parse_option.h @@ -0,0 +1,492 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_ + +#include +#include +#include +#include + +namespace seqan { + +// ---------------------------------------------------------------------------- +// Class ArgParseOption +// ---------------------------------------------------------------------------- + +/*! + * @class ArgParseOption + * @extends ArgParseArgument + * @headerfile + * @brief Store information for a specific command line option. + * + * @signature class ArgParseOption : ArgParseArgument; + * + * You can use the shortcut @link ArgumentParser#addOption @endlink for adding options to @link ArgumentParser @endlink + * object. + */ + +/*! + * @fn ArgParseOption::ArgParseOption + * @brief Constructor. + * + * @signature ArgParseOption::ArgParseOption(shortName, longName, helpText, argumentType[, argumentLabel[, isList[, numValues]]]); + * + * @param[in] shortName The short name of the argument. + * @param[in] longName The long name of the argument (std::string). + * @param[in] helpText The text to display as help (std::string). + * @param[in] argumentType The type of the argument (@link ArgParseArgument::ArgumentType @endlink). + * @param[in] argumentLabel The label for the value to use in the help display, e.g. 'INT' in '--value INT' + * (std::string). + * @param[in] isList Flag for whether this option can be given multiple times (bool, true for + * allowing multiple values). + * @param[in] numValues Number of command line arguments that each option should bind (unsigned). + * + * @section Short and Long Option Names + * + * Short option names are passed to the program following one dash (e.g. '-i', '-e'). Long optiongs are passed + * following two dashes (e.g. '--num-threads', '--error-rate'). The leading one or two dashes are not passed to the + * constructor of ArgParseOption, however. + * + * @section Naming Conventions + * + *
    + *
  • Keep the short name short, ideally to one character.
    • + *
  • Only use lower-case characters in the long name, use dashes to separate words, only use alphanumeric characters + * and dashes, no underline characters
    • . + *
+ */ + +class ArgParseOption : + public ArgParseArgument +{ +public: + // ---------------------------------------------------------------------------- + // Members to specify the names of the ArgParseOption + // ---------------------------------------------------------------------------- + std::string shortName; // short option name + std::string longName; // long option name + + // ---------------------------------------------------------------------------- + // Members representing type, content and restrictions of the ArgParseOption + // ---------------------------------------------------------------------------- + bool _isFlag; // true if this a bool option, that has no + // argument we will internally represent it as a + // string option set to either "true" or "false" + bool _isRequired; // true if this ArgParseOption must be set + bool _isHidden; // true if this ArgParseOption should not be + // shown on the command line + bool _isAdvanced; // true if this ArgParseOption should only + // be shown in the full help + + // ---------------------------------------------------------------------------- + // Constructors + // ---------------------------------------------------------------------------- + ArgParseOption(std::string const & _shortName, + std::string const & _longName, + std::string const & _help, + ArgumentType argumentType, + std::string const & argumentLabel = "", + bool isListArgument = false, + unsigned numberOfValues = 1) : + ArgParseArgument(argumentType, argumentLabel, isListArgument, numberOfValues), + shortName(_shortName), + longName(_longName), + _isFlag(false), + _isRequired(false), + _isHidden(false), + _isAdvanced(false) + { + _helpText = _help; + } + + ArgParseOption(std::string const & _shortName, + std::string const & _longName, + std::string const & _help) : + ArgParseArgument(ArgParseArgument::STRING), + shortName(_shortName), + longName(_longName), + _isFlag(true), + _isRequired(false), + _isHidden(false), + _isAdvanced(false) + { + defaultValue.push_back("false"); + setValidValues(*this, "true false"); + _helpText = _help; + } + +}; + +// ---------------------------------------------------------------------------- +// Function isStringArgument() +// ---------------------------------------------------------------------------- + +inline bool isStringArgument(ArgParseOption const & me) +{ + return isStringArgument(static_cast(me)) && !me._isFlag; +} + +// ---------------------------------------------------------------------------- +// Function isFlagOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#isFlagOption + * @headerfile + * @brief Returns whether an option is a flag. + * + * @signature bool isFlagOption(option); + * + * @param[in] option The ArgParseOption object to query. + * + * @return bool true if option is a flag/switch and false otherwise. + * + * Flags are given without arguments, e.g. the -l flag in the Unix ls command. + */ + +inline bool isFlagOption(ArgParseOption const & me) +{ + return me._isFlag; +} + +// ---------------------------------------------------------------------------- +// Function isHidden() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#isHidden + * @headerfile + * @brief Return whether an option is hidden on the help screen. + * + * @signature bool isHidden(option); + * + * @param[in] option The ArgParseOption object to query. + * + * @return bool true if it is hidden, false otherwise. + * + * By default, options are not hidden. + */ + +inline bool isHidden(ArgParseOption const & me) +{ + return me._isHidden; +} + +// ---------------------------------------------------------------------------- +// Function hideOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#hideOption + * @headerfile + * @brief Hides the ArgParseOption from the help screen (or shows it again). + * + * @signature void hideOption(option[, hide]); + * + * @param[in,out] option The ArgParseOption object to set the hidden flag of. + * @param[in] hide bool that indicates whether to hide the flag (default: true) + */ + +inline void hideOption(ArgParseOption & me, bool hide = true) +{ + me._isHidden = hide; +} + +// ---------------------------------------------------------------------------- +// Function isHidden() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#isAdvanced + * @headerfile + * @brief Return whether an option is only shown in the full help screen. + * + * @signature bool isAdvanced(option); + * + * @param[in] option The ArgParseOption object to query. + * + * @return bool true if it is hidden, false otherwise. + * + * By default, options are not marked as advanced. + */ + +inline bool isAdvanced(ArgParseOption const & me) +{ + return me._isAdvanced; +} + +// ---------------------------------------------------------------------------- +// Function hideOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#setAdvanced + * @headerfile + * @brief Shows the ArgParseOption only on the full help screen. + * + * @signature void setAdvanced(option[, advanced]); + * + * @param[in,out] option The ArgParseOption object to set the advanced flag of. + * @param[in] advanced bool that indicates whether to hide the flag (default: true) + */ + +inline void setAdvanced(ArgParseOption & me, bool advanced = true) +{ + me._isAdvanced = advanced; +} + +// ---------------------------------------------------------------------------- +// Function isRequired() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#isRequired + * @headerfile + * @brief Returns whether the option is mandatory. + * + * @signature bool isRequired(option); + * + * @param[in] option The ArgParseOption object to query. + * + * @return bool true if the option is mandatory and false if it not. + * + * By default, options are not mandatory. + */ + +inline bool isRequired(ArgParseOption const & me) +{ + return me._isRequired; +} + +// ---------------------------------------------------------------------------- +// Function setDefaultValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#setDefaultValue + * @headerfile + * @brief Set the default value for the given option. + * + * @signature void setDefaultValue(option, v); + * + * @param[in,out] option The ArgParseOption to set the default value for. + * @param[in] v The value to set, (any type that can be streamed into an std::stringstream). + */ + +// TODO(holtgrew): Deprecate in favour of string-only variant? + +template +inline void setDefaultValue(ArgParseOption & me, const TValue & value) +{ + SEQAN_TRY + { + std::stringstream strm; + strm << value; + + // clear old values + me.defaultValue.clear(); + + // add defaultValue + me.defaultValue.push_back(strm.str()); + + // check if all constraints are satisfied + _checkValue(me, strm.str()); + } + SEQAN_CATCH(ParseError & ex) + { + SEQAN_FAIL("Default value does not satisfy the restrictions:\n %s", ex.what()); + } +} + +// ---------------------------------------------------------------------------- +// Function addDefaultValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#addDefaultValue + * @headerfile + * @brief Adds/appends a new value to the list of default values. + * + * @signature void setDefaultValue(option, v); + * + * @param[in,out] option The ArgParseOption to appen the default value for. + * @param[in] v The value to append, (any type that can be streamed into an std::stringstream). + * + * @section Remarks + * + * This function does not check any length restrictions for this value. + */ + + +template +inline void addDefaultValue(ArgParseOption & me, const TValue & value) +{ + SEQAN_TRY + { + std::stringstream strm; + strm << value; + + // add defaultValue + me.defaultValue.push_back(strm.str()); + + // check if all constraints are satisfied + _checkValue(me, strm.str(), me.defaultValue.size() - 1); + } + SEQAN_CATCH(ParseError & ex) + { + SEQAN_FAIL("Default value does not satisfy the restrictions:\n %s", ex.what()); + } +} + +// ---------------------------------------------------------------------------- +// Function setRequired() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#setRequired + * @headerfile + * @brief Sets whether or not the option is mandatory. + * + * @signature void setRequired(option, required); + * + * @param[in,out] option The ArgParseOption to modify. + * @param[in] required Flag whether the option is mandatory (bool). + * + * By default, options are not mandatory. + */ + +inline void setRequired(ArgParseOption & me, bool required) +{ + me._isRequired = required; +} + +// ---------------------------------------------------------------------------- +// Function getArgumentLabel() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#getArgumentLabel + * @headerfile + * @brief Returns the argument label. + * + * @signature std::string getArgumentLabel(option); + * + * @param[in] option The ArgParseOption object to query. + * + * @return std::string The argument label string. + */ + +inline std::string const getArgumentLabel(ArgParseOption const & me) +{ + if (isFlagOption(me)) + return ""; + else + return getArgumentLabel(static_cast(me)); +} + +// ---------------------------------------------------------------------------- +// Function getOptionName() [ArgParseOption] +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#getOptionName + * @headerfile + * @brief Returns the name of the ArgParseOption in a well-formatted way. + * + * @signature std::string getOptionName(option); + * + * @param[in] option The ArgParseOption object to query. + * + * @return std::string The option name string. + */ + +inline std::string getOptionName(ArgParseOption const & me) +{ + std::stringstream stream; + + stream << (empty(me.shortName) ? "" : "-"); + stream << me.shortName; + stream << ((empty(me.shortName) || empty(me.longName) ? "" : ", ")); + if (!empty(me.longName)) + { + stream << "--"; + stream << me.longName; + } + return stream.str(); +} + +// ---------------------------------------------------------------------------- +// Function write() [ArgParseOption] +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgParseOption#write + * @headerfile + * @brief Writes the basic informationa bout the ArgParseOption to the provided stream. + * + * @signature void write(stream, option); + * + * @param[in,out] stream The @link StreamConcept stream @endlink to write to. + * @param[out] option The ArgParseOption object to write to stream. + */ + +template +inline void write(TStream & target, ArgParseOption const & me) +{ + writeValue(target, '\t'); + write(target, getOptionName(me)); + writeValue(target, '\t'); + writeValue(target, '\t'); + write(target, me._helpText); +} + +// ---------------------------------------------------------------------------- +// operator<<() [ArgParseOption] +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We need to work out a consistent scheme with operator<<(). + +template +inline TStream & operator<<(TStream & target, ArgParseOption const & source) +{ + typename DirectionIterator::Type it = directionIterator(target, Output()); + write(it, source); + return target; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_OPTION_H_ diff --git a/seqan/arg_parse/arg_parse_parse.h b/seqan/arg_parse/arg_parse_parse.h new file mode 100644 index 0000000..5afe27a --- /dev/null +++ b/seqan/arg_parse/arg_parse_parse.h @@ -0,0 +1,395 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_ +#define SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_ + +#include +#include +#include +#include + +namespace seqan { + +// ---------------------------------------------------------------------------- +// Function parse() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#parse + * @headerfile + * @brief Parse command line parameters. + * + * @signature TResult parse(parser, argc, argv[, outStream[, errStream]]); + * + * @param[in,out] parser The ArgumentParser to use for parsing and for storing parse results. + * @param[in] argc The number of arguments (int). + * @param[in] argv The arguments (const char * argv[]). + * @param[in,out] outStream The std::ostream to use for output. + * @param[in,out] errStream The std::ostream to use for error output. + * + * @return TResult The parse result, of type @link ArgumentParser::ParseResult @endlink. + * + * This function must be called before retrieving any options or arguments from the parser. + */ + +// Helper class for parsing command line arguments. +// +// Putting things into its a class allows us to structure the parsing in a fine way. + +template +class ArgumentParserHelper_ +{ +public: + typedef ArgumentParser::TArgumentMapSize TArgumentPosition; + + // Reference to the ArgumentParser to parse for. + ArgumentParser & parser; + // The argc and argv from the main() method. + int argc; + TChar ** argv; + + // The parser's state is stored in the following variables. + + // The special argument "--" is ignored as an option and only arguments can follow. The following flag holds the + // state that this token was seen. + bool seenDashDash; + // The index of the current positional argument. + TArgumentPosition currentArgument; + + ArgumentParserHelper_(ArgumentParser & parser, int argc, TChar * argv[]) + : parser(parser), argc(argc), argv(argv), seenDashDash(false), currentArgument(0) + {} + + void reset() + { + seenDashDash = false; + currentArgument = 0; + } + + // Perform the argument parsing. + void parseArgs() + { + reset(); // reset state + + // Parse binary name from command line if it was not set. + if (empty(getAppName(parser))) + _parseAppName(parser, argv[0]); + + for (int argi = 1; argi < argc; ++argi) + { + // after "--" ever arg is treated as argument (not as option), e.g. "rm -rf -- --file-name" + // "-" is a treated as argument as for a filename arguments it represents stdin + // everything else that begins with "-" is an option + + size_t argLen = strlen(argv[argi]); + if (seenDashDash || argLen == 0 || ((argv[argi][0] != '-') || (argLen == 1))) // + // Handle as position argument if we have seen "--" or does not start with dash. + handleArgument(argv[argi]); + else if (strcmp(argv[argi], "--") == 0) + // If this is "--" then ignore the argument itself but set the seen flag for it. + seenDashDash = true; + else + // This is an option. + handleOption(argi, argv[argi]); + } + } + +private: + + // Handle the given string as an argument. + // + // Throw ParseError in case of too many arguments. + void handleArgument(char const * argStr) + { + // Check whether we have the largest number of allowed arguments already. + if (parser.argumentList.size() <= currentArgument) + SEQAN_THROW(ParseError("Too many arguments!")); + + ArgParseArgument & argument = getArgument(parser, currentArgument); + _assignArgumentValue(argument, argStr); + + if (!isListArgument(argument)) + ++currentArgument; + } + + // Handle the given string as an option. + // + // Throw InvalidOption if there is a formal error (== "-") or invalid option naparser. + // + // Throw MissingArgument in case of --key=value option but the option requires multiple values. + void handleOption(int & argi, std::string arg) + { + if (arg == "-") + SEQAN_THROW(InvalidOption("-")); + + if (arg[1] == '-') + handleLongOption(argi, arg); + else + handleShortOption(argi, arg); + } + + // Handle the given string as a long option. + void handleLongOption(int & argi, std::string const & arg) + { + // We will store the option name and the value in these variables. + std::string longOpt = arg; + std::string val; + + // Split option in case of --key=value format. + size_t t = arg.find('='); + if (t != std::string::npos) // is --key=value option + { + val = arg.substr(t + 1); + longOpt = arg.substr(0, t); + } + longOpt.erase(0, 2); + + // Guard against invalid option names. + if (!hasOption(parser, longOpt)) + SEQAN_THROW(InvalidOption(longOpt)); + + // Parse out the values for the option from the command line arguments. + ArgParseOption & opt = getOption(parser, longOpt); + if (t != std::string::npos) // was --key=value option + { + // We can only assign one value in this case. If the option expected more than one value then this is an + // error. + if (numberOfAllowedValues(opt) != 1) + SEQAN_THROW(MissingArgument(longOpt)); + // If everything is fine then we can assign the value to the option. + _assignArgumentValue(opt, val); + } + else if (isFlagOption(opt)) + { + // Handling flag options is simple. + _assignArgumentValue(opt, "true"); + } + else + { + // If we reach here, we have a --key value option and might require multiple values. + + // Guard against missing values. + if (argi + (int)numberOfAllowedValues(opt) >= argc) + SEQAN_THROW(MissingArgument(longOpt)); + // We have sufficient values, get them from argv and assign them to the option. + for (int t = 0; t < (int)numberOfAllowedValues(opt); ++t) + _assignArgumentValue(opt, argv[++argi]); + } + } + + // Handle the given string as a short option. + void handleShortOption(int & argi, std::string const & arg) + { + // Parse out the short option. This is made complicated because the user can concatenate multiple short options + // into one. NB: we do not check for and warn about possible ambiguities. + // + // We enumerate the possible option names starting from left to right, then sorted descendingly by length. + // Boolean options can be squished together in this way without further restrictions. If the option requires + // additional arguments then it has to be the last in the short options. + + for (unsigned s = 1; s < arg.size(); ++s) + { + unsigned e = arg.size(); + for (; s < e; --e) + { + if (hasOption(parser, arg.substr(s, e - s))) + { + ArgParseOption & opt = getOption(parser, arg.substr(s, e - s)); + s = --e; // advance in squished options; s > e if at end + + // Flag options are easy to handle. + if (isFlagOption(opt)) + { + _assignArgumentValue(opt, "true"); + continue; + } + + // Handle option with values. + if (e < arg.size() - 1) + { + std::stringstream what; + what << "invalid combination of arguments -- " << arg << std::endl; + SEQAN_THROW(ParseError(what.str())); + } + + // Handle the case of too few options. + if (argi + (int)numberOfAllowedValues(opt) >= argc) + SEQAN_THROW(MissingArgument(opt.shortName)); + + // Assign the required option value.s + for (int t = 0; t < (int)numberOfAllowedValues(opt); ++t) + _assignArgumentValue(opt, argv[++argi]); + } + } + + // No option was found. + if (s == e) + SEQAN_THROW(InvalidOption(arg.substr(s))); + } + } +}; + +// Parser driver function. +template +ArgumentParser::ParseResult parse(ArgumentParser & me, + int argc, + TChar * argv[], + std::ostream & outputStream, + std::ostream & errorStream) +{ + SEQAN_TRY + { + // Perform the parsing without any valid value checking on the argument values. + ArgumentParserHelper_ parserHelper(me, argc, argv); + parserHelper.parseArgs(); + + // Copy the file extensions from the "--${NAME}-file-ext" options to "--${NAME}". + for (unsigned i = 0; i < me.optionMap.size(); ++i) + { + ArgParseOption & opt = me.optionMap[i]; + std::string longExtName = opt.longName + "-file-ext"; + std::string shortExtName = opt.shortName + "-file-ext"; + if (!opt.longName.empty() && hasOption(me, longExtName)) + opt._fileExtensions = getArgumentValues(getOption(me, longExtName)); + else if (!opt.shortName.empty() && hasOption(me, shortExtName)) + opt._fileExtensions = getArgumentValues(getOption(me, longExtName)); + } + // Copy the file extensions from the "--arg-${NUM}-file-ext" options to the argument. + for (unsigned i = 0; i < me.argumentList.size(); ++i) + { + ArgParseArgument & arg = me.argumentList[i]; + std::stringstream ss; + ss << "arg-" << (i + 1) << "-file-ext"; + if (hasOption(me, ss.str())) + arg._fileExtensions = getArgumentValues(getOption(me, ss.str())); + } + + // Check all arguments for their values. + for (unsigned i = 0; i < me.optionMap.size(); ++i) + _checkValue(me.optionMap[i]); + for (unsigned i = 0; i < me.argumentList.size(); ++i) + _checkValue(me.argumentList[i]); + } + SEQAN_CATCH(ParseError & ex) + { + errorStream << getAppName(me) << ": " << ex.what() << std::endl; + return ArgumentParser::PARSE_ERROR; + } + +#ifndef SEQAN_DISABLE_VERSION_CHECK + // do version check if not turned off by the user + bool check_version = false; + getOptionValue(check_version, me, "version-check"); + + if (check_version) + { + VersionCheck app_version(toCString(me._toolDoc._name), + toCString(me._toolDoc._version), + errorStream); + std::promise appVersionProm; + me.appVersionCheckFuture = appVersionProm.get_future(); + app_version(std::move(appVersionProm)); + } +#endif // !SEQAN_DISABLE_VERSION_CHECK + + // Handle the special options. + if (hasOption(me, "version") && isSet(me, "version")) + { + printVersion(me, outputStream); + return ArgumentParser::PARSE_VERSION; + } + else if (hasOption(me, "copyright") && isSet(me, "copyright")) + { + printLongCopyright(me, outputStream); + return ArgumentParser::PARSE_COPYRIGHT; + } + else if (hasOption(me, "write-ctd") && isSet(me, "write-ctd")) + { + if (writeCTD(me)) + return ArgumentParser::PARSE_WRITE_CTD; + else + return ArgumentParser::PARSE_ERROR; + } + else if (isSet(me, "help")) + { + printHelp(me, outputStream); + return ArgumentParser::PARSE_HELP; + } + else if (isSet(me, "full-help")) + { + printHelp(me, outputStream, "txt", true); + return ArgumentParser::PARSE_HELP; + } + else if (isSet(me, "export-help")) + { + std::string format; + getOptionValue(format, me, "export-help"); + printHelp(me, outputStream, format, true); + return ArgumentParser::PARSE_EXPORT_HELP; + } + else if (argc == 1 && !(_allRequiredSet(me) && _allArgumentsSet(me))) + { + // print short help and exit + printShortHelp(me, errorStream); + return ArgumentParser::PARSE_HELP; + } + + // In case that everything is fine, we can now return OK. + if (_allRequiredSet(me) && _allArgumentsSet(me)) + return ArgumentParser::PARSE_OK; + + // Otherwise, we check which options missed values. + if (!_allRequiredSet(me)) + for (unsigned o = 0; o < length(me.optionMap); ++o) + if (!isSet(me.optionMap[o]) && isRequired(me.optionMap[o])) + errorStream << getAppName(me) << ": Missing value for option: " << getOptionName(me.optionMap[o]) << std::endl; + // and arguments + if (!_allArgumentsSet(me)) + errorStream << getAppName(me) << ": Not enough arguments were provided." << std::endl; + errorStream << "Try '" << getAppName(me) << " --help' for more information.\n"; + return ArgumentParser::PARSE_ERROR; +} + +template +ArgumentParser::ParseResult parse(ArgumentParser & me, + int argc, + TChar * argv[]) +{ + return parse(me, argc, argv, std::cout, std::cerr); +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_ARG_PARSE_ARG_PARSE_PARSE_H_ diff --git a/seqan/arg_parse/arg_parse_type_support.h b/seqan/arg_parse/arg_parse_type_support.h new file mode 100644 index 0000000..9b1192d --- /dev/null +++ b/seqan/arg_parse/arg_parse_type_support.h @@ -0,0 +1,236 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +// TODO(aiche): check if parts of the functionality could be merged with lexicalCast in stream module + +#ifndef SEQAN_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_ +#define SEQAN_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_ + +#include +#include + +#include + +namespace seqan { + + +// ========================================================================== +// Tags, Classes, Enums +// ========================================================================== + +template +struct BooleanArgumentValues_ +{ + static constexpr std::array LIST_TRUE{{"1", "ON", "TRUE", "T", "YES"}}; + static constexpr std::array LIST_FALSE{{"0", "OFF", "FALSE", "F", "NO"}}; +}; + +template +constexpr std::array BooleanArgumentValues_::LIST_TRUE; + +template +constexpr std::array BooleanArgumentValues_::LIST_FALSE; + +// ========================================================================== +// Functions +// ========================================================================== + +// ---------------------------------------------------------------------------- +// Function _tryCast() +// ---------------------------------------------------------------------------- +template +inline bool _tryCast(TTarget & dest, TString const source) +{ + std::istringstream stream(toCString(source)); + bool result = (!(stream >> dest).fail()) && (stream.rdbuf()->in_avail() == 0); + return result; +} + +template +inline bool _tryCast(bool & dst, TString const & s) +{ + // since the validValue check already verifies that the value is one of + // BooleanArgumentValues_<>::LIST_TRUE and BooleanArgumentValues_<>::LIST_FALSE, + // one only needs to check one equivalent class + std::string s_uppercase{s}; + std::transform(s.begin(), s.end(), s_uppercase.begin(), ::toupper); // allow for lowercase letters + dst = (std::find(BooleanArgumentValues_<>::LIST_TRUE.begin(), + BooleanArgumentValues_<>::LIST_TRUE.end(), + s_uppercase) + != BooleanArgumentValues_<>::LIST_TRUE.end()); + return true; +} + +// ---------------------------------------------------------------------------- +// Function _cast() +// ---------------------------------------------------------------------------- +template +inline TTarget _cast(TString const s) +{ + // We are sing additional braces here for "most vexing parse" resolution + // when enforcing default initialization also for built-in types. + TTarget dst((TTarget())); + std::istringstream stream(toCString(s)); + bool result = (!(stream >> dst).fail()) && (stream.rdbuf()->in_avail() == 0); + SEQAN_CHECK(result, "could not cast %s", toCString(s)); + return dst; +} + +// ---------------------------------------------------------------------------- +// Function _isCastable() +// ---------------------------------------------------------------------------- +template +inline bool _isCastable(TString const s) +{ + TTarget dst; + std::istringstream stream(toCString(s)); + return (!(stream >> dst).fail()) && (stream.rdbuf()->in_avail() == 0); +} + +// ---------------------------------------------------------------------------- +// Function _isDouble() +// ---------------------------------------------------------------------------- + +template +inline bool _isDouble(TString const s) +{ + return _isCastable(s); +} + +// ---------------------------------------------------------------------------- +// Function _isInt() +// ---------------------------------------------------------------------------- + +template +inline bool _isInt(TString const s) +{ + return _isCastable(s); +} + +// ---------------------------------------------------------------------------- +// Function _convertFlagValue() +// ---------------------------------------------------------------------------- + +inline bool _convertFlagValue(bool & dst, std::string const & src) +{ + dst = !empty(src) && (src != "false"); + return true; +} + +template +inline bool _convertFlagValue(TObject & /*dst*/, std::string const & /*s*/) +{ + return false; +} + +// ---------------------------------------------------------------------------- +// Function _convertArgumentValue() +// ---------------------------------------------------------------------------- + +class ArgParseArgument; +inline bool isIntegerArgument(ArgParseArgument const & me); +inline bool isInt64Argument(ArgParseArgument const & me); +inline bool isDoubleArgument(ArgParseArgument const & me); +inline bool isStringArgument(ArgParseArgument const & me); +inline bool isBooleanArgument(ArgParseArgument const & me); + +inline bool _convertArgumentValue(bool & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isBooleanArgument(opt)) + return false; + + return _tryCast(dst, src); +} + +inline bool _convertArgumentValue(int & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isIntegerArgument(opt)) + return false; + + return _tryCast(dst, src); +} + +inline bool _convertArgumentValue(unsigned int & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isIntegerArgument(opt)) + return false; + + return _tryCast(dst, src); +} + +inline bool _convertArgumentValue(int64_t & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isIntegerArgument(opt) && !isInt64Argument(opt)) + return false; + + return _tryCast(dst, src); +} + +inline bool _convertArgumentValue(uint64_t & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isIntegerArgument(opt) && !isInt64Argument(opt)) + return false; + + return _tryCast(dst, src); +} + +inline bool _convertArgumentValue(float & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isDoubleArgument(opt)) + return false; + + return _tryCast(dst, src); +} + +inline bool _convertArgumentValue(double & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isDoubleArgument(opt)) + return false; + + return _tryCast(dst, src); +} + +template +inline bool _convertArgumentValue(TObject & dst, ArgParseArgument const & opt, std::string const & src) +{ + if (!isStringArgument(opt)) + return false; + + assign(dst, src); + return true; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_ARG_PARSE_ARG_PARSE_TYPE_SUPPRT_H_ diff --git a/seqan/arg_parse/arg_parse_version_check.h b/seqan/arg_parse/arg_parse_version_check.h new file mode 100644 index 0000000..bb10cc8 --- /dev/null +++ b/seqan/arg_parse/arg_parse_version_check.h @@ -0,0 +1,480 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Svenja Mehringer +// ========================================================================== + +#ifndef SEQAN_INCLUDE_ARG_PARSE_VERSION_CHECK_H_ +#define SEQAN_INCLUDE_ARG_PARSE_VERSION_CHECK_H_ + +#include + +#include +#include +#include +#include +#include + +namespace seqan +{ + +// ========================================================================== +// Forwards +// ========================================================================== + +// NOTE(rrahn): In-file forward for function call operator. +struct VersionCheck; +inline void _checkForNewerVersion(VersionCheck &, std::promise); +inline std::string _getPath(); +constexpr const char * _getOS(); +constexpr const char * _getBitSys(); + +// ========================================================================== +// Tags, Classes, Enums +// ========================================================================== + +template +struct VersionControlTags_ +{ + static constexpr char const * const SEQAN_NAME = "seqan"; + static constexpr char const * const UNREGISTERED_APP = "UNREGISTERED_APP"; + + static constexpr char const * const MESSAGE_SEQAN_UPDATE = + "[SEQAN INFO] :: There is a newer SeqAn version available!\n" + "[SEQAN INFO] :: Please visit www.seqan.de for an update or inform the developer of this app.\n" + "[SEQAN INFO] :: If you don't want to recieve this message again set --version-check OFF\n\n"; + static constexpr char const * const MESSAGE_APP_UPDATE = + "[APP INFO] :: There is a newer version of this application available.\n" + "[APP INFO] :: If this app is developed by SeqAn, visit www.seqan.de for updates.\n" + "[APP INFO] :: If you don't want to recieve this message again set --version_check OFF\n\n"; + static constexpr char const * const MESSAGE_UNREGISTERED_APP = + "[SEQAN INFO] :: Thank you for using SeqAn!\n" + "[SEQAN INFO] :: You might want to regsiter you app for support and version check features?\n" + "[SEQAN INFO] :: Just send us an email to seqan@team.fu-berlin.de with your app name and version number.\n" + "[SEQAN INFO] :: If you don't want to recieve this message anymore set --version_check OFF\n\n"; + static constexpr char const * const MESSAGE_REGISTERED_APP_UPDATE = + "[APP INFO] :: We noticed the app version you use is newer than the one registered with us.\n" + "[APP INFO] :: Please send us an email with the new version so we can correct it (support@seqan.de)\n\n"; +}; + +template +constexpr char const * const VersionControlTags_::SEQAN_NAME; +template +constexpr char const * const VersionControlTags_::UNREGISTERED_APP; +template +constexpr char const * const VersionControlTags_::MESSAGE_SEQAN_UPDATE; +template +constexpr char const * const VersionControlTags_::MESSAGE_APP_UPDATE; +template +constexpr char const * const VersionControlTags_::MESSAGE_UNREGISTERED_APP; +template +constexpr char const * const VersionControlTags_::MESSAGE_REGISTERED_APP_UPDATE; + +struct VersionCheck +{ + // ---------------------------------------------------------------------------- + // Member Variables + // ---------------------------------------------------------------------------- + std::string _url; + std::string _name; + std::string _version = "0.0.0"; + std::string _program; + std::string _command; + std::string _path = _getPath(); + std::string _timestamp_filename; + std::ostream & errorStream; + + // ---------------------------------------------------------------------------- + // Constructors + // ---------------------------------------------------------------------------- + + VersionCheck(std::string name, + std::string const & version, + std::ostream & errorStream) : + _name{std::move(name)}, + errorStream(errorStream) + { + std::smatch versionMatch; +#if defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) + _timestamp_filename = _path + "/" + _name + "_usr.timestamp"; +#else + _timestamp_filename = _path + "/" + _name + "_dev.timestamp"; +#endif + if (!version.empty() && + std::regex_search(version, versionMatch, std::regex("^([[:digit:]]+\\.[[:digit:]]+\\.[[:digit:]]+).*"))) + { + _version = versionMatch.str(1); // in case the git revision number is given take only version number + } + _url = static_cast("http://seqan-update.informatik.uni-tuebingen.de/check/SeqAn_") + _getOS() + _getBitSys() + _name + "_" + _version; + _getProgram(); + _updateCommand(); + } + + // ---------------------------------------------------------------------------- + // Member Functions + // ---------------------------------------------------------------------------- + +#if defined(STDLIB_VS) + void _getProgram() + { + _program = "powershell.exe -NoLogo -NonInteractive -Command \"& {Invoke-WebRequest -erroraction 'silentlycontinue' -OutFile"; + } +#else // Unix based platforms. + void _getProgram() + { + // ask if system call for version or help is successfull + if (!system("wget --version > /dev/null 2>&1")) + _program = "wget -q -O"; + else if (!system("curl --version > /dev/null 2>&1")) + _program = "curl -o"; +#ifndef __linux // ftp call does not work on linux + else if (!system("which ftp > /dev/null 2>&1")) + _program = "ftp -Vo"; +#endif + else + _program.clear(); + } +#endif // defined(STDLIB_VS) + + void _updateCommand() + { + if (!_program.empty()) + { + _command = _program + " " + _path + "/" + _name + ".version " + _url; +#if defined(STDLIB_VS) + _command = _command + "; exit [int] -not $?}\" > nul 2>&1"; +#else + _command = _command + " > /dev/null 2>&1"; +#endif + } + } + + inline void operator()(std::promise versionCheckProm) + { + _checkForNewerVersion(*this, std::move(versionCheckProm)); + } +}; + +// ========================================================================== +// Metafunctions +// ========================================================================== + +// ========================================================================== +// Functions +// ========================================================================== + +// ---------------------------------------------------------------------------- +// Function setURL() +// ---------------------------------------------------------------------------- + +inline void setURL(VersionCheck & me, std::string url) +{ + std::swap(me._url, url); + me._updateCommand(); +} + +// ---------------------------------------------------------------------------- +// Function _getOS() +// ---------------------------------------------------------------------------- + +constexpr const char * _getOS() +{ + //get system information +#ifdef __linux + return "Linux"; +#elif __APPLE__ + return "MacOS"; +#elif defined(STDLIB_VS) + return "Windows"; +#elif __FreeBSD__ + return "FreeBSD"; +#elif __OpenBSD__ + return "OpenBSD"; +#else + return "unknown"; +#endif +} + +// ---------------------------------------------------------------------------- +// Function _getBitSys() +// ---------------------------------------------------------------------------- + +constexpr const char * _getBitSys() +{ +#if SEQAN_IS_32_BIT + return "_32_"; +#else + return "_64_"; +#endif +} + +// ---------------------------------------------------------------------------- +// Function _checkWritability() +// ---------------------------------------------------------------------------- + +#if defined(STDLIB_VS) +inline bool _checkWritability(std::string const & path) +{ + DWORD ftyp = GetFileAttributesA(path.c_str()); + if (ftyp == INVALID_FILE_ATTRIBUTES || !(ftyp & FILE_ATTRIBUTE_DIRECTORY)) + { + if (!CreateDirectory(path.c_str(), NULL)) + return false; + } + + HANDLE dummyFile; // check writablity by trying to create a file in GENERIC_WRITE mode + std::string fileName(path + "/dummy.txt"); + dummyFile = CreateFile(fileName.c_str(), GENERIC_WRITE, 0, NULL, CREATE_ALWAYS, FILE_ATTRIBUTE_NORMAL, NULL); + + if (dummyFile == INVALID_HANDLE_VALUE) + return false; + + CloseHandle(dummyFile); + bool successful_deletion = DeleteFile(fileName.c_str()); + SEQAN_ASSERT(successful_deletion); + if (!successful_deletion) + return false; + + return true; +} +#else +inline bool _checkWritability(std::string const & path) +{ + struct stat d_stat; + if (stat(path.c_str(), &d_stat) < 0) + { + // try to make dir + std::string makeDir("mkdir -p " + path); + if (system(makeDir.c_str())) + return false; // could not create home dir + + if (stat(path.c_str(), &d_stat) < 0) // repeat stat + return false; + } + + if (!(d_stat.st_mode & S_IWUSR)) + return false; // dir not writable + + return true; +} +#endif + +// ---------------------------------------------------------------------------- +// Function _getPath() +// ---------------------------------------------------------------------------- + +inline std::string _getPath() +{ + std::string path; +#if defined(STDLIB_VS) + path = std::string(getenv("UserProfile")) + "/.config/seqan"; +#else + path = std::string(getenv("HOME")) + "/.config/seqan"; +#endif + + // check if user has permission to write to home path + if (!_checkWritability(path)) + { +#if defined(STDLIB_VS) + TCHAR tmp_path [MAX_PATH]; + if (GetTempPath(MAX_PATH, tmp_path) != 0) + { + path = tmp_path; + } + else + { //GetTempPath() returns 0 on failure + path.clear(); + } +# else // unix + path = "/tmp"; +#endif + } + return path; +} + +// ---------------------------------------------------------------------------- +// Function _getFileTimeDiff() +// ---------------------------------------------------------------------------- + +inline double _getFileTimeDiff(VersionCheck const & me) +{ + double curr = static_cast(std::chrono::duration_cast(std::chrono::system_clock::now().time_since_epoch()).count()); + std::ifstream timestamp_file; + timestamp_file.open(me._timestamp_filename.c_str()); + + if (timestamp_file.is_open()) + { + std::string str_time; + std::getline(timestamp_file, str_time); + timestamp_file.close(); + double d_time; + lexicalCast(d_time, str_time); + return curr - d_time; + } + return curr; +} + +// ---------------------------------------------------------------------------- +// Function _getNumbersFromString() +// ---------------------------------------------------------------------------- + +inline String _getNumbersFromString(std::string const & str) +{ + String numbers; + StringSet set; + strSplit(set, str, EqualsChar<'.'>(), false); + for (auto & num : set) + { + appendValue(numbers, lexicalCast(num)); + } + return numbers; +} + +// ---------------------------------------------------------------------------- +// Function _readVersionString() +// ---------------------------------------------------------------------------- + +inline void _readVersionStrings(std::vector & versions, std::string const & version_file) +{ + std::ifstream myfile; + myfile.open(version_file.c_str()); + std::string app_version; + std::string seqan_version; + if (myfile.is_open()) + { + std::getline(myfile, app_version); // get first line which should only contain the version number of the app + +#if !defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) + if (app_version == VersionControlTags_<>::UNREGISTERED_APP) + versions[0] = app_version; +#endif // !defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) + + if (std::regex_match(app_version, std::regex("^[[:digit:]]+\\.[[:digit:]]+\\.[[:digit:]]+$"))) + versions[0] = app_version; + + std::getline(myfile, seqan_version); // get second line which should only contain the version number of seqan + + if (std::regex_match(seqan_version, std::regex("^[[:digit:]]+\\.[[:digit:]]+\\.[[:digit:]]+$"))) + versions[1] = seqan_version; + + myfile.close(); + } +} + +// ---------------------------------------------------------------------------- +// Function _callServer() +// ---------------------------------------------------------------------------- + +inline void _callServer(VersionCheck const me, std::promise prom) +{ + // update timestamp + std::ofstream timestamp_file(me._timestamp_filename.c_str()); + if (timestamp_file.is_open()) + { + timestamp_file << std::chrono::duration_cast(std::chrono::system_clock::now().time_since_epoch()).count(); + timestamp_file.close(); + } + + // system call + // http response is stored in a file '.config/seqan/{app_name}_version' + if (system(me._command.c_str())) + prom.set_value(false); + else + prom.set_value(true); +} + +// ---------------------------------------------------------------------------- +// Function checkForNewerVersion() +// ---------------------------------------------------------------------------- + +inline void _checkForNewerVersion(VersionCheck & me, std::promise prom) +{ + if (me._path.empty()) // neither home dir nor temp dir are writable + { + prom.set_value(false); + return; + } + + std::string version_filename(me._path + "/" + me._name + ".version"); + double min_time_diff(86400); // one day = 86400 seonds + double file_time_diff(_getFileTimeDiff(me)); // time difference in seconds + + if (file_time_diff < min_time_diff) + { + prom.set_value(false); // only check for newer version once a day + return; + } + + std::vector str_server_versions{"", ""}; + _readVersionStrings(str_server_versions, version_filename); + +#if !defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) // only check seqan version in debug or testing mode + if (!str_server_versions[1].empty()) // seqan version + { + std::string seqan_version = std::to_string(SEQAN_VERSION_MAJOR) + "." + + std::to_string(SEQAN_VERSION_MINOR) + "." + + std::to_string(SEQAN_VERSION_PATCH); + Lexical<> version_comp(_getNumbersFromString(seqan_version), _getNumbersFromString(str_server_versions[1])); + + if (isLess(version_comp)) + me.errorStream << VersionControlTags_<>::MESSAGE_SEQAN_UPDATE; + } + if (str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP) + me.errorStream << VersionControlTags_<>::MESSAGE_UNREGISTERED_APP; +#endif + + if (!str_server_versions[0].empty() & !(str_server_versions[0] == VersionControlTags_<>::UNREGISTERED_APP)) // app version + { + Lexical<> version_comp(_getNumbersFromString(me._version), _getNumbersFromString(str_server_versions[0])); + +#if defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) // only check app version in release or testing mode + if (isLess(version_comp)) + me.errorStream << VersionControlTags_<>::MESSAGE_APP_UPDATE; +#endif // defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) + +#if !defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) // only notify developer that app version should be updated on server + if (isGreater(version_comp)) + me.errorStream << VersionControlTags_<>::MESSAGE_REGISTERED_APP_UPDATE; +#endif // !defined(NDEBUG) || defined(SEQAN_TEST_VERSION_CHECK_) + } + + if (me._program.empty()) + { + prom.set_value(false); + return; + } + + // launch a seperate thread to not defer runtime. + std::thread(_callServer, me, std::move(prom)).detach(); +} + +} // namespace seqan +#endif //SEQAN_INCLUDE_ARG_PARSE_VERSION_CHECK_H_ diff --git a/seqan/arg_parse/argument_parser.h b/seqan/arg_parse/argument_parser.h new file mode 100644 index 0000000..92467a3 --- /dev/null +++ b/seqan/arg_parse/argument_parser.h @@ -0,0 +1,1192 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== + +#ifndef SEQAN_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_ +#define SEQAN_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_ + +#include +#include +#include + +#include +#include +#include +#include + +#include + +#include +#include +#include +#include +#include + +namespace seqan { + +// ========================================================================== +// Forwards +// ========================================================================== + +// friend declaration to make addOption() and hideOption() available +// in ArgumentParser::init() +class ArgumentParser; +class ArgParseOption; +void addOption(ArgumentParser & me, ArgParseOption const & opt); +void hideOption(ArgumentParser & me, std::string const & name, bool hide); +void setValidValues(ArgumentParser & me, std::string const & name, std::string const & values); +template +void setDefaultValue(ArgumentParser & me, std::string const & name, const TValue & value); + +// Required in addOption() and addArgument(). +inline void hideOption(ArgumentParser & me, std::string const & name, bool hide = true); +inline ArgParseOption & getOption(ArgumentParser & me, std::string const & name); +inline void setValidValues(ArgumentParser & me, std::string const & name, std::vector const & values); +inline ArgParseArgument & getArgument(ArgumentParser & me, unsigned position); + +// ========================================================================== +// Tags, Classes, Enums +// ========================================================================== + +/*! + * @class ArgumentParser + * @headerfile + * @brief Parse the command line. + * + * @signature class ArgumentParser; + * + * Options are stored as @link ArgParseOption @endlink and @link ArgParseArgument @endlink objects. + * + * @section Remarks + * + * See the documentation of @link ToolDoc @endlink on how to format text. Wherever possible, formatting is added + * automatically for you. You have to use formatting in the following places: (1) usage lines, (2) option help texts, + * (3) description and additional text sections. + * + * @section Examples + * + * The following gives a simple example of how to use the ArgumentParser class. + * + * @include demos/dox/arg_parse/argument_parser.cpp + * + * @code{.console} + * $ demo_arg_parse_argument_parser in.fa out.txt --id 0 + * Built target seqan_core + * Built target demo_arg_parse + * Verbose: off + * Identity: 0 + * Input-File: in.fa + * Output-File: out.txt + * @endcode + * + * @see ArgParseArgument + * @see ArgParseOption + * @see ToolDoc + */ + +/*! + * @fn ArgumentParser::ArgumentParser + * @brief Constructor + * + * @signature ArgumentParser::ArgumentParser([appName]); + * + * @param[in] appName The name of the application (std::string), defaults to argv[0]. + */ + +/*! + * @enum ArgumentParser::ParseResult + * @brief Argument parsing result. + * + * @signature enum ArgumentParser::ParseResult; + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_OK; + * @brief Parsing the program's arguments was successful and no builtin command was triggered. + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_ERROR; + * @brief There were errors parsing the arguments. + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_HELP; + * @brief Parsing was successful, built-in --help or --full-help option was used. + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_VERSION; + * @brief Parsing was successful, built-in --version option was used. + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_COPYRIGHT; + * @brief Parsing was successful, built-in --copyright option was used. + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_WRITE_CTD; + * @brief Parsing was successful, built-in --write-ctd option was used. + * + * @val ArgumentParser::ParseResult ArgumentParser::PARSE_EXPORT_HELP; + * @brief Parsing was successful, built-in --export-help option was used. + */ + +class ArgumentParser +{ +public: + + // ---------------------------------------------------------------------------- + // Enum ParseResult + // ---------------------------------------------------------------------------- + + // will be used as return value of parse(..) to indicate whether parsing worked + enum ParseResult + { + PARSE_OK, + PARSE_ERROR, + PARSE_HELP, + PARSE_VERSION, + PARSE_COPYRIGHT, + PARSE_WRITE_CTD, + PARSE_EXPORT_HELP + }; + + // ---------------------------------------------------------------------------- + // Class Typedefs + // ---------------------------------------------------------------------------- + + typedef std::vector TOptionMap; + typedef std::vector TArgumentMap; + typedef Size::Type TOptionMapSize; + typedef Size::Type TArgumentMapSize; + + typedef std::map TStringMap; + typedef std::vector TValueMap; + + // ---------------------------------------------------------------------------- + // Mapping of option names to options + // ---------------------------------------------------------------------------- + + TStringMap shortNameMap; + TStringMap longNameMap; + TOptionMap optionMap; + TArgumentMap argumentList; + + // ---------------------------------------------------------------------------- + // Documentation Members + // ---------------------------------------------------------------------------- + + ToolDoc _toolDoc; // the tool doc for all user specified + // text + std::vector _description; // the description which we need to + // separate to put it on top of the rest + std::vector _usageText; // the usage lines as strings, to avoid + // interference with the rest of the doc + + std::future appVersionCheckFuture; + // ---------------------------------------------------------------------------- + // Function init() + // ---------------------------------------------------------------------------- + + void init() + { + addOption(*this, ArgParseOption("h", "help", "Display the help message.")); + addOption(*this, ArgParseOption("hh", "full-help", "Display the help message with advanced options.")); + hideOption(*this, "full-help", true); // hidden by default + + // hidden flags used for export of man pages and ctd formats + addOption(*this, ArgParseOption("", + "write-ctd", + "Exports the app's interface description to a .ctd file.", + ArgParseArgument::OUTPUT_FILE)); + hideOption(*this, "write-ctd", true); + + addOption(*this, ArgParseOption("", + "export-help", + "Export help to a format. One of {'html', 'man', 'txt'}.", + ArgParseArgument::STRING, + "FORMAT")); + hideOption(*this, "export-help", true); + setValidValues(*this, "export-help", "html man txt"); + +#ifndef SEQAN_DISABLE_VERSION_CHECK + addOption(*this, ArgParseOption("", + "version-check", + "Turn this option off to disable version update notifications of the application. ", + ArgParseArgument::BOOL)); +#ifdef SEQAN_VERSION_CHECK_OPT_IN + setDefaultValue(*this, "version-check", false); +#else // Make version update opt out. + setDefaultValue(*this, "version-check", true); +#endif // SEQAN_VERSION_CHECK_OPT_IN +#endif // !SEQAN_DISABLE_VERSION_CHECK + } + + // ---------------------------------------------------------------------------- + // Constructors + // ---------------------------------------------------------------------------- + + ArgumentParser() + { + init(); + } + + ArgumentParser(std::string const & _appName) + { + setName(_toolDoc, _appName); + init(); + } + + ~ArgumentParser() + { + // wait for another 3 seconds + if (appVersionCheckFuture.valid()) + appVersionCheckFuture.wait_for(std::chrono::seconds(3)); + } + +}; + +// ========================================================================== +// Metafunctions +// ========================================================================== + +// ========================================================================== +// Functions +// ========================================================================== + +// ---------------------------------------------------------------------------- +// Function hasOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#hasOption + * @headerfile + * @brief Query whether a certain option is registered in the parser. + * + * @signature bool hasOption(parser, name); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] name The name to query for (std::string). + * + * @return bool true if there is such an option, false otherwise. + */ + +inline bool hasOption(ArgumentParser const & me, std::string const & name) +{ + return hasKey(me.shortNameMap, name) || hasKey(me.longNameMap, name); +} + +// ---------------------------------------------------------------------------- +// Function addOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addOption + * @headerfile + * @brief Adds an @link ArgParseOption @endlink to an ArgumentParser. + * + * @signature void addOption(parser, option); + * + * @param[in,out] parser The ArgumentParser to add the option to. + * @param[in] option The ArgParseOption to add to parser. + */ + +inline void _copyValidValuesToFileExt(ArgumentParser & me, std::string const & name) +{ + // Copy valid values, remove leading dots. + ArgParseOption & option = getOption(me, name); + if (isInputFileArgument(option) || isOutputFileArgument(option)) + { + std::string longName = option.longName.empty() ? option.shortName : option.longName; + longName += "-file-ext"; + std::vector validValues = option.validValues; + for (unsigned i = 0; i < length(validValues); ++i) + if (!validValues[i].empty() && validValues[i][0] == '.') + validValues[i].erase(0, 1); + setValidValues(me, longName, validValues); + } +} + +inline void addOption(ArgumentParser & me, ArgParseOption const & opt) +{ + // check if an option with the same identifiers was already registered + SEQAN_CHECK(!hasOption(me, opt.shortName), "There already is an option with the name %s!", toCString(opt.shortName)); + SEQAN_CHECK(!hasOption(me, opt.longName), "There already is an option with the name %s!", toCString(opt.longName)); + + // finally append the option + appendValue(me.optionMap, opt); + + if (!empty(opt.shortName)) + me.shortNameMap.insert(std::make_pair(opt.shortName, length(me.optionMap) - 1)); + if (!empty(opt.longName)) + me.longNameMap.insert(std::make_pair(opt.longName, length(me.optionMap) - 1)); + + // handle the case of input and output option: add a string option --${name}-file-ext. + if (isInputFileArgument(opt) || isOutputFileArgument(opt)) + { + std::string longName = opt.longName.empty() ? opt.shortName : opt.longName; + longName += "-file-ext"; + std::string helpText = "Override file extension for --"; + helpText += opt.longName; + + // Add option, copy list argument, number of allowed values. + addOption(me, ArgParseOption("", longName, helpText, ArgParseOption::STRING, "EXT", + isListArgument(opt), numberOfAllowedValues(opt))); + getOption(me, longName.c_str()).tags.push_back("file-ext-override"); + getOption(me, longName.c_str()).tags.push_back("gkn-ignore"); + // Hide option. + hideOption(me, longName); + // Copy valid values, remove leading dots. + _copyValidValuesToFileExt(me, opt.longName); + } +} + +// ---------------------------------------------------------------------------- +// Function addArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addArgument + * @headerfile + * @brief Adds an @link ArgParseArgument @endlink to an ArgumentParser. + * + * @signature void addArgument(parser, arg); + * + * @param[in,out] parser The ArgumentParser to add the argument to. + * @param[in] arg The ArgParseArgument to add to parser. + */ + +inline void _copyValidValuesToFileExt(ArgumentParser & me, unsigned no) +{ + // Copy valid values, remove leading dots. + ArgParseArgument & arg = getArgument(me, no); + if (isInputFileArgument(arg) || isOutputFileArgument(arg)) + { + std::stringstream longNameSS; + longNameSS << "arg-" << (no + 1) << "-file-ext"; + std::string longName = longNameSS.str(); + std::vector validValues = arg.validValues; + for (unsigned i = 0; i < length(validValues); ++i) + if (!validValues[i].empty() && validValues[i][0] == '.') + validValues[i].erase(0, 1); + setValidValues(me, longName, validValues); + } +} + +inline void addArgument(ArgumentParser & me, ArgParseArgument const & arg) +{ + // check previous arguments + // .. lists can only be last argument + if (!me.argumentList.empty()) + { + SEQAN_CHECK(!isListArgument(me.argumentList[me.argumentList.size() - 1]), + "You cannot add an additional argument after a list argument."); + } + + // check current argument + // .. arguments should not have default values + SEQAN_CHECK(arg.defaultValue.empty(), "Arguments cannot have default values."); + SEQAN_CHECK(arg._numberOfValues == 1, "n-Tuple of arguments are not supported."); + + me.argumentList.push_back(arg); + + // handle the case of input and output option: add a string option --${name}-file-ext. + if (isInputFileArgument(arg) || isOutputFileArgument(arg)) + { + std::stringstream longNameSS; + longNameSS << "arg-" << me.argumentList.size() << "-file-ext"; + std::string longName = longNameSS.str(); + std::stringstream helpTextSS; + helpTextSS << "Override file extension for argument " << me.argumentList.size(); + std::string helpText = helpTextSS.str(); + + // Add option, copy list argument, number of allowed values. + addOption(me, ArgParseOption("", longName, helpText, ArgParseOption::STRING, "EXT", + isListArgument(arg), numberOfAllowedValues(arg))); + getOption(me, longName.c_str()).tags.push_back("file-ext-override"); + getOption(me, longName.c_str()).tags.push_back("gkn-ignore"); + // Hide option. + hideOption(me, longName); + // Copy valid values, remove leading dots. + _copyValidValuesToFileExt(me, me.argumentList.size() - 1); + } +} + +// ---------------------------------------------------------------------------- +// Function _getOptionIndex() +// ---------------------------------------------------------------------------- +// note that it is assumed that the option exists if this method is called + +inline ArgumentParser::TOptionMapSize _getOptionIndex(ArgumentParser const & me, + std::string const & name) +{ + ArgumentParser::TOptionMapSize option_index; + if (me.shortNameMap.find(name) != me.shortNameMap.end()) + { + option_index = me.shortNameMap.find(name)->second; + } + else + { + option_index = me.longNameMap.find(name)->second; + } + return option_index; +} + +// ---------------------------------------------------------------------------- +// Function getOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getOption + * @headerfile + * @brief Returns a reference to the specified option. + * + * @signature TOption getOption(parser, name); + * + * @param[in] parser The parser to query. + * @param[in] name The short or long name of the option (std::string). + * + * @return TOption Reference to the @link ArgParseOption @endlink with the given short or long name. + */ + +inline ArgParseOption & getOption(ArgumentParser & me, std::string const & name) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + return me.optionMap[_getOptionIndex(me, name)]; +} + +inline ArgParseOption const & getOption(ArgumentParser const & me, std::string const & name) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + return me.optionMap[_getOptionIndex(me, name)]; +} + +// ---------------------------------------------------------------------------- +// Function setRequired() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setRequired + * @headerfile + * @brief Sets whether or not the option with the givne name is mandatory. + * + * @signature void setRequired(parser, name[, required]). + * + * @param[in,out] parser The ArgumentParser to set the flag of. + * @param[in] name The short or long name of the option (std::string). + * @param[in] required Whether or not the option is required (bool, default to true). + */ + +inline void setRequired(ArgumentParser & me, std::string const & name, bool required = true) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setRequired(getOption(me, name), required); +} + +// ---------------------------------------------------------------------------- +// Function hideOption() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#hideOption + * @headerfile + * @brief Hides the ArgParseOption with the given name. + * + * @signature void hideOption(parser, name[, hide]). + * + * @param[in,out] parser The ArgParseOption to the the hidden flag of. + * @param[in] name The short or long name of the option to modify. + * @param[in] hide Whether or not to hide the flag (bool, defaults to true). + */ + +inline void hideOption(ArgumentParser & me, std::string const & name, bool hide) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + hideOption(getOption(me, name), hide); +} + +// ---------------------------------------------------------------------------- +// Function setAdvanced() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setAdvanced + * @headerfile + * @brief Sets whether or not the option with the givne name is advanced. + * + * @signature void setAdvanced(parser, name[, required]). + * + * @param[in,out] parser The ArgumentParser to set the flag of. + * @param[in] name The short or long name of the option (std::string). + * @param[in] required Whether or not the option is required (bool, default to true). + */ + +inline void setAdvanced(ArgumentParser & me, std::string const & name, bool advanced = true) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setAdvanced(getOption(me, name), advanced); + // make sure the full-help options is visible so advanced options can be shown + if (advanced) + hideOption(me, "full-help", false); +} + +// ---------------------------------------------------------------------------- +// Function getArgument() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getArgument + * @headerfile + * @brief Returns a reference to the given positional argument. + * + * @signature TArgument getArgument(parser, pos); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] pos The position of the argument to return (unsigned, starting at 0). + * + * @return TArgument Reference to the @link ArgParseArgument @endlink with the given position. + */ + +inline ArgParseArgument & getArgument(ArgumentParser & me, unsigned position) +{ + SEQAN_CHECK(position < me.argumentList.size(), + "ArgumentParser: Only %d arguments available", me.argumentList.size()); + return me.argumentList[position]; +} + +inline ArgParseArgument const & getArgument(ArgumentParser const & me, unsigned position) +{ + SEQAN_CHECK(position < me.argumentList.size(), + "ArgumentParser: Only %d arguments available", me.argumentList.size()); + return me.argumentList[position]; +} + +// ---------------------------------------------------------------------------- +// Function isSet() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#isSet + * @headerfile + * @brief Query whether an option was set on the command line. + * + * @signature bool isSet(parser, name); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] name The short or long name of the option (std::string). + * + * @return bool Whether or not the option was set on the command line or not. + */ + +inline bool isSet(ArgumentParser const & me, std::string const & name) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + return isSet(getOption(me, name)); +} + +// ---------------------------------------------------------------------------- +// Function hasDefault() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#hasDefault + * @headerfile + * @brief Query whether an option has a default value. + * + * @signature bool hasDefault(parser, name); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] name The short or long name of the option (std::string). + * + * @return bool Whether or not the option has a default value. + */ + +inline bool hasDefault(ArgumentParser const & me, std::string const & name) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + return hasDefault(getOption(me, name)); +} + +// ---------------------------------------------------------------------------- +// Function _allRequiredSet() +// ---------------------------------------------------------------------------- + +inline bool _allRequiredSet(ArgumentParser const & me) +{ + for (unsigned o = 0; o < length(me.optionMap); ++o) + if (!isSet(me.optionMap[o]) && isRequired(me.optionMap[o])) + return false; + + return true; +} + +// ---------------------------------------------------------------------------- +// Function _allArgumentsSet() +// ---------------------------------------------------------------------------- + +inline bool _allArgumentsSet(ArgumentParser const & me) +{ + for (unsigned a = 0; a < me.argumentList.size(); ++a) + if (!isSet(me.argumentList[a])) + return false; + + return true; +} + +// ---------------------------------------------------------------------------- +// Function getOptionValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getOptionValue + * @headerfile + * @brief Retrieve the value of an option. + * + * @signature bool getOptionValue(dest, parser, name[, pos]); + * + * @param[in] dest The variable to write the result to (the type is a template parameter and the value type of the + * option must be convertible in the type of dest for the retrieval to work, also see + * result value). + * @param[in] parser The ArgumentParser to get the value from. + * @param[in] name The short or long name of the option (std::string). + * @param[in] pos Optional position for multi-value options (unsigned, defaults to 0). + * + * @return bool true if the requested option was given on the command line and could be coverted to the type of + * dest. + */ + +template +inline bool getOptionValue(TValue & val, + ArgumentParser const & me, + std::string const & name, + unsigned argNo) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + + if (isSet(me, name) || hasDefault(me, name)) + { + if (isFlagOption(getOption(me, name))) + { + return _convertFlagValue(val, getArgumentValue(getOption(me, name), argNo)); + } + else + { + return _convertArgumentValue(val, + getOption(me, name), + getArgumentValue(getOption(me, name), argNo)); + } + } + else + { + return false; + } +} + +template +inline bool getOptionValue(TValue & val, + ArgumentParser const & me, + std::string const & name) +{ + return getOptionValue(val, me, name, 0); +} + +// ---------------------------------------------------------------------------- +// Function getOptionFileExtension() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getOptionFileExtension + * @headerfile + * @brief Retrieve the file extension of a file option. + * + * @signature std::string getOptionFileExtension(parser, name[, pos]); + * + * @param[in] parser The ArgumentParser to get the value from. + * @param[in] name The short or long name of the option (std::string). + * @param[in] pos Optional position for multi-value options (unsigned, defaults to 0). + * + * @return std::string The extension of the option. Empty if not set or no extension. + * + * @see ArgumentParser#getArgumentFileExtension + * + * @section Overriding File Extension on the Command Line + * + * For each option with type INPUT_FILE and OUTPUT_FILE, an option with the name + * ${name}-file-ext is automatically added to the ArgumentParser (where ${name} is the name + * of the original option). The extension can be overridden by specifying the argument. Thus, the user of + * the program could give the value "file.ext" to the parameter "fname" and override the extension on the + * command line to "ext2" as follows: + * + * @code{.console} + * # program_name --fname file.ext --fname-file-ext ext2 + * @endcode + */ + +inline std::string getOptionFileExtension(ArgumentParser const & me, + std::string const & name, + unsigned argNo = 0) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + + return getFileExtension(getOption(me, name), argNo); +} + +// ---------------------------------------------------------------------------- +// Function getOptionValueCount() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getOptionValueCount + * @headerfile + * @brief Query number of values stored for the specified option. + * + * @signature unsigned getOptionValueCount(parser, name); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] name The short or long name of the option (string). + * + * @return unsigned The number of values for the option with the given name. + */ + +inline unsigned getOptionValueCount(ArgumentParser const & me, std::string const & name) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + return getArgumentValues(getOption(me, name)).size(); +} + +// ---------------------------------------------------------------------------- +// Function getArgumentValueCount() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getArgumentValueCount + * @headerfile + * @brief Query number of values stored for the specified argument. + * + * @signature unsigned getArgumentValueCount(parser, pos); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] name The position of the argument (unsigned, 0-based). + * + * @return unsigned The number of values for the argument with the given position. + */ + +inline unsigned getArgumentValueCount(ArgumentParser const & me, unsigned argumentPosition) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + return getArgumentValues(getArgument(me, argumentPosition)).size(); +} + +// ---------------------------------------------------------------------------- +// Function getArgumentValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getArgumentValue + * @headerfile + * @brief Retrieves the value of an argument given by its position. + * + * @signature bool getArgumentValue(dest, parser, pos[, no]); + * + * @param[in] dest The variable to write the result to (the type is a template parameter and the value type of the + * argument must be convertible in the type of dest for the retrieval to work, also see + * result value). + * @param[in] parser The ArgumentParser to get the value from. + * @param[in] pos The position of the argument to get the value of. + * @param[in] no Optional position for multi-value arguments (unsigned, defaults to 0). + * + * @return bool true if the retrieval was successful, false otherwise. + */ + +template +inline bool getArgumentValue(TValue & value, + ArgumentParser const & me, + unsigned argumentPosition, + unsigned argNo) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + return _convertArgumentValue(value, getArgument(me, argumentPosition), getArgumentValue(getArgument(me, argumentPosition), argNo)); +} + +template +inline bool getArgumentValue(TValue & value, + ArgumentParser const & me, + unsigned argumentPosition) +{ + return getArgumentValue(value, me, argumentPosition, 0); +} + +// ---------------------------------------------------------------------------- +// Function getArgumentFileExtension() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getArgumentFileExtension + * @headerfile + * @brief Retrieve the file extension of a file argument. + * + * @signature std::string argumentFileExtension(parser, pos[, argNo]); + * + * @param[in] parser The ArgumentParser to get the value from. + * @param[in] pos The position of the argument to query (unsigned). + * @param[in] argNo Optional position for multi-value options (unsigned, defaults to 0). + * + * @return std::string The extension of the argument if any. + * + * @see ArgumentParser#getOptionFileExtension + * + * @section Overriding File Extensions on the Command Line + * + * For each argument with type INPUT_FILE and OUTPUT_FILE, an option with the index + * arg-${idx}-file-ext is automatically added to the ArgumentParser (where ${idx} is the index + * of the original option). The extension can be overridden by specifying the argument. Thus, the user of + * the program could give the value "file.ext" to the parameter "0" and override the extension on the + * command line to "ext2" as follows: + * + * @code{.console} + * # program_name file.ext --arg-0-file-ext ext2 + * @endcode + */ + +inline std::string getArgumentFileExtension(ArgumentParser const & me, + unsigned argumentPosition, + unsigned argNo = 0) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + + + return getFileExtension(getArgument(me, argumentPosition), argNo); +} + +// ---------------------------------------------------------------------------- +// Function getOptionValues() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getOptionValues + * @headerfile + * @brief Returns all values of an option given on the command line. + * + * @signature TVector getOptionValues(parser, name); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] name The short or long name of the option to get (std::string). + * + * @return TVector The resulting values (std::vector<std::string>). + */ + +inline std::vector const & getOptionValues(ArgumentParser const & me, + std::string const & name) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + return getArgumentValues(getOption(me, name)); +} + +// ---------------------------------------------------------------------------- +// Function getArgumentValues() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getArgumentValues + * @headerfile + * @brief Returns all values of an argument given on the command line. + * + * @signature TVector getArgumentValues(parser, pos); + * + * @param[in] parser The ArgumentParser to query. + * @param[in] pos The position of the argument (unsigned, 0-based). + * + * @return TVector The resulting values (std::vector<std::string>). + */ + +inline std::vector const & getArgumentValues(ArgumentParser const & me, + unsigned argumentPosition) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + return getArgumentValues(getArgument(me, argumentPosition)); +} + +// ---------------------------------------------------------------------------- +// Function setDefaultValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setDefaultValue + * @headerfile + * @brief Set the default value of an option of an ArgumentParser. + * + * @signature void setDefaultValue(parser, name, v); + * + * @param[in] parser The ArgumentParser to set the default value to. + * @param[in] name The short or long name of the argument (std::string). + * @param[in] v The value to set (template parameter, must be streamable into a std::stringstream). + */ + +template +inline void setDefaultValue(ArgumentParser & me, + std::string const & name, + const TValue & value) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setDefaultValue(getOption(me, name), value); +} + +// ---------------------------------------------------------------------------- +// Function addDefaultValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#addDefaultValue + * @headerfile + * @brief Add/append a value to the default values for an option in an ArgumentParser. + * + * @signature void addDefaultValue(parser, name, v); + * + * @param[in,out] parser The ArgumentParser to append the default value to. + * @param[in] name The short or long name of the argument (std::string). + * @param[in] v The value to append (template parameter, must be streamable into a std::stringstream). + */ + +template +inline void addDefaultValue(ArgumentParser & me, + std::string const & name, + const TValue & value) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + addDefaultValue(getOption(me, name), value); +} + +// ---------------------------------------------------------------------------- +// Function setMinValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setMinValue + * @headerfile + * @brief Set smallest allowed value for an option or argument of an ArgumentParser. + * + * @signature void setMinValue(parser, name, v); + * @signature void setMinValue(parser, pos, v); + * + * @param[in,out] parser The ArgumentParser to set the minimal value for. + * @param[in] name The name of the option to set the minimal value for (std::string). + * @param[in] pos The position of the argument to set the minimal value for (unsigned, 0-based). + * @param[in] v The minimal value to set (std::string). + * + * @section Remarks + * + * The option/argument must have an integer or double type. + */ + +inline void setMinValue(ArgumentParser & me, + std::string const & name, + std::string const & _minValue) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setMinValue(getOption(me, name), _minValue); +} + +inline void setMinValue(ArgumentParser & me, + unsigned argumentPosition, + std::string const & _minValue) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + setMinValue(getArgument(me, argumentPosition), _minValue); +} + +// ---------------------------------------------------------------------------- +// Function setMaxValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setMaxValue + * @headerfile + * @brief Set largest allowed value for an option or argument of an ArgumentParser. + * + * @signature void setMaxValue(parser, name, v); + * @signature void setMaxValue(parser, pos, v); + * + * @param[in,out] parser The ArgumentParser to set the maximal value for. + * @param[in] name The name of the option to set the maximal value for (std::string). + * @param[in] pos The position of the argument to set the maximal value for (unsigned, 0-based). + * @param[in] v The maximal value to set (std::string). + * + * @section Remarks + * + * The option/argument must have an integer or double type. + */ + +inline void setMaxValue(ArgumentParser & me, + std::string const & name, + std::string const & _maxValue) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setMaxValue(getOption(me, name), _maxValue); +} + +inline void setMaxValue(ArgumentParser & me, + unsigned argumentPosition, + std::string const & _minValue) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + setMaxValue(getArgument(me, argumentPosition), _minValue); +} + +// ---------------------------------------------------------------------------- +// Function setValidValues() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setValidValues + * @headerfile + * @brief Set valid values for an argumetn or option of an ArgumentParser. + * + * @signature void setValidValues(parser, name, values); + * @signature void setValidValues(parser, pos, values); + * + * @param[in,out] parser The ArgumentParser to set the default values to. + * @param[in] name The name of the option (std::string). + * @param[in] pos The position of the argument (unsigned, 0-based). + * @param[in] values The values to set. Either a std::string with the values as space-separated list + * or a std::vector<std::string> with the values. + */ + +inline void setValidValues(ArgumentParser & me, + std::string const & name, + std::vector const & values) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setValidValues(getOption(me, name), values); + _copyValidValuesToFileExt(me, name); +} + +inline void setValidValues(ArgumentParser & me, + std::string const & name, + std::string const & values) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setValidValues(getOption(me, name), values); + _copyValidValuesToFileExt(me, name); +} + +inline void setValidValues(ArgumentParser & me, + unsigned argumentPosition, + std::vector const & values) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + setValidValues(getArgument(me, argumentPosition), values); + _copyValidValuesToFileExt(me, argumentPosition); +} + +inline void setValidValues(ArgumentParser & me, + unsigned argumentPosition, + std::string const & values) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + setValidValues(getArgument(me, argumentPosition), values); + _copyValidValuesToFileExt(me, argumentPosition); +} + +// ---------------------------------------------------------------------------- +// Function setHelpText() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#setHelpText + * @headerfile + * @brief Set the help text of an option or argument. + * + * @signature void setHelpText(parser, name, text); + * @signature void setHelpText(parser, pos, text); + * + * @param[in,out] parser The ArgumentParser object. + * @param[in] name The name of the option to set the help text for (std::string). + * @param[in] pos The position of the argument to set the help text for. + * @param[in] text The string to use for the help text (std::string). + */ + +inline void setHelpText(ArgumentParser & me, + std::string const & name, + std::string const & text) +{ + SEQAN_CHECK(hasOption(me, name), "Unknown option: %s", toCString(name)); + setHelpText(getOption(me, name), text); +} + +inline void setHelpText(ArgumentParser & me, + unsigned argumentPosition, + std::string const & text) +{ + SEQAN_CHECK(me.argumentList.size() > argumentPosition, + "Argument Parser has only %d arguments.", + me.argumentList.size()); + setHelpText(getArgument(me, argumentPosition), text); +} + +// ---------------------------------------------------------------------------- +// Function getFileExtensions() +// ---------------------------------------------------------------------------- + +/*! + * @fn ArgumentParser#getFileExtensions + * @headerfile + * @brief Returns file format extension given a format tag. + * + * @signature TVector getFormatExtension(tag); + * @signature TVector getFormatExtension(tagList); + * @signature TVector getFormatExtension(tagSelector); + * + * @param[in] tag A single file foramt, e.g. Fastq(). + * @param[in] tagList A list of file format (@link TagList @endlink). + * @param[in] tagSelector A file format selector (@link TagSelector @endlink). + * + * @return TVector A std::vector<std::string> with the allowed file format extensions. + */ + +template +inline std::vector +getFileExtensions(T const formatTag) +{ + std::vector extensions; + _getFileExtensions(extensions, formatTag); + return extensions; +} + + +} // namespace seqan + +#endif // SEQAN_INCLUDE_ARG_PARSE_ARGUMENT_PARSER_H_ diff --git a/seqan/arg_parse/tool_doc.h b/seqan/arg_parse/tool_doc.h new file mode 100644 index 0000000..a19a983 --- /dev/null +++ b/seqan/arg_parse/tool_doc.h @@ -0,0 +1,1613 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_ARG_PARSE_TOOL_DOC_H_ +#define SEQAN_INCLUDE_ARG_PARSE_TOOL_DOC_H_ + +#include + +#include +#include +#include + +namespace seqan { + +// ========================================================================== +// Forwards +// ========================================================================== + +class ToolDoc; +inline void clearEntries(ToolDoc & doc); +inline void append(ToolDoc & a, ToolDoc const & b); + +// ========================================================================== +// Tags, Classes, Enums +// ========================================================================== + +// -------------------------------------------------------------------------- +// Class ToolDocEntry_ +// -------------------------------------------------------------------------- + +// Base class for entries in the ToolDoc class. + +class ToolDocEntry_ +{ +public: + enum EntryType + { + SUBSECTION, SECTION, LINE, LIST_ITEM + }; + + virtual ~ToolDocEntry_() {} + + virtual EntryType getType() const = 0; +}; + +// -------------------------------------------------------------------------- +// Class ToolDocSection_ +// -------------------------------------------------------------------------- + +// A section in the ToolDoc class. + +class ToolDocSection_ : + public ToolDocEntry_ +{ +public: + CharString _title; + + ToolDocSection_(ToolDocSection_ const & sec) : + ToolDocEntry_(sec), _title(sec._title) + {} + + ToolDocSection_(CharString const & title) : + _title(title) + {} + + virtual EntryType getType() const + { + return SECTION; + } + +}; + +// -------------------------------------------------------------------------- +// Class ToolDocSubSection_ +// -------------------------------------------------------------------------- + +// A subsection. + +class ToolDocSubSection_ : + public ToolDocSection_ +{ +public: + ToolDocSubSection_(ToolDocSubSection_ const & sec) : + ToolDocSection_(sec) + {} + + ToolDocSubSection_(CharString const & title) : + ToolDocSection_(title) + {} + + virtual EntryType getType() const + { + return SUBSECTION; + } + +}; + +// -------------------------------------------------------------------------- +// Class ToolDocLine__ +// -------------------------------------------------------------------------- + +// A Line/Paragraph in ToolDoc documents. + +class ToolDocLine_ : + public ToolDocEntry_ +{ +public: + CharString _text; + // Evaluates to true if it is a paragraph and separated by .sp, false if it is a line, separated by .br. + bool _isPar; + + ToolDocLine_(ToolDocLine_ const & line) : + ToolDocEntry_(line), _text(line._text), _isPar(line._isPar) + {} + + ToolDocLine_(CharString const & text, bool isParagraph) : + _text(text), _isPar(isParagraph) + {} + + virtual EntryType getType() const + { + return LINE; + } + + bool isParagraph() const + { + return _isPar; + } + +}; + +// -------------------------------------------------------------------------- +// Class ToolDocListItem_ +// -------------------------------------------------------------------------- + +// A list item in ToolDoc documents. + +class ToolDocListItem_ : + public ToolDocEntry_ +{ +public: + CharString _term; + CharString _description; + + ToolDocListItem_(ToolDocListItem_ const & item) : + ToolDocEntry_(item), _term(item._term), _description(item._description) + {} + + ToolDocListItem_(CharString const & term, CharString const & description) : + _term(term), _description(description) + {} + + virtual EntryType getType() const + { + return LIST_ITEM; + } + +}; + +// -------------------------------------------------------------------------- +// Class ToolDocPrinter_ +// -------------------------------------------------------------------------- + +// Abstrace base class for ToolDoc printers. + +class ToolDocPrinter_ +{ +public: + virtual void print(std::ostream & stream, ToolDoc const & doc) = 0; +}; + +// -------------------------------------------------------------------------- +// Class ManToolDocPrinter_ +// -------------------------------------------------------------------------- + +// Print ToolDoc instance in man format. + +class ManToolDocPrinter_ : + public ToolDocPrinter_ +{ +public: + virtual void print(std::ostream & stream, ToolDoc const & doc); +}; + +// -------------------------------------------------------------------------- +// Class HtmlToolDocPrinter_ +// -------------------------------------------------------------------------- + +// Print ToolDoc instance in HTML format. + +class HtmlToolDocPrinter_ : + public ToolDocPrinter_ +{ +public: + void _maybeCloseList(std::ostream & stream, bool & isListOpen) + { + if (!isListOpen) + return; + + stream << "\n"; + isListOpen = false; + } + + void _maybeCloseParagraph(std::ostream & stream, bool & isParOpen) + { + if (!isParOpen) + return; + + stream << "

\n"; + isParOpen = false; + } + + // Converts formatting with \fI, \fB, and \fP to HTML. + template + TSequence _toHtml(TSequence const & input) const + { + TSequence buffer = xmlEscape(input); + TSequence result; + String openTags; + + typedef typename Iterator::Type TIterator; + TIterator endIt = end(input, Standard()); + for (TIterator it = begin(input, Standard()); it != endIt; goNext(it)) + { + if (*it == '\\') + { + // Handle escape sequence, we interpret only "\-", "\fI", and "\fB". + goNext(it); + SEQAN_ASSERT_NOT(it == endIt); + if (*it == '-') + { + appendValue(result, *it); + } + else if (*it == 'f') + { + goNext(it); + SEQAN_ASSERT_NOT(it == endIt); + if (*it == 'I') + { + appendValue(openTags, "em"); + append(result, ""); + } + else if (*it == 'B') + { + appendValue(openTags, "strong"); + append(result, ""); + } + else if (*it == 'P') + { + SEQAN_ASSERT_NOT(empty(openTags)); + append(result, ""); + eraseBack(openTags); + } + else + { + append(result, "\\f"); + appendValue(result, *it); + } + } + else + { + appendValue(result, '\\'); + appendValue(result, *it); + } + } + else + { + appendValue(result, *it); + } + } + + return result; + } + + virtual void print(std::ostream & stream, ToolDoc const & doc); +}; + +// -------------------------------------------------------------------------- +// Class TextToolDocPrinter_ +// -------------------------------------------------------------------------- + +// Print ToolDoc objects in Text format, suitable for console output. + +class TextToolDocPrinter_ : + public ToolDocPrinter_ +{ +public: + // Stores the relevant parameters of the documentation on the screen. + struct Layout_ + { + unsigned screenWidth; + unsigned defaultScreenWidth; + unsigned maximalScreenWidth; + unsigned minimalScreenWidth; + unsigned leftPadding; + unsigned centerPadding; + unsigned rightPadding; + unsigned leftColumnWidth; + unsigned rightColumnWidth; + unsigned rightColumnTab; + + Layout_() : + screenWidth(0), defaultScreenWidth(80), maximalScreenWidth(120), minimalScreenWidth(40), + leftPadding(4), centerPadding(2), rightPadding(2), leftColumnWidth(4), rightColumnWidth(0) + { + // Guess terminal screen width and set into layout. + unsigned cols = 0, rows = 0; + bool success = getTerminalSize(cols, rows); + screenWidth = (success && cols > 0) ? cols : defaultScreenWidth; + screenWidth = std::max(screenWidth, minimalScreenWidth); + screenWidth = std::min(screenWidth, maximalScreenWidth); + screenWidth -= rightPadding; + + rightColumnWidth = screenWidth - leftPadding - leftColumnWidth - centerPadding - rightPadding; + rightColumnTab = leftPadding + leftColumnWidth + centerPadding; + + // std::cerr << "screen width\t" << screenWidth << std::endl; + } + + }; + + Layout_ _layout; + + virtual void print(std::ostream & stream, ToolDoc const & doc); + + void _printSection(std::ostream & stream, ToolDocSection_ const & section) + { + std::ostream_iterator out(stream); + stream << '\n' << _toText("\\fB"); + std::transform(begin(section._title), end(section._title), out, static_cast < int(*)(int) > (toupper)); + stream << _toText("\\fP") << '\n'; + } + + void _printSubSection(std::ostream & stream, ToolDocSection_ const & section) + { + std::ostream_iterator out(stream); + stream << '\n' << _toText("\\fB"); + std::fill_n(out, _layout.leftPadding / 2, ' '); + stream << section._title << _toText("\\fP") << '\n'; + } + + void _printLine(std::ostream & stream, ToolDocLine_ const & line) + { + std::ostream_iterator out(stream); + std::fill_n(out, _layout.leftPadding, ' '); + + _printText(stream, line._text, _layout.leftPadding); + } + + CharString _toText(CharString const & str) const + { + CharString result; + + typedef Iterator::Type TIterator; + for (TIterator it = begin(str, Rooted()); !atEnd(it); goNext(it)) + { + if (*it == '\\') + { + // Handle escape sequence, we interpret only "\-", "\fI", and "\fB". + goNext(it); + SEQAN_ASSERT_NOT(atEnd(it)); + if (*it == '-') + { + appendValue(result, *it); + } + else if (*it == 'f') + { + goNext(it); + SEQAN_ASSERT_NOT(atEnd(it)); + if (*it == 'I') + { + if (isTerminal()) + append(result, "\033[4m"); + } + else if (*it == 'B') + { + if (isTerminal()) + append(result, "\033[1m"); + } + else if (*it == 'P') + { + if (isTerminal()) + append(result, "\033[0m"); + } + else + { + append(result, "\\f"); + appendValue(result, *it); + } + } + else + { + appendValue(result, '\\'); + appendValue(result, *it); + } + } + else + { + appendValue(result, *it); + } + } + + return result; + } + + void _printListItem(std::ostream & stream, ToolDocListItem_ const & listItem) + { + std::ostream_iterator out(stream); + + // Print term. + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText(listItem._term); + unsigned pos = _layout.leftPadding + length(listItem._term); + if (pos + _layout.centerPadding > _layout.rightColumnTab) + { + stream << '\n'; + pos = 0; + } + std::fill_n(out, _layout.rightColumnTab - pos, ' '); + + _printText(stream, listItem._description, _layout.rightColumnTab); + } + + // Returns width of text if printed, i.e. "\-" has length 1, "\fI", "\fB", "\fP" have length 0. + unsigned _textWidth(CharString const & text) + { + unsigned result = 0; + + for (unsigned i = 0; i < length(text); ++i) + { + if (text[i] != '\\') + { + result += 1; + continue; + } + + if (i + 1 == length(text)) + { + result += 1; // Will print "\\". + continue; + } + + if (text[i + 1] == '\\' || text[i + 1] == '-') + { + i += 1; + result += 1; + continue; // Will print '\\' or '-'. + } + + if (i + 2 == length(text)) + { + i += 1; + result += 2; // Will print two chars. + continue; + } + + if (text[i + 1] == 'f') + { + if (text[i + 2] == 'B' || text[i + 2] == 'I' || text[i + 2] == 'P') + i += 2; // Skip f and {B, I, P}. + else + result += 1; + } + } + + return result; + } + + // Print text, must be at tab already. + void _printText(std::ostream & stream, CharString const & text, unsigned tab) + { + unsigned pos = tab; + std::ostream_iterator out(stream); + + // Tokenize the text. + std::istringstream iss(toCString(text)); + std::vector tokens; + std::copy(std::istream_iterator(iss), std::istream_iterator(), + std::back_inserter >(tokens)); + + // Print the text. + SEQAN_ASSERT_LEQ(pos, tab); + std::fill_n(out, tab - pos, ' '); // go to tab + + pos = tab; + typedef std::vector::const_iterator TConstIter; + for (TConstIter it = tokens.begin(); it != tokens.end(); ++it) + { + if (it == tokens.begin()) + { + stream << _toText(*it); + pos += _textWidth(*it); + if (pos > _layout.screenWidth) + { + stream << '\n'; + std::fill_n(out, tab, ' '); + pos = tab; + } + } + else + { + if (pos + 1 + _textWidth(*it) > _layout.screenWidth) + { + // Would go over screen with next, print current word on next line. + stream << '\n'; + fill_n(out, tab, ' '); + stream << _toText(*it); + pos = tab + _textWidth(*it); + } + else + { + stream << ' '; + stream << _toText(*it); + pos += _textWidth(*it) + 1; + } + } + } + if (!empty(tokens)) + stream << '\n'; + } + +}; + +// -------------------------------------------------------------------------- +// Class ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @class ToolDoc + * @implements AssignableConcept + * @headerfile + * @brief Container for string documentation on a command line tool. + * + * @signature class ToolDoc; + * + * @section Remarks + * + * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows one to store + * and represent all information related to a command line tool that would normally go into a man page. It can be + * printed to STL streams in different formats, currently plain text, HTML and man pages are supported. + * + * You can also use basic formatting in text. This formatting is tailored to the usage on the command line. Use + * \fB to start bold font, \fI to start italic font and \fP to use the previous font (of + * course, use correct escaping of the backslash in C strings, so use "\\fB", "\\fI", and + * "\\fP" in your code. + * + * @section Examples + * + * The following shows a brief example of how to use @link ToolDoc @endlink. + * + * @code{.cpp} + * ToolDoc doc; + * setName(doc, "RazerS"); + * setShortDescription(doc, "Read mapping with controllable sensitivity."); + * setDate(doc, "04 March 2012"); + * setVersion(doc, "1.0"); + * setCategory(doc, "Read Mapping"); + * setManTitle(doc, "SeqAn Apps Reference Manual"); + * + * addSection(doc, "Synopsis"); + * addText(doc, "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fIREADS\\fP", false); + * addText(doc, + * "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fILEFT_READS\\fP " + * "\\fIRIGHT_READS\\fP", false); + * + * addSection(doc, "Description"); + * addText(doc, + * "RazerS is a read mapper with controllable, sensitivity. This " + * "means that you can find all read matches in the reference sequence " + * "and optionally, you can trade lower sensitivity for better " + * "performance."); + * addText(doc, + * "What's special about RazerS is that you can control the sensitivity."); + * + * addSection(doc, "Options"); + * addSubSection(doc, "Main Options"); + * addListItem(doc, "\\fB-id\\fP, \\fB--indels\\fP", + * "Enable mapping with indels enabled."); + * addListItem(doc, "\\fB-i\\fP, \\fB--identity\\fP \\fIIDENTITY\\fP", + * "Set minimal identity of matches to find."); + * + * print(std::cout, doc, "text"); + * @endcode + * + * @see ToolDoc#addText + * @see ToolDoc#addListItem + * @see ArgumentParser + */ + +/*! + * @fn ToolDoc::ToolDoc + * @brief Constructor + * + * @signature ToolDoc::ToolDoc() + */ + +class ToolDoc +{ +public: + CharString _name; + CharString _shortDescription; + CharString _url; + CharString _date; + CharString _version; + CharString _shortCopyright; + CharString _longCopyright; + CharString _citation; + CharString _manTitle; + CharString _category; + unsigned _manSection; + + String _entries; + + enum Format {FORMAT_HTML, FORMAT_MAN, FORMAT_TXT}; + + ToolDoc() : + _manSection(1) {} + + ToolDoc(ToolDoc const & toolDoc) : + _name(toolDoc._name), _shortDescription(toolDoc._shortDescription), _url(toolDoc._url), + _date(toolDoc._date), _version(toolDoc._version), _shortCopyright(toolDoc._shortCopyright), + _longCopyright(toolDoc._longCopyright), _citation(toolDoc._citation), _manTitle(toolDoc._manTitle), + _category(toolDoc._category), _manSection(1) + { + append(*this, toolDoc); + } + + ~ToolDoc() + { + clearEntries(*this); + } + + void print(std::ostream & stream, Format format) const + { + switch (format) + { + case FORMAT_HTML: + { + HtmlToolDocPrinter_ p; + p.print(stream, *this); + } + break; + + case FORMAT_MAN: + { + ManToolDocPrinter_ p; + p.print(stream, *this); + } + break; + + case FORMAT_TXT: + { + TextToolDocPrinter_ p; + p.print(stream, *this); + } + break; + } + } + + void print(std::ostream & stream, CharString const & format) const + { + if (format == "html") + print(stream, FORMAT_HTML); + else if (format == "man") + print(stream, FORMAT_MAN); + else + print(stream, FORMAT_TXT); + } + +}; + +// ========================================================================== +// Metafunctions +// ========================================================================== + +// ========================================================================== +// Functions +// ========================================================================== + +// -------------------------------------------------------------------------- +// Function append() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#append + * @headerfile + * @brief Append two @link ToolDoc @endlink objects. + * + * @signature void append(a, b); + * + * @param[in,out] a This object is updated + * @param[in] b This object is appended to b. + */ + +inline void append(ToolDoc & a, ToolDoc const & b) +{ + for (unsigned i = 0; i < length(b._entries); ++i) + { + // TODO(holtgrew): This is quite ugly and can be made better with shared_ptr<> in C++11. + switch (b._entries[i]->getType()) + { + case ToolDocEntry_::SUBSECTION: + appendValue(a._entries, new ToolDocSubSection_(*static_cast(b._entries[i]))); + break; + + case ToolDocEntry_::SECTION: + appendValue(a._entries, new ToolDocSection_(*static_cast(b._entries[i]))); + break; + + case ToolDocEntry_::LINE: + appendValue(a._entries, new ToolDocLine_(*static_cast(b._entries[i]))); + break; + + case ToolDocEntry_::LIST_ITEM: + appendValue(a._entries, new ToolDocListItem_(*static_cast(b._entries[i]))); + break; + } + } +} + +// -------------------------------------------------------------------------- +// Function setName() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setName + * @headerfile + * @brief Set the tool name. + * + * @signature void setName(toolDoc, name); + * + * @param[in,out] toolDoc The ToolDoc object to the set the name for. + * @param[in] name The name of the tool (@link CharString @endlink). + */ + +inline void setName(ToolDoc & doc, CharString const & name) +{ + doc._name = name; +} + +// -------------------------------------------------------------------------- +// Function getName() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getName + * @headerfile + * @brief Get the tool name. + * + * @signature CharString getName(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the name for. + * + * @return CharString Resulting name (@link CharString @endlink). + */ + +inline CharString const & getName(ToolDoc const & doc) +{ + return doc._name; +} + +// -------------------------------------------------------------------------- +// Function setCategory() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setCategory + * @headerfile + * @brief Set the tool name. + * + * @signature void setName(toolDoc, name); + * + * @param[in,out] toolDoc The ToolDoc object to the set the name for. + * @param[in] name The name of the tool (@link CharString @endlink). + */ + +inline void setCategory(ToolDoc & doc, CharString const & category) +{ + doc._category = category; +} + +// -------------------------------------------------------------------------- +// Function getCategory() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getCategory + * @headerfile + * @brief Get the tool category. + * + * @signature CharString getCategory(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the category for. + * + * @return CharString Resulting category (@link CharString @endlink). + */ + +inline CharString const & getCategory(ToolDoc const & doc) +{ + return doc._category; +} + +// -------------------------------------------------------------------------- +// Function setShortDescription() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setShortDescription + * @headerfile + * @brief Set the tool short description. + * + * @signature void setShortDescription(toolDoc, text); + * + * @param[in,out] toolDoc The ToolDoc object to the set the short description for. + * @param[in] text The short description of the tool (@link CharString @endlink). + */ + +inline void setShortDescription(ToolDoc & doc, CharString const & shortDescription) +{ + doc._shortDescription = shortDescription; +} + +// -------------------------------------------------------------------------- +// Function getShortDescription() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getShortDescription + * @headerfile + * @brief Get the tool short description. + * + * @signature CharString getShortDescription(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the short description for. + * + * @return CharString Resulting short description (@link CharString @endlink). + */ + +inline CharString const & getShortDescription(ToolDoc const & doc) +{ + return doc._shortDescription; +} + +// -------------------------------------------------------------------------- +// Function setUrl() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setUrl + * @headerfile + * @brief Set the url string to the app repository or website. + * + * @signature void setUrl(toolDoc, str); + * + * @param[in,out] toolDoc The ToolDoc object to the set the version string for. + * @param[in] str The url string of the tool (@link CharString @endlink). + */ + +inline void setUrl(ToolDoc & doc, CharString url) +{ + std::swap(doc._url, url); +} + +// -------------------------------------------------------------------------- +// Function getUrl() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getUrl + * @headerfile + * @brief Get the url string to the app repository or website. + * + * @signature CharString getUrl(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the version string. + * + * @return CharString Resulting url string (@link CharString @endlink). + */ + +inline CharString const & getUrl(ToolDoc const & doc) +{ + return doc._url; +} + +// -------------------------------------------------------------------------- +// Function setDate() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setDate + * @headerfile + * @brief Set the date string. + * + * @signature void setName(toolDoc, str); + * + * @param[in,out] toolDoc The ToolDoc object to the set the date string for. + * @param[in] str The date string of the tool (@link CharString @endlink). + */ + +inline void setDate(ToolDoc & doc, CharString const & date) +{ + doc._date = date; +} + +// -------------------------------------------------------------------------- +// Function getDate() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getDate + * @headerfile + * @brief Get the date. + * + * @signature CharString getDate(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the date from. + * + * @return CharString Resulting date string (@link CharString @endlink). + */ + +inline CharString const & getDate(ToolDoc const & doc) +{ + return doc._date; +} + +// -------------------------------------------------------------------------- +// Function setVersion() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setVersion + * @headerfile + * @brief Set the tool version string. + * + * @signature void setVersion(toolDoc, str); + * + * @param[in,out] toolDoc The ToolDoc object to the set the version string for. + * @param[in] str The version string of the tool (@link CharString @endlink). + */ + +inline void setVersion(ToolDoc & doc, CharString const & version) +{ + doc._version = version; +} + +// -------------------------------------------------------------------------- +// Function getVersion() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getVersion + * @headerfile + * @brief Get the tool version string. + * + * @signature CharString getVersion(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the version string. + * + * @return CharString Resulting version string (@link CharString @endlink). + */ + +inline CharString const & getVersion(ToolDoc const & doc) +{ + return doc._version; +} + +// -------------------------------------------------------------------------- +// Function setShortCopyright() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setShortCopyright + * @headerfile + * @brief Set the tool short copyright string. + * + * @signature void setShortCopyright(toolDoc, str); + * + * @param[in,out] toolDoc The ToolDoc object to the set the short copyright string for. + * @param[in] str The short copyright string of the tool (@link CharString @endlink). + */ + +inline void setShortCopyright(ToolDoc & doc, CharString const & shortCopyright) +{ + doc._shortCopyright = shortCopyright; +} + +// -------------------------------------------------------------------------- +// Function getShortCopyright() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getShortCopyright + * @headerfile + * @brief Get the tool short copyright string. + * + * @signature CharString getShortCopyright(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the short copyright string. + * + * @return CharString Resulting short copyright string (@link CharString @endlink). + */ + +inline CharString const & getShortCopyright(ToolDoc const & doc) +{ + return doc._shortCopyright; +} + +// -------------------------------------------------------------------------- +// Function setLongCopyright() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setLongCopyright + * @headerfile + * @brief Set the tool long copyright string. + * + * @signature void setLongCopyright(toolDoc, str); + * + * @param[in,out] toolDoc The ToolDoc object to the set the long copyright string for. + * @param[in] str The long copyright string of the tool (@link CharString @endlink). + */ + +inline void setLongCopyright(ToolDoc & doc, CharString const & longCopyright) +{ + doc._longCopyright = longCopyright; +} + +// -------------------------------------------------------------------------- +// Function getLongCopyright() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getLongCopyright + * @headerfile + * @brief Get the tool long copyright string. + * + * @signature CharString getLongCopyright(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the long copyright string. + * + * @return CharString Resulting long copyright string (@link CharString @endlink). + */ + +inline CharString const & getLongCopyright(ToolDoc const & doc) +{ + return doc._longCopyright; +} + +// -------------------------------------------------------------------------- +// Function setCitation() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setCitation + * @headerfile + * @brief Set the tool citation string. + * + * @signature void setCitation(toolDoc, str); + * + * @param[in,out] toolDoc The ToolDoc object to the set the citation string for. + * @param[in] str The citation string of the tool (@link CharString @endlink). + */ + +inline void setCitation(ToolDoc & doc, CharString const & citation) +{ + doc._citation = citation; +} + +// -------------------------------------------------------------------------- +// Function getCitation() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getCitation + * @headerfile + * @brief Get the tool citation string. + * + * @signature CharString getCitation(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the citation string. + * + * @return CharString Resulting citation string (@link CharString @endlink). + */ + +inline CharString const & getCitation(ToolDoc const & doc) +{ + return doc._citation; +} + + +// -------------------------------------------------------------------------- +// Function setManTitle() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#setManTitle + * @headerfile + * @brief Set the man title. + * + * @signature void setTitle(toolDoc, title); + * + * @param[in,out] toolDoc The ToolDoc object to the set the title for. + * @param[in] title The title of the tool (@link CharString @endlink). + */ + +inline void setManTitle(ToolDoc & doc, CharString const & title) +{ + doc._manTitle = title; +} + +// -------------------------------------------------------------------------- +// Function getManTitle() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#getManTitle + * @headerfile + * @brief Get the tool man page title of. + * + * @signature CharString getManTitle(toolDoc); + * + * @param[in] toolDoc The ToolDoc object to the get the man page title. + * + * @return CharString Resulting man page title (@link CharString @endlink). + */ + +inline CharString const & getManTitle(ToolDoc & doc) +{ + return doc._manTitle; +} + +// -------------------------------------------------------------------------- +// Function addSection()ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#addSection + * @headerfile + * @brief Add a section with the given title. + * + * @signature void addSection(toolDoc, title); + * + * @param[in,out] toolDoc The ToolDoc object to add a section for. + * @param[in] title The section title (@link CharString @endlink). + */ + +inline void addSection(ToolDoc & doc, CharString const & title) +{ + appendValue(doc._entries, new ToolDocSection_(title)); +} + +// -------------------------------------------------------------------------- +// Function addSubSection() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#addSubSection + * @headerfile + * @brief Add a subsection with the given title. + * + * @signature void addSubSection(toolDoc, title); + * + * @param[in,out] toolDoc The ToolDoc object to add a subsection for. + * @param[in] title The subsection title (@link CharString @endlink). + */ + +inline void addSubSection(ToolDoc & doc, CharString const & title) +{ + appendValue(doc._entries, new ToolDocSubSection_(title)); +} + +// -------------------------------------------------------------------------- +// Function addText() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#addText + * @headerfile + * @brief Add a text line/paragraph to ToolDoc. + * + * @signature void addText(toolDoc, text[, isParagraph]); + * + * @param[in,out] toolDoc The ToolDoc to add the text to. + * @param[in] text The text to add (@link CharString @endlink). + * @param[in] isParagraph Whether to insert as paragraph or just a line (only one line break if not a paragraph). + */ + +inline void addText(ToolDoc & doc, CharString const & text, bool isParagraph) +{ + appendValue(doc._entries, new ToolDocLine_(text, isParagraph)); +} + +inline void addText(ToolDoc & doc, CharString const & text) +{ + addText(doc, text, true); +} + +// -------------------------------------------------------------------------- +// Function addListItem() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#addListItem + * @headerfile + * @brief Add a list item to a ToolDoc. + * + * @signature void addListItem(toolDoc, key, value); + * + * @param[in,out] toolDoc The ToolDoc object to add the list item to. + * @param[in] key The key for the list (@link CharString @endlink). + * @param[in] value The value for the list (@link CharString @endlink). + */ + +inline void addListItem(ToolDoc & doc, CharString const & key, CharString const & value) +{ + appendValue(doc._entries, new ToolDocListItem_(key, value)); +} + +// -------------------------------------------------------------------------- +// Function print() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#print + * @headerfile + * @brief Print ToolDoc object in a given format. + * + * @signature void print(stream, toolDoc, format); + * + * @param[in,out] stream The std::ostream to write to. + * @param[in] toolDoc The ToolDoc to print. + * @param[in] format The format, one of {"html", "man", "txt"}. + */ + +inline void print(std::ostream & stream, ToolDoc const & doc, CharString const & format) +{ + doc.print(stream, format); +} + +// -------------------------------------------------------------------------- +// Function clearEntries() ToolDoc +// -------------------------------------------------------------------------- + +/*! + * @fn ToolDoc#clearEntries + * @headerfile + * @brief Clear entries from ToolDoc. + * + * @signature void clearEntries(toolDoc); + * + * @param[in,out] toolDoc The ToolDoc object to clear entries from. + */ + +inline void clearEntries(ToolDoc & doc) +{ + typedef Iterator, Rooted>::Type TIter; + for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it)) + delete *it; + clear(doc._entries); +} + +// -------------------------------------------------------------------------- +// Function HtmlDocPrinter_::print() +// -------------------------------------------------------------------------- + +inline +void HtmlToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc) +{ + // Print HTML boilerplate header. + stream << "\n" + << "\n" + << "\n" + << "\n" + << "" << xmlEscape(doc._name) << " — " << xmlEscape(doc._shortDescription) << "\n" + << "\n" + << "\n"; + + stream << "

" << _toHtml(doc._name) << "

\n" + << "
" << _toHtml(doc._shortDescription) << "
\n"; + + typedef Iterator const, Rooted>::Type TIter; + bool isDl = false; + bool isP = false; + for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it)) + { + SEQAN_ASSERT_NOT_MSG(isDl && isP, "Current
and

are mutually exclusive."); + ToolDocEntry_ * entry = *it; + + switch (entry->getType()) + { + case ToolDocEntry_::SECTION: + { + _maybeCloseList(stream, isDl); + _maybeCloseParagraph(stream, isP); + ToolDocSection_ const * sec = static_cast(entry); + stream << "

" << _toHtml(sec->_title) << "

\n"; + } + break; + + case ToolDocEntry_::SUBSECTION: + { + _maybeCloseList(stream, isDl); + _maybeCloseParagraph(stream, isP); + ToolDocSection_ const * sec = static_cast(entry); + stream << "

" << _toHtml(sec->_title) << "

\n"; + } + break; + + case ToolDocEntry_::LINE: + { + ToolDocLine_ const * line = static_cast(entry); + _maybeCloseList(stream, isDl); + if (!isP) + { + stream << "

\n"; + isP = true; + } + stream << _toHtml(line->_text) << "\n"; + if (line->isParagraph()) + _maybeCloseParagraph(stream, isP); + else + stream << "
\n"; + } + break; + + case ToolDocEntry_::LIST_ITEM: + { + _maybeCloseParagraph(stream, isP); + ToolDocListItem_ const * item = static_cast(entry); + if (!isDl) + { + stream << "

\n"; + isDl = true; + } + stream << "
" << _toHtml(item->_term) << "
\n" + << "
" << _toHtml(item->_description) << "
\n"; + } + break; + } + } + _maybeCloseList(stream, isDl); + + // Print version, date and url. + stream << "

Version

\n" + << "Last update: " << _toHtml(doc._date) << "
\n" + << doc._name << " version: " << doc._version << "
\n" + << "SeqAn version: " << SEQAN_VERSION_MAJOR << '.' << SEQAN_VERSION_MINOR << '.' + << SEQAN_VERSION_PATCH; + if (SEQAN_VERSION_PRE_RELEASE != 0) + stream << "-pre" << SEQAN_VERSION_PRE_RELEASE; + if (!empty(doc._url)) + { + stream << "

Url

\n" + << doc._url << "
\n"; + } + stream << "
\n"; + + // Print legal stuff + if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation))) + { + stream << "

Legal

\n"; + + if (!empty(doc._shortCopyright)) + stream << doc._name << " Copyright: " + << doc._shortCopyright << "
\n"; + + stream << "SeqAn Copyright: 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
\n"; + + if (!empty(doc._citation)) + stream << "In your academic works please cite: " << doc._citation << "
\n"; + else + stream << ""; + + if (!empty(doc._longCopyright)) + stream << "For full copyright and/or warranty information see --copyright.\n"; + } + + // Print HTML boilerplate footer. + stream << ""; +} + +// -------------------------------------------------------------------------- +// Function TextDocPrinter_::print() +// -------------------------------------------------------------------------- + +inline +void TextToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc) +{ + std::ostream_iterator out(stream); + + stream << doc._name; + if (!empty(doc._shortDescription)) + stream << " - " << doc._shortDescription; + stream << "\n"; + unsigned len = _textWidth(doc._name) + (empty(doc._shortDescription) ? 0 : 3) + _textWidth(doc._shortDescription); + std::fill_n(out, len, '='); + stream << '\n'; + + typedef Iterator const, Rooted>::Type TIter; + bool prevWasParagraph = false; // Stores whether to add a line break. + for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it)) + { + ToolDocEntry_ * entry = *it; + + switch (entry->getType()) + { + case ToolDocEntry_::SECTION: + { + ToolDocSection_ const * sec = static_cast(entry); + _printSection(stream, *sec); + prevWasParagraph = false; + } + break; + + case ToolDocEntry_::SUBSECTION: + { + ToolDocSection_ const * sec = static_cast(entry); + _printSubSection(stream, *sec); + prevWasParagraph = false; + } + break; + + case ToolDocEntry_::LINE: + { + if (prevWasParagraph) + stream << '\n'; + ToolDocLine_ const * line = static_cast(entry); + _printLine(stream, *line); + prevWasParagraph = line->isParagraph(); + } + break; + + case ToolDocEntry_::LIST_ITEM: + { + if (prevWasParagraph) + stream << '\n'; + ToolDocListItem_ const * item = static_cast(entry); + _printListItem(stream, *item); + prevWasParagraph = false; + } + break; + } + } + + // Print version, date and url. + stream << "\n" << _toText("\\fB") << "VERSION" << _toText("\\fP") << "\n"; + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText("\\fB") << "Last update: " << _toText("\\fP") << doc._date << "\n"; + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText("\\fB") << doc._name << " version: " << _toText("\\fP") << doc._version << "\n"; + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText("\\fB") << "SeqAn version: " << _toText("\\fP") << SEQAN_VERSION_MAJOR << '.' + << SEQAN_VERSION_MINOR << '.' << SEQAN_VERSION_PATCH; + if (SEQAN_VERSION_PRE_RELEASE != 0) + stream << "-pre" << SEQAN_VERSION_PRE_RELEASE; + if (!empty(doc._url)) + { + stream << "\n" << _toText("\\fB") << "URL" << _toText("\\fP") << "\n"; + std::fill_n(out, _layout.leftPadding, ' '); + stream << doc._url << "\n"; + } + stream << "\n"; + + // Print legal stuff + if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation))) + { + stream << "\n" << _toText("\\fB") << "LEGAL" << _toText("\\fP") << "\n"; + + if (!empty(doc._shortCopyright)) + { + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText("\\fB") << doc._name << " Copyright: " + << _toText("\\fP") << doc._shortCopyright << "\n"; + } + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText("\\fB") << "SeqAn Copyright: " << _toText("\\fP") + << "2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n"; + if (!empty(doc._citation)) + { + std::fill_n(out, _layout.leftPadding, ' '); + stream << _toText("\\fB") << "In your academic works please cite: " << _toText("\\fP") + << doc._citation << "\n"; + } + if (!empty(doc._longCopyright)) + { + std::fill_n(out, _layout.leftPadding, ' '); + stream << "For full copyright and/or warranty information see " << _toText("\\fB") + << "--copyright" << _toText("\\fP") << ".\n"; + } + } +} + +inline +void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc) +{ + std::ostream_iterator out(stream); + + // Print .TH line. + stream << ".TH "; + std::transform(begin(doc._name), end(doc._name), out, static_cast < int(*)(int) > (toupper)); + stream << " " << doc._manSection << " \"" << doc._date << "\" \""; + std::transform(begin(doc._name), end(doc._name), out, static_cast < int(*)(int) > (tolower)); + stream << " " << doc._version << "\" \"" << doc._manTitle << "\"\n"; + + // Print NAME section. + stream << ".SH NAME\n" + << doc._name << " \\- " << doc._shortDescription << std::endl; + + // Print text. + typedef Iterator const, Rooted>::Type TIter; + bool isFirstInSection = true; + for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it)) + { + ToolDocEntry_ * entry = *it; + switch (entry->getType()) + { + case ToolDocEntry_::SUBSECTION: + { + ToolDocSubSection_ const * sec = static_cast(entry); + stream << ".SS " << sec->_title << "\n"; + isFirstInSection = true; + } + break; + + case ToolDocEntry_::SECTION: + { + ToolDocSection_ const * sec = static_cast(entry); + stream << ".SH "; + std::transform(begin(sec->_title), end(sec->_title), out, static_cast < int(*)(int) > (toupper)); + stream << "\n"; + isFirstInSection = true; + } + break; + + case ToolDocEntry_::LINE: + { + ToolDocLine_ const * line = static_cast(entry); + if (!isFirstInSection && line->isParagraph()) + stream << ".sp\n"; + else if (!isFirstInSection && !line->isParagraph()) + stream << ".br\n"; + stream << line->_text << "\n"; + isFirstInSection = false; + } + break; + + case ToolDocEntry_::LIST_ITEM: + { + ToolDocListItem_ const * item = static_cast(entry); + stream << ".TP\n" + << item->_term << "\n" + << item->_description << "\n"; + isFirstInSection = false; + } + break; + } + } + + // Print legal stuff + if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation))) + { + stream << ".SH LEGAL\n"; + + if (!empty(doc._shortCopyright)) + stream << "\\fB" << doc._name << " Copyright:\\fR " << doc._shortCopyright << "\n.br\n"; + + stream << "\\fBSeqAn Copyright:\\fR 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n.br\n"; + + if (!empty(doc._citation)) + stream << "\\fBIn your academic works please cite:\\fR " << doc._citation << "\n.br\n"; + + if (!empty(doc._longCopyright)) + stream << "For full copyright and/or warranty information see \\fB--copyright\\fR.\n"; + } +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_MISC_TOOL_DOC_H_ diff --git a/seqan/arg_parse/xml_support.h b/seqan/arg_parse/xml_support.h new file mode 100644 index 0000000..6e14d40 --- /dev/null +++ b/seqan/arg_parse/xml_support.h @@ -0,0 +1,95 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Stephan Aiche +// ========================================================================== + +#ifndef INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_ +#define INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function _xmlEscape() +// ---------------------------------------------------------------------------- + +/* + * make sure that the text we put into the XML does not break the XML + * candidates are + * " -> " + * ' -> ' + * & -> & + * < -> < + * > -> > + */ +template +TSequence xmlEscape(TSequence const & original) +{ + typedef typename Iterator::Type TSequenceIterator; + TSequence escaped; + TSequenceIterator endIter = end(original, Standard()); + for (TSequenceIterator ch = begin(original, Standard()); ch != endIter; goNext(ch)) + { + if (value(ch) == '"') + append(escaped, """); + else if (value(ch) == '\'') + append(escaped, "'"); + else if (value(ch) == '&') + append(escaped, "&"); + else if (value(ch) == '<') + append(escaped, "<"); + else if (value(ch) == '>') + append(escaped, ">"); + else + appendValue(escaped, *ch); + } + return escaped; +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_ARG_PARSE_XML_SUPPORT_H_ diff --git a/seqan/bam_io.h b/seqan/bam_io.h new file mode 100644 index 0000000..f9f9842 --- /dev/null +++ b/seqan/bam_io.h @@ -0,0 +1,96 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// Author: David Weese +// ========================================================================== +// Facade header for module bam_io. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_H_ +#define INCLUDE_SEQAN_BAM_IO_H_ + +// =========================================================================== +// Prerequisites. +// =========================================================================== + +#include +#include +#include +#include +#include +#include + +// =========================================================================== +// Data Structures & Conversion. +// =========================================================================== + +#include +#include +#include +#include +#include +#include + +// =========================================================================== +// Actual I/O Code. +// =========================================================================== + +#include +#include +#include +#include + +// =========================================================================== +// Easy BAM / SAM I/O. +// =========================================================================== + +#include + +// =========================================================================== +// Utility Routines. +// =========================================================================== + +#include + +// Not included by default, requires C++11 +//#include + +// =========================================================================== +// BAM Index Related. +// =========================================================================== + +// BAM indices are only available when ZLIB is available. +#if SEQAN_HAS_ZLIB +#include +#endif // #if SEQAN_HAS_ZLIB + +#endif // INCLUDE_SEQAN_BAM_IO_H_ diff --git a/seqan/bam_io/bam_alignment_record.h b/seqan/bam_io/bam_alignment_record.h new file mode 100644 index 0000000..4e694d5 --- /dev/null +++ b/seqan/bam_io/bam_alignment_record.h @@ -0,0 +1,612 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// The class BamAlignmentRecord, flag checking methods, flag constants. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +class BamAlignmentRecord; +inline void clear(BamAlignmentRecord & record); + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @enum BamFlags + * @headerfile + * @brief Shortcuts to the bitmask flags for BAM/SAM files. + * + * @signature enum BamFlags; + * + * @val BamFlags BAM_FLAG_MULTIPLE = 0x0001; + * @brief Template has multiple fragments in sequencing. + * + * @val BamFlags BAM_FLAG_ALL_PROPER = 0x0002; + * @brief All fragments in the template are properly mapped. + * + * @val BamFlags BAM_FLAG_UNMAPPED = 0x0004; + * @brief This fragment is unmapped. + * + * @val BamFlags BAM_FLAG_NEXT_UNMAPPED = 0x0008; + * @brief Next fragment in template is unmapped. + * + * @val BamFlags BAM_FLAG_RC = 0x0010; + * @brief Fragment is reverse-complemented. + * + * @val BamFlags BAM_FLAG_NEXT_RC = 0x0020; + * @brief Next fragment in template is reverse-complemented. + * + * @val BamFlags BAM_FLAG_FIRST = 0x0040; + * @brief This fragment is the first one in its template. + * + * @val BamFlags BAM_FLAG_LAST = 0x0080; + * @brief This fragment is the last one in its template (second in case of paired sequencing). + * + * @val BamFlags BAM_FLAG_SECONDARY = 0x0100; + * @brief Secondary alignment. + * + * @val BamFlags BAM_FLAG_QC_NO_PASS = 0x0200; + * @brief Does not pass quality controls. + * + * @val BamFlags BAM_FLAG_DUPLICATE = 0x0400; + * @brief PCR or optical duplicate. + * + * @var BamFlags BAM_FLAG_SUPPLEMENTARY = 0x0800; + * @brief Supplementary alignment. + */ + +enum BamFlags +{ + BAM_FLAG_MULTIPLE = 0x0001, + BAM_FLAG_ALL_PROPER = 0x0002, + BAM_FLAG_UNMAPPED = 0x0004, + BAM_FLAG_NEXT_UNMAPPED = 0x0008, + BAM_FLAG_RC = 0x0010, + BAM_FLAG_NEXT_RC = 0x0020, + BAM_FLAG_FIRST = 0x0040, + BAM_FLAG_LAST = 0x0080, + BAM_FLAG_SECONDARY = 0x0100, + BAM_FLAG_QC_NO_PASS = 0x0200, + BAM_FLAG_DUPLICATE = 0x0400, + BAM_FLAG_SUPPLEMENTARY = 0x0800 +}; + +template +struct BamTypeChar +{ + enum + { + VALUE = + (IsSameType::VALUE)? 'A': + (IsSameType::VALUE)? 'c': + (IsSameType::VALUE)? 'C': + (IsSameType::VALUE)? 's': + (IsSameType::VALUE)? 'S': + (IsSameType::VALUE)? 'i': + (IsSameType::VALUE)? 'I': + (IsSameType::VALUE)? 'f': +// (IsSameType::VALUE)? 'd': + (IsSequence::VALUE)? 'Z': + '?' + }; +}; + +// List of primitive BAM types (ordered by expected usage frequency) +typedef TagList > > > > > > > BamTagTypes; + +// ---------------------------------------------------------------------------- +// Class BamAlignmentRecord +// ---------------------------------------------------------------------------- + +/*! + * @class BamAlignmentRecord + * @headerfile + * @implements FormattedFileRecordConcept + * @signature class BamAlignmentRecord; + * @brief Represent a record from a BAM or SAM file. + * + * @section Remarks + * + * While also used to represent SAM records, the type is called BamAlignmentRecord since the data directly + * reflects a BAM records (0-based positions, identify references by id, and tags are stored in BAM format. + * + * @see BamFileIn + * @see BamFileOut + */ + +/*! + * @var uint32_t BamAlignmentRecord::INVALID_POS + * @brief Static member with invalid sentinel/position value (-1). + * + * @var uint32_t BamAlignmentRecord::INVALID_REFID + * @brief Static member with invalid sentinel/position value (-1). + * + * @var uint32_t BamAlignmentRecord::INVALID_LEN + * @brief Static member with invalid/sentinel reference ids (0 as in BAM/SAM). + * + * @var CharString BamAlignmentRecord::qName; + * @brief The query/read name. + * + * Note that the reads of a template all of the same query name and are differentiated by their position + * and the BAM_FLAG_FIRST/BAM_FLAG_LAST flag values. + * + * @var uint16_t BamAlignmentRecord::flag; + * @brief The flag of this mapping. + * + * See @link BamFlags @endlink for flag constants and also see the hasFlag*() functions. + * + * @var int32_t BamAlignmentRecord::rID + * @brief ID of reference for this fragment mapping (0-based, INVALID_REFID for '*' in SAM). + * + * @var int32_t BamAlignmentRecord::beginPos + * @brief Begin position of the alignment (0-based, INVALID_POS for '0' in SAM). + * + * @var uint8_t BamAlignmentRecord::mapQ; + * @brief Mapping quality (255 for '*'). + * + * @var uint16_t BamAlignmentRecord::bin; + * @brief The bin of the alignment, automatically computed when writing BAM. + * + * @var TCigarString BamAlignmentRecord::cigar; + * @brief The CIGAR string for the BAM alignment (of type String >). + * + * @var int32_t BamAlignmentRecord::rNextId; + * @brief The ID of the reference where the next fragment in this template aligns. + * + * INVALID_REFID for '*'. + * + * @var int32_t BamAlignmentRecord::pNext; + * @brief Position on the reference where the next fragment in this template aligns. + * + * INVALID_POS for '*'. + * + * @var int32_t BamAlignmentRecord::tLen; + * @brief The inferred template size. + * + * INVALID_LEN for '*'. + * + * @var CharString BamAlignmentRecord::seq; + * @brief The fragment sequence. + * + * @var CharString BamAlignmentRecord::qual; + * @brief The PHRED quality values of the sequence (as in SAM), empty for '*'. + * + * @var CharString BamAlignmentRecord::tags; + * @brief Raw BAM tag string, use @link BamTagsDict @endlink for comfortable access. + */ + +struct BamAlignmentRecordCore +{ + int32_t rID; + int32_t beginPos; + mutable uint32_t _l_qname:8; + uint32_t mapQ:8; + mutable uint32_t bin:16; + mutable uint32_t _n_cigar:16; + uint32_t flag:16; + mutable int32_t _l_qseq; // _l_qname, _n_cigar and _l_qseq for internal usage + int32_t rNextId; + int32_t pNext; + int32_t tLen; +}; + +class BamAlignmentRecord : public BamAlignmentRecordCore +{ +public: + uint32_t _qID; // TODO(holtgrew): Undocumented as of yet. + String > cigar; + CharString qName; + IupacString seq; + CharString qual; + CharString tags; // raw tags in BAM format + CharString _buffer; // reusable internal buffer (used for I/O) + + static int32_t const INVALID_POS = -1; + static int32_t const INVALID_REFID = -1; // TODO(holtgrew): Rename to ...REF_ID. + static int32_t const INVALID_LEN = 0; + static uint32_t const INVALID_QID = 4294967295u; // TODO(holtgrew): Undocumented as of yet. + + BamAlignmentRecord() : _qID(MaxValue::VALUE) { clear(*this); } +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#clear + * @brief Clear BamAlignmentRecord. + * + * @signature void clear(record); + * + * @param[in,out] record The BamAlignmentRecord to clear. + * + * Clears all strings and resets it to default initialization state. + */ + +inline void +clear(BamAlignmentRecord & record) +{ + clear(record.qName); + record.flag = 0; + record._qID = MaxValue::VALUE; + record.rID = BamAlignmentRecord::INVALID_REFID; + record.beginPos = BamAlignmentRecord::INVALID_POS; + record.mapQ = 255; + record.bin = 0; + clear(record.cigar); + record.rNextId = BamAlignmentRecord::INVALID_REFID; + record.pNext = BamAlignmentRecord::INVALID_POS; + record.tLen = BamAlignmentRecord::INVALID_LEN; + clear(record.seq); + clear(record.qual); + clear(record.tags); +} + +// ---------------------------------------------------------------------------- +// Function hasFlagMultiple() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagMultiple + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "multiple" flag set. + * + * @signature bool hasFlagMultiple(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagMultiple(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_MULTIPLE) == BAM_FLAG_MULTIPLE; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagAllProper() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagAllProper + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "all properly aligned" flag set. + * + * @signature bool hasFlagAllProper(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagAllProper(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_ALL_PROPER) == BAM_FLAG_ALL_PROPER; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagUnmapped() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagUnmapped + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "unmapped" flag set. + * + * @signature bool hasFlagUnmapped(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagUnmapped(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_UNMAPPED) == BAM_FLAG_UNMAPPED; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagNextUnmapped() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagNextUnmapped + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "next unmapped" flag set. + * + * @signature bool hasFlagNextUnmapped(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagNextUnmapped(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_NEXT_UNMAPPED) == BAM_FLAG_NEXT_UNMAPPED; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagRC() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagRC + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "reverse-complemented" flag set. + * + * @signature bool hasFlagRC(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagRC(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_RC) == BAM_FLAG_RC; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagNextRC() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagNextRC + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "next reverse-complemented" flag set. + * + * @signature bool hasFlagNextRC(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagNextRC(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_NEXT_RC) == BAM_FLAG_NEXT_RC; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagFirst() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagFirst + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "first in template" flag set. + * + * @signature bool hasFlagFirst(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagFirst(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_FIRST) == BAM_FLAG_FIRST; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagLast() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagLast + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "last in template" flag set. + * + * @signature bool hasFlagLast(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagLast(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_LAST) == BAM_FLAG_LAST; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagSecondary() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagSecondary + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "secondary" flag set. + * + * @signature bool hasFlagSecondary(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagSecondary(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_SECONDARY) == BAM_FLAG_SECONDARY; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagQCNoPass() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagQCNoPass + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "did not pass QC" flag set. + * + * @signature bool hasFlagQCNoPass(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagQCNoPass(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_QC_NO_PASS) == BAM_FLAG_QC_NO_PASS; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagDuplicate() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagDuplicate + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "duplicate" flag set. + * + * @signature bool hasFlagDuplicate(record); + * + * @param[in] record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + * + * @see BamFlags + */ + +inline bool +hasFlagDuplicate(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_DUPLICATE) == BAM_FLAG_DUPLICATE; +} + +// ---------------------------------------------------------------------------- +// Function hasFlagSupplementary() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#hasFlagSupplementary + * @headerfile + * @brief Return true if a @link BamAlignmentRecord @endlink has the "supplementary" flag set. + * + * @signature bool hasFlagSupplementary(record); + * + * @param record The BamAlignmentRecord to query. + * + * @return bool true if the flag is set, false otherwise. + */ + +inline bool +hasFlagSupplementary(BamAlignmentRecord const & record) +{ + return (record.flag & BAM_FLAG_SUPPLEMENTARY) == BAM_FLAG_SUPPLEMENTARY; +} + +// ---------------------------------------------------------------------------- +// Function getAlignmentLengthInRef() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#getAlignmentLengthInRef + * @headerfile + * @brief Return the alignment length in the record's projection in the reference. + * + * @signature unsigned getAlignmentLengthInRef(record); + * + * @param[in] record The BamAlignmentRecord to compute length for. + * + * @return unsigned The alignment length. + * + * @see BamFlags + */ + +inline unsigned +getAlignmentLengthInRef(BamAlignmentRecord const & record) +{ + unsigned l = 0; + _getLengthInRef(l, record.cigar); + return l; +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_RECORD_H_ diff --git a/seqan/bam_io/bam_alignment_record_util.h b/seqan/bam_io/bam_alignment_record_util.h new file mode 100644 index 0000000..1a7a02f --- /dev/null +++ b/seqan/bam_io/bam_alignment_record_util.h @@ -0,0 +1,253 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_ + +namespace seqan { + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function getContigName() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#getContigName + * @brief Return the name of the reference contig of a @link BamAlignmentRecord @endlink. + * + * @signature TNameString getContigName(record, file); + * + * @param[in] record The @link BamAlignmentRecord @endlink to query. + * @param[in] file The @link BamFileIn @endlink or @link BamFileOut @endlink where the record belongs to. + * + * @return TNameString The name of the reference contig. TNameString is the @link Value @endlink type of the NameStore. + * The NameStore type can be determined using the @link Member @endlink metafunction + * for the @link BamIOContext @endlink in conjunction with the @link BamIOContextMemberTag#NameStoreMember @endlink tag. + */ + +template +inline typename Value, Dependent<> >::Type, NameStoreMember>::Type>::Type const & +getContigName(BamAlignmentRecord const & record, FormattedFile const & file) +{ + return contigNames(context(file))[record.rID]; +} + +// ---------------------------------------------------------------------------- +// Function getContigLength() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamAlignmentRecord#getContigLength + * @brief Return the length of the reference contig of a @link BamAlignmentRecord @endlink. + * + * @signature TLength getContigLength(record, file); + * + * @param[in] record The @link BamAlignmentRecord @endlink to query. + * @param[in] file The @link BamFileIn @endlink or @link BamFileOut @endlink where the record belongs to. + * + * @return TLength The length of the reference contig. TLength is the @link Value @endlink type of the LengthStore. + * The LengthStore type can be determined using the @link Member @endlink metafunction + * for the @link BamIOContext @endlink in conjunction with the @link BamIOContextMemberTag#LengthStoreMember @endlink tag. + */ + +template +inline typename Value, Dependent<> >::Type, LengthStoreMember>::Type>::Type +getContigLength(BamAlignmentRecord const & record, FormattedFile const & file) +{ + return contigLengths(context(file))[record.rID]; +} + +// ---------------------------------------------------------------------------- +// Function getClippedPos() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Test me! +// TODO(holtgrew): Document me! + +// Extract positions of soft clipping. + +inline bool +getClippedPos(unsigned & posBegin, unsigned & posEnd, BamAlignmentRecord const & record) +{ + posBegin = 0; + posEnd = length(record.seq); + + for (unsigned j = 0; j < length(record.cigar); ++j) + { + if (record.cigar[j].operation == 'S') + posBegin += record.cigar[j].count; + else + break; + } + for (unsigned j = 0; j < length(record.cigar); ++j) + { + if (record.cigar[length(record.cigar) - j - 1].operation == 'S') + posEnd -= record.cigar[length(record.cigar) - j - 1].count; + else + break; + } + SEQAN_ASSERT_LEQ(posBegin, posEnd); + SEQAN_ASSERT_LEQ(posBegin, length(record.seq)); + SEQAN_ASSERT_LEQ(posEnd, length(record.seq)); + + return (posBegin != 0) || (posEnd != length(record.seq)); +} + +// ---------------------------------------------------------------------------- +// Function clippedSeqInfix() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Test me! +// TODO(holtgrew): Document me! + +// Returns clipped infix of seq member. + +inline Infix::Type +clippedSeqInfix(BamAlignmentRecord & record) +{ + unsigned begPos = 0, endPos = 0; + getClippedPos(begPos, endPos, record); + return infix(record.seq, begPos, endPos); +} + +inline Infix::Type +clippedSeqInfix(BamAlignmentRecord const & record) +{ + unsigned begPos = 0, endPos = 0; + getClippedPos(begPos, endPos, record); + return infix(record.seq, begPos, endPos); +} + +// ---------------------------------------------------------------------------- +// Function clippedQualInfix() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Test me! +// TODO(holtgrew): Document me! + +// Returns clipped infix of qual member. + +inline Infix::Type +clippedQualInfix(BamAlignmentRecord & record) +{ + unsigned begPos = 0, endPos = 0; + getClippedPos(begPos, endPos, record); + return infix(record.qual, begPos, endPos); +} + +inline Infix::Type +clippedQualInfix(BamAlignmentRecord const & record) +{ + unsigned begPos = 0, endPos = 0; + getClippedPos(begPos, endPos, record); + return infix(record.qual, begPos, endPos); +} + +// ---------------------------------------------------------------------------- +// Function countPaddings() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This actually belongs to wherever CigarElement is defined. + +inline unsigned countPaddings(String > const & cigarString) +{ + unsigned result = 0; + for (unsigned i = 0; i < length(cigarString); ++i) + if (cigarString[i].operation == 'P') + result += cigarString[i].count; + return result; +} + +// ---------------------------------------------------------------------------- +// Function bamRecordToAlignment() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Should rather be a global function? + +/*! + * @fn BamAlignmentRecord#bamRecordToAlignment + * @headerfile + * @brief Construct an @link Align @endlink object from a BamAlignmentRecord object. + * + * @signature void bamRecordToAlignment(align, reference, record); + * + * @param[out] align The @link Align @endlink object to create the alignment object in. + * @param[in] reference The string with the reference that record lies on. + * @param[in] record The @link BamAlignmentRecord @endlink to construct alignment from. + * + * The function will resize align to have two rows. The part of the reference that the read from + * record aligns to will be copied to the first row and the sequence from record will be copied to the second + * row (and reverse-complemented if appropriate). Then, the gaps from the CIGAR string in record will be + * copied to align. + * + * @section Example + * + * Here is an example: + * + * @code{.cpp} + * StringSet references; + * BamAlignment record; + * // Read references and record. + * Align align; + * if (record.rID != BamAlignmentRecord::INVALID_REFID) + * bamRecordToAlignment(align, references[record.refId], record); + * @endcode + */ + +// TODO(holtgrew): Convert into full example. + +template +void +bamRecordToAlignment(Align & result, TReference & reference, BamAlignmentRecord const & record) +{ + // TODO(holtgrew): Clipping better than copying infix? But is it generic? + resize(rows(result), 2); + + unsigned len = record.beginPos + getAlignmentLengthInRef(record) - countPaddings(record.cigar); + + setSource(row(result, 0), reference); + setClippedEndPosition(row(result, 0), record.beginPos + len); + setClippedBeginPosition(row(result, 0), record.beginPos); + cigarToGapAnchorContig(row(result, 0), record.cigar); + + assignSource(row(result, 1), record.seq); + cigarToGapAnchorRead(row(result, 1), record.cigar); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_ALIGNMENT_RECORD_UTIL_H_ diff --git a/seqan/bam_io/bam_file.h b/seqan/bam_io/bam_file.h new file mode 100644 index 0000000..bf1c681 --- /dev/null +++ b/seqan/bam_io/bam_file.h @@ -0,0 +1,363 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// ========================================================================== +// Class for reading/writing files in SAM or BAM format. +// ========================================================================== + +#ifndef SEQAN_BAM_IO_BAM_FILE_H_ +#define SEQAN_BAM_IO_BAM_FILE_H_ + +namespace seqan { + +// ============================================================================ +// Typedefs +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Type BamFileIn +// ---------------------------------------------------------------------------- + +/*! + * @class BamFileIn + * @signature typedef FormattedFile BamFileIn; + * @extends FormattedFileIn + * @headerfile + * @brief Class for reading SAM and BAM files. + * + * @see BamHeader + * @see BamAlignmentRecord + * + * @section Example + * + * Access SAM or BAM files. + * + * @include demos/tutorial/sam_and_bam_io/solution1.cpp + * + * The output is as follows: + * + * @include demos/tutorial/sam_and_bam_io/example.sam + */ + +typedef FormattedFile BamFileIn; + +// ---------------------------------------------------------------------------- +// Type BamFileOut +// ---------------------------------------------------------------------------- + +/*! + * @class BamFileOut + * @signature typedef FormattedFile BamFileOut; + * @extends FormattedFileOut + * @headerfile + * @brief Class for writing SAM and BAM files. + * + * @see BamHeader + * @see BamAlignmentRecord + * + * @section Example + * + * Access SAM or BAM files. + * + * @include demos/tutorial/sam_and_bam_io/solution1.cpp + * + * The output is as follows: + * + * @include demos/tutorial/sam_and_bam_io/example.sam + */ + +typedef FormattedFile BamFileOut; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction FormattedFileContext +// ---------------------------------------------------------------------------- + +template +struct FormattedFileContext, TStorageSpec> +{ + typedef StringSet TNameStore; + typedef NameStoreCache TNameStoreCache; + typedef BamIOContext Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction FileFormats +// ---------------------------------------------------------------------------- + +template +struct FileFormat > +{ +#if SEQAN_HAS_ZLIB + typedef TagSelector< + TagList > + > Type; +#else + typedef Sam Type; +#endif +}; + +// -------------------------------------------------------------------------- +// Function _mapBamFormatToCompressionFormat() +// -------------------------------------------------------------------------- + +inline BgzfFile +_mapFileFormatToCompressionFormat(Bam) +{ + return BgzfFile(); +} + +// ---------------------------------------------------------------------------- +// Function readHeader(); BamHeader +// ---------------------------------------------------------------------------- + +// support for dynamically chosen file formats +template +inline void +readHeader(BamHeader & /* header */, + BamIOContext & /* context */, + TForwardIter & /* iter */, + TagSelector<> const & /* format */) +{ + SEQAN_FAIL("BamFileIn: File format not specified."); +} + +template +inline void +readHeader(BamHeader & header, + BamIOContext & context, + TForwardIter & iter, + TagSelector const & format) +{ + typedef typename TTagList::Type TFormat; + + if (isEqual(format, TFormat())) + readHeader(header, context, iter, TFormat()); + else + readHeader(header, context, iter, static_cast::Base const &>(format)); +} + +// convenient BamFile variant +template +inline void +readHeader(BamHeader & header, FormattedFile & file) +{ + readHeader(header, context(file), file.iter, file.format); +} + +// ---------------------------------------------------------------------------- +// Function readRecord(); BamAlignmentRecord +// ---------------------------------------------------------------------------- + +// support for dynamically chosen file formats +template +inline void +_readBamRecord(TBuffer & /* rawRecord */, TForwardIter & /* iter */, TagSelector<> const & /* format */) +{ + SEQAN_FAIL("BamFileIn: File format not specified."); +} + +template +inline void +_readBamRecord(TBuffer & rawRecord, TForwardIter & iter, TagSelector const & format) +{ + typedef typename TTagList::Type TFormat; + + if (isEqual(format, TFormat())) + _readBamRecord(rawRecord, iter, TFormat()); + else + _readBamRecord(rawRecord, iter, static_cast::Base const &>(format)); +} + +// ---------------------------------------------------------------------------- +// Function readRecord(); BamAlignmentRecord +// ---------------------------------------------------------------------------- + +// support for dynamically chosen file formats +template +inline void +readRecord(BamAlignmentRecord & /* record */, + BamIOContext & /* context */, + TForwardIter & /* iter */, + TagSelector<> const & /* format */) +{ + SEQAN_FAIL("BamFileIn: File format not specified."); +} + +template +inline void +readRecord(BamAlignmentRecord & record, + BamIOContext & context, + TForwardIter & iter, + TagSelector const & format) +{ + typedef typename TTagList::Type TFormat; + + if (isEqual(format, TFormat())) + readRecord(record, context, iter, TFormat()); + else + readRecord(record, context, iter, static_cast::Base const &>(format)); +} + +// convenient BamFile variant +template +inline void +readRecord(BamAlignmentRecord & record, FormattedFile & file) +{ + readRecord(record, context(file), file.iter, file.format); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And::Type, BamAlignmentRecord>, + IsInteger >, TSize) +readRecords(TRecords & records, FormattedFile & file, TSize maxRecords) +{ + String & buffers = context(file).buffers; + if (static_cast(length(buffers)) < maxRecords) + resize(buffers, maxRecords, Exact()); + if (static_cast(length(records)) < maxRecords) + resize(records, maxRecords, Exact()); + + TSize numRecords = 0; + for (; numRecords < maxRecords && !atEnd(file.iter); ++numRecords) + _readBamRecord(buffers[numRecords], file.iter, file.format); + +// SEQAN_OMP_PRAGMA(parallel for) + for (int i = 0; i < (int)numRecords; ++i) + { + CharIterator bufIter = begin(buffers[i]); + readRecord(records[i], context(file), bufIter, file.format); + } + return numRecords; +} + +// ---------------------------------------------------------------------------- +// Function writeHeader(); BamHeader +// ---------------------------------------------------------------------------- + +// support for dynamically chosen file formats +template +inline void +write(TTarget & /* target */, + BamHeader const & /* header */, + BamIOContext & /* context */, + TagSelector<> const & /* format */) +{ + SEQAN_FAIL("BamFileOut: File format not specified."); +} + +template +inline void +write(TTarget & target, + BamHeader const & header, + BamIOContext & context, + TagSelector const & format) +{ + typedef typename TTagList::Type TFormat; + + if (isEqual(format, TFormat())) + write(target, header, context, TFormat()); + else + write(target, header, context, static_cast::Base const &>(format)); +} + +// convenient BamFile variant +template +inline void +writeHeader(FormattedFile & file, BamHeader const & header) +{ + write(file.iter, header, context(file), file.format); +} + +// ---------------------------------------------------------------------------- +// Function writeRecord(); BamAlignmentRecord +// ---------------------------------------------------------------------------- + +// support for dynamically chosen file formats +template +inline void +write(TTarget & /* target */, + BamAlignmentRecord const & /* record */, + BamIOContext & /* context */, + TagSelector<> const & /* format */) +{ + SEQAN_FAIL("BamFileOut: File format not specified."); +} + +template +inline void +write(TTarget & target, + BamAlignmentRecord const & record, + BamIOContext & context, + TagSelector const & format) +{ + typedef typename TTagList::Type TFormat; + + if (isEqual(format, TFormat())) + write(target, record, context, TFormat()); + else + write(target, record, context, static_cast::Base const &>(format)); +} + +template +inline void +writeRecord(FormattedFile & file, BamAlignmentRecord const & record) +{ + write(file.iter, record, context(file), file.format); +} + +template +inline SEQAN_FUNC_ENABLE_IF(IsSameType::Type, BamAlignmentRecord>, void) +writeRecords(FormattedFile & file, TRecords const & records) +{ + String & buffers = context(file).buffers; + if (length(buffers) < length(records)) + resize(buffers, length(records)); + + SEQAN_OMP_PRAGMA(parallel for) + for (int i = 0; i < (int)length(records); ++i) + { + clear(buffers[i]); + write(buffers[i], records[i], context(file), file.format); + } + for (int i = 0; i < (int)length(records); ++i) + write(file.iter, buffers[i]); +} + +} // namespace seqan + +#endif // SEQAN_BAM_IO_BAM_FILE_H_ diff --git a/seqan/bam_io/bam_header_record.h b/seqan/bam_io/bam_header_record.h new file mode 100644 index 0000000..0854d33 --- /dev/null +++ b/seqan/bam_io/bam_header_record.h @@ -0,0 +1,483 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// BamHeaderRecord class, supporting types and functions for accessing tags +// in headers. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_ + +namespace seqan { + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Enum BamHeaderRecordType +// ---------------------------------------------------------------------------- + +/*! + * @enum BamHeaderRecordType + * @headerfile + * @brief Enumeration for the header record type. + * + * @signature enum BamHeaderRecordType; + * + * @val BamHeaderRecordType BAM_HEADER_FIRST = 0; + * @brief Is the first header (HD). + * + * @val BamHeaderRecordType BAM_HEADER_REFERENCE = 1; + * @brief Is a reference (SQ) header. + * + * @val BamHeaderRecordType BAM_HEADER_READ_GROUP = 2; + * @brief Is a read group (RG) header. + * + * @val BamHeaderRecordType BAM_HEADER_PROGRAM = 3; + * @brief Is a program (PG) header. + * + * @val BamHeaderRecordType BAM_HEADER_COMMENT = 4; + * @brief Is a comment (CO) header. + */ + +enum BamHeaderRecordType +{ + BAM_HEADER_FIRST = 0, + BAM_HEADER_REFERENCE = 1, + BAM_HEADER_READ_GROUP = 2, + BAM_HEADER_PROGRAM = 3, + BAM_HEADER_COMMENT = 4 +}; + +// ---------------------------------------------------------------------------- +// Enum BamSortOrder +// ---------------------------------------------------------------------------- + +/*! + * @enum BamSortOrder + * @headerfile + * @brief Enumeration for the header record type. + * + * @signature enum BamSortOrder; + * + * @val BamSortOrder BAM_SORT_UNKNOWN = 0; + * @brief BAM file sort order is unknown. + * + * @val BamSortOrder BAM_SORT_UNSORTED = 1; + * @brief BAM file is unsorted. + * + * @val BamSortOrder BAM_SORT_QUERYNAME = 2; + * @brief BAM file is sorted by query name; + * + * @val BamSortOrder BAM_SORT_COORDINATE = 3; + * @brief BAM file is sorted by coordinate. + */ + +enum BamSortOrder +{ + BAM_SORT_UNKNOWN = 0, + BAM_SORT_UNSORTED = 1, + BAM_SORT_QUERYNAME = 2, + BAM_SORT_COORDINATE = 3 +}; + +// ---------------------------------------------------------------------------- +// Class BamHeaderRecord +// ---------------------------------------------------------------------------- + +/*! + * @class BamHeaderRecord + * @headerfile + * @brief Represents a header entry in a SAM file or the header section of the BAM header. + * + * @signature class BamHeaderRecord; + * + * @section Remarks + * + * Comment records are stored with one tag where the key is empty and the value is the comment. + */ + +/*! + * @fn BamHeaderRecord::BamHeaderRecord + * @brief Constructor. + * @signature BamHeaderRecord::BamRecord(); + * + * Only the default constructor is provided. + */ + +/*! + * @typedef BamHeaderRecord::TTagName + * @brief Type of the tag keys (@link CharString @endlink). + * @signature BamHeaderRecord::TTagName; + * + * @typedef BamHeaderRecord::TTagValue + * @brief Type of the tag values (@link CharString @endlink). + * @signature BamHeaderRecord::TTagValue; + * + * @typedef BamHeaderRecord::TTag + * @brief Type of the tag keys (@link Pair @endlink of TTagName and TTagValue). + * @signature BamHeaderRecord::TTag; + * + * @typedef BamHeaderRecord::TTags + * @brief Type of the tags string (@link AllocString @endlink of TTag). + * @signature BamHeaderRecord::TTags; + * + * @var BamHeaderRecordType BamHeaderRecord::type; + * @brief Type of the record. + * + * @var TRecordString BamHeaderRecord::tags; + * @brief The header record's tags, of type @link BamHeaderRecord::TTags @endlink. + */ + +class BamHeaderRecord +{ +public: + typedef CharString TTagName; + typedef CharString TTagValue; + typedef Pair TTag; + typedef String TTags; + + BamHeaderRecordType type; + TTags tags; + + BamHeaderRecord() : type(BAM_HEADER_FIRST) {} +}; + +// ---------------------------------------------------------------------------- +// Class BamHeader +// ---------------------------------------------------------------------------- + +/*! + * @class BamHeader + * @headerfile + * @implements FormattedFileHeaderConcept + * @signature typedef String BamHeader; + * @brief Represent the information of the BAM header. + * + * @see BamFileIn + * @see BamFileOut + */ + +typedef String BamHeader; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function std::swap() +// ---------------------------------------------------------------------------- + +inline void +swap(BamHeaderRecord &a, BamHeaderRecord &b) +{ + std::swap(a.type, b.type); + swap(a.tags, b.tags); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamHeaderRecord::clear + * @brief Clear BamHeaderRecord object. + * + * @signature void clear(record); + * + * @param[in,out] record The record to clear. + */ + +inline void +clear(BamHeaderRecord & record) +{ + clear(record.tags); +} + +// ---------------------------------------------------------------------------- +// Function findTagKey() +// ---------------------------------------------------------------------------- + +template +inline bool +findTagKey(unsigned & idx, TKeyName const & key, BamHeaderRecord const & record) +{ + typedef BamHeaderRecord::TTags const TTags; + typedef Iterator::Type TIterator; + + idx = 0; + TIterator itEnd = end(record.tags, Standard()); + for (TIterator it = begin(record.tags, Standard()); it != itEnd; goNext(it), ++idx) + if (it->i1 == key) + return true; + + return false; +} + +// ---------------------------------------------------------------------------- +// Function getTagValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamHeaderRecord::getTagValue + * @brief Return tag value from a @link BamHeaderRecord @endlink. + * + * @signature bool getTagValue(tagValue, idx, record); + * @signature bool getTagValue(tagValue, key, record); + * + * @param[out] tagValue The @link CharString @endlink to write the tag value to. + * @param[in] idx An integer with the index of the tag in the header record. + * @param[in] key A two-letter sequence with the key of the tag in the header record. + * + * @return bool true in case the value could be retrieved, false otherwise. + * + * @section Example + * + * @code{.cpp} + * CharString tagValue; + * bool keyFound = getTagValue(tagValue, "SN", record); + * @endcode + */ + +template +SEQAN_FUNC_ENABLE_IF( + IsInteger, + bool) +inline getTagValue(CharString & value, TId idx, BamHeaderRecord const & record) +{ + if ((unsigned)idx >= length(record.tags)) + return false; + value = record.tags[idx].i2; + return true; +} + +template +SEQAN_FUNC_ENABLE_IF( + IsSequence, + bool) +inline getTagValue(CharString & value, TKeyName const & key, BamHeaderRecord const & record) +{ + unsigned idx = 0; + if (!findTagKey(idx, key, record)) + return false; + return getTagValue(value, idx, record); +} + +/*! + * @fn BamHeaderRecord::setTagValue + * @brief Sets the value of a tag in a BamHeaderRecord. + * + * @signature void setTagValue(idx, value, record); + * @signature void setTagValue(key, value, record); + * + * @param[in,out] idx The index of the tag in the header record to set the value for. + * @param[in] key The name of the tag (two-letter sequence) to set. + * @param[in] record The header record to set the value for. + */ + +// TODO(holtgrew): Parameter order! + +template +SEQAN_FUNC_ENABLE_IF( + IsInteger, + void) +inline setTagValue(TId idx, CharString const & value, BamHeaderRecord & record) +{ + if (idx >= length(record.tags)) + return; + record.tags[idx].i2 = value; +} + +template +SEQAN_FUNC_ENABLE_IF( + IsSequence, + void) +inline setTagValue(TKeyName const & key, CharString const & value, BamHeaderRecord & record) +{ + unsigned idx = 0; + if (!findTagKey(idx, key, record)) + { + idx = length(record.tags); + resize(record.tags, idx + 1); + record.tags[idx].i1 = key; + } + setTagValue(idx, value, record); +} + +// ---------------------------------------------------------------------------- +// Function getSortOrder() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Document me! Test me! + + +inline bool +searchRecord(unsigned & recordIdx, + BamHeader const & header, + BamHeaderRecordType recordType, + unsigned startIdx) +{ + for (recordIdx = startIdx; recordIdx < length(header); ++recordIdx) + if (header[recordIdx].type == recordType) + return true; + return false; +} + +inline bool +searchRecord(unsigned & recordIdx, + BamHeader const & header, + BamHeaderRecordType recordType) +{ + return searchRecord(recordIdx, header, recordType, 0); +} + + +struct BamHeaderRecordTypeLess +{ + bool operator() (BamHeaderRecord const &a, BamHeaderRecord const &b) const + { + return a.type < b.type; + } +}; + +struct BamHeaderRecordEqual +{ + bool operator() (BamHeaderRecord const &a, BamHeaderRecord const &b) const + { + return a.type == b.type && a.tags == b.tags; + } +}; + + +inline void +removeDuplicates(BamHeader & header) +{ + BamHeaderRecordTypeLess less; + BamHeaderRecordEqual pred; + + std::stable_sort(begin(header, Standard()), end(header, Standard()), less); + + for (size_t uniqueBegin = 0, uniqueEnd = 1; uniqueEnd < length(header);) + { + if (less(header[uniqueBegin], header[uniqueEnd])) + uniqueBegin = uniqueEnd; + + size_t j; + for (j = uniqueBegin; j < uniqueEnd; ++j) + if (pred(header[j], header[uniqueEnd])) + { + erase(header, uniqueEnd); + break; + } + + if (j == uniqueEnd) + ++uniqueEnd; + } +} + +inline BamSortOrder +getSortOrder(BamHeader const & header) +{ + CharString soString; + for (unsigned recIdx = 0; searchRecord(recIdx, header, BAM_HEADER_FIRST, recIdx); ++recIdx) + { + if (getTagValue(soString, "SO", header[recIdx])) + { + if (soString == "unsorted") + return BAM_SORT_UNSORTED; + else if (soString == "queryname") + return BAM_SORT_QUERYNAME; + else if (soString == "coordinate") + return BAM_SORT_COORDINATE; + else + return BAM_SORT_UNKNOWN; + } + } + return BAM_SORT_UNKNOWN; +} + +inline void +setSortOrder(BamHeader & header, BamSortOrder sortOrder) +{ + char const * soString; + switch (sortOrder) + { + case BAM_SORT_UNSORTED: + soString = "unsorted"; + break; + + case BAM_SORT_QUERYNAME: + soString = "queryname"; + break; + + case BAM_SORT_COORDINATE: + soString = "coordinate"; + break; + + default: + soString = "unknown"; + } + + bool notFound = true; + for (unsigned recIdx = 0; searchRecord(recIdx, header, BAM_HEADER_FIRST, recIdx); ++recIdx) + { + unsigned idx = 0; + if (findTagKey(idx, "SO", header[recIdx])) + { + notFound = false; + setTagValue(idx, soString, header[recIdx]); + } + } + + if (notFound) + { + unsigned recIdx = 0; + if (searchRecord(recIdx, header, BAM_HEADER_FIRST)) + { + setTagValue("SO", soString, header[recIdx]); + } + else + { + BamHeaderRecord rec; + rec.type = BAM_HEADER_FIRST; + setTagValue("VN", "1.4", rec); + setTagValue("SO", soString, rec); + insert(header, 0, rec); + } + } +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_HEADER_RECORD_H_ diff --git a/seqan/bam_io/bam_index_bai.h b/seqan/bam_io/bam_index_bai.h new file mode 100644 index 0000000..db5ed68 --- /dev/null +++ b/seqan/bam_io/bam_index_bai.h @@ -0,0 +1,794 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +// The index building algorithm is based on the samtools implementation which +// is under the MIT License: + +/* The MIT License + + Copyright (c) 2008-2009 Genome Research Ltd. + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_ + +namespace seqan { + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class BamIndex +// ---------------------------------------------------------------------------- + +/*! + * @class BamIndex + * @headerfile + * + * @brief Access to BAM indices. + * + * @signature template + * class BamIndex; + * + * This is an abstract class; don't use it itself but its specializations. + * + * @see BamFileIn + */ + +template +class BamIndex; + +// ---------------------------------------------------------------------------- +// Tag Bai +// ---------------------------------------------------------------------------- + +struct Bai_; +typedef Tag Bai; + +// ---------------------------------------------------------------------------- +// Helper Class BaiBamIndexBinData_ +// ---------------------------------------------------------------------------- + +// Store the information of a bin. + +struct BaiBamIndexBinData_ +{ + String > chunkBegEnds; +}; + +// ---------------------------------------------------------------------------- +// Spec BAI BamIndex +// ---------------------------------------------------------------------------- + +/*! + * @class BaiBamIndex + * @headerfile + * @extends BamIndex + * @brief Access to BAI (samtools-style). + * + * @signature template <> + * class BamIndex; + */ + +/*! + * @fn BaiBamIndex::BamIndex + * @brief Constructor. + * + * @signature BamIndex::BamIndex(); + * + * @section Remarks + * + * Only the default constructor is provided. + */ + +template <> +class BamIndex +{ +public: + typedef std::map TBinIndex_; + typedef String TLinearIndex_; + + uint64_t _unalignedCount; + + // 1<<14 is the size of the minimum bin. + static const int32_t BAM_LIDX_SHIFT = 14; + + String _binIndices; + String _linearIndices; + + BamIndex() : _unalignedCount(maxValue()) + {} +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function jumpToRegion() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamFileIn#jumpToRegion + * @brief Seek in BamFileIn using an index. + * + * You provide a region [pos, posEnd) on the reference refID that you want to jump to and the function + * jumps to the first alignment in this region, if any. + * + * @signature bool jumpToRegion(bamFileIn, hasAlignments, refID, pos, posEnd, index); + * + * @param[in,out] bamFileIn The @link BamFileIn @endlink to jump with. + * @param[out] hasAlignments A bool that is set true if the region [pos, posEnd) has any + * alignments. + * @param[in] refID The reference id to jump to (int32_t). + * @param[in] pos The begin of the region to jump to (int32_t). + * @param[in] posEnd The end of the region to jump to (int32_t). + * @param[in] index The @link BamIndex @endlink to use for the jumping. + * + * @return bool true if seeking was successful, false if not. + * + * @section Remarks + * + * This function fails if refID/pos are invalid. + */ + +static inline void +_baiReg2bins(String & list, uint32_t beg, uint32_t end) +{ + unsigned k; + if (beg >= end) return; + if (end >= 1u<<29) end = 1u<<29; + --end; + appendValue(list, 0); + for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) appendValue(list, k); + for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) appendValue(list, k); + for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) appendValue(list, k); + for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) appendValue(list, k); + for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) appendValue(list, k); +} + +template +inline bool +jumpToRegion(FormattedFile & bamFile, + bool & hasAlignments, + int32_t refId, + int32_t pos, + int32_t posEnd, + BamIndex const & index) +{ + if (!isEqual(format(bamFile), Bam())) + return false; + + hasAlignments = false; + if (refId < 0) + return false; // Cannot seek to invalid reference. + if (static_cast(refId) >= length(index._binIndices)) + return false; // Cannot seek to invalid reference. + + // ------------------------------------------------------------------------ + // Compute offset in BGZF file. + // ------------------------------------------------------------------------ + uint64_t offset = MaxValue::VALUE; + + // Retrieve the candidate bin identifiers for [pos, posEnd). + String candidateBins; + _baiReg2bins(candidateBins, pos, posEnd); + + // Retrieve the smallest required offset from the linear index. + unsigned windowIdx = pos >> 14; // Linear index consists of 16kb windows. + uint64_t linearMinOffset = 0; + if (windowIdx >= length(index._linearIndices[refId])) + { + // TODO(holtgrew): Can we simply always take case 1? + + // This is the case were we want to jump in a non-existing window. + // + // If there are no linear indices for this reference then we use the linear min offset of the next + // reference that has an linear index. + if (empty(index._linearIndices[refId])) + { + for (unsigned i = refId; i < length(index._linearIndices); ++i) + { + if (!empty(index._linearIndices[i])) + { + linearMinOffset = front(index._linearIndices[i]); + if (linearMinOffset != 0u) + break; + for (unsigned j = 1; j < length(index._linearIndices[i]); ++j) + { + if (index._linearIndices[i][j] > linearMinOffset) + { + linearMinOffset = index._linearIndices[i][j]; + break; + } + } + if (linearMinOffset != 0u) + break; + } + } + } + else + { + linearMinOffset = back(index._linearIndices[refId]); + } + } + else + { + linearMinOffset = index._linearIndices[refId][windowIdx]; + } + + // Combine candidate bins and smallest required offset from linear index into candidate offset. + typedef std::set TOffsetCandidates; + TOffsetCandidates offsetCandidates; + typedef typename Iterator, Rooted>::Type TCandidateIter; + for (TCandidateIter it = begin(candidateBins, Rooted()); !atEnd(it); goNext(it)) + { + typedef typename std::map::const_iterator TMapIter; + TMapIter mIt = index._binIndices[refId].find(*it); + if (mIt == index._binIndices[refId].end()) + continue; // Candidate is not in index! + + typedef typename Iterator > const, Rooted>::Type TBegEndIter; + for (TBegEndIter it2 = begin(mIt->second.chunkBegEnds, Rooted()); !atEnd(it2); goNext(it2)) + if (it2->i2 >= linearMinOffset) + offsetCandidates.insert(it2->i1); + } + + // Search through candidate offsets, find rightmost possible. + // + // Note that it is not necessarily the first. + // + // TODO(holtgrew): Can this be optimized similar to how bamtools does it? + typedef typename TOffsetCandidates::const_iterator TOffsetCandidateIter; + BamAlignmentRecord record; + for (TOffsetCandidateIter candIt = offsetCandidates.begin(); candIt != offsetCandidates.end(); ++candIt) + { + setPosition(bamFile, *candIt); + + readRecord(record, bamFile); + + // std::cerr << "record.beginPos == " << record.beginPos << "\n"; + // int32_t endPos = record.beginPos + getAlignmentLengthInRef(record); + if (record.rID != refId) + continue; // Wrong contig. + if (!hasAlignments || record.beginPos <= pos) + { + // Found a valid alignment. + hasAlignments = true; + offset = *candIt; + } + + if (record.beginPos >= posEnd) + break; // Cannot find overlapping any more. + } + + if (offset != MaxValue::VALUE) + setPosition(bamFile, offset); + + // Finding no overlapping alignment is not an error, hasAlignments is false. + return true; +} + +// ---------------------------------------------------------------------------- +// Function jumpToOrphans() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamFileIn#jumpToOrphans + * @brief Seek to orphans block in BamFileIn using an index. + * + * @signature bool jumpToOrphans(bamFileIn, hasAlignments, index); + * + * @param[in,out] bamFileIn The @link BamFileIn @endlink object to jump with. + * @param[out] hasAlignments A bool that is set to true if there are any orphans. + * @param[in] index The @link BamIndex @endlink to use for jumping. + */ + +template +bool jumpToOrphans(FormattedFile & bamFile, + bool & hasAlignments, + BamIndex const & index) +{ + if (!isEqual(format(bamFile), Bam())) + return false; + + hasAlignments = false; + + // Search linear indices for the largest entry of all references. + uint64_t aliOffset = MaxValue::VALUE; + for (int i = length(index._linearIndices) - 1; i >= 0; --i) + if (!empty(index._linearIndices[i])) + { + aliOffset = back(index._linearIndices[i]); + break; + } + if (aliOffset == MaxValue::VALUE) + return false; // No offset found. + + // Get index of the first orphan alignment by seeking from linear index bucket. + BamAlignmentRecord record; + uint64_t offset = MaxValue::VALUE; + uint64_t result = 0; + if (!setPosition(bamFile, aliOffset)) + return false; // Error while seeking. + while (!atEnd(bamFile)) + { + result = position(bamFile); + readRecord(record, bamFile); + if (record.rID == -1) + { + // Found alignment. + hasAlignments = true; + offset = result; + break; + } + } + + // Jump back to the first alignment. + if (offset != MaxValue::VALUE) + { + if (!setPosition(bamFile, offset)) + return false; // Error while seeking. + } + + // Finding no orphan alignment is not an error, hasAilgnments is false then. + return true; +} + +// ---------------------------------------------------------------------------- +// Function getUnalignedCount() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamIndex#getUnalignedCount + * @brief Query index for number of unaligned reads. + * + * @signature uint64_t getUnalignedCount(index); + * + * @param[in] index Index to query. + * @return uint64_t The number of unaligned reads. + */ + +inline uint64_t +getUnalignedCount(BamIndex const & index) +{ + return index._unalignedCount; +} + +// ---------------------------------------------------------------------------- +// Function open() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamIndex#open + * @brief Load a BAM index from a given file name. + * @signature bool open(index, filename); + + * @param[in,out] index Target data structure. + * @param[in] filename Path to file to load. Types: char const * + * + * @return bool Returns true on success, false otherwise. + */ + +inline bool +open(BamIndex & index, char const * filename) +{ + std::fstream fin(filename, std::ios::binary | std::ios::in); + if (!fin.good()) + return false; // Could not open file. + + // Read magic number. + CharString buffer; + resize(buffer, 4); + fin.read(&buffer[0], 4); + if (!fin.good()) + return false; + if (buffer != "BAI\1") + return false; // Magic number is wrong. + + int32_t nRef = 0; + fin.read(reinterpret_cast(&nRef), 4); + if (!fin.good()) + return false; + + resize(index._linearIndices, nRef); + resize(index._binIndices, nRef); + + for (int i = 0; i < nRef; ++i) // For each reference. + { + // Read bin index. + int32_t nBin = 0; + fin.read(reinterpret_cast(&nBin), 4); + if (!fin.good()) + return false; + index._binIndices[i].clear(); + BaiBamIndexBinData_ data; + for (int j = 0; j < nBin; ++j) // For each bin. + { + clear(data.chunkBegEnds); + + uint32_t bin = 0; + fin.read(reinterpret_cast(&bin), 4); + if (!fin.good()) + return false; + + int32_t nChunk = 0; + fin.read(reinterpret_cast(&nChunk), 4); + if (!fin.good()) + return false; + reserve(data.chunkBegEnds, nChunk); + for (int k = 0; k < nChunk; ++k) // For each chunk; + { + uint64_t chunkBeg = 0; + uint64_t chunkEnd = 0; + fin.read(reinterpret_cast(&chunkBeg), 8); + fin.read(reinterpret_cast(&chunkEnd), 8); + if (!fin.good()) + return false; + appendValue(data.chunkBegEnds, Pair(chunkBeg, chunkEnd)); + } + + // Copy bin data into index. + index._binIndices[i][bin] = data; + } + + // Read linear index. + int32_t nIntv = 0; + fin.read(reinterpret_cast(&nIntv), 4); + if (!fin.good()) + return false; + clear(index._linearIndices[i]); + reserve(index._linearIndices[i], nIntv); + for (int j = 0; j < nIntv; ++j) + { + uint64_t ioffset = 0; + fin.read(reinterpret_cast(&ioffset), 8); + if (!fin.good()) + return false; + appendValue(index._linearIndices[i], ioffset); + } + } + + if (!fin.good()) + return false; + + // Read (optional) number of alignments without coordinate. + uint64_t nNoCoord = 0; + fin.read(reinterpret_cast(&nNoCoord), 8); + if (!fin.good()) + { + fin.clear(); + nNoCoord = 0; + } + index._unalignedCount = nNoCoord; + + return true; +} + +// TODO(holtgrew): This is only here because of the read() function with TSequence in old file.h. + +inline bool +open(BamIndex & index, char * filename) +{ + return open(index, static_cast(filename)); +} + +// --------------------------------------------------------------------------- +// Function save() +// --------------------------------------------------------------------------- + +/*! + * @fn BamIndex#save + * @brief Save a BamIndex object. + * + * @signature bool save(baiIndex, baiFileName); + * + * @param[in] baiIndex The BamIndex to write out. + * @param[in] baiFileName The name of the BAI file to write to. + * + * @return bool true on success, false otherwise. + */ + +inline bool save(BamIndex const & index, char const * baiFilename) +{ + // Open output file. + std::ofstream out(baiFilename, std::ios::binary | std::ios::out); + + SEQAN_ASSERT_EQ(length(index._binIndices), length(index._linearIndices)); + + // Write header. + out.write("BAI\1", 4); + int32_t numRefSeqs = length(index._binIndices); + out.write(reinterpret_cast(&numRefSeqs), 4); + + // Write out indices. + typedef BamIndex const TBamIndex; + typedef TBamIndex::TBinIndex_ const TBinIndex; + typedef TBinIndex::const_iterator TBinIndexIter; + typedef TBamIndex::TLinearIndex_ TLinearIndex; + for (int i = 0; i < numRefSeqs; ++i) + { + TBinIndex const & binIndex = index._binIndices[i]; + TLinearIndex const & linearIndex = index._linearIndices[i]; + + // Write out binning index. + int32_t numBins = binIndex.size(); + out.write(reinterpret_cast(&numBins), 4); + for (TBinIndexIter itB = binIndex.begin(), itBEnd = binIndex.end(); itB != itBEnd; ++itB) + { + // Write out bin id. + out.write(reinterpret_cast(&itB->first), 4); + // Write out number of chunks. + uint32_t numChunks = length(itB->second.chunkBegEnds); + out.write(reinterpret_cast(&numChunks), 4); + // Write out all chunks. + typedef Iterator > const, Rooted>::Type TChunkIter; + for (TChunkIter itC = begin(itB->second.chunkBegEnds); !atEnd(itC); goNext(itC)) + { + out.write(reinterpret_cast(&itC->i1), 8); + out.write(reinterpret_cast(&itC->i2), 8); + } + } + + // Write out linear index. + int32_t numIntervals = length(linearIndex); + out.write(reinterpret_cast(&numIntervals), 4); + typedef Iterator const, Rooted>::Type TLinearIndexIter; + for (TLinearIndexIter it = begin(linearIndex, Rooted()); !atEnd(it); goNext(it)) + out.write(reinterpret_cast(&*it), 8); + } + + // Write the number of unaligned reads if set. + //std::cerr << "UNALIGNED\t" << index._unalignedCount << std::endl; + if (index._unalignedCount != maxValue()) + out.write(reinterpret_cast(&index._unalignedCount), 8); + + return out.good(); // false on error, true on success. +} + + +inline void _baiAddAlignmentChunkToBin(BamIndex & index, + uint32_t currBin, + uint32_t currOffset, + uint64_t prevOffset) +{ + // If this is not the first reference sequence then add previous reference data. + Pair newChunk(currOffset, prevOffset); + + // If no interest exists yet for this bin, create one and store alignment chunk. + BamIndex::TBinIndex_::iterator binIter = back(index._binIndices).find(currBin); + if (binIter == back(index._binIndices).end()) + { + BaiBamIndexBinData_ binData; + appendValue(binData.chunkBegEnds, newChunk); + back(index._binIndices).insert(std::make_pair(currBin, binData)); + } + else + { + // Otherwise, just append alignment chunk. + appendValue(binIter->second.chunkBegEnds, newChunk); + } +} + +// --------------------------------------------------------------------------- +// Function build() +// --------------------------------------------------------------------------- +// TODO(dadi): uncomment when BamIndex.build index is fixed. DOX commented out +/* + * @fn BamIndex#build + * @brief Create a BamIndex from BAM file. + * + * @signature bool build(baiIndex, bamFileName); + * + * @param[out] baiIndex The BamIndex to build into. + * @param[in] bamFileName Path to the BAM file to build an index for. Type: char const *. + * + * @return bool true on success, false otherwise. + */ +inline bool build(BamIndex & index, char const * bamFilename) +{ + // SEQAN_FAIL("This does not work yet!"); + + index._unalignedCount = 0; + clear(index._binIndices); + clear(index._linearIndices); + + // Open BAM file for reading. + BamFileIn bamFile; + if (!open(bamFile, bamFilename)) + return false; // Could not open BAM file. + + // Read BAM header. + BamHeader header; + readHeader(header, bamFile); + + uint32_t numRefSeqs = length(contigNames(context(bamFile))); + + // Scan over BAM file and create index. + BamAlignmentRecord record; + uint32_t currBin = maxValue(); + uint32_t prevBin = maxValue(); + int32_t currRefId = BamAlignmentRecord::INVALID_REFID; + int32_t prevRefId = BamAlignmentRecord::INVALID_REFID; + uint64_t currOffset = position(bamFile); + uint64_t prevOffset = currOffset; + int32_t prevPos = minValue(); + + while (!atEnd(bamFile)) + { + // Load next record. + readRecord(record, bamFile); + + // Check ordering. + if (prevRefId == record.rID && prevPos > record.beginPos) + return false; + + // The reference sequence changed, close bins for previous reference. + if (prevRefId != record.rID) + { + if (prevRefId != BamAlignmentRecord::INVALID_REFID) + { + _baiAddAlignmentChunkToBin(index, currBin, currOffset, prevOffset); + + // Add an index for all empty references between prevRefId (excluded) and record.rID (included). + for (int i = prevRefId + 1; i < record.rID; ++i) + { + BamIndex::TBinIndex_ binIndex; + appendValue(index._binIndices, binIndex); + BamIndex::TLinearIndex_ linearIndex; + appendValue(index._linearIndices, linearIndex); + } + + // Update bin book keeping. + currOffset = prevOffset; + currBin = record.bin; + prevBin = record.bin; + currRefId = record.rID; + } + else + { + // Otherwise, this is the first pass. Create an index for all empty references up to and including + // current refId. + for (int i = 0; i < record.rID; ++i) + { + BamIndex::TBinIndex_ binIndex; + appendValue(index._binIndices, binIndex); + BamIndex::TLinearIndex_ linearIndex; + appendValue(index._linearIndices, linearIndex); + } + } + + // Update reference book keeping. + prevRefId = record.rID; + prevBin = minValue(); + } + + // If the alignment's reference id is valid and its bin is not a leaf. + if (record.rID >= 0 && record.bin < 4681) + { + int32_t beginOffset = record.beginPos >> BamIndex::BAM_LIDX_SHIFT; + int32_t endPos = getAlignmentLengthInRef(record); + int32_t endOffset = (endPos - 1) >> BamIndex::BAM_LIDX_SHIFT; + + // Resize linear index if necessary. + unsigned oldSize = length(index._linearIndices); + unsigned newSize = endOffset + 1; + if (oldSize < newSize) + resize(back(index._linearIndices), newSize, 0); + + // Store offset. + for (int i = beginOffset + 1; i <= endOffset; ++i) + if (back(index._linearIndices)[i] == 0u) + back(index._linearIndices)[i] = prevOffset; + } + + // Handle the case if we changed to a new BAI bin. + if (record.bin != prevBin) + { + // If not first bin of reference, save previous bin data. + if (currBin != maxValue()) + _baiAddAlignmentChunkToBin(index, currBin, currOffset, prevOffset); + + // Update markers. + currOffset = prevOffset; + currBin = record.bin; + prevBin = record.bin; + currRefId = record.rID; + + // If the reference id is invalid then break out. + if (currRefId < 0) + break; + } + + // Make sure that the current file pointer is beyond prevOffset. + if (position(bamFile) <= static_cast(prevOffset)) + return false; // Calculating offsets failed. + + // Update prevOffset and prevPos. + prevOffset = position(bamFile); + prevPos = record.beginPos; + } + + // Count remaining unaligned records. + while (!atEnd(bamFile)) + { + SEQAN_ASSERT_GT(index._unalignedCount, 0u); + + readRecord(record, bamFile); + if (record.rID >= 0) + return false; // Could not read record. + + index._unalignedCount += 1; + } + + // After loading all alignments, if any data was read, perform checks. + if (currRefId >= 0) + { + // Store last alignment chunk to its bin and then write last reference entry with data. + _baiAddAlignmentChunkToBin(index, currBin, currOffset, prevOffset); + + // Finally, write any empty references remaining at end of file. + SEQAN_ASSERT_GEQ(numRefSeqs, length(index._binIndices)); + BamIndex::TBinIndex_ binIndex; + resize(index._binIndices, numRefSeqs, binIndex); // TODO(holtgrew): binIndex is unnecessary if resize used T() as default value as vector.resize() does. + } + + // Merge small bins if possible. + // SEQAN_FAIL("TODO: Merge bins!"); + return true; +} + + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_INDEX_BAI_H_ diff --git a/seqan/bam_io/bam_io_context.h b/seqan/bam_io/bam_io_context.h new file mode 100644 index 0000000..3bdf2e3 --- /dev/null +++ b/seqan/bam_io/bam_io_context.h @@ -0,0 +1,353 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Class BamIOContext, accessor functions. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_ + +namespace seqan { + +// ============================================================================ +// Tags +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Tag NameStoreMember +// ---------------------------------------------------------------------------- + +/*! + * @defgroup BamIOContextMemberTag BamIOContext Member Tags + * @brief Defines standard tags used to get the type of the members of the @link BamIOContext @endlink using the @link Member @endlink metafunction. + */ + +/*! + * @tag BamIOContextMemberTag#NameStoreMember + * @brief Tag used to get the type for the NameStore. + * @headerfile + * + * @signature typedef Tag NameStoreMember; + */ + +struct NameStoreMember_; +typedef Tag NameStoreMember; + +// ---------------------------------------------------------------------------- +// Tag NameStoreCacheMember +// ---------------------------------------------------------------------------- + +/*! + * @tag BamIOContextMemberTag#NameStoreCacheMember + * @brief Tag used to get the type for the NameStoreCache. + * @headerfile + * + * @signature typedef Tag NameStoreCacheMember; + */ + +struct NameStoreCacheMember_; +typedef Tag NameStoreCacheMember; + +// ---------------------------------------------------------------------------- +// Tag LengthStoreMember +// ---------------------------------------------------------------------------- + +/*! + * @tag BamIOContextMemberTag#LengthStoreMember + * @brief Tag used to get the type for the LengthStore. + * @headerfile + * + * @signature typedef Tag LengthStoreMember; + */ + +struct LengthStoreMember_; +typedef Tag LengthStoreMember; + +// ============================================================================ +// Classes +// ============================================================================ + +/*! + * @class BamIOContext + * @headerfile + * @brief The I/O context to use for BAM I/O. + * + * @signature template + * class BamIOContext; + * + * @tparam TNameStore The type used to represent the names. + * @tparam TNameStoreCache The type used to cache the names. Defaults to @link NameStoreCache @endlink <TNameStore>l;. + * + * BamIOContext objects store the names of (and provide a cache for) reference contig names. + * + * @section Examples + * + * Creating a @link BamIOContext @endlink for a raw @link StringSet @endlink of @link CharString @endlink. + * + * @code{.cpp} + * StringSet contigNames; + * NameStoreCache > contigNamesCache(contigNames); + * BamIOContext > bamIOContext(contigNames, contigNamesCache); + * // ... + * @endcode + * + * Using a @link BamIOContext @endlink with a @link FragmentStore @endlink. + * + * @code{.cpp} + * typedef FragmentStore<>::TContigNameStore TNameStore; + * typedef NameStoreCache TNameStoreCache; + * FragmentStore<> store; + * // Optionally, do something with store. + * typedef BamIOContext TBamIOContext; + * TBamIOContext bamIOContext(store.contigNameStore, store.contigNameStoreCache); + * // ... + * @endcode + */ + +/*! + * @fn BamIOContext::BamIOContext + * @headerfile + * @brief Constructor. + * + * @signature BamIOContext::BamIOContext(); + * @signature BamIOContext::BamIOContext(contigNameStore, contigNamesStoreCache); + * + * Default constructor or construction with references to sequence and sample names. + */ + +template , + typename TNameStoreCache_ = NameStoreCache, + typename TStorageSpec = void> +class BamIOContext +{ +public: + typedef typename Member::Type TNameStore; + typedef typename Member::Type TNameStoreCache; + typedef typename Member::Type TLengthStore; + + typedef typename If, + Dependent<>, TStorageSpec>::Type TNSStorageSpec; + typedef typename If, + Owner<>, TStorageSpec>::Type TSLStorageSpec; + + typedef typename StorageSwitch::Type TNameStoreMember; + typedef typename StorageSwitch::Type TNameStoreCacheMember; + typedef typename StorageSwitch::Type TLengthStoreMember; + + TNameStoreMember _contigNames; + TNameStoreCacheMember _contigNamesCache; + TLengthStoreMember _contigLengths; + CharString buffer; + String buffers; + String translateFile2GlobalRefId; + + BamIOContext() : + _contigNames(TNameStoreMember()), + _contigNamesCache(ifSwitch(typename IsPointer::Type(), + (TNameStoreCache*)NULL, + _contigNames)), + _contigLengths(TLengthStoreMember()) + {} + + BamIOContext(TNameStore & contigNames_, TNameStoreCache & contigNamesCache_) : + _contigNames(_referenceCast::Type>(contigNames_)), + _contigNamesCache(ifSwitch(typename IsPointer::Type(), + &contigNamesCache_, + _contigNames)), + _contigLengths(TLengthStoreMember()) + {} + + template + BamIOContext(BamIOContext & other) : + _contigNames(_referenceCast::Type>(contigNames(other))), + _contigNamesCache(ifSwitch(typename IsPointer::Type(), + &contigNamesCache(other), + _contigNames)), + _contigLengths(_referenceCast::Type>(contigLengths(other))) + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction NameStore +// ---------------------------------------------------------------------------- + +template +struct Member, + NameStoreMember> +{ + typedef TNameStore Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction NameStoreCache +// ---------------------------------------------------------------------------- + +template +struct Member, + NameStoreCacheMember> +{ + typedef TNameStoreCache Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction LengthStore +// ---------------------------------------------------------------------------- + +template +struct Member, + LengthStoreMember> +{ + typedef String Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function contigNames() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamIOContext#contigNames + * @brief Return reference to contig names from @link BamIOContext @endlink. + * + * @signature TNameStoreRef contigNames(context); + * + * @param[in] context The @link BamIOContext @endlink to query. + * + * @return TNameStoreRef A reference to the TNameStore of the context. + */ + +template +inline TNameStore & +contigNames(BamIOContext & context) +{ + return _referenceCast(context._contigNames); +} + +template +inline TNameStore const & +contigNames(BamIOContext const & context) +{ + return _referenceCast(context._contigNames); +} + +template +inline void +setContigNames(BamIOContext > & context, TNameStore & contigNames) +{ + context._contigNames = &contigNames; +} + +// ---------------------------------------------------------------------------- +// Function contigLengths() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamIOContext#contigLengths + * @brief Return reference to contig lengths from @link BamIOContext @endlink. + * + * @signature TLengthStoreRef contigLengths(context); + * + * @param[in] context The @link BamIOContext @endlink to query. + * + * @return TLengthStoreRef A reference to the TLengthStore of the context. + */ + +template +inline typename BamIOContext::TLengthStore & +contigLengths(BamIOContext & context) +{ + typedef typename BamIOContext::TLengthStore TLengthStore; + return _referenceCast(context._contigLengths); +} + +template +inline typename BamIOContext::TLengthStore const & +contigLengths(BamIOContext const & context) +{ + typedef typename BamIOContext::TLengthStore TLengthStore; + return _referenceCast(context._contigLengths); +} + +template +inline void +setContigLengths(BamIOContext > & context, TLengthStore & contigLengths) +{ + context._contigLengths = &contigLengths; +} + +// ---------------------------------------------------------------------------- +// Function contigNamesCache() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamIOContext#contigNamesCache + * @brief Return reference to contig names cache from @link BamIOContext @endlink. + * + * @signature TNameStoreCacheRef contigNamesCache(context); + * + * @param[in] context The @link BamIOContext @endlink to query. + * + * @return TNameStoreCacheRef A reference to the TNameStoreCache of the context. + */ + +template +inline TNameStoreCache & +contigNamesCache(BamIOContext & context) +{ + return _referenceCast(context._contigNamesCache); +} + +template +inline TNameStoreCache const & +contigNamesCache(BamIOContext const & context) +{ + return _referenceCast(context._contigNamesCache); +} + +template +inline void +setContigNamesCache(BamIOContext > & context, TNameStoreCache & contigNamesCache) +{ + context._contigNamesCache = &contigNamesCache; +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_IO_CONTEXT_H_ diff --git a/seqan/bam_io/bam_sam_conversion.h b/seqan/bam_io/bam_sam_conversion.h new file mode 100644 index 0000000..4cec8de --- /dev/null +++ b/seqan/bam_io/bam_sam_conversion.h @@ -0,0 +1,369 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// Author: David Weese +// ========================================================================== +// Code to convert between SAM and BAM format tags (textual <-> binary). +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function assignTagsSamToBam() +// ---------------------------------------------------------------------------- + +template +struct AppendTagsSamToBamOneTagHelper_ +{ + TTarget ⌖ + TBuffer buffer; + char typeC; + + AppendTagsSamToBamOneTagHelper_(TTarget &target, TBuffer buffer, char typeC): + target(target), + buffer(buffer), + typeC(typeC) + {} + + template + bool operator() (Type) + { + if (BamTypeChar::VALUE != typeC) + return false; + + appendRawPod(target, lexicalCast(buffer)); + return true; + } +}; + +template +void _appendTagsSamToBamOneTag(TTarget & target, TForwardIter & iter, CharString & buffer) +{ + write(target, iter, 2); + + clear(buffer); + write(buffer, iter, 3); + SEQAN_ASSERT_EQ(buffer[0], ':'); + SEQAN_ASSERT_EQ(buffer[2], ':'); + + char typeC = buffer[1]; + appendValue(target, typeC); + + switch (typeC) + { + case 'Z': + case 'H': + // BAM string + // TODO(holtgrew): Could test on even length in case of 'H'. + readUntil(target, iter, OrFunctor()); + appendValue(target, '\0'); + break; + + case 'B': + { + // BAM array + + // Read type. + readOne(typeC, iter); + appendValue(target, typeC); + + // Read array contents. + clear(buffer); + readUntil(buffer, iter, OrFunctor()); + + size_t len = length(buffer); + + // Count number of entries (== number of commas after type character). + uint32_t nEntries = 0; + for (size_t i = 0; i != len; ++i) + if (buffer[i] == ',') + ++nEntries; + + // Write out array length. + appendRawPod(target, (uint32_t)nEntries); + + // Write out array values. + size_t startPos = 1; + for (unsigned i = 0; i < nEntries; ++i) + { + SEQAN_ASSERT_LT(startPos, len); + + // search end of current entry + size_t endPos = startPos; + for (; endPos < len; ++endPos) + if (buffer[endPos] == ',') + { + buffer[endPos] = '\0'; + break; + } + + AppendTagsSamToBamOneTagHelper_ func(target, + toCString(buffer) + startPos, + typeC); + if (!tagApply(func, BamTagTypes())) + SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC); + + startPos = endPos + 1; + } + break; + } + + default: + { + // BAM simple value + clear(buffer); + readUntil(buffer, iter, OrFunctor()); + + AppendTagsSamToBamOneTagHelper_ func(target, buffer, typeC); + if (!tagApply(func, BamTagTypes())) + SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC); + } + } +} + +/*! + * @fn assignTagsSamToBam + * @headerfile + * @brief Assign tags in SAM format to tags in BAM format. + * + * @signature void assignTagsBamToSam(bamTags, samTags); + * + * @param[out] bamTags A sequence of char (e.g. @link CharString @endlink) for the target BAM tags. + * @param[in] samTags A sequence of char (e.g. @link CharString @endlink) for the source SAM tags. + * + * @see assignTagsBamToSam + */ + +template +void appendTagsSamToBam(TTarget & target, TSource const & source) +{ + // Handle case of empty source sequence. + if (empty(source)) + return; + + typedef typename Iterator::Type TSourceIter; + TSourceIter it = begin(source, Rooted()); + + CharString buffer; + + while (!atEnd(it)) + { + if (value(it) == '\t') + skipOne(it); + + _appendTagsSamToBamOneTag(target, it, buffer); + } +} + +template +void assignTagsSamToBam(TTarget & target, TSource const & source) +{ + clear(target); + appendTagsSamToBam(target, source); +} + +// ---------------------------------------------------------------------------- +// Function assignTagsBamToSam() +// ---------------------------------------------------------------------------- + +template +struct AssignTagsBamToSamOneTagHelper_ +{ + TTarget ⌖ + TSourceIter ⁢ + char typeC; + + AssignTagsBamToSamOneTagHelper_(TTarget &target, TSourceIter &it, char typeC): + target(target), + it(it), + typeC(typeC) + {} + + template + bool operator() (Type) + { + if (BamTypeChar::VALUE != typeC) + return false; + + appendNumber(target, reinterpret_cast(*it)); + it += sizeof(Type); + return true; + } + + bool operator() (char) + { + if (BamTypeChar::VALUE != typeC) + return false; + + writeValue(target, getValue(it)); + ++it; + return true; + } +}; + +template +void _appendTagsBamToSamOneTag(TTarget & target, TSourceIter & it) +{ + // Copy tag name. + SEQAN_ASSERT_NOT(atEnd(it)); + writeValue(target, *it++); + SEQAN_ASSERT_NOT(atEnd(it)); + writeValue(target, *it++); + + // Add ':'. + writeValue(target, ':'); + + char typeC = *it++; + char c = FunctorLowcase()(typeC); + + // The only integer type supported is a 32bit signed int (SAM Format Spec, 28 Feb 2014, Section 1.5) + // This sucks as this projection is not identically reversible + if (c == 'c' || c == 's' || c == 'i') + writeValue(target, 'i'); + else + writeValue(target, typeC); + + // Add ':'. + writeValue(target, ':'); + + switch (typeC) + { + case 'Z': + case 'H': + // BAM string + SEQAN_ASSERT_NOT(atEnd(it)); + while (*it != '\0') + { + writeValue(target, *it); + ++it; + SEQAN_ASSERT_NOT(atEnd(it)); + } + ++it; + break; + + case 'B': + { + // BAM array + typeC = *it++; + writeValue(target, typeC); + AssignTagsBamToSamOneTagHelper_ func(target, it, typeC); + + // Read array length. + union { + char raw[4]; + unsigned len; + } tmp; + for (unsigned i = 0; i < 4; ++i) + { + SEQAN_ASSERT_NOT(atEnd(it)); + tmp.raw[i] = *it++; + } + for (unsigned i = 0; i < tmp.len; ++i) + { + writeValue(target, ','); + if (!tagApply(func, BamTagTypes())) + SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC); + } + break; + } + + default: + { + // BAM simple value + AssignTagsBamToSamOneTagHelper_ func(target, it, typeC); + if (!tagApply(func, BamTagTypes())) + SEQAN_ASSERT_FAIL("Invalid tag type: %c!", typeC); + } + } +} + +/*! + * @fn assignTagsBamToSam + * @headerfile + * @brief Assign tags in BAM format to tags in SAM format. + * + * @signature void assignTagsBamToSam(samTags, bamTags); + * + * @param[out] samTags A sequence of char (e.g. @link CharString @endlink) for the target SAM tags. + * @param[in] bamTags A sequence of char (e.g. @link CharString @endlink) for the source BAM tags. + * + * @see assignTagsSamToBam + */ + +template +inline void +appendTagsBamToSam(TTarget & target, TSource const & source) +{ + if (empty(source)) + return; + + typedef typename Iterator::Type TSourceIter; + TSourceIter it = begin(source, Rooted()); + + while (true) + { + _appendTagsBamToSamOneTag(target, it); + if (atEnd(it)) + return; + writeValue(target, '\t'); + } +} + +template +void assignTagsBamToSam(TTarget & target, TSource const & source) +{ + clear(target); + appendTagsBamToSam(target, source); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_SAM_CONVERSION_H_ diff --git a/seqan/bam_io/bam_scanner_cache.h b/seqan/bam_io/bam_scanner_cache.h new file mode 100644 index 0000000..bbc1f42 --- /dev/null +++ b/seqan/bam_io/bam_scanner_cache.h @@ -0,0 +1,309 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_SCANNER_CACHE_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_SCANNER_CACHE_H_ + +#include +#include + +namespace seqan { + +using namespace std; + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +struct BamScannerCacheKey_ +{ + int32_t rID; + int32_t beginPos; + uint64_t qnameHash; + + bool operator== (BamScannerCacheKey_ const &other) const + { + return rID == other.rID && beginPos == other.beginPos && qnameHash == other.qnameHash; + } +}; + +struct BamScannerCacheSearchKey_ +{ + typedef uint16_t TFlag; + + BamScannerCacheKey_ cacheKey; + TFlag flags; + TFlag flagsMask; +}; + +struct BamScannerCacheHash_ : + std::unary_function +{ + size_t operator()(BamScannerCacheKey_ const &v) const + { + return std::hash()(v.rID) ^ std::hash()(v.beginPos) ^ std::hash()(v.qnameHash); + } +}; + +class BamScannerCache +{ +public: + // The Key is a pair of (genomic pos, name) where genomic pos is a pair of (rId, pos). + typedef String TRecords; + typedef Size::Type TRecordId; + typedef BamScannerCacheKey_ TKey; + + // A mapping from the key type to the BamAlignmentRecord at this position. + typedef unordered_multimap TMap; + typedef TMap::const_iterator TMapIter; + + TRecords records; + String unusedIds; + TMap map; + BamAlignmentRecord tmpRecord; + + static const TRecordId INVALID_ID = (TRecordId)-1; +}; + + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +template +uint64_t _suffixHash(TSequence const &sequence) +{ + typedef typename Iterator::Type TIter; + typedef typename Value::Type TValue; + typedef typename Size::Type TSize; + + const uint64_t ALPH_SIZE = ValueSize::VALUE; + const unsigned MAX_LEN = LogN<~(ALPH_SIZE - 1) / ALPH_SIZE, ALPH_SIZE>::VALUE + 1; + + TSize len = length(sequence); + TIter itEnd = end(sequence, Standard()); + + if (len > 2 && (sequence[len - 2] == ':' || sequence[len - 2] == '/')) + { + len -= 2; + itEnd -= 2; + } + + if (len > MAX_LEN) + len = MAX_LEN; + + TIter it = itEnd - len; + + uint64_t hash = 0; + for (; it != itEnd; ++it) + hash = hash * ALPH_SIZE + ordValue(*it); + return hash; +} + +inline void +insertRecord(BamScannerCache &cache, seqan::BamAlignmentRecord const &record) +{ + int _id; + if (empty(cache.unusedIds)) + { + _id = length(cache.records); + appendValue(cache.records, record); + } + else + { + _id = back(cache.unusedIds); + eraseBack(cache.unusedIds); + cache.records[_id] = record; + } + + BamScannerCache::TKey key = { record.rID, record.beginPos, _suffixHash(record.qName) }; + cache.map.insert(std::make_pair(key, _id)); +} + +template +inline bool +_qNamesEqual(TQName1 const &name1, TQName2 const &name2) +{ + unsigned len1 = length(name1); + unsigned len2 = length(name2); + + if (len1 != len2) + return false; + + if (len1 > 2 && len2 > 2) + { + if (name1[len1 - 2] == ':' || name1[len1 - 2] == '/') + return prefix(name1, len1 - 1) == prefix(name2, len2 - 1); + } + return name1 == name2; +} + + +// search a certain segment that might refer to lastRecord +// if recursively search for a intermediate segments that might refer to lastRecord +inline bool +_recursivelyFindSegmentGraph( + String &records, + BamScannerCacheSearchKey_ &searchKey, + unsigned segmentNo, + BamScannerCache &cache) +{ + typedef BamScannerCache::TMapIter TMapIter; + typedef BamScannerCacheSearchKey_::TFlag TFlag; + + // search for segment using contigId, position + std::pair range = cache.map.equal_range(searchKey.cacheKey); + for (TMapIter iter = range.first; iter != range.second;) + { + TMapIter it = iter; + ++iter; + BamAlignmentRecord &record = cache.records[it->second]; + + // ... additionally check flags and qName + if ((record.flag & searchKey.flagsMask) == searchKey.flags && + _qNamesEqual(record.qName, records[0].qName)) + { + if (record.rNextId == records[0].rID && record.pNext == records[0].beginPos) + { + resize(records, segmentNo + 2); + records[segmentNo + 1] = records[0]; + records[segmentNo] = record; + appendValue(cache.unusedIds, it->second); + cache.map.erase(it); + return true; + } + } + } + + for (; range.first != range.second; ++range.first) + { + BamAlignmentRecord &record = cache.records[range.first->second]; + + // ... additionally check flags and qName + if ((record.flag & searchKey.flagsMask) == searchKey.flags && + _qNamesEqual(record.qName, records[0].qName)) + { + BamScannerCacheSearchKey_ newSearchKey = { + { record.rNextId, record.pNext, searchKey.cacheKey.qnameHash }, + static_cast((record.flag & BAM_FLAG_MULTIPLE) | ((record.flag & BAM_FLAG_NEXT_RC) >> 1)), + BAM_FLAG_MULTIPLE | BAM_FLAG_RC + }; + if (_recursivelyFindSegmentGraph(records, newSearchKey, segmentNo + 1, cache)) + { + records[segmentNo] = record; + appendValue(cache.unusedIds, range.first->second); + cache.map.erase(range.first); + return true; + } + } + } + + return false; +} + + +inline void +readMultiRecords(String &records, BamFileIn &bamFile, BamScannerCache &cache) +{ + typedef BamScannerCacheSearchKey_::TFlag TFlag; + + if (empty(records)) + resize(records, 1); + + while (!atEnd(bamFile)) + { + // read next record + BamAlignmentRecord &record = records[0]; + readRecord(record, bamFile); + + // is this a single-end read or single alignment? + if (!hasFlagMultiple(record) || + record.rID == BamAlignmentRecord::INVALID_REFID || + record.beginPos == BamAlignmentRecord::INVALID_POS || + record.rNextId == BamAlignmentRecord::INVALID_REFID || + record.pNext == BamAlignmentRecord::INVALID_POS) + { + resize(records, 1); + return; + } + + if (record.rID < record.rNextId || (record.rID == record.rNextId && record.beginPos < record.pNext)) + { + // store record to retrieve it later + insertRecord(cache, record); + continue; + } + + // search mates in case of multiple templates + BamScannerCacheSearchKey_ searchKey = { + { record.rNextId, record.pNext, _suffixHash(record.qName) }, + static_cast((record.flag & BAM_FLAG_MULTIPLE) | ((record.flag & BAM_FLAG_NEXT_RC) >> 1)), + BAM_FLAG_MULTIPLE | BAM_FLAG_RC + }; + if (_recursivelyFindSegmentGraph(records, searchKey, 0, cache)) + { + // order paired-end reads by first and second segment in the template +// if (length(records) == 2) +// { +// if (hasFlagLast(records[0])) +// std::swap(records[0], records[1]); +// } + return; + } + else + { + // we could get here if both mates align to same position and we are the first + // hence, insert our record to be retrieved by the second. + if (records[0].beginPos != records[0].pNext) + { + std::cerr << "WARNING: Mate could not be found for:\n"; + write(std::cerr, records[0], context(bamFile), seqan::Sam()); + } + insertRecord(cache, records[0]); + } + } + clear(records); +} + +} // namespace seqan; + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_SCANNER_CACHE_H_ diff --git a/seqan/bam_io/bam_tags_dict.h b/seqan/bam_io/bam_tags_dict.h new file mode 100644 index 0000000..05ddae5 --- /dev/null +++ b/seqan/bam_io/bam_tags_dict.h @@ -0,0 +1,890 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// Author: David Weese +// ========================================================================== +// Code for read/write access to BAM tag dicts. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_ +#define INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +class BamTagsDict; + +inline bool hasIndex(BamTagsDict const & bamTags); +inline void buildIndex(BamTagsDict const & bamTags); + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Host +// ---------------------------------------------------------------------------- + +template <> +struct Host +{ + typedef CharString Type; +}; + +template <> +struct Host +{ + typedef CharString const Type; +}; + +template <> +struct Size +{ + typedef unsigned Type; +}; + +template <> +struct Position +{ + typedef unsigned Type; +}; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class BamTagsDict + * @headerfile + * @brief Indexes start positions of BAM tags in a @link CharString @endlink and provides a dict-like API. + * + * @signature class BamTagsDict; + * + * @section Example + * + * @include demos/dox/bam_io/bam_tags_dict.cpp + * + * Output is: + * + * @include demos/dox/bam_io/bam_tags_dict.cpp.stdout + * + * @see getBamTypeSize + * @see getBamTypeChar + */ + +/*! + * @fn BamTagsDict::BamTagsDict + * @brief Constructor + * + * @signature BamTagsDict::BamTagsDict(); + * @signature BamTagsDict::BamTagsDict(tags); + * + * @param[in,out] tags The tags string of a @link BamAlignmentRecord @endlink to be indexed and or modified. + * + * Note, the second constructor stores a reference to tags using a @link Holder @endlink. + * In case of modifying the BamTagsDict by adding or removing tags those changes will be transparently transferred + * to the origin of tags. + */ + +class BamTagsDict +{ +public: + typedef Host::Type TBamTagsSequence; + typedef RemoveConst::Type TBamTagsSeqNonConst; + typedef Position::Type TPos; + + Holder _host; + mutable String _positions; + + BamTagsDict() {} + + explicit + BamTagsDict(TBamTagsSeqNonConst & tags) : _host(tags) {} + + explicit + BamTagsDict(TBamTagsSeqNonConst const & tags) : _host(tags) {} + + template + inline Infix::Type>::Type + operator[] (TPos pos) const + { + if (!hasIndex(*this)) + buildIndex(*this); + return infix(host(*this), _positions[pos], _positions[pos + 1]); + } +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function host() +// ---------------------------------------------------------------------------- + +inline Host::Type & +host(BamTagsDict & bamTags) +{ + return value(bamTags._host); +} + +inline Host::Type & +host(BamTagsDict const & bamTags) +{ + return value(bamTags._host); +} + +// ---------------------------------------------------------------------------- +// Function hasIndex() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#hasIndex + * @brief Returns whether the BamTagsDict has an index. + * + * @signature bool hasIndex(tagsDict); + * + * @param[in] tagsDict The @link BamTagsDict @endlink to query. + * + * @return bool true if dict has an index and false otherwise. + */ + +inline bool +hasIndex(BamTagsDict const & bamTags) +{ + return !empty(bamTags._positions) || empty(host(bamTags)); +} + +// ---------------------------------------------------------------------------- +// Function getBamTypeSize() +// ---------------------------------------------------------------------------- + +/*! + * @fn getBamTypeSize + * @headerfile + * @brief Return size of the type identified by a type char. + * + * @signature int getBamTypeSize(c); + * + * @param[in] c A char that identifies a type. + * + * @return int The size of the type in bytes, -1 for variable-length types, -2 for invalid paramters. + * + * @see BamTagsDict + * @see getBamTypeChar + */ + +// Return sizeof() of the type identified with the given char. Returns -2 if not +// valid, -1 if of variable length. + +struct GetBamTypeSizeHelper_ +{ + int &resultSize; + char typeC; + + GetBamTypeSizeHelper_(int &resultSize, char typeC) : + resultSize(resultSize), + typeC(typeC) + {} + + template + bool operator() (Type) const + { + if (BamTypeChar::VALUE != typeC) + return false; + + resultSize = sizeof(Type); + return true; + } +}; + + +inline int +getBamTypeSize(char c) +{ + switch (toUpperValue(c)) + { + case 'Z': + case 'H': + case 'B': + return -1; + + default: + int result = -2; + GetBamTypeSizeHelper_ func(result, c); + tagApply(func, BamTagTypes()); + return result; + } +} + +// ---------------------------------------------------------------------------- +// Function buildIndex() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#buildIndex + * @brief Build index for a BamTagsDict object. + * + * @signature void buildIndex(tagsDict); + * + * @param[in,out] tagsDict The BamTagsDict object to build the index for. + */ + +inline void +buildIndex(BamTagsDict const & bamTags) +{ + typedef Host::Type TTagString; + typedef Iterator::Type TIter; + + clear(bamTags._positions); + if (empty(host(bamTags))) + return; // Done. + + appendValue(bamTags._positions, 0); + TIter itBegin = begin(host(bamTags), Standard()); + TIter itEnd = end(host(bamTags), Standard()); + for (TIter it = itBegin; it != itEnd; ) + { + SEQAN_ASSERT(it < itEnd); + // skip tag name (e.g. "NM") + it += 2; + + // get tag type (e.g. 'I') + char c = *(it++); + if (c == 'H' || c == 'Z') + { + // skip string and its end-of-string marker + while (*it != '\0') + { + ++it; + SEQAN_ASSERT(it != itEnd); + } + ++it; + } + else if (c == 'B') + { + // skip array of PODs + c = *(it++); + union { + char raw[4]; + uint32_t len; + } tmp; + arrayCopyForward(it, it + 4, tmp.raw); + it += 4 + tmp.len * getBamTypeSize(c); + } + else + { + // skip POD type (e.g. byte, int) + it += getBamTypeSize(c); + } + appendValue(bamTags._positions, it - itBegin); + } + // if (!empty(value(bamTags._host))) + // appendValue(bamTags._positions, length(host(bamTags)) + 1); // +1 since there is not tab at the end +} + +// ---------------------------------------------------------------------------- +// Function _dataHost() +// ---------------------------------------------------------------------------- + +inline Holder::Type> & +_dataHost(BamTagsDict & bamTags) +{ + return bamTags._host; +} + +inline Holder::Type> const & +_dataHost(BamTagsDict const & bamTags) +{ + return bamTags._host; +} + +// ---------------------------------------------------------------------------- +// Function setHost() +// ---------------------------------------------------------------------------- + +template +inline void +setHost(BamTagsDict & me, THost && host_) +{ + setValue(_dataHost(me), std::forward(host_)); + clear(me._positions); +} + +// ---------------------------------------------------------------------------- +// Function length() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#length + * @brief Returns the number of entries in a BamTagsDict. + * + * @signature unsigned length(tagsDict); + * + * @param[in] tagsDict The BamTagsDict object to query for its length. + * + * @return TSize The number of entries in the BamTagsDict. TSize is the result of + * Size<BamTagsDict>::Type. + */ + +inline Size::Type +length(BamTagsDict const & tags) +{ + if (empty(host(tags))) + return 0; + if (!hasIndex(tags)) + buildIndex(tags); + return length(tags._positions) - 1; +} + +// ---------------------------------------------------------------------------- +// Function getTagType() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#getTagType + * @brief Returns the tag type char for an entry of a BamTagsDict. + * + * @signature char getTagType(tagsDict, id); + * + * @param[in] tagsDict The BamTagsDict to query. + * @param[in] id The id of the tag for which to determine the type. See @link BamTagsDict#findTagKey @endlink. + * + * @return char A char that identifies the tag type. + */ + +template +inline char +getTagType(BamTagsDict const & tags, TId id) +{ + return tags[id][2]; +} + +// ---------------------------------------------------------------------------- +// Function getTagKey() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#getTagKey + * @brief Return key of a tag by index. + * + * @signature TKey getTagKey(tagsDict, id); + * + * @param[in] tagsDict The BamTagsDict to query. + * @param[in] id The index of the dict entry. + * + * @return TKey An infix of a @link CharString @endlink. Will be a two-character char sequence. + */ + +template +inline Infix::Type>::Type +getTagKey(BamTagsDict const & tags, TId id) +{ + return prefix(tags[id], 2); +} + +// ---------------------------------------------------------------------------- +// Function findTagKey() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#findTagKey + * @brief Find a tag by its key for a @link BamTagsDict @endlink object. + * + * @signature bool findTagKey(id, tagsDict, key); + * + * @param[out] id The id of the found tag. + * @param[in] tagsDict The BamTagsDict to query. + * @param[in] key The key to query for: @link CharString @endlink. + * + * @return bool true if the key could be found and false otherwise. + */ + +template +inline bool +findTagKey(TId & id, BamTagsDict const & tags, TKey const & key) +{ + for (id = 0; id < (TId)length(tags); ++id) + if (getTagKey(tags, id) == key) + return true; + return false; +} + +// ---------------------------------------------------------------------------- +// Function extractTagValue() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#extractTagValue + * @brief Extract and cast "atomic" value from tags string with index id. + * + * @signature bool extractTagValue(dest, tagsDict, id) + * + * @param[out] dest The variable to write the value to.The value is first copied in a variable of the type indicated in + * the BAM file. Then it is cast into the type of dest. + * + * @param[in] tagsDict The BamTagsDict object to query. + * @param[in] id The id of the tag to extract the value from. See @link BamTagsDict#findTagKey @endlink. + * + * @return bool true if the value could be extracted. + * + * @section Remarks + * + * The function only works for atomic types such as int, not for char* or arrays. + * + * See @link BamTagsDict @endlink for an example. + */ + +template +struct ExtractTagValueHelper_ +{ + TResultType &result; + TIter rawIter; + char typeC; + + ExtractTagValueHelper_(TResultType &result, char typeC, TIter rawIter) : + result(result), + rawIter(rawIter), + typeC(typeC) + {} + + template + bool operator() (Type) const + { + if (BamTypeChar::VALUE != typeC) + return false; + + union { + char raw[sizeof(Type)]; + Type i; + } tmp; + + arrayCopyForward(rawIter, rawIter + sizeof(Type), tmp.raw); + result = static_cast(tmp.i); + return true; + } +}; + +template +SEQAN_FUNC_ENABLE_IF(Is >, bool) +extractTagValue(TResultValue & val, BamTagsDict const & tags, TId id) +{ + typedef Infix::Type>::Type TInfix; + typedef Iterator::Type TIter; + + TInfix inf = tags[id]; + if (length(inf) < 4 || inf[2] == 'Z') + return false; + + TIter it = begin(inf, Standard()) + 2; + char typeC = getValue(it++); + ExtractTagValueHelper_ func(val, typeC, it); + + return tagApply(func, BamTagTypes()); +} + +template +SEQAN_FUNC_ENABLE_IF(IsSequence, bool) +extractTagValue(TResultValue & val, BamTagsDict const & tags, TId id) +{ + typedef Infix::Type>::Type TInfix; + + TInfix inf = tags[id]; + if (length(inf) < 4 || inf[2] != 'Z') + return false; + + val = infix(inf, 3, length(inf) - 1); + return true; +} + +// ---------------------------------------------------------------------------- +// Function getBamTypeChar() +// ---------------------------------------------------------------------------- + +/*! + * @fn getBamTypeChar + * @headerfile + * @brief Return char identifying the type of the argument type. + * + * @signature char getBamTypeChar(); + * @signature BamTypeChar::VALUE + * + * @tparam T The type to query for its type char. + * + * @section Remarks + * + * Note that this function is defined for the int16_t, uint16_t etc. but not for the types + * short, int etc. An exception are 8-bit characters/char, where it is defined for int8_t, + * uint8_t, and char unless char is equal to one of the other two types. This is important + * when used in @link BamTagsDict#setTagValue @endlink etc. since BAM gives type chars for printable characters, signed + * 8-bit numbers and unsigned 8-bit numbers. + * + * If int8_t and uint8_t are not identical to char, we can make this decision from the type, + * otherwise we cannot and we will give the integer types a higher precedence. + * + * In your programs, this should not make any difference, only the written SAM/BAM will differ. + * + * @see BamTagsDict + * @see getBamTypeSize + */ + +template +struct BamTypeChar : + BamTypeChar {}; + +template +inline char getBamTypeChar(T const &) +{ + return BamTypeChar::VALUE; +} + +// ---------------------------------------------------------------------------- +// Function setTagValue() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Test me! + +/*! + * @fn BamTagsDict#setTagValue + * + * @headerfile + * + * @brief Set the value of a tag through a @link BamTagsDict @endlink. + * + * @signature bool setTagValue(tagsDict, key, val[, typeC]); + * + * @param[in,out] tagsDict The BamTagsDict to modify. + * @param[in] key The key of the tag. Must be a sequence of length 2. + * @param[in] val The value to set the tag to. + * @param[in] typeC BAM type char to use. For portability (so the generated files are the same on all platforms), use + * a signed/unsigned qualified type for val or give typeC. Also see the remarks + * for @link getBamTypeChar @endlink. Types: getBamTypeChar@. + * + * @return bool true on success, false on failure. This function can fail if the key is not a valid tag id (e.g. does + * not have length 2) or if the type of val is not an atomic value or a string (anything but + * char *, char const *, a character, integer or float type is invalid). + * + * @section Remarks + * + * Note that setTagValue does not cast the type, so typeC only influences the type character written + * out but val is written out in binary without modification. + * + * @section Examples + * + * An example setting some atomic tag values. + * + * @code{.cpp} + * CharString rawTagsText; + * BamTagsDict tags(rawTagsText); + * setTagValue(tags, "XA", 9); // int + * setTagValue(tags, "XB", 9u); // unsigned int + * setTagValue(tags, "XC", 'X'); // char + * @endcode + * + * If char is equal to int8_t or uint8_t then the last line produces an entry with type 'c' + * or 'C'. To make sure that the type char 'A' (for "printable character") is written to the file, give it explicitely: + * + * @code{.cpp} + * setTagValue(tags, "XC", 'X', 'A'); // Overrwrite XC, enforce type 'printable character'. + * @endcode + * + * Note that on most systems ints have a width of 32 bytes, but the C++ standard leaves this open. For all + * types but characters, you should not give an explicit type char but use one of the types with explicit width and + * signed/unsigned qualifier such as int32_t, uint32_t etc. + * + * @code{.cpp} + * // The following is not recommended since the type of x is not "unsigned 32 bit int." + * int32_t x = -1; + * setTagValue(tags, "XB", x, 'I'); + * // Instead, explicitely use an unsigned type if you need one. Note that your compiler + * // might warn you about assigning -1 to an unsigned variable so you know that you are + * // probably doing something unintended. + * uint32_t y = -1; + * setTagValue(tags, "XB", y); + * + * // Do not do this! + * setTagValue(tags, "XA", 9, 'f'); // BOGUS since 9 is not a floating point number. + * @endcode + * + * @see getBamTypeChar + */ + +template +struct ToBamTagValueHelper_ +{ + TBamValueSequence &result; + TValue val; + char typeC; + + ToBamTagValueHelper_(TBamValueSequence &result, char typeC, TValue val) : + result(result), + val(val), + typeC(typeC) + {} + + template + bool operator() (Type) const + { + if (BamTypeChar::VALUE != typeC) + return false; + + union { + char raw[sizeof(Type)]; + Type i; + } tmp; + + tmp.i = static_cast(val); + append(result, toRange(&tmp.raw[0], &tmp.raw[sizeof(Type)])); + return true; + } +}; + +// Convert "atomic" value to BAM tag. Return whether val was atomic. +template +SEQAN_FUNC_ENABLE_IF(Is >, bool) +_toBamTagValue(TBamValueSequence & result, TValue const & val, char typeC) +{ + if (typeC == 'Z') + return false; + + appendValue(result, typeC); + ToBamTagValueHelper_ func(result, typeC, val); + if (tagApply(func, BamTagTypes())) + return true; + + resize(result, length(result) - 1); + return false; +} + +template +SEQAN_FUNC_ENABLE_IF(IsSequence, bool) +_toBamTagValue(TBamValueSequence & result, TValue const & val, char typeC) +{ + if (typeC != 'Z') + return false; + + appendValue(result, typeC); + append(result, val); + appendValue(result, '\0'); + return true; +} + + +// Sets an atomic value in a BamTagsDict. +// Returns true successful, can fail if val not atomic or key is not a valid tag id (2 chars). + +template +inline bool +setTagValue(BamTagsDict & tags, TKey const & key, TValue const & val, char typeC) +{ + if (!hasIndex(tags)) + buildIndex(tags); + + // Build value to insert/append. + if (length(key) != 2u) + return false; + + Position::Type id = 0; + if (findTagKey(id, tags, key)) + { + CharString bamTagVal; + if (!_toBamTagValue(bamTagVal, val, typeC)) + return false; + + replace(host(tags), tags._positions[id] + 2, tags._positions[id + 1], bamTagVal); + clear(tags._positions); + } + else + { + append(host(tags), key); + if (!_toBamTagValue(host(tags), val, typeC)) + { + resize(host(tags), length(host(tags)) - length(key)); + return false; + } + appendValue(tags._positions, length(host(tags))); + } + + return true; +} + +template +inline bool +setTagValue(BamTagsDict & tags, TKey const & key, TValue const & val) +{ + return setTagValue(tags, key, val, BamTypeChar::VALUE); +} + +/*! + * @fn BamTagsDict#appendTagValue + * + * @headerfile + * + * @brief Append a tag/value pair to a @link BamTagsDict @endlink. + * + * @signature bool appendTagValue(tagsDict, key, val[, typeC]); + * + * @param[in,out] tagsDict The BamTagsDict to modify. + * @param[in] key The key of the tag. Must be a sequence of length 2. + * @param[in] val The value to set the tag to. + * @param[in] typeC BAM type char to use. For portability (so the generated files are the same on all platforms), use + * a signed/unsigned qualified type for val or give typeC. Also see the remarks + * for @link getBamTypeChar @endlink. Types: getBamTypeChar@. + * + * @return bool true on success, false on failure. This function can fail if the key is not a valid tag id (e.g. does + * not have length 2) or if the type of val is not an atomic value or a string (anything but + * char *, char const *, a character, integer or float type is invalid). + * + * @section Remarks + * + * @link BamTagsDict#setTagValue @endlink behaves like appendTagValue if key was not part of tags + * before. However, in this case appendTagValue is faster. + */ + +template +inline bool +appendTagValue(TSequence & tags, TKey const & key, TValue const & val, char typeC) +{ + // Build value to insert/append. + if (length(key) != 2u) + return false; + + append(tags, key); + return _toBamTagValue(tags, val, typeC); +} + +template +inline bool +appendTagValue(BamTagsDict & tags, TKey const & key, TValue const & val, char typeC) +{ + if (appendTagValue(host(tags), key, val, typeC)) + { + appendValue(tags._positions, length(host(tags))); + return true; + } + return false; +} + + +template +inline bool +appendTagValue(TDictOrString & tags, TKey const & key, TValue const & val) +{ + return appendTagValue(tags, key, val, BamTypeChar::VALUE); +} + + +// ---------------------------------------------------------------------------- +// Function eraseTag() +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#eraseTag + * @brief Erase a tag from BamTagsDict. + * + * @signature bool eraseTag(tagsDict, key); + * + * @param[in,out] tagsDict The BamTagsDict to erase the tag from. + * @param[in] key The key of the tag to erase. + * + * @return bool true if the tag could be erased, false if the key wasn't present. + */ + +template +inline SEQAN_FUNC_DISABLE_IF(Is >, bool) +eraseTag(BamTagsDict & tags, TKey const & key) +{ + if (!hasIndex(tags)) + buildIndex(tags); + + Position::Type id = 0; + if (!findTagKey(id, tags, key)) + return false; + + erase(host(tags), tags._positions[id], tags._positions[id + 1]); + clear(tags._positions); + return true; +} + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, bool) +eraseTag(BamTagsDict & tags, TId const & id) +{ + typedef typename Iterator, Standard>::Type TIter; + if (!hasIndex(tags)) + buildIndex(tags); + + typename BamTagsDict::TPos delta = tags._positions[id + 1] - tags._positions[id]; + erase(host(tags), tags._positions[id], tags._positions[id + 1]); + erase(tags._positions, id); + TIter it = begin(tags._positions, Standard()) + id; + TIter itEnd = end(tags._positions, Standard()); + for (; it != itEnd; ++it) + *it -= delta; + return true; +} + +// ---------------------------------------------------------------------------- +// Function tagsToBamRecord(); +// ---------------------------------------------------------------------------- + +/*! + * @fn BamTagsDict#tagsToBamRecord + * @brief Writes bam tags to the tags field of the given @link BamAlignmentRecord @endlink. + * + * @signature void tagsToBamRecord(record, tagsDict) + * + * @param[out] record The @link BamAlignmentRecord @endlink whose tags field is overwritten. + * @param[in] tagsDict The @link BamTagsDict @endlink to get the tags from. + * + * This is semantically the same as: + * @code{.cpp} + * record.tags = host(tagsDict); + * @endcode + * + * See @link BamTagsDict @endlink for an example. + */ + + +inline void +tagsToBamRecord(BamAlignmentRecord & record, + BamTagsDict const & dict) +{ + record.tags = host(dict); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_BAM_TAGS_DICT_H_ diff --git a/seqan/bam_io/cigar.h b/seqan/bam_io/cigar.h new file mode 100644 index 0000000..8a61fef --- /dev/null +++ b/seqan/bam_io/cigar.h @@ -0,0 +1,696 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_CIGAR_H_ +#define INCLUDE_SEQAN_BAM_IO_CIGAR_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// struct CigarElement +// ---------------------------------------------------------------------------- + +/*! + * @class CigarElement + * @headerfile + * @brief One entry of a CIGAR string. + * + * @signature template <[typename TOperation[, typename TCount]]> + * class CigarElement; + * + * @tparam TOperation Type to use for storing operations, defaults to char. + * @tparam TCount Type to use for storing counts, defaults to unsigned. + */ + +/*! + * @fn CigarElement::CigarElement + * @brief Constructor + * + * @signature CigarElement::CigarElement(); + * @signature CigarElement::CigarElement(operation, count); + * + * @param[in] operation The operation to use, of type TOperation. + * @param[in] count The operation count, of type TCount. + * + * @section Remarks + * + * The default constructor initialized both @link CigarElement::operation @endlink and @link CigarElement::count + * @endlink with 0. + */ + +/*! + * @var TCount CigarElement::count; + * + * @brief The number of operations. + */ + +/*! + * @var TOperation CigarElement::operation; + * + * @brief The described operation. + */ + +template +struct CigarElement +{ + typedef TOperation_ TOperation; + typedef TCount_ TCount; + + TOperation operation; + TCount count; + + CigarElement() : operation(0), count(0) {} + + CigarElement(TOperation o, TCount c): + operation(o), + count(c) {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +template +struct Size > +{ + typedef TCount Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +template +inline bool operator>(CigarElement const & lhs, + CigarElement const & rhs) +{ + return lhs.operation > rhs.operation || (lhs.operation == rhs.operation && (lhs.count) > (rhs.count)); +} + +template +inline bool operator<(CigarElement const & lhs, + CigarElement const & rhs) +{ + return lhs.operation < rhs.operation || (lhs.operation == rhs.operation && (lhs.count) < (rhs.count)); +} + +template +inline bool operator==(CigarElement const & lhs, + CigarElement const & rhs) +{ + return lhs.operation == rhs.operation && (lhs.count) == (rhs.count); +} + +// ---------------------------------------------------------------------------- +// toBamCigarElement() +// ---------------------------------------------------------------------------- + +template +[[deprecated("The behavior is not clear. This function should not be used anymore.")]] +uint32_t toBamCigarElement(CigarElement const & cigarElement) +{ + char operation = 0; + switch (cigarElement.operation) { + case 'X': operation += 1; SEQAN_FALLTHROUGH + case '=': operation += 1; SEQAN_FALLTHROUGH + case 'P': operation += 1; SEQAN_FALLTHROUGH + case 'H': operation += 1; SEQAN_FALLTHROUGH + case 'S': operation += 1; SEQAN_FALLTHROUGH + case 'N': operation += 1; SEQAN_FALLTHROUGH + case 'D': operation += 1; SEQAN_FALLTHROUGH + case 'I': operation += 1; SEQAN_FALLTHROUGH + case 'M': break; + } + return (cigarElement.count << 4) | operation; +} + +// ---------------------------------------------------------------------------- +// getMDString() +// ---------------------------------------------------------------------------- + +template < + typename TMDString, + typename TGaps1, + typename TGaps2> +inline unsigned +getMDString( + TMDString &md, + TGaps1 &gaps1, // typically reference + TGaps2 &gaps2) // typically read +{ + typedef typename Value::Type TMDChar; + typedef typename Value::Type>::Type TVal1; + typedef typename Value::Type>::Type TVal2; + + typename Iterator::Type it1 = begin(gaps1); + typename Iterator::Type it2 = begin(gaps2); + char op, lastOp = ' '; + unsigned numOps = 0; + unsigned errors = 0; + + clear(md); + for (; !atEnd(it1) && !atEnd(it2); goNext(it1), goNext(it2)) + { + if (isGap(it1)) + { + if (!isGap(it2)) + ++errors; + continue; // insertion to the reference (gaps1) +// op = 'I'; // ignore insertions completely + } + if (isGap(it2)) + { + ++errors; +// if (op == 'I') // ignore paddings +// continue; + op = 'D'; // deletion from the reference (gaps1) + } + else + { + if ((TVal1)*it1 == (TVal2)*it2) + { + op = 'M'; + } + else + { + op = 'R'; + ++errors; + } + } + + // append match run + if (lastOp != op) + { + if (lastOp == 'M') + { + std::stringstream num; + num << numOps; + append(md, num.str()); + } + numOps = 0; + } + + // append deleted/replaced reference character + if (op != 'M') + { + // add ^ for deleted reference bases (from non-deletion to deletion) + if (op == 'D' && lastOp != 'D') + appendValue(md, '^'); + // add 0 for each replaced base that doesn't follow a match (for samtools/BWA compatibility) + else if (op == 'R' && lastOp != 'M') + appendValue(md, '0'); + appendValue(md, convert(*it1)); + } + + lastOp = op; + ++numOps; + } + SEQAN_ASSERT_EQ(atEnd(it1), atEnd(it2)); + if (lastOp == 'M') + { + std::stringstream num; + num << numOps; + append(md, num.str()); + } + return errors; +} + +// ---------------------------------------------------------------------------- +// getCigarString() +// ---------------------------------------------------------------------------- + +template < + typename TCigar, + typename TGaps1, + typename TGaps2, + typename TThresh> +inline void +getCigarString( + TCigar &cigar, + TGaps1 &gaps1, // typically reference + TGaps2 &gaps2, // typically read + TThresh splicedGapThresh) +{ + typename Iterator::Type it1 = begin(gaps1); + typename Iterator::Type it2 = begin(gaps2); +// typedef typename Value::Type>::Type TVal1; +// typedef typename Value::Type>::Type TVal2; + + clear(cigar); + char op, lastOp = ' '; + unsigned numOps = 0; + + // std::cout << "gaps1\t" << gaps1 << std::endl; + // std::cout << "gaps2\t" << gaps2 << "\t" << clippedBeginPosition(gaps2) << std::endl; + for (; !atEnd(it1) && !atEnd(it2); goNext(it1), goNext(it2)) + { + if (isGap(it1)) + { + if (isGap(it2)) + op = 'P'; + else if (isClipped(it2)) + op = '?'; + else + op = 'I'; + } + else if (isClipped(it1)) + { + op = '?'; + } + else + { + if (isGap(it2)) + op = 'D'; + else if (isClipped(it2)) + op = 'S'; + else + op = 'M'; +// op = ((TVal1)*it1 == (TVal2)*it2)? '=': 'X'; + } + + // append CIGAR operation + if (lastOp != op) + { + if (lastOp == 'D' && numOps >= (unsigned)splicedGapThresh) + lastOp = 'N'; + if (numOps > 0) + { + std::stringstream num; + num << numOps; + append(cigar, num.str()); + appendValue(cigar, lastOp); + } + numOps = 0; + lastOp = op; + } + ++numOps; + } +// if (atEnd(it1) != atEnd(it2)) +// std::cerr << "Invalid pairwise alignment:" << std::endl << gaps1 << std::endl << gaps2 << std::endl; + SEQAN_CHECK(atEnd(it1) == atEnd(it2), "Cannot get CIGAR from invalid pairwise alignment!"); + if (lastOp == 'D' && numOps >= (unsigned)splicedGapThresh) + lastOp = 'N'; + if (numOps > 0) + { + std::stringstream num; + num << numOps; + append(cigar, num.str()); + appendValue(cigar, lastOp); + } +} + +template < + typename TCigar, + typename TGaps1, + typename TGaps2> +inline void +getCigarString( + TCigar &cigar, + TGaps1 &gaps1, // typically reference + TGaps2 &gaps2) // typically read +{ + return getCigarString(cigar, gaps1, gaps2, 20); +} + +template < + typename TOperation, + typename TCount, + typename TSpec, + typename TGaps1, + typename TGaps2, + typename TThresh> +inline void +getCigarString( + String, TSpec> &cigar, + TGaps1 &gaps1, + TGaps2 &gaps2, + TThresh splicedGapThresh) +{ + typename Iterator::Type it1 = begin(gaps1); + typename Iterator::Type it2 = begin(gaps2); +// typedef typename Value::Type>::Type TVal1; +// typedef typename Value::Type>::Type TVal2; + + clear(cigar); + char op = '?', lastOp = ' '; + unsigned numOps = 0; + +// std::cout << gaps1 << std::endl; +// std::cout << gaps2 << std::endl; + for (; !atEnd(it1) && !atEnd(it2); goNext(it1), goNext(it2)) + { + if (isGap(it1)) + { + if (isGap(it2)) + op = 'P'; + else if (isClipped(it2)) + op = '?'; + else + op = 'I'; + } + else if (isClipped(it1)) + { + op = '?'; + } + else + { + if (isGap(it2)) + op = 'D'; + else if (isClipped(it2)) + op = 'S'; + else +// op = ((TVal1)*it1 == (TVal2)*it2)? '=': 'X'; + op = 'M'; + } + if (lastOp != op) + { + if (lastOp == 'D' && numOps >= (unsigned)splicedGapThresh) + lastOp = 'N'; + if (numOps > 0) + appendValue(cigar, CigarElement<>(lastOp, numOps)); + numOps = 0; + lastOp = op; + } + ++numOps; + } + SEQAN_ASSERT_EQ(atEnd(it1), atEnd(it2)); + if (lastOp == 'D' && numOps >= (unsigned)splicedGapThresh) + lastOp = 'N'; + if (numOps > 0) + appendValue(cigar, CigarElement<>(op, numOps)); +} + +// ---------------------------------------------------------------------------- +// alignAndGetCigarString() +// ---------------------------------------------------------------------------- + +template < + typename TCigar, typename TMDString, typename TContig, typename TReadSeq, + typename TAlignedRead, typename TErrors > +inline void +alignAndGetCigarString( + TCigar &cigar, TMDString &md, TContig &, TReadSeq &, + TAlignedRead &, TErrors &, Nothing const &) +{ + cigar = "*"; + clear(md); +} + +struct BamAlignFunctorEditDistance +{ + typedef String > TGapAnchors; + + TGapAnchors contigAnchors, readAnchors; + + template + inline int + align(TGaps1 &gaps1, TGaps2 &gaps2, TErrors maxErrors) + { + return -globalAlignment( + gaps1, gaps2, + Score(), + -(int)maxErrors, (int)maxErrors + ); + } +}; + +struct BamAlignFunctorSemiGlobalGotoh +{ + typedef String > TGapAnchors; + + Score score; + TGapAnchors contigAnchors, readAnchors; + + BamAlignFunctorSemiGlobalGotoh(Score score_) : + score(score_) + {} + + template + inline int + align(TGaps1 &gaps1, TGaps2 &gaps2, TErrors maxErrors) + { + return globalAlignment( + gaps1, gaps2, score, + AlignConfig(), + -(int)maxErrors, (int)maxErrors, + Gotoh() + ) / scoreMismatch(score); + } +}; + +struct BamAlignFunctorDefault +{ +}; + +template < + typename TCigar, typename TMDString, typename TContigInfix, typename TReadSeq, + typename TAlignedRead, typename TErrors, typename TAlignFunctor> +inline void +_alignAndGetCigarString( + TCigar &cigar, TMDString &md, TContigInfix const &contigInfix, TReadSeq const &fwdReadSeq, + TAlignedRead &, TErrors &errors, TAlignFunctor &functor) +{ + typedef Gaps > TContigGaps; + typedef Gaps > TReadGaps; + + clear(functor.contigAnchors); + clear(functor.readAnchors); + + TContigGaps contigGaps(contigInfix, functor.contigAnchors); + TReadGaps readGaps(fwdReadSeq, functor.readAnchors); + + // if there is already an alignment between contigInfix and fwdReadSeq with 0 or 1 error then + // we don't to realign as it contains no gaps + if (!(errors == 0 || (errors == 1 && length(contigInfix) == length(fwdReadSeq)))) + errors = functor.align(contigGaps, readGaps, errors); + + getCigarString(cigar, contigGaps, readGaps); + TErrors mdErrors = getMDString(md, contigGaps, readGaps); + + ignoreUnusedVariableWarning(mdErrors); + SEQAN_ASSERT_EQ(errors, mdErrors); +} + +template < + typename TCigar, typename TMDString, typename TContig, typename TReadSeq, + typename TAlignedRead, typename TErrors, typename TAlignFunctor> +inline void +alignAndGetCigarString( + TCigar &cigar, TMDString &md, TContig const &contig, TReadSeq const &readSeq, + TAlignedRead &alignedRead, TErrors &errors, TAlignFunctor &functor) +{ + typedef typename TContig::TContigSeq TContigSeq; + typedef typename Infix::Type TContigInfix; + + TContigInfix contigInfix; + + if (alignedRead.beginPos <= alignedRead.endPos) + { + contigInfix = infix(contig.seq, alignedRead.beginPos, alignedRead.endPos); + _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); + } + else + { + contigInfix = infix(contig.seq, alignedRead.endPos, alignedRead.beginPos); + _alignAndGetCigarString(cigar, md, contigInfix, reverseComplementString(readSeq), alignedRead, errors, functor); + } +} + +template < + typename TCigar, typename TMDString, typename TContig, typename TReadSeq, + typename TAlignedRead, typename TErrors> +inline void +alignAndGetCigarString( + TCigar &cigar, TMDString &md, TContig const &contig, TReadSeq const &readSeq, + TAlignedRead &alignedRead, TErrors &errors, BamAlignFunctorDefault &) +{ + typedef typename TContig::TContigSeq TContigSeq; + typedef Gaps > TContigGaps; + typedef typename ReverseComplementString::Type TRefCompReadSeq; + typedef Gaps > TReadGaps; + typedef Gaps > TRCReadGaps; + + TContigGaps contigGaps(contig.seq, contig.gaps); + + if (alignedRead.beginPos <= alignedRead.endPos) + { + setClippedBeginPosition(contigGaps, alignedRead.beginPos); + setClippedEndPosition(contigGaps, alignedRead.endPos); + + TReadGaps readGaps(readSeq, alignedRead.gaps); + + getCigarString(cigar, contigGaps, readGaps); + errors = getMDString(md, contigGaps, readGaps); + } + else + { + setClippedBeginPosition(contigGaps, alignedRead.endPos); + setClippedEndPosition(contigGaps, alignedRead.beginPos); + + TRCReadGaps readGaps(reverseComplementString(readSeq), alignedRead.gaps); + + getCigarString(cigar, contigGaps, readGaps); + errors = getMDString(md, contigGaps, readGaps); + } +} + +// ---------------------------------------------------------------------------- +// _getClippedLength() +// ---------------------------------------------------------------------------- + +template +inline void _getClippedLength(TNum & sum, TCigarString const & cigar) +{ + typedef typename Iterator::Type TCigarIter; + + TCigarIter it = begin(cigar, Standard()); + TCigarIter itEnd = end(cigar, Standard()); + + sum = 0; + for (; it != itEnd; ++it) + if (getValue(it).operation != 'S' && getValue(it).operation != 'H') + sum += getValue(it).count; +} + +// ---------------------------------------------------------------------------- +// _getLengthInRef() +// ---------------------------------------------------------------------------- + +template +inline void _getLengthInRef(TNum & sum, TCigarString const & cigar) +{ + typedef typename Iterator::Type TCigarIter; + + TCigarIter it = begin(cigar, Standard()); + TCigarIter itEnd = end(cigar, Standard()); + + sum = 0; + for (; it != itEnd; ++it) + if (getValue(it).operation != 'S' && getValue(it).operation != 'H' && getValue(it).operation != 'I') + sum += getValue(it).count; +} + +// ---------------------------------------------------------------------------- +// _getQueryLength() +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type>::Type +_getQueryLength(TCigarString const & cigar) +{ + typedef typename Iterator::Type TCigarIter; + typedef typename Size::Type>::Type TSize; + TCigarIter it = begin(cigar, Standard()); + TCigarIter itEnd = end(cigar, Standard()); + + TSize len = 0; + for (; it != itEnd; ++it) + if (getValue(it).operation != 'D' && getValue(it).operation != 'H' && getValue(it).operation != 'N' && getValue(it).operation != 'P') + len += getValue(it).count; + return len; +} + +// ---------------------------------------------------------------------------- +// cigarToGapAnchorRead() +// ---------------------------------------------------------------------------- + +template +unsigned cigarToGapAnchorRead(TGaps & gaps, TCigarString const & cigar) +{ + typename Iterator::Type it = begin(gaps); + bool atBegin = true; + unsigned beginGaps = 0; + for (unsigned i = 0; i < length(cigar); ++i) + { + switch (cigar[i].operation) + { + case 'D': + case 'N': + case 'P': + if (atBegin) + beginGaps += cigar[i].count; + insertGaps(it, cigar[i].count); + SEQAN_FALLTHROUGH + case 'I': + case 'M': + case 'S': + it += cigar[i].count; + atBegin = false; + } + } + return beginGaps; +} + +// ---------------------------------------------------------------------------- +// cigarToGapAnchorContig() +// ---------------------------------------------------------------------------- + +template +unsigned cigarToGapAnchorContig(TGaps & gaps, TCigarString const & cigar) +{ + typename Iterator::Type it = begin(gaps); + bool atBegin = true; + unsigned beginGaps = 0; + for (unsigned i = 0; i < length(cigar); ++i) + { + switch (cigar[i].operation) + { + case 'I': + case 'P': + if (atBegin) + beginGaps += cigar[i].count; + insertGaps(it, cigar[i].count); + SEQAN_FALLTHROUGH + case 'D': + case 'M': + case 'N': + case 'S': + it += cigar[i].count; + atBegin = false; + } + } + return beginGaps; +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_CIGAR_H_ diff --git a/seqan/bam_io/read_bam.h b/seqan/bam_io/read_bam.h new file mode 100644 index 0000000..71059c8 --- /dev/null +++ b/seqan/bam_io/read_bam.h @@ -0,0 +1,279 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Code for reading Bam. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_READ_BAM_H_ +#define INCLUDE_SEQAN_BAM_IO_READ_BAM_H_ + +namespace seqan { + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @tag FileFormats#Bam + * @brief Identify the BAM format. + * + * @tag FileFormats#Sam + * @brief Identify the SAM format. + */ + +struct Bam_; +typedef Tag Bam; + + +template +struct FileExtensions +{ + static char const * VALUE[1]; // default is one extension +}; + +template +char const * FileExtensions::VALUE[1] = +{ + ".bam" // default output extension +}; + + +template +struct MagicHeader +{ + static unsigned char const VALUE[4]; +}; + +template +unsigned char const MagicHeader::VALUE[4] = { 'B', 'A', 'M', '\1' }; // BAM's magic header + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function readHeader() BamHeader +// ---------------------------------------------------------------------------- + +template +inline void +readHeader(BamHeader & header, + BamIOContext & context, + TForwardIter & iter, + Bam const & /*tag*/) +{ + clear(header); + // Read BAM magic string. + String > magic; + read(magic, iter, 4); + if (magic != "BAM\1") + SEQAN_THROW(ParseError("Not in BAM format.")); + + // Read header text, including null padding. + int32_t lText; + readRawPod(lText, iter); + + CharString samHeader; + write(samHeader, iter, lText); + + // Truncate to first position of '\0'. + cropAfterFirst(samHeader, EqualsChar<'\0'>()); + + // Parse out header records. + BamHeaderRecord headerRecord; + Iterator::Type it = begin(samHeader); + while (!atEnd(it)) + { + clear(headerRecord); + readRecord(headerRecord, context, it, Sam()); + appendValue(header, headerRecord); + } + + // Read # reference sequences. + int32_t nRef; + readRawPod(nRef, iter); + CharString name; + + clear(context.translateFile2GlobalRefId); + resize(context.translateFile2GlobalRefId, nRef, -1); + + for (int32_t i = 0; i < nRef; ++i) + { + // Read length of the reference name. + int32_t nName; + readRawPod(nName, iter); + clear(name); + write(name, iter, nName); + resize(name, nName - 1); + // Read length of the reference sequence. + int32_t lRef; + readRawPod(lRef, iter); + + // Add entry to name store and sequenceInfos if necessary. + // Compute translation from local ids (used in the BAM file) to corresponding ids in the name store + size_t globalRefId = nameToId(contigNamesCache(context), name); + context.translateFile2GlobalRefId[i] = globalRefId; + if (length(contigLengths(context)) <= globalRefId) + resize(contigLengths(context), globalRefId + 1, 0); + contigLengths(context)[globalRefId] = lRef; + } +} + +// ---------------------------------------------------------------------------- +// Function readRecord() BamAlignmentRecord +// ---------------------------------------------------------------------------- + +template +inline int32_t +_readBamRecordWithoutSize(TBuffer & rawRecord, TForwardIter & iter) +{ + int32_t recordLen = 0; + readRawPod(recordLen, iter); + + // fail, if we read "BAM\1" (did you miss to call readRecord(header, bamFile) first?) + if (recordLen == 0x014D4142) + SEQAN_THROW(ParseError("Unexpected BAM header encountered.")); + + clear(rawRecord); + write(rawRecord, iter, (size_t)recordLen); + return recordLen; +} + +template +inline void +_readBamRecord(TBuffer & rawRecord, TForwardIter & iter, Bam) +{ + int32_t recordLen = 0; + readRawPod(recordLen, iter); + + // fail, if we read "BAM\1" (did you miss to call readRecord(header, bamFile) first?) + if (recordLen == 0x014D4142) + SEQAN_THROW(ParseError("Unexpected BAM header encountered.")); + + clear(rawRecord); + appendRawPod(rawRecord, recordLen); + write(rawRecord, iter, (size_t)recordLen); +} + +template +inline void +readRecord(BamAlignmentRecord & record, + BamIOContext & context, + TForwardIter & iter, + Bam const & /* tag */) +{ + typedef typename Iterator::Type TCharIter; + typedef typename Iterator >, Standard>::Type SEQAN_RESTRICT TCigarIter; + typedef typename Iterator::Type SEQAN_RESTRICT TSeqIter; + typedef typename Iterator::Type SEQAN_RESTRICT TQualIter; + + // Read size and data of the remaining block in one chunk (fastest). + int32_t remainingBytes = _readBamRecordWithoutSize(context.buffer, iter); + TCharIter it = begin(context.buffer, Standard()); + + // BamAlignmentRecordCore. + arrayCopyForward(it, it + sizeof(BamAlignmentRecordCore), reinterpret_cast(&record)); + it += sizeof(BamAlignmentRecordCore); + + remainingBytes -= sizeof(BamAlignmentRecordCore) + record._l_qname + + record._n_cigar * 4 + (record._l_qseq + 1) / 2 + record._l_qseq; + SEQAN_ASSERT_GEQ(remainingBytes, 0); + + // Translate file local rID into a global rID that is compatible with the context contigNames. + if (record.rID >= 0 && !empty(context.translateFile2GlobalRefId)) + record.rID = context.translateFile2GlobalRefId[record.rID]; + if (record.rID >= 0) + SEQAN_ASSERT_LT(static_cast(record.rID), length(contigNames(context))); + + // ... the same for rNextId + if (record.rNextId >= 0 && !empty(context.translateFile2GlobalRefId)) + record.rNextId = context.translateFile2GlobalRefId[record.rNextId]; + if (record.rNextId >= 0) + SEQAN_ASSERT_LT(static_cast(record.rNextId), length(contigNames(context))); + + // query name. + resize(record.qName, record._l_qname - 1, Exact()); + arrayCopyForward(it, it + record._l_qname - 1, begin(record.qName, Standard())); + it += record._l_qname; + + // cigar string. + resize(record.cigar, record._n_cigar, Exact()); + static char const * CIGAR_MAPPING = "MIDNSHP=X*******"; + TCigarIter cigEnd = end(record.cigar, Standard()); + for (TCigarIter cig = begin(record.cigar, Standard()); cig != cigEnd; ++cig) + { + unsigned opAndCnt; + readRawPod(opAndCnt, it); + SEQAN_ASSERT_LEQ(opAndCnt & 15, 8u); + cig->operation = CIGAR_MAPPING[opAndCnt & 15]; + cig->count = opAndCnt >> 4; + } + + // query sequence. + resize(record.seq, record._l_qseq, Exact()); + TSeqIter sit = begin(record.seq, Standard()); + TSeqIter sitEnd = sit + (record._l_qseq & ~1); + while (sit != sitEnd) + { + unsigned char ui = getValue(it); + ++it; + assignValue(sit, Iupac(ui >> 4)); + ++sit; + assignValue(sit, Iupac(ui & 0x0f)); + ++sit; + } + if (record._l_qseq & 1) + *sit++ = Iupac((uint8_t)*it++ >> 4); + + // phred quality + resize(record.qual, record._l_qseq, Exact()); + // If qual is a sequence of 0xff (heuristic same as samtools: Only look at first byte) then we clear it, to get the + // representation of '*'; + TQualIter qitEnd = end(record.qual, Standard()); + for (TQualIter qit = begin(record.qual, Standard()); qit != qitEnd;) + *qit++ = '!' + *it++; + if (!empty(record.qual) && record.qual[0] == '\xff') + clear(record.qual); + + // tags + resize(record.tags, remainingBytes, Exact()); + arrayCopyForward(it, it + remainingBytes, begin(record.tags, Standard())); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_READ_BAM_H_ diff --git a/seqan/bam_io/read_sam.h b/seqan/bam_io/read_sam.h new file mode 100644 index 0000000..ad30a46 --- /dev/null +++ b/seqan/bam_io/read_sam.h @@ -0,0 +1,399 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Code for reading SAM. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_READ_SAM_H_ +#define INCLUDE_SEQAN_BAM_IO_READ_SAM_H_ + +namespace seqan { + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +struct Sam_; +typedef Tag Sam; + + +template +struct FileExtensions +{ + static char const * VALUE[1]; // default is one extension +}; + +template +char const * FileExtensions::VALUE[1] = +{ + ".sam" // default output extension +}; + + +template +struct MagicHeader +{ + static unsigned char const * VALUE; +}; + +template +unsigned char const * MagicHeader::VALUE = NULL; // SAM has no magic header + + +enum SamTokenizeErrors_ +{ + SAM_INVALID_RECORD = 2048 +}; + +struct SamHeader_; +typedef Tag SamHeader; + +struct SamAlignment_; +typedef Tag SamAlignment; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function nextIs() SamHeader +// ---------------------------------------------------------------------------- + +template +inline bool nextIs(TForwardIter & iter, SamHeader const & /*tag*/) +{ + if (atEnd(iter)) + return false; + return value(iter) == '@'; +} + +//// ---------------------------------------------------------------------------- +//// Function skipRecord() SamHeader +//// ---------------------------------------------------------------------------- +// +//template +//inline void skipRecord(TForwardIter & iter, +// SamHeader const & /*tag*/) +//{ +// skipOne(iter, EqualsChar<'@'>()); +// skipLine(iter); +// return 0; +//} +// +//// ---------------------------------------------------------------------------- +//// Function skipRecord() SamAlignment +//// ---------------------------------------------------------------------------- +// +//template +//inline void skipRecord(TForwardIter & iter, +// SamAlignment const & /*tag*/) +//{ +// skipOne(iter, EqualsChar<'@'>()); +// skipLine(iter); +// return 0; +//} + +// ---------------------------------------------------------------------------- +// Function readRecord() BamHeaderRecord +// ---------------------------------------------------------------------------- + +template +inline void +readRecord(BamHeaderRecord & record, + BamIOContext & context, + TForwardIter & iter, + Sam const & /*tag*/) +{ + clear(record); + + // Make sure the first character is '@'. + skipOne(iter, EqualsChar<'@'>()); + + // Read the header tag. + char c1, c2; + readOne(c1, iter); + readOne(c2, iter); + + // Determine header type. + if (c1 == 'H' && c2 == 'D') + record.type = BAM_HEADER_FIRST; + else if (c1 == 'S' && c2 == 'Q') + record.type = BAM_HEADER_REFERENCE; + else if (c1 == 'R' && c2 == 'G') + record.type = BAM_HEADER_READ_GROUP; + else if (c1 == 'P' && c2 == 'G') + record.type = BAM_HEADER_PROGRAM; + else if (c1 == 'C' && c2 == 'O') + record.type = BAM_HEADER_COMMENT; + else + SEQAN_THROW(ParseError("Unknown SAM header type!")); + + CharString &buffer = context.buffer; + + if (record.type == BAM_HEADER_COMMENT) + { + skipOne(iter, IsTab()); + + appendValue(record.tags, Pair(), Exact()); + + clear(buffer); + readLine(buffer, iter); + assign(back(record.tags).i2, buffer, Exact()); + } + else + { + // Read the rest of the line into the tag field of record. + while (!atEnd(iter) && value(iter) == '\t') + { + skipOne(iter, IsTab()); + + appendValue(record.tags, Pair(), Exact()); + + clear(buffer); + readUntil(buffer, iter, EqualsChar<':'>()); + assign(back(record.tags).i1, buffer, Exact()); + + skipOne(iter, EqualsChar<':'>()); + + clear(buffer); + readUntil(buffer, iter, OrFunctor()); + assign(back(record.tags).i2, buffer, Exact()); + } + // Skip remaining line break + skipLine(iter); + } +} + +// ---------------------------------------------------------------------------- +// Function readRecord() BamHeader +// ---------------------------------------------------------------------------- + +template +inline void +readHeader(BamHeader & header, + BamIOContext & context, + TForwardIter & iter, + Sam const & tag) +{ + BamHeaderRecord record; + while (nextIs(iter, SamHeader())) + { + clear(record); + readRecord(record, context, iter, tag); + appendValue(header, record); + + // Get sequence information from @SQ header. + if (record.type == BAM_HEADER_REFERENCE) + { + CharString name; + unsigned lRef = 0; + for (unsigned i = 0; i < length(record.tags); ++i) + { + if (record.tags[i].i1 == "SN") + name = record.tags[i].i2; + else if (record.tags[i].i1 == "LN") + lexicalCast(lRef, record.tags[i].i2); + } + + // Add entry to name store and sequenceInfos if necessary. + size_t globalRefId = nameToId(contigNamesCache(context), name); + if (length(contigLengths(context)) <= globalRefId) + resize(contigLengths(context), globalRefId + 1, 0); + contigLengths(context)[globalRefId] = lRef; + } + } +} + +// ---------------------------------------------------------------------------- +// Function _readBamRecord() +// ---------------------------------------------------------------------------- + +template +inline void +_readBamRecord(TBuffer & rawRecord, TForwardIter & iter, Sam) +{ + clear(rawRecord); + readLine(rawRecord, iter); +} + +// ---------------------------------------------------------------------------- +// Function readRecord() BamAlignmentRecord +// ---------------------------------------------------------------------------- + +template +inline void +readRecord(BamAlignmentRecord & record, + BamIOContext & context, + TForwardIter & iter, + Sam const & /*tag*/) +{ + // fail, if we read "@" (did you miss to call readRecord(header, bamFile) first?) + if (nextIs(iter, SamHeader())) + SEQAN_THROW(ParseError("Unexpected SAM header encountered.")); + + OrFunctor, ParseError, Sam> > nextEntry; + + clear(record); + CharString &buffer = context.buffer; + + // QNAME + readUntil(record.qName, iter, nextEntry); + skipOne(iter, IsTab()); + + // FLAG + // TODO(holtgrew): Interpret hex and char as c-samtools -X does? + clear(buffer); + readUntil(buffer, iter, nextEntry); + record.flag = lexicalCast(buffer); + skipOne(iter, IsTab()); + + // RNAME + clear(buffer); + readUntil(buffer, iter, nextEntry); + if (buffer == "*") + record.rID = BamAlignmentRecord::INVALID_REFID; + else + record.rID = nameToId(contigNamesCache(context), buffer); + skipOne(iter, IsTab()); + + // POS + clear(buffer); + SEQAN_ASSERT_EQ((int32_t)0 - 1, (int32_t)BamAlignmentRecord::INVALID_POS); + readUntil(buffer, iter, nextEntry); + record.beginPos = (int32_t)lexicalCast(buffer) - 1; + skipOne(iter, IsTab()); + + // MAPQ + clear(buffer); + if (value(iter) == '*') + { + record.mapQ = 255; + skipOne(iter); + } + else + { + readUntil(buffer, iter, nextEntry); + record.mapQ = lexicalCast(buffer); + } + skipOne(iter, IsTab()); + + // CIGAR + CigarElement<> element; + if (value(iter) == '*') + skipOne(iter); + else + { + do + { + clear(buffer); + readUntil(buffer, iter, OrFunctor, AssertFunctor, ParseError, Sam> >()); + element.count = lexicalCast(buffer); + element.operation = value(iter); + skipOne(iter); + appendValue(record.cigar, element); + } while (value(iter) != '\t'); + } + skipOne(iter, IsTab()); + + // RNEXT + clear(buffer); + readUntil(buffer, iter, nextEntry); + if (buffer == "*") + record.rNextId = BamAlignmentRecord::INVALID_REFID; + else if (buffer == "=") + record.rNextId = record.rID; + else + record.rNextId = nameToId(contigNamesCache(context), buffer); + skipOne(iter, IsTab()); + + // PNEXT + if (value(iter) == '*') + { + record.pNext = BamAlignmentRecord::INVALID_POS; + skipOne(iter); + } + else + { + clear(buffer); + readUntil(buffer, iter, nextEntry); + record.pNext = (int32_t)lexicalCast(buffer) - 1; + } + skipOne(iter, IsTab()); + + // TLEN + if (value(iter) == '*') + { + record.tLen = MaxValue::VALUE; + skipOne(iter); + } + else + { + clear(buffer); + readUntil(buffer, iter, nextEntry); + record.tLen = lexicalCast(buffer); + } + skipOne(iter, IsTab()); + + // SEQ + readUntil(record.seq, iter, nextEntry); + // Handle case of missing sequence: Clear seq string as documented. + if (record.seq == "*") + clear(record.seq); + skipOne(iter, IsTab()); + + // QUAL + readUntil(record.qual, iter, OrFunctor()); + + // Handle case of missing quality: Clear qual string as documented. + if (record.qual == "*") + clear(record.qual); + + // The following list of tags is optional. A line break or EOF could also follow. + if (atEnd(iter)) + return; + if (value(iter) != '\t') + { + skipLine(iter); + return; + } + skipOne(iter, IsTab()); + + // TAGS + clear(buffer); + readLine(buffer, iter); + appendTagsSamToBam(record.tags, buffer); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_READ_SAM_H_ diff --git a/seqan/bam_io/write_bam.h b/seqan/bam_io/write_bam.h new file mode 100644 index 0000000..6eb1e1c --- /dev/null +++ b/seqan/bam_io/write_bam.h @@ -0,0 +1,276 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// Author: David Weese +// ========================================================================== +// Code for writing BAM. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_ +#define INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_ + +namespace seqan { + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function writeRecord() BamHeader +// ---------------------------------------------------------------------------- + +template +void write(TTarget & target, + BamHeader const & header, + BamIOContext & context, + Bam const & /*tag*/) +{ + write(target, "BAM\1"); + clear(context.buffer); + + // Create text of header. + for (unsigned i = 0; i < length(header); ++i) + write(context.buffer, header[i], context, Sam()); + + // Note that we do not write out a null-character to terminate the header. This would be valid by the SAM standard + // but the samtools do not expect this and write out the '\0' when converting from BAM to SAM. + // appendValue(context.buffer, '\0'); + + // Write text header. + appendRawPod(target, static_cast(length(context.buffer))); + write(target, context.buffer); + + // Write references. + if (!empty(context._contigNames)) + { + int32_t nRef = _max(length(contigNames(context)), length(contigLengths(context))); + appendRawPod(target, nRef); + + for (int32_t i = 0; i < nRef; ++i) + { + if (i < (int32_t)length(contigNames(context))) + { + appendRawPod(target, static_cast(length(contigNames(context)[i]) + 1)); + write(target, contigNames(context)[i]); + } + else + { + appendRawPod(target, static_cast(1)); + } + writeValue(target, '\0'); + int32_t lRef = 0; + if (i < (int32_t)length(contigLengths(context))) + lRef = contigLengths(context)[i]; + appendRawPod(target, lRef); + } + } +} + +// ---------------------------------------------------------------------------- +// Function writeRecord() BamAlignmentRecord +// ---------------------------------------------------------------------------- + +static inline int _reg2Bin(uint32_t beg, uint32_t end) +{ + --end; + if (beg >> 14 == end >> 14) + return 4681 + (beg >> 14); + + if (beg >> 17 == end >> 17) + return 585 + (beg >> 17); + + if (beg >> 20 == end >> 20) + return 73 + (beg >> 20); + + if (beg >> 23 == end >> 23) + return 9 + (beg >> 23); + + if (beg >> 26 == end >> 26) + return 1 + (beg >> 26); + + return 0; +} + +inline uint32_t +updateLengths(BamAlignmentRecord const & record) +{ + // update internal lengths. + record._l_qname = length(record.qName) + 1; + record._n_cigar = length(record.cigar); + record._l_qseq = length(record.seq); + + return sizeof(BamAlignmentRecordCore) + record._l_qname + + record._n_cigar * 4 + (record._l_qseq + 1) / 2 + record._l_qseq + + length(record.tags); +} + + +template +inline void +_writeBamRecord(TTarget & target, + BamAlignmentRecord const & record, + Bam const & /*tag*/) +{ + typedef typename Iterator > const, Standard>::Type SEQAN_RESTRICT TCigarIter; + typedef typename Iterator::Type SEQAN_RESTRICT TSeqIter; + typedef typename Iterator::Type SEQAN_RESTRICT TQualIter; + + // bin_mq_nl + unsigned l = 0; + _getLengthInRef(l, record.cigar); + record.bin =_reg2Bin(record.beginPos, record.beginPos + std::max(1u, l)); + + // Write fixed-size BamAlignmentRecordCore. + appendRawPod(target, (BamAlignmentRecordCore &)record); + + // read_name + write(target, record.qName); + writeValue(target, '\0'); + + // cigar + static unsigned char const MAP[256] = + { + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0, + 0, 0, 0, 0, 2, 0, 0, 0, 5, 1, 0, 0, 0, 0, 3, 0, + 6, 0, 0, 4, 0, 0, 0, 0, 8, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + TCigarIter citEnd = end(record.cigar, Standard()); + for (TCigarIter cit = begin(record.cigar, Standard()); cit != citEnd; ++cit) + appendRawPod(target, ((uint32_t)cit->count << 4) | MAP[(unsigned char)cit->operation]); + + // seq + TSeqIter sit = begin(record.seq, Standard()); + TSeqIter sitEnd = sit + (record._l_qseq & ~1); + while (sit != sitEnd) + { + unsigned char x = (ordValue(getValue(sit++)) << 4); + writeValue(target, x | ordValue(getValue(sit++))); + } + if (record._l_qseq & 1) + writeValue(target, ordValue(getValue(sit++)) << 4); + + // qual + SEQAN_ASSERT_LEQ(length(record.qual), length(record.seq)); + TQualIter qit = begin(record.qual, Standard()); + TQualIter qitEnd = end(record.qual, Standard()); + TQualIter qitVirtEnd = qit + record._l_qseq; + while (qit != qitEnd) + writeValue(target, *qit++ - '!'); + for (; qit != qitVirtEnd; ++qit) + writeValue(target, '\xff'); // fill with zero qualities + + // tags + write(target, record.tags); +} + +template +inline void +_writeBamRecordWrapper(TTarget & target, + BamAlignmentRecord const & record, + Nothing & /* range */, + uint32_t size, + Bam const & tag) +{ + appendRawPod(target, size); + _writeBamRecord(target, record, tag); +} + +template +inline void +_writeBamRecordWrapper(TTarget & target, + BamAlignmentRecord const & record, + Range & range, + uint32_t size, + Bam const & tag) +{ + if (SEQAN_LIKELY(size + 4 <= length(range))) + { + appendRawPod(range.begin, size); + _writeBamRecord(range.begin, record, tag); + advanceChunk(target, size + 4); + } + else + { + appendRawPod(target, size); + _writeBamRecord(target, record, tag); + } +} + +template +void write(TTarget & target, + BamAlignmentRecord const & record, + BamIOContext & context, + Bam const & tag) +{ +#ifdef SEQAN_DEBUG_OR_TEST_ + // Check for valid IO Context. + if (record.rID != BamAlignmentRecord::INVALID_REFID) + { + SEQAN_ASSERT_LT_MSG(record.rID, static_cast(length(contigNames(context))), + "BAM IO Assertion: Unknown REF ID!"); + } + if (record.rNextId != BamAlignmentRecord::INVALID_REFID) + { + SEQAN_ASSERT_LT_MSG(record.rNextId, static_cast(length(contigNames(context))), + "BAM IO Assertion: Unknown NEXT REF ID!"); + } +#endif + ignoreUnusedVariableWarning(context); + + // Update internal lengths + uint32_t size = updateLengths(record); + + // Reserve chunk memory + reserveChunk(target, 4 + size, Output()); + + // Write length and record + typename Chunk::Type ochunk; + getChunk(ochunk, target, Output()); + _writeBamRecordWrapper(target, record, ochunk, size, tag); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_WRITE_BAM_H_ diff --git a/seqan/bam_io/write_sam.h b/seqan/bam_io/write_sam.h new file mode 100644 index 0000000..3191e9a --- /dev/null +++ b/seqan/bam_io/write_sam.h @@ -0,0 +1,221 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Code for writing SAM. +// ========================================================================== + +#ifndef INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_ +#define INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_ + +namespace seqan { + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function write() BamHeaderRecord +// ---------------------------------------------------------------------------- + +template +inline void write(TTarget & target, + BamHeaderRecord const & header, + BamIOContext const & /*context*/, + Sam const & /*tag*/) +{ + char const * headerTypes[] = {"@HD", "@SQ", "@RG", "@PG", "@CO"}; + write(target, headerTypes[header.type]); + + if (header.type == BAM_HEADER_COMMENT && !empty(header.tags)) + { + writeValue(target, '\t'); + write(target, header.tags[0].i2); + } + else + { + for (unsigned i = 0; i < length(header.tags); ++i) + { + writeValue(target, '\t'); + write(target, header.tags[i].i1); + writeValue(target, ':'); + write(target, header.tags[i].i2); + } + } + + writeValue(target, '\n'); +} + +// ---------------------------------------------------------------------------- +// Function write() BamHeader +// ---------------------------------------------------------------------------- + +template +inline void write(TTarget & target, + BamHeader const & header, + BamIOContext const & context, + Sam const & tag) +{ + String writtenSeqInfos; + resize(writtenSeqInfos, length(contigNames(context)), false); + + size_t globalRefId = 0; + for (unsigned i = 0; i < length(header); ++i) + { + BamHeaderRecord const & record = header[i]; + if (record.type == BAM_HEADER_REFERENCE) + for (unsigned j = 0; j < length(record.tags); ++j) + if (record.tags[j].i1 == "SN") + { + if (getIdByName(globalRefId, contigNamesCache(context), record.tags[j].i2)) + writtenSeqInfos[globalRefId] = true; + break; + } + + write(target, record, context, tag); + } + + // Write missing @SQ header records. + SEQAN_ASSERT_LEQ(length(contigLengths(context)), length(contigNames(context))); + for (unsigned i = 0; i < length(contigLengths(context)); ++i) + { + if (writtenSeqInfos[i]) + continue; + write(target, "@SQ\tSN:"); + write(target, contigNames(context)[i]); + write(target, "\tLN:"); + appendNumber(target, contigLengths(context)[i]); + writeValue(target, '\n'); + } +} + +// ---------------------------------------------------------------------------- +// Function write() BamAlignmentRecord +// ---------------------------------------------------------------------------- + +template +inline void write(TTarget & target, + BamAlignmentRecord const & record, + BamIOContext const & context, + Sam const & /*tag*/) +{ +#ifdef SEQAN_DEBUG_OR_TEST_ + // Check for valid IO Context. + if (record.rID != BamAlignmentRecord::INVALID_REFID) + { + SEQAN_ASSERT_LT_MSG(record.rID, static_cast(length(contigNames(context))), + "SAM IO Assertion: Unknown REF ID!"); + } + if (record.rNextId != BamAlignmentRecord::INVALID_REFID) + { + SEQAN_ASSERT_LT_MSG(record.rNextId, static_cast(length(contigNames(context))), + "SAM IO Assertion: Unknown NEXT REF ID!"); + } +#endif + + write(target, record.qName); + writeValue(target, '\t'); + + appendNumber(target, record.flag); + writeValue(target, '\t'); + + if (record.rID == BamAlignmentRecord::INVALID_REFID) + writeValue(target, '*'); + else + write(target, contigNames(context)[record.rID]); + + writeValue(target, '\t'); + + SEQAN_ASSERT_EQ((int32_t)BamAlignmentRecord::INVALID_POS + 1, (int32_t)0); + appendNumber(target, record.beginPos + 1); + + writeValue(target, '\t'); + + appendNumber(target, static_cast(record.mapQ)); + writeValue(target, '\t'); + + if (empty(record.cigar)) + writeValue(target, '*'); + else + for (unsigned i = 0; i < length(record.cigar); ++i) + { + appendNumber(target, record.cigar[i].count); + writeValue(target, record.cigar[i].operation); + } + + writeValue(target, '\t'); + + if (record.rNextId == BamAlignmentRecord::INVALID_REFID) + writeValue(target, '*'); + else if (record.rID == record.rNextId) + writeValue(target, '='); + else + write(target, contigNames(context)[record.rNextId]); + + writeValue(target, '\t'); + + appendNumber(target, record.pNext + 1); + + writeValue(target, '\t'); + + if (record.tLen == BamAlignmentRecord::INVALID_LEN) + writeValue(target, '0'); + else + appendNumber(target, record.tLen); + + writeValue(target, '\t'); + + if (empty(record.seq)) + writeValue(target, '*'); // Case of empty seq string / "*". + else + write(target, record.seq); + + writeValue(target, '\t'); + + + if (empty(record.qual)) // Case of empty quality string / "*". + writeValue(target, '*'); + else + write(target, record.qual); + + if (!empty(record.tags)) + { + writeValue(target, '\t'); + appendTagsBamToSam(target, record.tags); + } + + writeValue(target, '\n'); +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BAM_IO_WRITE_SAM_H_ diff --git a/seqan/basic.h b/seqan/basic.h new file mode 100644 index 0000000..0cf12db --- /dev/null +++ b/seqan/basic.h @@ -0,0 +1,112 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Umbrella header for the basic module. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_H_ + +// -------------------------------------------------------------------------- +// Prerequisites +// -------------------------------------------------------------------------- + +#include + +// -------------------------------------------------------------------------- +// Include Sub Modules +// -------------------------------------------------------------------------- + +// Code for debugging and testing (assertions, test system) and profiling. +#include + +// C++ Metaprogramming Support Code, generally independent of SeqAn. +#include + +// Basic functors. +#include + +// Fundamental meta and global functions. This is what makes SeqAn SeqAn. +#include + +// Basic exceptions. +#include + +// More advanced debug system constructs. +// TODO(holtgrew): Move into basic_debug subsystem, some stuff from metaprogramming and fundamental required, those should not depend on debug system. +#include + +// SeqAn Concept Checking Library (ported from Boost). +#include + +// Container concept and supporting code. +#include + +// Memory allocation code. +#include + +// High level parallelism support. +#include + +// Mathematical functions and utilities. +#include + +// Smart pointers, including Holder<> class hierarchy. +#include + +// Iterator concept and implementation. +#include + +// Functions to efficiently move data between containers/iterators/streams +#include + +// Alphabet concept and biological implementations. +#include + +// Proxy class and supporting code. +#include + +// Aggregate data types (pairs, triples, tuples). +#include + +// Remaining code with cyclic dependencies. +#include + +// Basic views functions and metafunctions. +#include + +// Basic device metafunctions. +#include + +// Basic SIMD vector implementation using intrinsics. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_H_ diff --git a/seqan/basic/aggregate_concept.h b/seqan/basic/aggregate_concept.h new file mode 100644 index 0000000..f79a7d1 --- /dev/null +++ b/seqan/basic/aggregate_concept.h @@ -0,0 +1,132 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @concept AggregateConcept + * + * @brief Aggregate types contain a fixed number of fixed-size values (pairs, triples, tuples). + * + * Stream output operators are not shown in the function list below, but required. + * + * Comparison operators are not shown in the function list below, but required. + */ + +/*! + * @fn AggregateConcept#operator<< + * @brief Stream output operator. + * + * @signature TStream AggregateConcept::operator<<(stream, aggregate); + * + * @param[in,out] stream The std::ostream to write to. + * @param[in] aggregate The aggregate type to write to the stream. + * + * @return TStream Reference to stream after writing aggregate to it. + */ + +/*! + * @defgroup AggregateTags Aggregate Tags + * @brief Tags to use in aggregate (e.g. Pair, Triple, and Tuple) types. + */ + +/*! + * @tag AggregateTags#Pack + * @headerfile + * @brief Tag to mark a packed specialization that disables address alignment for members. + * + * @signature typedef Tag Pack; + */ + +struct Pack_; +typedef Tag Pack; + +// TODO(holtgrew): We need @tparam for tag in the Dox system. + +/*! + * @tag AggregateTags#BitPacked + * @headerfile + * @brief Tag to mark a bit-packed specialization that avoids to waste bits. + * + * @signature template <[unsinged BITSIZE1[, unsigned BITSIZE2]]> + * struct BitPacked; + * + * BITSIZE1 The number of bits for the first entry. + * + * BITSIZE2 The number of bits for the second entry. + */ + +template +struct BitPacked; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +/*! + * @mfn MakePacked + * @headerfile + * @brief Return the corresponding packed type for a type. + * + * @signature MakePacked::Type; + * + * @tparam TAggregate The aggregate type to transform. + * + * @return Type The resulting packed type. + */ + +template +struct MakePacked +{ + typedef T Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_AGGREGATE_CONCEPT_H_ diff --git a/seqan/basic/allocator_chunkpool.h b/seqan/basic/allocator_chunkpool.h new file mode 100644 index 0000000..d41f433 --- /dev/null +++ b/seqan/basic/allocator_chunkpool.h @@ -0,0 +1,245 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Allocator that pools one or more consecutive memory blocks of a specific +// size. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +template < + size_t SIZE, + size_t MAX_COUNT = 26, + typename TParentAllocator = Allocator > > +struct ChunkPool; + +template +struct Allocator > +{ + enum + { + STORAGE_SIZE_1 = 0x1000UL, + STORAGE_SIZE_2 = SIZE * MAX_COUNT * 8, + STORAGE_SIZE_UPPER = (STORAGE_SIZE_1 > STORAGE_SIZE_2) ? STORAGE_SIZE_1 : STORAGE_SIZE_2, + ITEMS_PER_STORAGE = STORAGE_SIZE_UPPER / SIZE, + STORAGE_SIZE = ITEMS_PER_STORAGE * SIZE, + + STORAGE_SIZE_MIN = SIZE * MAX_COUNT //minimal storage size + }; + + char * data_recycled_blocks [MAX_COUNT]; + char * data_current_begin; + char * data_current_end; + char * data_current_free; + Holder data_parent_allocator; + + Allocator() + { + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + data_current_end = data_current_free = 0; + //dont need to initialize data_current_begin + } + + Allocator(size_t reserve_item_count) + { + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + + size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN; + allocate( parentAllocator( *this ), data_current_begin, storage_size ); + data_current_end = data_current_begin + storage_size; + data_current_free = data_current_begin; + } + + Allocator(TParentAllocator & parent_alloc) + { + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + data_current_end = data_current_free = 0; + //dont need to initialize data_current_begin + + setValue(data_parent_allocator, parent_alloc); + } + + Allocator(size_t reserve_item_count, TParentAllocator & parent_alloc) + { + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + + setValue(data_parent_allocator, parent_alloc); + + size_t storage_size = (reserve_item_count * SIZE > STORAGE_SIZE_MIN) ? reserve_item_count * SIZE : STORAGE_SIZE_MIN; + allocate( parentAllocator( *this ), data_current_begin, storage_size ); + data_current_end = data_current_begin + storage_size; + data_current_free = data_current_begin; + } + + //Dummy copy + Allocator(Allocator const &) + { + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + data_current_end = data_current_free = 0; + //dont need to initialize data_current_begin + } + inline Allocator & + operator=(Allocator const &) + { + clear(*this); + return *this; + } + + ~Allocator() + { + clear(*this); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function parentAllocator() +// ---------------------------------------------------------------------------- + +template +inline TParentAllocator & +parentAllocator(Allocator > & me) +{ + return value(me.data_parent_allocator); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +void +clear(Allocator > & me) +{ + std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks)); + me.data_current_end = me.data_current_free = 0; + + clear(parentAllocator(me)); +} + +// ---------------------------------------------------------------------------- +// Function allocate() +// ---------------------------------------------------------------------------- + +template +inline void +allocate(Allocator > & me, + TValue * & data, + TSize count, + Tag const tag_) +{ + SEQAN_ASSERT_GT(count, static_cast(0)); + + typedef Allocator > TAllocator; + + char * ptr; + + if ((sizeof(TValue) != SIZE) || ((size_t) count > MAX_COUNT)) + {//no blocking + return allocate(parentAllocator(me), data, count, tag_); + } + + size_t bytes_needed = count * SIZE; + if (me.data_recycled_blocks[count - 1]) + {//use recycled + ptr = me.data_recycled_blocks[count - 1]; + me.data_recycled_blocks[count - 1] = * reinterpret_cast(ptr); + } + else + {//use new + ptr = me.data_current_free; + if (ptr + bytes_needed > me.data_current_end) + {//not enough free space in current storage: allocate new + size_t rest_block_number = (me.data_current_end - me.data_current_free) / SIZE; + if (ptr && rest_block_number) + {//link rest to recycle list + *reinterpret_cast(ptr) = me.data_recycled_blocks[rest_block_number - 1]; + me.data_recycled_blocks[rest_block_number - 1] = reinterpret_cast(ptr); + } + + allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_); + me.data_current_begin = ptr; + me.data_current_end = ptr + TAllocator::STORAGE_SIZE; + } + me.data_current_free = ptr + bytes_needed; + } + + data = reinterpret_cast(ptr); +} + +// ---------------------------------------------------------------------------- +// Function deallocate() +// ---------------------------------------------------------------------------- + +template +inline void +deallocate(Allocator > & me, + TValue * data, + TSize count, + Tag const tag_) +{ + SEQAN_ASSERT_GT(count, 0); + + if ((sizeof(TValue) != SIZE) || (static_cast(count) > MAX_COUNT)) + {//no blocking + return deallocate(parentAllocator(me), data, count, tag_); + } + + //link in recycling list + *reinterpret_cast(data) = me.data_recycled_blocks[count - 1]; + me.data_recycled_blocks[count - 1] = reinterpret_cast(data); +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_CHUNKPOOL_H_ diff --git a/seqan/basic/allocator_interface.h b/seqan/basic/allocator_interface.h new file mode 100644 index 0000000..41d7169 --- /dev/null +++ b/seqan/basic/allocator_interface.h @@ -0,0 +1,432 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Allocator class definition and generic interface. +// ========================================================================== + +// TODO(holtgrew): Perform some benchmarks and use a better malloc, e.g. tcmalloc and see whether our allocator infrastructure is worth keeping around. +// TODO(holtgrew): Rename to allocator_base.h? + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +struct Tristate_; +typedef Tag Tristate; +template struct Holder; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @defgroup AllocatorUsageTags Allocator Usage Tags + * @brief The purpose of an allocated memory block. + * + * @tag AllocatorUsageTags#TagAllocateUnspecified + * @headerfile + * @brief Not specified. + * + * @tag AllocatorUsageTags#TagAllocateTemp + * @headerfile + * @brief Temporary memory. + * + * @tag AllocatorUsageTags#TagAllocateStorage + * @headerfile + * @brief Memory for storing container content. + */ + +// TODO(holtgrew): ANY use/difference? + +struct AllocateUnspecified_; +typedef Tag TagAllocateUnspecified; + +struct AllocateTemp_; +typedef Tag TagAllocateTemp; + +struct AllocateStorage_; +typedef Tag TagAllocateStorage; + +struct AllocateAlignedMalloc_; +typedef Tag TagAllocateAlignedMalloc; + +/*! + * @class Allocator + * @headerfile + * @brief Manager for allocated memory. + * + * @signature template + * class Allocator; + * + * @tparam TSpec The specializing type. + * + * @section Remarks + * + * There are two reasons for using non-trivial allocators: + * + *
    + *
  1. Allocators support the function @link Allocator#clear @endlink for a fast deallocation of all allocated + * memory blocks.
    2. + *
  2. Some allocators are faster in allocating an deallocating memory. Pool allocators like e.g. + * @link SinglePoolAllocator @endlink or @link MultiPoolAllocator @endlink speed up + * @link Allocator#allocate @endlink, @link Allocator#deallocate * @endlink, and + * @link Allocator#clear @endlink for pooled memory blocks.
    3. + *
+ */ + +template +struct Allocator; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +//.Metafunction.Spec.param.T.type:Class.Allocator + +template +struct Spec > +{ + typedef TSpec Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function allocate() +// ---------------------------------------------------------------------------- + +/*! + * @fn Allocator#allocate + * @headerfile + * @brief Allocates memory from heap. + * + * @signature void allocate(allocator, data, count[, usageTag]); + * + * @param[in] count Number of items that could be stored in the allocated memory. The type of the allocated + * items is given by the type of data. + * @param[in] usageTag A tag the specifies the purpose for the allocated memory. Values: + * @link AllocatorUsageTags @endlink. + * @param[in,out] allocator Allocator object. allocator is conceptually the "owner" of the allocated + * memory. Objects of all types can be used as allocators. If no special behavior is + * implemented, default functions allocation/deallocation are applied that uses standard + * new and delete operators. Types: Allocator + * + * @section Remarks + * + * The function allocates at least count*sizeof(data) bytes. The allocated memory is large enough to hold + * count objects of type T, where T * is type of data. + * + * These objects are not constructed by allocate. + * + * Use e.g. one of the functions @link valueConstruct @endlink, @link arrayConstruct @endlink, @link arrayConstructCopy + * @endlink or @link arrayFill @endlink to construct the objects. A new operator which is part of the C++ + * standard (defined in <new>) can also be used to construct objects at a given memory address. + * + * @section Remarks + * + * All allocated memory blocks should be deallocated by the corresponding function @link Allocator#deallocate @endlink. + */ + +template +inline void +allocate(T const & me, + TValue * & data, + TSize count) +{ + allocate(me, data, count, TagAllocateUnspecified()); +} + +template +inline void +allocate(T & me, + TValue * & data, + TSize count) +{ + allocate(me, data, count, TagAllocateUnspecified()); +} + +template +inline void +allocate(T const &, + TValue * & data, + TSize count, + Tag const &) +{ +// data = (TValue *) operator new(count * sizeof(TValue)); +#ifdef STDLIB_VS + data = (TValue *) _aligned_malloc(count * sizeof(TValue), __alignof(TValue)); +#else +/*#if _POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600 + const size_t align = (__alignof__(TValue) < sizeof(void*)) ? sizeof(void*): __alignof__(TValue); + if (posix_memalign(&(void* &)data, align, count * sizeof(TValue))) + data = NULL; +#else + data = (TValue *) malloc(count * sizeof(TValue)); +#endif*/ + data = (TValue *) operator new(count * sizeof(TValue)); +#endif + +#ifdef SEQAN_PROFILE + if (data) + SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue)); +#endif +} + +template +inline void +allocate(T &, + TValue * & data, + TSize count, + Tag const &) +{ +// data = (TValue *) operator new(count * sizeof(TValue)); +#ifdef STDLIB_VS + data = (TValue *) _aligned_malloc(count * sizeof(TValue), __alignof(TValue)); +#else +/*#if _POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600 + const size_t align = (__alignof__(TValue) < sizeof(void*)) ? sizeof(void*) : __alignof__(TValue); + if (posix_memalign(&(void* &)data, align, count * sizeof(TValue))) + data = NULL; +#else + data = (TValue *) malloc(count * sizeof(TValue)); +#endif*/ + data = (TValue *) operator new(count * sizeof(TValue)); +#endif + +#ifdef SEQAN_PROFILE + if (data) + SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue)); +#endif +} + +// NOTE(rrahn): Currently *new* does not support aligned memory, but we need it for dynamically +// allocated SimdVector class, so we overload the allocation to use mem_alloc for simd vector types. +// See following discussion: http://stackoverflow.com/questions/6973995/dynamic-aligned-memory-allocation-in-c11 +template +inline void +allocate(T const &, + TValue * & data, + TSize count, + TagAllocateAlignedMalloc const &) +{ +#ifdef PLATFORM_WINDOWS_VS + data = (TValue *) _aligned_malloc(count * sizeof(TValue), __alignof(TValue)); +#else + #if _POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600 + const size_t align = (__alignof__(TValue) < sizeof(void*)) ? sizeof(void*): __alignof__(TValue); + if (posix_memalign(&(void* &)data, align, count * sizeof(TValue))) + data = NULL; + #else + data = (TValue *) malloc(count * sizeof(TValue)); + #endif +#endif +} + +template +inline void +allocate(T &, + TValue * & data, + TSize count, + TagAllocateAlignedMalloc const &) +{ +#ifdef PLATFORM_WINDOWS_VS + data = (TValue *) _aligned_malloc(count * sizeof(TValue), __alignof(TValue)); +#else + #if _POSIX_C_SOURCE >= 200112L || _XOPEN_SOURCE >= 600 + const size_t align = (__alignof__(TValue) < sizeof(void*)) ? sizeof(void*) : __alignof__(TValue); + if (posix_memalign(&(void* &)data, align, count * sizeof(TValue))) + data = NULL; + #else + data = (TValue *) malloc(count * sizeof(TValue)); + #endif +#endif +} + +// ---------------------------------------------------------------------------- +// Function deallocate() +// ---------------------------------------------------------------------------- + +/*! + * @fn Allocator#deallocate + * @headerfile + * @brief Deallocates memory. + * + * @signature void deallocate(object, data, count[, usageTag]) + * + * @param[in,out] object Allocator object.object is conceptually the "owner" of the allocated memory. + * Objects of all types can be used as allocators. If no special behavior is implemented, + * default functions allocation/deallocation are applied that uses standard new + * and delete operators. Types: Allocator + * @param[out] data Pointer to allocated memory that was allocated by allocate. + * @param[in] count Number of items that could be stored in the allocated memory. + * @param[in] usageTag A tag the specifies the purpose for the allocated memory. + * Values: @link AllocatorUsageTags @endlink. + * + * The values for object, count and usageTag should be the same that was used when + * allocate was called. The value of data should be the same that was returned by allocate. + * + * deallocate does not destruct objects. + * + * Use e.g. one of the functions @link valueDestruct @endlink or @link arrayDestruct @endlink to destruct the objects. + * delete and delete [] operators which are part of the C++ standard (defined in <new>) + * can also be used to destruct objects at a given memory address. + */ + +template +inline void +deallocate(T const & me, + TValue * data, + TSize const count) +{ + deallocate(me, data, count, TagAllocateUnspecified()); +} + +template +inline void +deallocate(T & me, + TValue * data, + TSize const count) +{ + deallocate(me, data, count, TagAllocateUnspecified()); +} + +template +inline void +deallocate( + T const & /*me*/, + TValue * data, +#ifdef SEQAN_PROFILE + TSize count, +#else + TSize, +#endif + Tag const) +{ +#ifdef SEQAN_PROFILE + if (data && count) // .. to use count if SEQAN_PROFILE is not defined + SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue)); +#endif +// operator delete ((void *) data); +#ifdef STDLIB_VS + _aligned_free((void *) data); +#else +// free((void *) data); + operator delete ((void *) data); +#endif +} + +template +inline void +deallocate( + T & /*me*/, + TValue * data, +#ifdef SEQAN_PROFILE + TSize count, +#else + TSize, +#endif + Tag const) +{ +#ifdef SEQAN_PROFILE + if (data && count) // .. to use count if SEQAN_PROFILE is not defined + SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue)); +#endif +// operator delete ((void *) data); +#ifdef STDLIB_VS + _aligned_free((void *) data); +#else +// free((void *) data); + operator delete ((void *) data); +#endif +} + +// NOTE(rrahn): Currently *new* does not support aligned memory, but we need it for dynamically +// allocated SimdVector class, so we overload the allocation to use mem_alloc for simd vector types. +// See following discussion: http://stackoverflow.com/questions/6973995/dynamic-aligned-memory-allocation-in-c11 +template +inline void +deallocate( + T const & /*me*/, + TValue * data, +#ifdef SEQAN_PROFILE + TSize count, +#else + TSize, +#endif + TagAllocateAlignedMalloc const) +{ +#ifdef SEQAN_PROFILE + if (data && count) // .. to use count if SEQAN_PROFILE is not defined + SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue)); +#endif +#ifdef PLATFORM_WINDOWS_VS + _aligned_free((void *) data); +#else + free((void *) data); +#endif +} + +template +inline void +deallocate( + T & /*me*/, + TValue * data, +#ifdef SEQAN_PROFILE + TSize count, +#else + TSize, +#endif + TagAllocateAlignedMalloc const) +{ +#ifdef SEQAN_PROFILE + if (data && count) // .. to use count if SEQAN_PROFILE is not defined + SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue)); +#endif + // operator delete ((void *) data); +#ifdef PLATFORM_WINDOWS_VS + _aligned_free((void *) data); +#else + free((void *) data); +#endif +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_INTERFACE_H_ diff --git a/seqan/basic/allocator_multipool.h b/seqan/basic/allocator_multipool.h new file mode 100644 index 0000000..a93cbd1 --- /dev/null +++ b/seqan/basic/allocator_multipool.h @@ -0,0 +1,262 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Allocator that pools blocks up to a given size. +// ========================================================================== + +#ifndef SEQAN_BASIC_BASIC_ALLOCATOR_MULTIPOOL_H_ +#define SEQAN_BASIC_BASIC_ALLOCATOR_MULTIPOOL_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class MultiPoolAllocator + * @extends Allocator + * @headerfile + * @brief Allocator that pools memory blocks. + * + * @signature template + * class Allocator >; + * + * @tparam TParentAllocator The parent allocator. + * @tparam BLOCKING_LIMIT The maximum size for memory blocks to be pooled (default is 256). + * + * Freed blocks are not immediately deallocated but recycled in subsequential allocations. This way, the number of + * calls to the heap manager is reduced and that might speed up memory management. + * + * Note that memory block larger than BLOCKING_LIMIT are not pooled but immediately allocated and deallocated + * using ParentAllocator. + */ + +template >, unsigned int BLOCKING_LIMIT = 0x100> +struct MultiPool; + +typedef Allocator >, 0x100> > PoolAllocator; + +template +struct Allocator > +{ + enum + { + BLOCKING_LIMIT = BLOCKING_LIMIT_, + GRANULARITY_BITS = 2, + BLOCKING_COUNT = BLOCKING_LIMIT >> GRANULARITY_BITS, + STORAGE_SIZE = 0xf80 + }; + + char * data_recycled_blocks [BLOCKING_COUNT]; + char * data_current_begin [BLOCKING_COUNT]; + char * data_current_free [BLOCKING_COUNT]; + Holder data_parent_allocator; + + Allocator() + { + // TODO(holtrew): Why not SeqAn's memset? or use using? + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + std::memset(data_current_begin, 0, sizeof(data_current_begin)); + std::memset(data_current_free, 0, sizeof(data_current_free)); + } + + Allocator(TParentAllocator & parent_alloc) + { + // TODO(holtrew): Why not SeqAn's memset? or use using? + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + std::memset(data_current_begin, 0, sizeof(data_current_begin)); + std::memset(data_current_free, 0, sizeof(data_current_free)); + + setValue(data_parent_allocator, parent_alloc); + } + + //Dummy copy + Allocator(Allocator const &) + { + // TODO(holtrew): Why not SeqAn's memset? or use using? + std::memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks)); + std::memset(data_current_begin, 0, sizeof(data_current_begin)); + std::memset(data_current_free, 0, sizeof(data_current_free)); + } + + inline Allocator & + operator=(Allocator const &) + { + clear(*this); + return *this; + } + + ~Allocator() + { + clear(*this); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function parentAllocator() +// ---------------------------------------------------------------------------- + +template +inline TParentAllocator & +parentAllocator(Allocator > & me) +{ + return value(me.data_parent_allocator); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +void +clear(Allocator > & me) +{ + std::memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks)); + std::memset(me.data_current_begin, 0, sizeof(me.data_current_begin)); + std::memset(me.data_current_free, 0, sizeof(me.data_current_free)); + + clear(parentAllocator(me)); +} + +// ---------------------------------------------------------------------------- +// Helper function _allocatorBlockNumber() +// ---------------------------------------------------------------------------- + +template +inline unsigned int +_allocatorBlockNumber(Allocator > &, + size_t size_) +{ + typedef Allocator > TAllocator; + + SEQAN_ASSERT_GT(size_, 0u); + + if (size_ < BLOCKING_LIMIT) + {//blocks + return size_ >> TAllocator::GRANULARITY_BITS; + } + else + {//no blocking + return TAllocator::BLOCKING_COUNT; + } +} + +// ---------------------------------------------------------------------------- +// Function allocate() +// ---------------------------------------------------------------------------- + +template +inline void +allocate(Allocator > & me, + TValue * & data, + TSize count, + Tag const & tag_) +{ + typedef Allocator > TAllocator; + + size_t bytes_needed = count * sizeof(TValue); + char * ptr; + + unsigned int block_number = _allocatorBlockNumber(me, bytes_needed); + if (block_number == TAllocator::BLOCKING_COUNT) + {//no blocking + return allocate(parentAllocator(me), data, count, tag_); + } + + bytes_needed = (block_number + 1) << TAllocator::GRANULARITY_BITS; + + if (me.data_recycled_blocks[block_number]) + {//use recycled + ptr = me.data_recycled_blocks[block_number]; + me.data_recycled_blocks[block_number] = * reinterpret_cast(ptr); + } + else + {//use new + ptr = me.data_current_free[block_number]; + if (!ptr || (ptr + bytes_needed > me.data_current_begin[block_number] + TAllocator::STORAGE_SIZE)) + {//not enough free space in current storage: allocate new + allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_); + me.data_current_begin[block_number] = ptr; + } + me.data_current_free[block_number] = ptr + bytes_needed; + } + + data = reinterpret_cast(ptr); +} + +// ---------------------------------------------------------------------------- +// Function deallocate() +// ---------------------------------------------------------------------------- + +template +inline void +deallocate(Allocator > & me, + TValue * data, + TSize count, + Tag const tag_) +{ + typedef Allocator > TAllocator; + + size_t bytes_needed = count * sizeof(TValue); + + unsigned int block_number = _allocatorBlockNumber(me, bytes_needed); + if (block_number == TAllocator::BLOCKING_COUNT) + {//no blocking + return deallocate(parentAllocator(me), data, count, tag_); + } + + bytes_needed = (block_number + 1) << TAllocator::GRANULARITY_BITS; + + //link in recycling list + *reinterpret_cast(data) = me.data_recycled_blocks[block_number]; + me.data_recycled_blocks[block_number] = reinterpret_cast(data); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_BASIC_ALLOCATOR_MULTIPOOL_H_ diff --git a/seqan/basic/allocator_simple.h b/seqan/basic/allocator_simple.h new file mode 100644 index 0000000..37d45ce --- /dev/null +++ b/seqan/basic/allocator_simple.h @@ -0,0 +1,239 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// General purpose allocator. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class SimpleAllocator + * @extends Allocator + * @headerfile + * @brief General purpose allocator. + * + * @signature template + * class Allocator >; + * + * @tparam TParentAllocator An allocator that is used by the simple allocator to allocate memory. + * + * The tag Default used as TparentAllocator means that the default implementations of allocate and + * deallocate are used. + */ + +template +struct SimpleAlloc; + +typedef Allocator > SimpleAllocator; + +template +struct Allocator > +{ + struct Header + { + Header * left; + Header * right; + size_t size; + }; + + Header * data_storages; + Holder data_parent_allocator; + + Allocator() + : data_storages(0) + { + } + + Allocator(TParentAllocator & parent_alloc) + : data_storages(0) + { + setValue(data_parent_allocator, parent_alloc); + } + + //Dummy copy + Allocator(Allocator const &) + : data_storages(0) + { + } + + inline Allocator & + operator = (Allocator const &) + { + clear(*this); + return *this; + } + + ~Allocator() + { + clear(*this); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function parentAllocator() +// ---------------------------------------------------------------------------- + +template +inline TParentAllocator & +parentAllocator(Allocator > & me) +{ + return value(me.data_parent_allocator); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +/*! + * @fn Allocator#clear + * @brief Deallocates all memory blocks. + * + * @signature void clear(allocator); + * + * @param[in,out] The allocator to clear. + * + * @section Remarks + * + * This function deallocates all memory block sthat were allocated using allocate() for allocator. + * The memory is not pooled but directly passed back to the heap manager. + */ + +// TODO(holtgrew): Using #-functions messes up search results. +template +void +clear(Allocator > & me) +{ + typedef Allocator > TAllocator; + + while (me.data_storages) + { + typename TAllocator::Header * next_storage = me.data_storages->right; + deallocate(parentAllocator(me), reinterpret_cast(me.data_storages), me.data_storages->size); + me.data_storages = next_storage; + } +} + +// ---------------------------------------------------------------------------- +// Function allocate() +// ---------------------------------------------------------------------------- + +template +inline void +allocate(Allocator > & me, + TValue * & data, + TSize count, + Tag const &) +{ + typedef Allocator > TAllocator; + typedef typename TAllocator::Header THeader; + + //compute needed bytes + size_t bytes_needed = count * sizeof(TValue) + sizeof(THeader); + + //allocate storage from parent + char * ptr; + allocate(parentAllocator(me), ptr, bytes_needed, TagAllocateStorage()); + + THeader * new_block = reinterpret_cast(ptr); + new_block->left = 0; + new_block->right = me.data_storages; + new_block->size = bytes_needed; + + if (me.data_storages) + { + me.data_storages->left = new_block; + } + me.data_storages = new_block; + + //return data + data = reinterpret_cast(ptr + sizeof(THeader)); +} + +// ---------------------------------------------------------------------------- +// Function deallocate() +// ---------------------------------------------------------------------------- + +template +inline void +deallocate(Allocator > & me, + TValue * data, + TSize, + Tag const &) +{ + typedef Allocator > TAllocator; + typedef typename TAllocator::Header THeader; + + //update links + THeader & header = *(reinterpret_cast(data) - 1); + if (header.left) + { + header.left->right = header.right; + } + else + { + me.data_storages = header.right; + } + if (header.right) + { + header.right->left = header.left; + } + + //deallocate storage using parent + char * ptr = reinterpret_cast(& header); + deallocate(parentAllocator(me), ptr, header.size); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_SIMPLE_H_ diff --git a/seqan/basic/allocator_singlepool.h b/seqan/basic/allocator_singlepool.h new file mode 100644 index 0000000..314cdab --- /dev/null +++ b/seqan/basic/allocator_singlepool.h @@ -0,0 +1,250 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Allocator that pools blocks of a given size; Different-sized blocks are +// not pooled. +// ========================================================================== + +#ifndef SEQAN_BASIC_BASIC_ALLOCATOR_SINGLE_POOL_H_ +#define SEQAN_BASIC_BASIC_ALLOCATOR_SINGLE_POOL_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class SinglePoolAllocator + * @extends Allocator + * @headerfile + * @brief Allocator that pools memory blocks of a specific size. + * + * @signature template + * class Allocator; + * + * @tparam SIZE The size of the blocks. + * @tparam TParentAllocator The parent allocator to use. + * + * A pool allocator allocates several memory blocks at once. Freed blocks are not immediately deallocated but + * recycled in subsequential allocations. This way, the number of calls to the heap manager is reduced, and that + * might speed up memory management. + * + * The single pool allocator only pools memory blocks of size at most $SIZE$. Blocks of other sizes are allocated and + * deallocated using an allocator of type $ParentAllocator$. Using the single pool allocator for blocksizes larger + * than a few KB is not advised. + */ + +template +struct SinglePool; + +template +struct Allocator > +{ + enum + { + // item must be large enough to keep a pointer to the next free item + SIZE_PER_ITEM = SIZE < sizeof(void*)? sizeof(void*) : SIZE, + ITEMS_PER_BLOCK = (SIZE_PER_ITEM < 0x0100) ? 0x01000 / SIZE_PER_ITEM : 16, + STORAGE_SIZE = SIZE_PER_ITEM * ITEMS_PER_BLOCK, + STORAGE_SIZE_MIN = SIZE_PER_ITEM + }; + + char * data_recycled_blocks; + char * data_current_begin; + char * data_current_end; + char * data_current_free; + Holder data_parent_allocator; + + Allocator() : data_recycled_blocks(), data_current_begin(), data_current_end(), data_current_free() + {} + + Allocator(size_t reserve_item_count) : data_recycled_blocks() + { + size_t storage_size = std::max(reserve_item_count * SIZE_PER_ITEM, STORAGE_SIZE_MIN); + allocate(parentAllocator(*this), data_current_begin, storage_size); + data_current_end = data_current_begin + storage_size; + data_current_free = data_current_begin; + } + + Allocator(TParentAllocator & parent_alloc) + { + setValue(data_parent_allocator, parent_alloc); + + data_recycled_blocks = data_current_end = data_current_free = 0; + //dont need to initialize data_current_begin + } + + Allocator(size_t reserve_item_count, TParentAllocator & parent_alloc) + { + data_recycled_blocks = 0; + + setValue(data_parent_allocator, parent_alloc); + + size_t storage_size = std::max(reserve_item_count * SIZE_PER_ITEM, STORAGE_SIZE_MIN); + allocate(parentAllocator(*this), data_current_begin, storage_size); + data_current_end = data_current_begin + storage_size; + data_current_free = data_current_begin; + } + + // Dummy copy + Allocator(Allocator const &) : + data_recycled_blocks(), data_current_begin(), data_current_end(), + data_current_free() + { + data_recycled_blocks = data_current_end = data_current_free = 0; + } + + inline Allocator & + operator=(Allocator const &) + { + clear(*this); + return *this; + } + + ~Allocator() + { + clear(*this); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function parentAllocator() +// ---------------------------------------------------------------------------- + +template +inline TParentAllocator & +parentAllocator(Allocator > & me) +{ + return value(me.data_parent_allocator); +} + +// ---------------------------------------------------------------------------- +// Function clear() +// ---------------------------------------------------------------------------- + +template +void +clear(Allocator > & me) +{ + me.data_recycled_blocks = me.data_current_end = me.data_current_free = 0; + clear(parentAllocator(me)); +} + +// ---------------------------------------------------------------------------- +// Function allocate() +// ---------------------------------------------------------------------------- + +template +inline void +allocate(Allocator > & me, + TValue * & data, + TSize count, + Tag const tag_) +{ + typedef Allocator > TAllocator; + size_t bytes_needed = count * sizeof(TValue); + + if (bytes_needed > TAllocator::SIZE_PER_ITEM) + {//no blocking + allocate(parentAllocator(me), data, count, tag_); + return; + } + + if (bytes_needed < TAllocator::SIZE_PER_ITEM) + bytes_needed = TAllocator::SIZE_PER_ITEM; + + char * ptr; + if (me.data_recycled_blocks) + {//use recycled + ptr = me.data_recycled_blocks; + me.data_recycled_blocks = * reinterpret_cast(ptr); + } + else + {//use new + ptr = me.data_current_free; + if (ptr + bytes_needed > me.data_current_end) + {//not enough free space in current storage: allocate new + allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_); + me.data_current_begin = ptr; + me.data_current_end = ptr + TAllocator::STORAGE_SIZE; + } + me.data_current_free = ptr + bytes_needed; + } + + data = reinterpret_cast(ptr); +} + +// ---------------------------------------------------------------------------- +// Function deallocate() +// ---------------------------------------------------------------------------- + +template +inline void +deallocate(Allocator > & me, + TValue * data, + TSize count, + Tag const tag_) +{ + typedef Allocator > TAllocator; + + size_t bytes_needed = count * sizeof(TValue); + + if (bytes_needed > TAllocator::SIZE_PER_ITEM) + {//no blocking + deallocate(parentAllocator(me), data, count, tag_); + return; + } + + //link in recycling list + *reinterpret_cast(data) = me.data_recycled_blocks; + me.data_recycled_blocks = reinterpret_cast(data); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_BASIC_ALLOCATOR_SINGLE_POOL_H_ diff --git a/seqan/basic/allocator_to_std.h b/seqan/basic/allocator_to_std.h new file mode 100644 index 0000000..b7d07a5 --- /dev/null +++ b/seqan/basic/allocator_to_std.h @@ -0,0 +1,206 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Wrapper that adapts SeqAn allocators to STL allocators. +// ========================================================================== + +// TODO(holtgrew): Rename STD to STL? +// TODO(holtgrew): Rename to allocator_to_stl.h, remove basic_ prefix of all other allocator headers. + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class ToStdAllocator + * @headerfile + * @brief Emulates standard conform allocator. + * + * @signature template + * class ToStdAllocator; + * + * @tparam TValue Type of allocated items. + * @tparam THost Type of the host allocator object.This object is used to call @link Allocator#allocate @endlink and + * @link Allocator#deallocate @endlink. + * + * The member functions allocate and deallocate of ToStdAllocator call the (globale) + * functions @link Allocator#allocate @endlink and @link Allocator#deallocate @endlink, respectively. The globale + * functions get an allocator object as their first arguments. This allocator object is not the ToStdAllocator + * object itself, but the host object that was given to the constructor. + * + * @fn ToStdAllocator#ToStdAllocator + * @brief Constructor + * + * @signature ToStdAllocator::ToStdAllocator(host); + * + * @param[in] host The host object that is used as allocator for @link Allocator#allocate @endlink and @link + * Allocator#deallocate @endlink. + */ + +template +struct ToStdAllocator +{ + typedef TValue value_type; // nolint + typedef value_type * pointer; // nolint + typedef value_type & reference; // nolint + typedef value_type const * const_pointer; // nolint + typedef value_type const & const_reference; // nolint + + typedef size_t size_type; // nolint + typedef ptrdiff_t difference_type; // nolint + + ToStdAllocator(THost & host): m_host(& host) + {} + + template + ToStdAllocator(ToStdAllocator const & alloc) + : m_host(alloc.m_host) + {} + + ToStdAllocator & operator= (ToStdAllocator const & alloc) + { + m_host = alloc.m_host; + return *this; + } + + pointer allocate(size_type count) + { + value_type * ptr; + seqan::allocate(*m_host, ptr, count); + return pointer(ptr); + } + + pointer allocate(size_type count, const void *) + { + value_type * ptr; + seqan::allocate(*m_host, ptr, count); + return pointer(ptr); + } + + void deallocate(pointer data, size_type count) + { + seqan::deallocate(*m_host, data, count); + } + + void construct(pointer ptr, const_reference data) + { + new(ptr) TValue(data); + } + + void destroy(pointer ptr) + { + ptr->~TValue(); + } + + pointer address(reference value) const + { + return (&value); + } + + const_pointer address(const_reference value) const + { + return (&value); + } + + size_type max_size() const + { + return ~0UL / sizeof(value_type); + } + + template + struct rebind // nolint + { + typedef ToStdAllocator other; // nolint + }; + + template + friend + struct ToStdAllocator; + +private: + THost * m_host; +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction ToStdAllocator() +// ---------------------------------------------------------------------------- + +template +struct StdAllocator +{ + typedef ToStdAllocator Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function host() +// ---------------------------------------------------------------------------- + +/*! + * @fn ToStdAllocator#host + * @headerfile + * @brief The object a given object depends on. + * + * @signature THost host(allocator); + * + * @param[in] allocator The allocator to query. + * + * @return THost The host object. + */ + +template +THost & +host(ToStdAllocator & me) +{ + return *me.m_host; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALLOCATOR_TO_STD_H_ diff --git a/seqan/basic/alphabet_adapt_builtins.h b/seqan/basic/alphabet_adapt_builtins.h new file mode 100644 index 0000000..a5db639 --- /dev/null +++ b/seqan/basic/alphabet_adapt_builtins.h @@ -0,0 +1,236 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Döring +// ========================================================================== +// Adaptions of builting types such as bool, int, but also "builtin-level" +// user defined types such as wchar_t, int64_t, uint64_t to the alphabet +// concepts they are in. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_ +#define SEQAN_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunctions MaxValue_, MinValue_ +// ---------------------------------------------------------------------------- + +// We would want to have this here, however this is not possible with the +// current implementation. + +// ---------------------------------------------------------------------------- +// Metafunction BitsPerValue +// ---------------------------------------------------------------------------- + +template <> +struct BitsPerValue +{ + typedef int Type; + enum { VALUE = 1 }; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IsCharType +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This should probably become a concept. + +/*! + * @mfn IsCharType + * @headerfile + * + * @brief Return whether the argument is char, wchar_t, char const, or wchar_t + * const. + * + * @signature IsCharType::Type; + * @signature IsCharType::VALUE; + * + * @tparam T Type to check type of. + * + * This metafunction is used to enable and disable templated adaptions of arrays to sequences for builtin character + * types only. + * + * The return value is True/true for char, wchar_t, char const, and + * wchar_t const. + */ + +template +struct IsCharType; + +template +struct IsCharType +{ + typedef False Type; + enum { VALUE = 0 }; +}; + +template +struct IsCharType + : IsCharType {}; + +template <> +struct IsCharType +{ + typedef True Type; + enum { VALUE = 1 }; +}; + +template <> +struct IsCharType +{ + typedef True Type; + enum { VALUE = 1 }; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function gapValueImpl() [char] +// ---------------------------------------------------------------------------- + +inline char const & +gapValueImpl(char *) +{ + static char const _gap = '-'; + return _gap; +} + +inline char const & +gapValueImpl(char const *) +{ + static char const _gap = '-'; + return _gap; +} + +// ---------------------------------------------------------------------------- +// Function unknownValueImpl() [char] +// ---------------------------------------------------------------------------- + +inline char const & +unknownValueImpl(char *) +{ + static char const _unknown = 'N'; + return _unknown; +} + +inline char const & +unknownValueImpl(char const *) +{ + static char const _unknown = 'N'; + return _unknown; +} + +// ---------------------------------------------------------------------------- +// Function supremumValueImpl() +// ---------------------------------------------------------------------------- + +template +inline T const & +supremumValueImpl(T *) +{ + static T const x = MaxValue::VALUE; + return x; +} + +inline long double const & +supremumValueImpl(long double *) +{ + static long double const _value = std::numeric_limits::infinity( ); + return _value; +} + +inline double const & +supremumValueImpl(double *) +{ + static double const _value = std::numeric_limits::infinity( ); + return _value; +} +inline float const & +supremumValueImpl(float *) +{ + static float const _value = std::numeric_limits::infinity( ); + return _value; +} + +// ---------------------------------------------------------------------------- +// Function infimumValueImpl() +// ---------------------------------------------------------------------------- + +template +inline T const & +infimumValueImpl(T *) +{ + static T const x = MinValue::VALUE; + return x; +} + +inline float const & +infimumValueImpl(float *) +{ + static float const _value = -std::numeric_limits::infinity( ); + return _value; +} + +inline double const & +infimumValueImpl(double *) +{ + static double const _value = -std::numeric_limits::infinity( ); + return _value; +} + +inline long double const & +infimumValueImpl(long double *) +{ + static long double const _value = -std::numeric_limits::infinity( ); + return _value; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_BASIC_ALPHABET_ADAPT_BUILTINS_H_ diff --git a/seqan/basic/alphabet_bio.h b/seqan/basic/alphabet_bio.h new file mode 100644 index 0000000..0339e34 --- /dev/null +++ b/seqan/basic/alphabet_bio.h @@ -0,0 +1,101 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== +// Alphabet concepts stemming from biological applications. +// ========================================================================== + +// TODO(holtgrew): Where is the documentation, shouldnt it be here? + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function gapValueImpl +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This looks wrong. + +template +inline T +gapValueImpl(T *) +{ + static T const _gap = T(); + return _gap; +} + +// ---------------------------------------------------------------------------- +// Function gapValue +// ---------------------------------------------------------------------------- + +template +inline T +gapValue() +{ + static T * _tag = 0; + return gapValueImpl(_tag); +} + +// ---------------------------------------------------------------------------- +// Function unknownValue +// ---------------------------------------------------------------------------- + +template +inline T +unknownValue() +{ + static T * _tag = 0; + return unknownValueImpl(_tag); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_BIO_H_ diff --git a/seqan/basic/alphabet_concept.h b/seqan/basic/alphabet_concept.h new file mode 100644 index 0000000..50e5164 --- /dev/null +++ b/seqan/basic/alphabet_concept.h @@ -0,0 +1,586 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// Author: Manuel Holtgrewe +// ========================================================================== +// Concept definitions for alphabets. +// ========================================================================== + +// SEQAN_NO_GENERATED_FORWARDS + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_ + +namespace seqan { + +// ============================================================================ +// Concepts for generic alphabets +// ============================================================================ + +/*! + * @concept AlphabetConcept + * @extends AssignableConcept + * @extends DefaultConstructibleConcept + * @extends CopyConstructibleConcept + * @headerfile + * @brief Natural container value. + * + * @signature concept AlphabetConcept; + * + * @section Examples + * + * Valid expressions (v is of type T): + * + * @code{.cpp} + * unsigned bpv = BitsPerValue::VALUE; + * @endcode + */ + +/*! + * @mfn AlphabetConcept#BitsPerValue + * @headerfile + * @brief Number of bits needed to store a value. + * + * @signature BitsPerValue::VALUE + * + * @tparam T A class. + * + * @return VALUE The number of bits needed to store a value. + */ + +// Forwards for Metafunctions and Functions. +template struct BitsPerValue; + +// minimal requirements for the alphabet of a String class +SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructible)(CopyConstructible)) +{ + typedef typename BitsPerValue::Type TBitsPerValue; + + TValue val, val2; + + SEQAN_CONCEPT_USAGE(AlphabetConcept) + { + SEQAN_STATIC_ASSERT_MSG(BitsPerValue::VALUE != 0, "Alphabet types must implement the BitsPerValue metafunction with non-zero value."); + + // assign must be available as an equivalent to '=' + assign(val, val2); +// swap(val, val2); + + TBitsPerValue b = BitsPerValue::VALUE; + + ignoreUnusedVariableWarning(b); + } +}; + +// ============================================================================ +// Concepts For Alphabets From The Mathematics Domain. +// ============================================================================ + +/*! + * @concept OrderedAlphabetConcept + * @extends AlphabetConcept + * @extends ComparableConcept + * @headerfile + * + * @brief Totally strict ordered alphabet. + * + * @signature concept OrderedAlphabetConcept; + */ + +/*! + * @fn OrderedAlphabetConcept::operator< + * @brief Less-than operator. + * + * @signature bool OrderedAlphabetConcept::operator<(other); + * + * @param[in] other Object of the same type to compare to this. + * + * @return bool True in case of this object being smaller than other + */ + +/*! + * @mfn OrderedAlphabetConcept#MaxValue + * @headerfile + * @brief Supremum for a given type. + * + * @signature MaxValue::VALUE + * + * @tparam T An ordered type. + * + * @return VALUE The largest value that T can represent. + * + * @see OrderedAlphabetConcept#maxValue + */ + +/*! + * @mfn OrderedAlphabetConcept#MinValue + * @headerfile + * @brief Infimum for a given type. + * + * @signature MinValue::VALUE + * + * @tparam T An ordered type. + * + * @return VALUE The smallest value that T can represent. + * + * @see OrderedAlphabetConcept#minValue + */ + +/*! + * @fn OrderedAlphabetConcept#supremumValueImpl + * @brief Implements maxValue. + * + * @signature T supremumValueImpl(valuePointerTag); + * + * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type. The pointer needs not to point + * to a valid object, so it is possible to use a null pointer here. + * + * @return T A value inf that holds: inf >= i for all values i. + * + * This function implements OrderedAlphabetConcept#maxValue. It is recommended to use OrderedAlphabetConcept#maxValue + * rather than supremumValueImpl. + * + * @section Status + * + * Deprecated, will be removed in favour of OrderedAlphabetConcept#MaxValue. + * + * @see OrderedAlphabetConcept#maxValue + */ + +/*! + * @fn OrderedAlphabetConcept#maxValue + * @brief Supremum for a given type. + * + * @signature T maxValue(); + * + * @tparam T The type to get the max value of. + * + * @return T A value inf that holds: inf >= i for all values i of type T. + * + * The function is implemented in supremumValueImpl. Do not specialize maxValue, specialize supremumValueImpl + * instead! + * + * @section Status + * + * Deprecated, will be removed in favour of MaxValue. + * + * @see OrderedAlphabetConcept#supremumValueImpl + * @see OrderedAlphabetConcept#minValue + * @see OrderedAlphabetConcept#MaxValue + */ + +/*! + * @fn OrderedAlphabetConcept#infimumValueImpl + * @brief Implements minValue. + * + * @signature T infimumValueImpl(valuePointerTag); + * + * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type. The pointer needs not to point + * to a valid object, so it is possible to use a null pointer here. + * + * @return T A value inf that holds: inf <= i for all values i. + * + * This function implements minValue. It is recommended to use minValue rather than infimumValueImpl. + * + * @section Status + * + * Deprecated, will be removed in favour of MinValue. + * + * @see OrderedAlphabetConcept#minValue + */ + +/*! + * @fn OrderedAlphabetConcept#minValue + * @brief Infimum for a given type. + * + * @signature T minValue(); + * + * @tparam T An ordered type. + * + * @return T A value inf that holds: inf <= i for all values i of type T. + * + * The function is implemented in infimumValueImpl. Do not specialize minValue, specialize infimumValueImpl + * instead! + * + * @section Status + * + * Deprecated, will be removed in favour of MinValue. + * + * @see OrderedAlphabetConcept#infimumValueImpl + * @see OrderedAlphabetConcept#maxValue + * @see OrderedAlphabetConcept#MinValue + */ + +// Forwards for Metafunctions and Functions. +template struct MinValue; +template struct MaxValue; +template T const & minValue(); +template T const & minValue(T); +template T const & maxValue(); +template T const & maxValue(T); + +SEQAN_CONCEPT_REFINE(OrderedAlphabetConcept, (TValue), (AlphabetConcept)(Comparable)) +{ + TValue val; + + SEQAN_CONCEPT_USAGE(OrderedAlphabetConcept) + { + // type consistency checks + sameType(minValue(val), val); + sameType(minValue(), val); + sameType(MinValue::VALUE, val); + sameType(maxValue(val), val); + sameType(maxValue(), val); + sameType(MaxValue::VALUE, val); + + // TODO(holtgrew): This does not work in C++98, we need C++11 with constexpr. + // TODO(holtgrew): Do these tests for each alphabet in runtime tests. + // sanity checks + // SEQAN_STATIC_ASSERT_MSG(MinValue::VALUE <= MaxValue::VALUE, "Minimal alphabet value must be less or equal to the maximal value."); + + // TODO(holtgrew): This does not work in C++98, we need C++11 with constexpr, cannot cast non-integral and non-enumeration types at compile time in C++98. + // 0 must be an element of the alphabet, as we want to be able + // to initialize a TValue variable to omit uninitialized warnings. + // SEQAN_STATIC_ASSERT_MSG(MinValue::VALUE <= static_cast(0), "0 must be convertible to a valid alphabet value."); + // SEQAN_STATIC_ASSERT_MSG(static_cast(0) <= MaxValue::VALUE, "0 must be convertible to a valid alphabet value."); + } +}; + +/*! + * @concept FiniteOrderedAlphabetConcept + * @headerfile + * @extends OrderedAlphabetConcept + * @brief An type that is of finite domain and totally ordered and thus has a minimum and maximum value. + */ + +/*! + * @mfn FiniteOrderedAlphabetConcept#ValueSize + * @brief Number of different values a value type object can have. + * + * @signature ValueSize::Type; + * @signature ValueSize::VALUE; + * + * @tparam T A type to query for its value size. + * + * @return VALUE The number of different values a value of type T can have. The type is Type. + * @return Type The type of the result VALUE. + * + * This function is only defined for integral types like unsigned, int, or Dna. For floating point + * numbers and the 64 bit types int64_t and uint64_t, it returns 0 since there is no standard + * compliant way to return the number of values for these types. + * + * Note that you cannot get pointers or references to ValueSize<T>::VALUE in your program. You can use + * @link FiniteOrderedAlphabetConcept#valueSize @endlink in your programs without problems, though. When you get + * problems in your tests, use the "unary plus" workaround from the examples section. + * + * @section Examples + * + * The temporary assignment workaround. + * + * @code{.cpp} + * SEQAN_ASSERT_EQ(ValueSize::VALUE, 2u); // Linker error. + * SEQAN_ASSERT_EQ(+ValueSize::VALUE, 2u); // OK + * SEQAN_ASSERT_EQ(valueSize(), 2u); // OK + * @endcode + */ + +/*! + * @fn FiniteOrderedAlphabetConcept#ordValue + * @headerfile + * @brief Maps an alphabet 1-to-1 to the interval [0..ValueSize). + * + * @signature T ordValue(value); + * + * @param[in] value Arbitrary character value. Types: SimpleType + * + * @return T An unsigned value (result of Size<typeof(value)> between 0 and ValueSize of the type of value. + * + * This function first converts value to its unsigned value type and after that to an unsigned int. You can't + * use (unsigned int)c for a character c as on some systems char is signed and a -1 + * would be mapped to 0xffffffff instead of 0x000000ff. + */ + +/*! + * @fn FiniteOrderedAlphabetConcept#valueSize + * @brief Returns size of an alphabet. + * + * @signature T1 valueSize(); + * + * @tparam T2 Type to query for value size. + * + * @return T1 Number of values in type T2. + * + * @see FiniteOrderedAlphabetConcept#ValueSize + */ + +// Forwards for Metafunctions and Functions. +template struct ValueSize; +template typename ValueSize::Type valueSize(); +// Forwards for Metafunctions and Functions. +template inline typename ValueSize::Type ordValue(TValue const & c); + +SEQAN_CONCEPT_REFINE(FiniteOrderedAlphabetConcept, (TValue), (OrderedAlphabetConcept)) +{ + typedef typename ValueSize::Type TSize; + + TValue val; + TSize size; + + SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept)); + + SEQAN_CONCEPT_USAGE(FiniteOrderedAlphabetConcept) + { + // a finite alphabet must be countable + sameType(ordValue(val), size); + sameType(valueSize(), size); + sameType(ValueSize::VALUE, size); + + // alphabet must be non-empty + SEQAN_STATIC_ASSERT_MSG(static_cast(0) < ValueSize::VALUE, "Alphabet size be greater than zero."); + + // convert integer to alphabet value + val = 0; + val = size; + TValue val2(0); + TValue val3(size); + + ignoreUnusedVariableWarning(val2); + ignoreUnusedVariableWarning(val3); + } +}; + +// ============================================================================ +// Concepts For Alphabets From The Bioinformatics Domain. +// ============================================================================ +/*! + * @concept AlphabetWithGapsConcept + * @extends AlphabetConcept + * @headerfile + * + * @brief An alphabet that includes a specific gap character. + */ + +/*! + * @fn AlphabetWithGapsConcept#gapValueImpl + * @brief Implements gapValue. + * + * @signature T gapValueImpl(valuePointerTag); + * + * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type. The pointer needs not to + * point to a valid object, so it is possible to use a null pointer here. + * + * @return T A gap character. + * + * This function implements gapValue. It is recommended to use gapValue rather than gapValueImpl. + * + * @see AlphabetWithGapsConcept#gapValue + */ + +/*! + * @fn AlphabetWithGapsConcept#gapValue + * @brief Return the "gap" value from an alphabet. + * + * @signature T gapValue(); + * + * @tparam T The alphabet type to query the gap value from. + * + * @return T The gap character. + * + * The function is implemented in gapValueImpl. Do not specialize gapValue, specialize link gapValueImpl + * instead! + * + * @see AlphabetWithGapsConcept#gapValueImpl + */ + +// Forwards for Metafunctions and Functions. +template T gapValue(); +template T gapValueImpl(T *); + +SEQAN_CONCEPT_REFINE(AlphabetWithGapsConcept, (TValue), (AlphabetConcept)) +{ + TValue val; + + SEQAN_CONCEPT_USAGE(AlphabetWithGapsConcept) + { + // Test the availability and return type of gapValue() and gapValueImpl(). + sameType(gapValue(), val); + sameType(gapValueImpl(static_cast(0)), val); + } +}; + +/*! + * @concept AlphabetWithUnknownValueConcept + * @extends AlphabetConcept + * @headerfile + * + * @brief An alphabet which includes a specific "unknown" character. + */ + +/*! + * @fn AlphabetWithUnknownValueConcept#unknownValue + * + * @brief Return the "unknown" value from an alphabet. + * + * @signature T unknownValue(); + * + * @tparam T The alphabet type to query the unknown value from. + * + * @return TReturn The "unknown" value. + * + * @see AlphabetWithUnknownValueConcept#unknownValueImpl + */ + +/*! + * @fn AlphabetWithUnknownValueConcept#unknownValueImpl + * @brief Implements unknownValue. + * + * @signature T gapValueImpl(valuePointerTag) + * + * @param[in] valuePointerTag A pointer that is used as a tag to specify the value type. The pointer needs not to + * point to a valid object, so it is possible to use a null pointer here. + * + * @return TReturn A "unknown" character. + * + * This function implements unknownValue. It is recommended to use gapValue rather than gapValueImpl. + * + * @see AlphabetWithUnknownValueConcept#unknownValue + */ + +// Forwards for Metafunctions and Functions. +template T unknownValue(); +template T unknownValueImpl(T *); + +SEQAN_CONCEPT_REFINE(AlphabetWithUnknownValueConcept, (TValue), (AlphabetConcept)) +{ + TValue val; + + SEQAN_CONCEPT_USAGE(AlphabetWithUnknownValueConcept) + { + // Test the availability and return type of unknownValue() and unknownValueImpl(). + sameType(unknownValue(), val); + sameType(unknownValueImpl(static_cast(0)), val); + } +}; + +/*! + * @concept AlphabetWithQualitiesConcept + * @extends AlphabetConcept + * @headerfile + * + * @brief An alphabet where qualities can be attached to the characters. + */ + +/*! + * @mfn AlphabetWithQualitiesConcept#HasQualities + * @headerfile + * @brief Return whether the given type stores qualities besides the alphabet. + * + * @signature HasQualities::VALUE; + * @signature HasQualities::Type; + * + * @tparam TAlphabet The alphabe to query. + * + * @return VALUE true or false + * @return Type True or False + */ + +/*! + * @mfn AlphabetWithQualitiesConcept#QualityValueSize + * @brief Return the number of quality values in characters from alphabet with qualities. + * + * @signature QualityValueSize::VALUE; + * + * @tparam TAlphabet The alphabet to query for its value size. + * + * @return VALUE The cardinality of the set of qualities. + */ + +/*! + * @fn AlphabetWithQualitiesConcept#getQualityValue + * @brief Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with + * a specified element from a sequence. + * @signature int getQualityValue(c); + * + * @param[in] c Character to retrieve the quality from. + * + * @return int Quality value of c. The quality value is an int value between 0 and 62 (inclusive). + * + * @section Examples + * + * @code{.cpp} + * String seq = "TATA"; + * // Assign quality value to first 'T' in sequence seq + * assignQualityValue(seq[0], 35); + * // Print quality value of first 'T', and default quality value of first 'A' + * std::cout << getQualityValue(seq[0]) << std::endl; // Defined as 35 + * std::cout << getQualityValue(seq[1]) << std::endl; // Default value 60 + * @endcode + * + * @see AlphabetWithQualitiesConcept#assignQualityValue + * @see convertQuality + */ + +/*! + * @fn AlphabetWithQualitiesConcept#assignQualityValue + * @brief Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a + * sequence. + * + * @signature void assignQualityValue(c, q); + * + * @param[out] c Target character to assign quality to. + * @param[in] q Quality to assign to the character. The quality value is an integral value between 0 and 62 + * (inclusive). + * + * If q is a char then '!' is subtracted from q. This is useful for ASCII encoded + * PHRED scores. + * + * @see AlphabetWithQualitiesConcept#getQualityValue + * @see convertQuality + * @see assignQualities + */ + +// TODO(holtgrew): What about different quality types? Guess scaling? Look at how other packages do this. + +SEQAN_CONCEPT_REFINE(AlphabetWithQualitiesConcept, (TValue), (AlphabetConcept)) +{ + TValue val; + + SEQAN_CONCEPT_USAGE(AlphabetWithQualitiesConcept) + { + // TODO(holtgrew): Write me! + } +}; + + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_CONCEPT_H_ diff --git a/seqan/basic/alphabet_math.h b/seqan/basic/alphabet_math.h new file mode 100644 index 0000000..c77afdb --- /dev/null +++ b/seqan/basic/alphabet_math.h @@ -0,0 +1,294 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== +// Math functions for alphabets. +// ========================================================================== + +#include +#include + +#ifndef SEQAN_BASIC_ALPHABET_MATH_H_ +#define SEQAN_BASIC_ALPHABET_MATH_H_ + +// TODO(holtgrew): Move actual implementations to alphabet_adapt_builtins. IF POSSIBLE + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction MaxValue +// ---------------------------------------------------------------------------- + +template +struct MaximumValueUnsigned_ { static const T VALUE; }; + +template +const T MaximumValueUnsigned_::VALUE = ~(T)0; + +template +struct MaximumValueSigned_ { static const T VALUE; }; +template +struct MaximumValueFloat_ { static const float VALUE; }; +template +struct MaximumValueDouble_ { static const double VALUE; }; + +template +const T MaximumValueSigned_::VALUE = ((((T)1 << (BitsPerValue::VALUE - 2)) - 1) << 1) + 1; +template +const float MaximumValueFloat_::VALUE = FLT_MAX; +template +const double MaximumValueDouble_::VALUE = DBL_MAX; + +template <> +struct MaximumValueSigned_ +{ + static const bool VALUE = true; +}; + +// template <> +// const char MaximumValueUnsigned_::VALUE = CHAR_MAX; +// template <> +// const char MaximumValueSigned_::VALUE = CHAR_MAX; + +template < + typename T, + typename TParent = typename IfC< + IsSameType::VALUE, + MaximumValueDouble_<>, + typename IfC< + IsSameType::VALUE, + MaximumValueFloat_<>, + typename IfC< + IsSameType::Type, T>::VALUE, + MaximumValueSigned_, + MaximumValueUnsigned_ + >::Type + >::Type + >::Type + > +struct MaxValue_ : TParent {}; + +// We use two levels here, so we can forward declare MaxValue with one +// template parameter. + +template +struct MaxValue : MaxValue_ {}; + +// ---------------------------------------------------------------------------- +// Metafunction MinValue +// ---------------------------------------------------------------------------- + +template +struct MinimumValueUnsigned_ { static const T VALUE; }; +template +struct MinimumValueSigned_ { static const T VALUE; }; + +template +struct MinimumValueFloat_ { static const float VALUE; }; +template +struct MinimumValueDouble_ { static const double VALUE; }; + +template +const T MinimumValueUnsigned_::VALUE = T(0); +template +const T MinimumValueSigned_::VALUE = ~(T)MaximumValueSigned_::VALUE; +template +const float MinimumValueFloat_::VALUE = -FLT_MAX; +template +const double MinimumValueDouble_::VALUE = -DBL_MAX; + +template <> +struct MinimumValueSigned_ +{ + static const bool VALUE = false; +}; + +// template <> +// const char MinimumValueUnsigned_::VALUE = 0; +// template <> +// const char MinimumValueSigned_::VALUE = 0; + +template < + typename T, + typename TParent = typename IfC< + IsSameType::VALUE, + MinimumValueDouble_<>, + typename IfC< + IsSameType::VALUE, + MinimumValueFloat_<>, + typename IfC< + IsSameType::Type, T>::VALUE, + MinimumValueSigned_, + MinimumValueUnsigned_ + >::Type + >::Type + >::Type + > +struct MinValue_ : TParent {}; + +// We use two levels here, so we can forward declare MinValue with one +// template parameter. + +template +struct MinValue : MinValue_ {}; + +// ============================================================================ +// Functions +// ============================================================================ + +// -------------------------------------------------------------------------- +// Function toUpperValue() +// -------------------------------------------------------------------------- + +template +inline +TValue toUpperValue(TValue c) +{ + return c; +} + +inline +char toUpperValue(char c) +{ + return c >= 'a' && c <= 'z' ? c + 'A' - 'a' : c; +} + +inline +signed char toUpperValue(signed char c) +{ + return toUpperValue(static_cast(c)); +} + +inline +unsigned char toUpperValue(unsigned char c) +{ + return toUpperValue(static_cast(c)); +} + +// ---------------------------------------------------------------------------- +// Function supremumValueImpl +// ---------------------------------------------------------------------------- + +template inline T const & supremumValueImpl(T *); + +// ---------------------------------------------------------------------------- +// Function maxValue +// ---------------------------------------------------------------------------- + +// Forward to supremumValueImpl() only. + +template +inline T const & +maxValue() +{ + T * _tag = 0; + return supremumValueImpl(_tag); +} + +template +inline T const & +maxValue(T /*tag*/) +{ + T * _tag = 0; + return supremumValueImpl(_tag); +} + +// ---------------------------------------------------------------------------- +// Function infimumValueImpl +// ---------------------------------------------------------------------------- + +template inline T const & infimumValueImpl(T *); + +// ---------------------------------------------------------------------------- +// Function minValue +// ---------------------------------------------------------------------------- + +// Forward to infimumValueImpl() only. + +template +inline T const & +minValue() +{ + T * _tag = 0; + return infimumValueImpl(_tag); +} + +template +inline T const & +minValue(T /*tag*/) +{ + T * _tag = 0; + return infimumValueImpl(_tag); +} + +// ---------------------------------------------------------------------------- +// Function isNegative() +// ---------------------------------------------------------------------------- + +// to remove '... < 0 is always false' warning +template +inline bool +isNegative(T, False) +{ + return false; +} + +template +inline bool +isNegative(T t, True) +{ + return t < 0; +} + +template +inline bool +isNegative(T t) +{ + return isNegative(t, typename IsSameType::Type>::Type()); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_ALPHABET_MATH_H_ diff --git a/seqan/basic/alphabet_profile.h b/seqan/basic/alphabet_profile.h new file mode 100644 index 0000000..ac81662 --- /dev/null +++ b/seqan/basic/alphabet_profile.h @@ -0,0 +1,382 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Tobias Rausch +// ========================================================================== +// Profile alphabet character code. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +class Proxy; + +template +struct IteratorProxy; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +/*! + * @class ProfileChar + * + * @headerfile + * + * @brief Alphabet type for profiles over another alphabet. + * + * @signature template + * class ProfileChar; + * + * @tparam TValue The underlying alphabet type. + * @tparam TCount The type to use for counting, default: unsigned int. + * @tparam TSpec Specialization tag, default: void + */ + +/*! + * @var VariableType ProfileChar::count[] + * + * @brief Array of ValueSize elements, giving counts in profile. + */ + +template +class ProfileChar; + +template +class ProfileChar +{ +public: + typedef typename ValueSize::Type TSize; + + TCount count[ValueSize::VALUE]; + + // ------------------------------------------------------------------------ + // Constructors + // ------------------------------------------------------------------------ + + ProfileChar() + { + memset::VALUE * sizeof(TCount), (unsigned char) 0>(count); + } + + ProfileChar(ProfileChar const & other_data) + { + for (TSize i = 0; i < ValueSize::VALUE; ++i) + count[i] = other_data.count[i]; + } + + // TODO(holtgrew): Limit TOther to SourceValue? + template + ProfileChar(TOther const & other_data) + { + memset::VALUE * sizeof(TCount), (unsigned char) 0>(count); + count[ordValue(TValue(other_data))] = 1; + } + + template + ProfileChar(Proxy const & proxy) + { + memset::VALUE * sizeof(TCount), (unsigned char) 0>(count); + assign(*this, getValue(proxy)); + } + + // ------------------------------------------------------------------------ + // Assignment operators; Have to be defined in class. + // ------------------------------------------------------------------------ + + ProfileChar & + operator=(ProfileChar const & other_data) + { + if (this == &other_data) return *this; + + for (TSize i = 0; i < ValueSize::VALUE; ++i) + count[i] = other_data.count[i]; + return *this; + } + + template + ProfileChar & + operator=(TOther const & other_data) + { + memset::VALUE * sizeof(TCount), 0u>(count); + count[ordValue(TValue(other_data))] = 1; + return *this; + } + + // ------------------------------------------------------------------------ + // Type conversion operators; Have to be defined in class. + // ------------------------------------------------------------------------ + + operator char() + { + typename Size::Type maxIndex = getMaxIndex(*this); + return (maxIndex == ValueSize::VALUE - 1) ? gapValue() : (char) TValue(maxIndex); + } +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction ValueSize +// ---------------------------------------------------------------------------- + +/*! + * @mfn ProfileChar#ValueSize + * @brief Number of different values a value type object can have. + * + * @signature ValueSize::VALUE; + * + * @tparam T The type to query. + * + * @return VALUE Number of different values T can have. + */ + +template +struct ValueSize > +{ + enum { VALUE = ValueSize::VALUE + 1 }; + typedef unsigned Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction SourceValue +// ---------------------------------------------------------------------------- + +/*! + * @mfn ProfileChar#SourceValue + * @brief Returns underlying value for ProfileChar. + * + * @signature SourceValue::Type + * + * @tparam T Type to query. + * + * @return Type The type of the underlying character. + * + * @section Examples + * + * @code{.cpp} + * typedef ProfileChar TProfileChar; + * typedef SourceValue::Type TType; // Is Dna. + * @endcode + */ + +template +struct SourceValue; + +template +struct SourceValue > +{ + typedef TValue Type; +}; + +template +struct SourceValue const> : + SourceValue > +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool +operator==(ProfileChar const & lhs, + ProfileChar const & rhs) +{ + typedef ProfileChar TProfileChar; + typedef typename ValueSize::Type TValueSize; + + for (TValueSize i = 0; i < ValueSize::VALUE; ++i) + if (lhs.count[i] != rhs.count[i]) + return false; + return true; +} + +// ---------------------------------------------------------------------------- +// Function operator!=() +// ---------------------------------------------------------------------------- + +template +inline +bool +operator!=(ProfileChar const & lhs, + ProfileChar const & rhs) +{ + typedef ProfileChar TProfileChar; + typedef typename ValueSize::Type TSize; + + for (TSize i = 0; i < ValueSize::VALUE; ++i) + if (lhs.count[i] != rhs.count[i]) + return true; + return false; +} + +// ---------------------------------------------------------------------------- +// Function empty() +// ---------------------------------------------------------------------------- + +/*! + * @fn ProfileChar#empty + * @brief Check whether there are only gaps in the representation of the ProfileChar. + * + * @signature bool empty(c); + * + * @param c ProfileChar to query. + * @return bool Whether or not the ProfileChar only contains gaps. + */ +template +bool empty(ProfileChar const & source) +{ + typedef typename ValueSize const>::Type TSize; + + for (TSize i = 0; i < ValueSize::VALUE; ++i) + if (source.count[i]) + return false; + return true; +} + +// ---------------------------------------------------------------------------- +// Helper Function getMaxIndex() +// ---------------------------------------------------------------------------- + +/*! + * @fn ProfileChar#getMaxIndex + * @brief Return number of dominating entry in ProfileChar. + * + * @signature TSize getMaxIndex(c); + * + * @param[in] c ProfileChar to query for its dominating entry. + * @return TSize index (with the @link FiniteOrderedAlphabetConcept#ordValue @endlink) of the dominating character + * in c + */ +template +typename Size const>::Type +getMaxIndex(ProfileChar const & source) +{ + typedef ProfileChar TProfileChar; + typedef typename Size::Type TSize; + TSize maxIndex = 0; + TSourceCount maxCount = source.count[0]; + for (TSize i = 1; i < ValueSize::VALUE; ++i) + { + if (source.count[i] > maxCount) + { + maxIndex = i; + maxCount = source.count[i]; + } + } + return maxIndex; +} + +// ---------------------------------------------------------------------------- +// Helper Function totalCount() +// ---------------------------------------------------------------------------- + +/*! + * @fn ProfileChar#totalCount + * @brief Return sum of counts in ProfileChar. + * + * @signature TCount totalCount(c); + * + * @param[in] c ProfileChar to query. + * @return TCount Total number of characters represented by c. + */ +template +TSourceCount totalCount(ProfileChar const & source) +{ + typedef ProfileChar TProfileChar; + typedef typename Size::Type TSize; + TSourceCount totalCount = source.count[0]; + for (TSize i = 1; i < ValueSize::VALUE; ++i) + totalCount += source.count[i]; + return totalCount; +} + + +// ---------------------------------------------------------------------------- +// Function assign() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): What if there only are gaps? + +template +inline void +assign(SimpleType & target, + ProfileChar const & source) +{ + target.value = getMaxIndex(source); +} + +// ---------------------------------------------------------------------------- +// Function convertImpl() +// ---------------------------------------------------------------------------- + +template +inline typename Convert >::Type +convertImpl(Convert const &, + ProfileChar const & source) +{ + return (getMaxIndex(source) == ValueSize::VALUE) ? convertImpl(Convert(), '-') : convertImpl(Convert(), TSourceValue(getMaxIndex(source))); +} + +// ---------------------------------------------------------------------------- +// Function operator<<(); Stream output. +// ---------------------------------------------------------------------------- + +template +inline TStream & +operator<<(TStream & os, ProfileChar const & rhs) +{ + typedef ProfileChar TProfileChar; + typedef typename Size::Type TSize; + for (TSize i = 0; i < ValueSize::VALUE; ++i) + os << i << ':' << rhs.count[i] << ' ' << ';'; + return os; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_PROFILE_H_ diff --git a/seqan/basic/alphabet_qualities.h b/seqan/basic/alphabet_qualities.h new file mode 100644 index 0000000..b3b79de --- /dev/null +++ b/seqan/basic/alphabet_qualities.h @@ -0,0 +1,129 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// Author: Manuel Holtgrewe +// ========================================================================== +// Definitions for piggybacking qualities in free bits of bytes. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_ + +// TODO(holtgrew): Should the documentation be here? + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction QualityValueSize +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Do we want a default specialization? Should it return 0? +template +struct QualityValueSize +{ + enum { VALUE = ValueSize::VALUE }; +}; + +template +struct QualityValueSize : QualityValueSize +{}; + +// ---------------------------------------------------------------------------- +// Metafunction HasQualities +// ---------------------------------------------------------------------------- + +template +struct HasQualities +{ + typedef False Type; + static const bool VALUE = false; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function assignQualityValue() +// ---------------------------------------------------------------------------- + +// Documentation is in alphabet_concept.h. + +// ---------------------------------------------------------------------------- +// Function getQualityValue() +// ---------------------------------------------------------------------------- + +// Documentation is in alphabet_concept.h. + +// ---------------------------------------------------------------------------- +// Function convertQuality() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This could use some thought, what about other scales? + +/*! + * @fn convertQuality + * @headerfile + * + * @brief Convert an integer quality value into its ASCII representation for FASTQ (Phred scale). + * + * @signature void convertQuality(c, q); + * + * @param[in] q Value of the quality to convert. The quality value is an integral value between 0 and 62 + * (inclusive), int. + * @param[out] c Character to store the quality in, char. + * + * @see AlphabetWithQualitiesConcept#getQualityValue + * @see AlphabetWithQualitiesConcept#assignQualityValue + */ + +inline +void convertQuality(char & c, int q) +{ + c = '!' + char(q); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_ diff --git a/seqan/basic/alphabet_residue.h b/seqan/basic/alphabet_residue.h new file mode 100644 index 0000000..fae9710 --- /dev/null +++ b/seqan/basic/alphabet_residue.h @@ -0,0 +1,1493 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Implementation of the biological SimpleType specializations Dna, Dna5, +// DnaQ, Dna5Q, Rna, Rna5, Iupac, and AminoAcid. The conversion tables are +// in alphabet_residue_tabs.h. +// +// This header's structure is an exception to the standard. Because +// splitting into one header for each specialization is a bit too much, we +// define all types in one header. We define the classes, metafunctions and +// functions in one section, one subsection for reach type to make the whole +// thing more readable. Conversion through assignment is defined in the +// Function section. +// ========================================================================== + +// TODO(holtgrew): Add RnaQ and Rna5Q? Can we create a tag/type for Dna and Rna that is then differentiated with one additional tag? + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template struct BaseAlphabet; + +// ============================================================================ +// Classes, Metafunctions, Functions +// ============================================================================ + +// Also see comment at the top for more information on this exceptional +// structure. +// +// We define the SimpleType specializations, the metafunctions ValueSize and +// BitsPerValue and the functions unknownValueImpl() for each specialization in +// this section. + +// ---------------------------------------------------------------------------- +// Specialization Dna +// ---------------------------------------------------------------------------- + +/*! + * @class Dna + * @extends SimpleType + * @headerfile + * @brief Alphabet for DNA. + * + * @signature typedef SimpleType Dna; + * + * The ValueSize of Dna is 4. The nucleotides are enumerated this way: 'A' = 0, 'C' = 1, 'G' = 2, 'T' = + * 3. + * + * Objects of type Dna can be converted to various other types and vice versa. An object that has a value not + * in {'A', 'C', 'G', 'T'} is converted to 'A'. + * + * @see Dna5 + * @see DnaString + * @see DnaIterator + */ + +struct Dna_ {}; +typedef SimpleType Dna; + +template <> +struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 4; +}; + +template <> +struct BitsPerValue< Dna > +{ + typedef uint8_t Type; + static const Type VALUE = 2; +}; + +// ---------------------------------------------------------------------------- +// Specialization Dna5 +// ---------------------------------------------------------------------------- + +/*! + * @class Dna5 + * @extends SimpleType + * @headerfile + * @brief Alphabet for DNA including 'N' character. + * + * @signature typedef SimpleType Dna5; + * + * The @link FiniteOrderedAlphabetConcept#ValueSize @endlink of Dna5 is 5. The nucleotides are enumerated this + * way: 'A' = 0, 'C' = 1, 'G' = 2, 'T' = 3. The 'N' character ("unkown nucleotide") is encoded by 4. + * + * Objects of type Dna5 can be converted to various other types and vice versa. An object that has a value not + * in {'A', 'C', 'G', 'T'} is converted to 'N'. + * + * @see Dna5Iterator + * @see Dna5String + * @see Dna + */ + +struct Dna5_ {}; +typedef SimpleType Dna5; + +template <> +struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 5; +}; + +template <> +struct BitsPerValue +{ + typedef uint8_t Type; + static const Type VALUE = 3; +}; + +inline Dna5 +unknownValueImpl(Dna5 *) +{ + static const Dna5 _result = Dna5('N'); + return _result; +} + +// ---------------------------------------------------------------------------- +// Specialization DnaQ +// ---------------------------------------------------------------------------- + +/*! + * @class DnaQ + * @extends SimpleType + * @headerfile + * @implements AlphabetWithQualitiesConcept + * @brief Alphabet for DNA plus PHRED quality. + * + * @signature typedef SimpleType DnaQ; + * + * The ValueSize of DnaQ is 4. The nucleotides are enumerated this way: 'A' = 0, 'C' = 1, 'G' = 2, 'T' = + * 3. + * + * Objects of type DnaQ can be converted to various other types and vice versa. + * + * Note that the default quality value is set to 60. + * + * @see Dna5Q + * @see Dna + */ + +#ifndef SEQAN_DEFAULT_QUALITY +#define SEQAN_DEFAULT_QUALITY 40 +#endif + +struct DnaQ_ {}; +typedef SimpleType DnaQ; + +template <> struct ValueSize +{ + typedef uint8_t Type; + static const ValueSize::Type VALUE = 4; // Considering nucleotides. +}; + +template <> struct InternalValueSize_ +{ + enum { VALUE = 252 }; // Considering nucleotides x Quality 0..62. +}; + +template <> struct BitsPerValue +{ + enum { VALUE = 8 }; + typedef uint8_t Type; +}; + +template <> struct HasQualities +{ + typedef True Type; + static const bool VALUE = true; +}; + +template <> +struct BaseAlphabet +{ + typedef Dna Type; +}; + +template <> +struct QualityValueSize +{ + enum { VALUE = 63 }; // 64 - 1 (N) +}; + +template +inline int getQualityValue(TValue const &) +{ + return 0; +} + +inline int getQualityValue(DnaQ const & c) +{ + return c.value >> 2; +} + +inline +void assignQualityValue(DnaQ & c, int q) +{ + if (q < 0) q = 0; + if (q >= QualityValueSize::VALUE) + q = QualityValueSize::VALUE - 1; + c.value = (c.value & 3) | (q << 2); +} + +inline +void assignQualityValue(DnaQ & c, char q) +{ + int q1 = static_cast(q - '!'); + if (q1 < 0) q1 = 0; + if (q1 >= QualityValueSize::VALUE) + q1 = QualityValueSize::VALUE - 1; + assignQualityValue(c, q1); +} + +inline +void assignQualityValue(char & q, DnaQ c) +{ + q = '!' + getQualityValue(c); +} + + +// ---------------------------------------------------------------------------- +// Specialization Dna5Q +// ---------------------------------------------------------------------------- + +/*! + * @class Dna5Q + * @extends SimpleType + * @headerfile + * @implements AlphabetWithQualitiesConcept + * @brief Alphabet for DNA plus PHRED quality including 'N' character. + * + * @signature typedef SimpleType Dna5Q; + * + * The ValueSize of Dna5Q is 5. The nucleotides are enumerated this way: 'A' = 0, 'C' = 1, 'G' = 2, 'T' = + * 3. The 'N' character ("unknown nucleotide") is encoded by 4. + * + * Objects of type Dna5 can be converted to various other types and vice versa. + * + * Note that the default quality value is set to 40. + * + * @see Dna5 + * @see DnaQ + */ + +struct Dna5Q_ {}; +typedef SimpleType Dna5Q; + +static const unsigned char Dna5QValueN_ = 252; // value representing N + +template <> struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 5; // Considering nucleotides + N. +}; + +template <> struct InternalValueSize_ +{ + enum { VALUE = 253 }; // Considering (nucleotides x Quality 0..62) + N. +}; + +template <> struct BitsPerValue +{ + enum { VALUE = 8 }; + typedef uint8_t Type; +}; + +template <> struct HasQualities +{ + typedef True Type; + static const bool VALUE = true; +}; + +template <> +struct BaseAlphabet +{ + typedef Dna5 Type; +}; + +template <> struct +QualityValueSize +{ + enum { VALUE = 63 }; +}; + +inline Dna5Q +unknownValueImpl(Dna5Q *) +{ + static const Dna5Q _result = Dna5Q('N'); + return _result; +} + +inline int getQualityValue(Dna5Q const &c) +{ + // We use a lookup table to extract the qualities from DNA5Q. The lookup + // table based code is equivalent to the following line: + // return (c.value == Dna5QValueN_)? 0: c.value >> 2; + + static const unsigned table[] = { + 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, + 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, + 8, 8, 9, 9, 9, 9, 10, 10, 10, 10, 11, 11, 11, 11, 12, 12, 12, + 12, 13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, + 17, 17, 17, 17, 18, 18, 18, 18, 19, 19, 19, 19, 20, 20, 20, 20, 21, + 21, 21, 21, 22, 22, 22, 22, 23, 23, 23, 23, 24, 24, 24, 24, 25, 25, + 25, 25, 26, 26, 26, 26, 27, 27, 27, 27, 28, 28, 28, 28, 29, 29, 29, + 29, 30, 30, 30, 30, 31, 31, 31, 31, 32, 32, 32, 32, 33, 33, 33, 33, + 34, 34, 34, 34, 35, 35, 35, 35, 36, 36, 36, 36, 37, 37, 37, 37, 38, + 38, 38, 38, 39, 39, 39, 39, 40, 40, 40, 40, 41, 41, 41, 41, 42, 42, + 42, 42, 43, 43, 43, 43, 44, 44, 44, 44, 45, 45, 45, 45, 46, 46, 46, + 46, 47, 47, 47, 47, 48, 48, 48, 48, 49, 49, 49, 49, 50, 50, 50, 50, + 51, 51, 51, 51, 52, 52, 52, 52, 53, 53, 53, 53, 54, 54, 54, 54, 55, + 55, 55, 55, 56, 56, 56, 56, 57, 57, 57, 57, 58, 58, 58, 58, 59, 59, + 59, 59, 60, 60, 60, 60, 61, 61, 61, 61, 62, 62, 62, 62, + 0, 0, 0, 0}; + return table[c.value]; +} + +inline +void assignQualityValue(Dna5Q &c, int q) +{ + if (q < 0) q = 0; + if (q >= QualityValueSize::VALUE) + q = QualityValueSize::VALUE - 1; + if (c.value != Dna5QValueN_) + c.value = (c.value & 3) | (q << 2); +} + +inline +void assignQualityValue(Dna5Q &c, char q) +{ + int q1 = static_cast(q - '!'); + if (q1 < 0) q1 = 0; + if (q1 >= QualityValueSize::VALUE) + q1 = QualityValueSize::VALUE - 1; + assignQualityValue(c, q1); +} + +inline +void assignQualityValue(char & q, Dna5Q c) +{ + q = '!' + getQualityValue(c); +} + +// ---------------------------------------------------------------------------- +// Specialization Rna +// ---------------------------------------------------------------------------- + +/*! + * @class Rna + * @extends SimpleType + * @headerfile + * @brief Alphabet for RNA. + * + * @signature typedef SimpleType Rna; + * + * The ValueSize of Rna is 4. The nucleotides are enumerated this way: 'A' = 0, 'C' = 1, 'G' = 2, 'U' = + * 3. + * + * Objects of type Rna can be converted to various other types and vice versa. An object that has a value not + * in {'A', 'C', 'G', 'U'} is converted to 'A'. + * + * Rna is typedef for SimpleType, while Rna_ is a helper specialization tag class. + * + * @see Rna5 + * @see RnaString + * @see RnaIterator + */ + +struct Rna_ {}; +typedef SimpleType Rna; + +template <> +struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 4; +}; + +template <> +struct BitsPerValue +{ + typedef uint8_t Type; + static const Type VALUE = 2; +}; + +// ---------------------------------------------------------------------------- +// Specialization Rna5 +// ---------------------------------------------------------------------------- + +/*! + * @class Rna5 + * @extends SimpleType + * @headerfile + * @brief Alphabet for RNA including 'N' character. + * + * @signature typedef SimpleType Rna5; + * + * The ValueSize of Rna5 is 5. The nucleotides are enumerated this way: 'A' = 0, 'C' = 1, 'G' = 2, 'U' = + * 3. The 'N' character ("unkown nucleotide") is encoded by 4. + * + * Objects of type Rna5 can be converted to various other types and vice versa. An object that has a value not + * in {'A', 'C', 'G', 'U'} is converted to 'N'. + * + * @see Rna5Iterator + * @see Rna5String + * @see Rna + */ + +struct Rna5_ {}; +typedef SimpleType Rna5; + +template <> +struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 5; +}; + +template <> struct BitsPerValue +{ + typedef uint8_t Type; + static const Type VALUE = 3; +}; + +inline Rna5 +unknownValueImpl(Rna5 *) +{ + static const Rna5 _result = Rna5('N'); + return _result; +} + +// ---------------------------------------------------------------------------- +// Specialization Iupac +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): We should support retrieval of nucleotides represented by a IUPAC char. + +/*! + * @class Iupac + * @extends SimpleType + * @headerfile + * @brief Iupac code for DNA. + * + * @signature typedef SimpleType Iupac; + * + * The ValueSize of Iupac is 16. The nucleotides are enumerated from 0 to 19 in this order: 'U'=0, 'T', 'A', + * 'W', 'C', 'Y', 'M', 'H', 'G', 'K', 'R', 'D', 'S', 'B', 'V', 'N'=15. + * + * Objects of type Iupac can be converted to various other types and vice versa. Unknown values are converted + * to 'N'. + * + * @see IupacString + * @see IupacIterator + */ + +struct Iupac_ {}; +typedef SimpleType Iupac; + +template <> struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 16; +}; + +template <> struct BitsPerValue +{ + typedef uint8_t Type; + static const Type VALUE = 4; +}; + +inline Iupac +unknownValueImpl(Iupac *) +{ + static const Iupac _result = Iupac('N'); + return _result; +} + +// ---------------------------------------------------------------------------- +// Specialization AminoAcid +// ---------------------------------------------------------------------------- + +/*! + * @class AminoAcid + * @extends SimpleType + * @headerfile + * @brief IUPAC code for amino acids. + * @signature typedef SingleType AminoAcid; + * + * The ValueSize of AminoAcid is 27. + * + * The amino acid symbols are as follows, i.e. they are sorted alphabetically + * up until the last two symbols: + * + * 'A' = 0, 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y', 'Z', 'X'. '*' + * + * Of these 'B' is a wildcard for (Aspartic Acid, Asparagine), + * 'J' for (Leucine, Isoleucine), 'Z' for (Glutamic Acid, Glutamine) and + * 'X' for "any amino acid". + * + * 'O' refers to the rare Pyrrolysine, 'U' refers to the rare Selenocysteine and '*' to the terminator tRNA. + * + * Objects of type AminoAcid can be converted to char and vice versa. Unknown values are converted to + * 'X'. + * + * @see FiniteOrderedAlphabetConcept#ValueSize + * @see PeptideIterator + * @see Peptide + */ + +struct AminoAcid_ {}; +typedef SimpleType AminoAcid; + +template <> struct ValueSize +{ + typedef uint8_t Type; + static const Type VALUE = 27; +}; + +template <> struct BitsPerValue +{ + typedef uint8_t Type; + static const Type VALUE = 5; +}; + +inline AminoAcid +unknownValueImpl(AminoAcid *) +{ + static const AminoAcid _result = AminoAcid('X'); + return _result; +} + +// ---------------------------------------------------------------------------- +// Specialization Finite +// ---------------------------------------------------------------------------- + +/*! + * @class Finite + * @extends SimpleType + * @headerfile + * + * @brief A finite alphabet of a fixed size. + * + * @signature template + * class SimpleType >; + * + * @tparam TValue The type that is use to store the values. + * @tparam SIZE The ValueSize of the alphabet. + */ + +template +struct Finite; + +template +struct ValueSize > > +{ + typedef unsigned Type; + static const Type VALUE = SIZE; +}; + +template +struct BitsPerValue > > +{ + typedef uint8_t Type; + static const Type VALUE = Log2::VALUE; +}; + +// ============================================================================ +// Assignment / Conversion Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// char +// ---------------------------------------------------------------------------- + +inline void assign(char & c_target, + Dna const & source) +{ + c_target = TranslateTableDna5ToChar_<>::VALUE[source.value]; +} + +inline void assign(char & c_target, + Dna5 const & source) +{ + c_target = TranslateTableDna5ToChar_<>::VALUE[source.value]; +} + +inline void assign(char & c_target, + Rna const & source) +{ + c_target = TranslateTableRna5ToChar_<>::VALUE[source.value]; +} + +inline void assign(char & c_target, + Rna5 const & source) +{ + c_target = TranslateTableRna5ToChar_<>::VALUE[source.value]; +} + +inline void assign(char & c_target, Iupac const & source) +{ + c_target = TranslateTableIupacToChar_<>::VALUE[source.value]; +} + +inline void assign(char & c_target, AminoAcid const & source) +{ + c_target = TranslateTableAAToChar_<>::VALUE[source.value]; +} + +// ---------------------------------------------------------------------------- +// Dna +// ---------------------------------------------------------------------------- + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna & target, uint8_t c_source) +{ + target.value = TranslateTableByteToDna_<>::VALUE[c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna & target, char c_source) +{ + target.value = TranslateTableCharToDna_<>::VALUE[(unsigned char) c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna & target, Dna5 const & c_source) +{ + target.value = c_source.value & 0x03; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna & target, Iupac const & source) +{ + target.value = TranslateTableIupacToDna_<>::VALUE[source.value]; +} + +// ---------------------------------------------------------------------------- +// Dna5 +// ---------------------------------------------------------------------------- + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5 & target, uint8_t c_source) +{ + target.value = TranslateTableByteToDna5_<>::VALUE[c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5 & target, char c_source) +{ + target.value = TranslateTableCharToDna5_<>::VALUE[(unsigned char) c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5 & target, Iupac const & source) +{ + target.value = TranslateTableIupacToDna5_<>::VALUE[source.value]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna5 & target, Dna const & c_source) +{ + target.value = c_source.value; +} + +// ---------------------------------------------------------------------------- +// Rna +// ---------------------------------------------------------------------------- + +template <> +struct CompareTypeImpl +{ + typedef Rna Type; +}; + +inline void assign(Rna & target, uint8_t c_source) +{ + target.value = TranslateTableByteToDna_<>::VALUE[c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Rna Type; +}; + +inline void assign(Rna & target, char c_source) +{ + target.value = TranslateTableCharToDna_<>::VALUE[(unsigned char)c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Rna Type; +}; + +inline void assign(Rna & target, Rna5 const & c_source) +{ + target.value = c_source.value & 0x03; +} + +// --------------------------------------------------------------------------- +// Rna5 +// --------------------------------------------------------------------------- + +template <> +struct CompareTypeImpl +{ + typedef Rna5 Type; +}; + +inline void assign(Rna5 & target, uint8_t c_source) +{ + target.value = TranslateTableByteToDna5_<>::VALUE[c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Rna5 Type; +}; + +inline void assign(Rna5 & target, char c_source) +{ + target.value = TranslateTableCharToDna5_<>::VALUE[(unsigned char)c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Rna5 & target, Rna const & c_source) +{ + target.value = c_source.value; +} + +// --------------------------------------------------------------------------- +// Iupac +// --------------------------------------------------------------------------- + +template <> +struct CompareTypeImpl +{ + typedef Iupac Type; +}; + +inline void assign(Iupac & target, uint8_t c_source) +{ + target.value = TranslateTableByteToIupac_<>::VALUE[c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef Iupac Type; +}; + +inline void assign(Iupac & target, char c_source) +{ + target.value = TranslateTableCharToIupac_<>::VALUE[(unsigned char) c_source]; +} + +inline void assign(Iupac & target, Dna const & source) +{ + target.value = TranslateTableDna5ToIupac_<>::VALUE[source.value]; +} + +inline void assign(Iupac & target, Dna5 const & source) +{ + target.value = TranslateTableDna5ToIupac_<>::VALUE[source.value]; +} + +// --------------------------------------------------------------------------- +// Amino Acid +// --------------------------------------------------------------------------- + +template <> +struct CompareTypeImpl +{ + typedef AminoAcid Type; +}; + +inline void assign(AminoAcid & target, uint8_t c_source) +{ + target.value = TranslateTableByteToAA_<>::VALUE[c_source]; +} + +template <> +struct CompareTypeImpl +{ + typedef AminoAcid Type; +}; + +inline void assign(AminoAcid & target, char c_source) +{ + target.value = TranslateTableCharToAA_<>::VALUE[(unsigned char) c_source]; +} + +// --------------------------------------------------------------------------- +// DnaQ +// --------------------------------------------------------------------------- + +// template +// struct CompareTypeImpl, SimpleType > +// { +// typedef SimpleType Type; +// }; +// +// template +// struct CompareTypeImpl, SimpleType > +// { +// typedef SimpleType Type; +// }; + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(DnaQ & target, Dna const & source) +{ + target.value = source.value | (SEQAN_DEFAULT_QUALITY << 2); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna & target, DnaQ const & source) +{ + target.value = source.value & 3; +} + +template <> +struct CompareTypeImpl +{ + typedef Iupac Type; +}; + +inline void assign(DnaQ & target, Iupac const & source) +{ + assign(target, (Dna) source); +} + +template <> +struct CompareTypeImpl +{ + typedef Iupac Type; +}; + +inline void assign(Iupac & target, DnaQ const & source) +{ + assign(target, (Dna) source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(DnaQ & target, Dna5 const & source) +{ + assign(target, (Dna) source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(DnaQ & target, uint8_t c_source) +{ + assign(target, (Dna) c_source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(DnaQ & target, char c_source) +{ + assign(target, (Dna) c_source); +} + +inline void +assign(DnaQ & target, DnaQ const & source) +{ + target.value = source.value; +} + +template +inline void +assign(DnaQ & target, TSource const & source) +{ + target.value = (Dna)source; +} + +inline void +assign(int64_t & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(int64_t & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// uint64_t + +inline void +assign(uint64_t & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(uint64_t & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// int + +inline void +assign(int & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(int & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// unsigned int + +inline void +assign(unsigned int & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(unsigned int & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// short + +inline void +assign(short & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(short & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// unsigned short + +inline void +assign(unsigned short & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(unsigned short & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// char + +inline void +assign(char & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(char & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// signed char + +inline void +assign(signed char & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(signed char & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// unsigned char + +inline void +assign(unsigned char & c_target, + DnaQ & source) +{ + c_target = Dna(source); +} + +inline void +assign(unsigned char & c_target, + DnaQ const & source) +{ + c_target = Dna(source); +} + +// --------------------------------------------------------------------------- +// Dna5Q +// --------------------------------------------------------------------------- + +// template +// struct CompareTypeImpl, SimpleType > +// { +// typedef SimpleType Type; +// }; +// +// template +// struct CompareTypeImpl, SimpleType > +// { +// typedef SimpleType Type; +// }; + + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(DnaQ & target, Dna5Q const & source) +{ + // We perform the converstion from DNA5 to DNA5 with qualities by a simple + // table lookup. The lookup below is equivalent to the following line: + // + // target.value = (source.value == Dna5QValueN_)? 0: source.value; + + static const unsigned table[] = { + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, + 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, + 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, + 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, + 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, + 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, + 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, + 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, + 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, + 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, + 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, + 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, + 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, + 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, + 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, + 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 0, 0, 0, 0 + }; + target.value = table[source.value]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna5Q & target, DnaQ const & source) +{ + target.value = source.value; +} + + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5 & target, Dna5Q const & source) +{ + + // We perform the conversion from DNA5 to DNA5 with qualities by a simple + // table lookup. The lookup below is equivalent to the following line: + // + // target.value = (source.value == Dna5QValueN_)? 4: source.value & 3; + + static const unsigned table[] = { + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, + 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 4, 4, 4, 4 // <-- note the 4 + }; + target.value = table[source.value]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5Q & target, Dna5 const & source) +{ + + // We perform the conversion from DNA5 with qualities to DNA5 by a simple + // table lookup. The lookup below is equivalent to the following line: + // + // target.value = (source.value == 4)? Dna5QValueN_ : source.value | (40 << 2); + + static const unsigned table[] = { + (SEQAN_DEFAULT_QUALITY << 2) + 0, (SEQAN_DEFAULT_QUALITY << 2) + 1, + (SEQAN_DEFAULT_QUALITY << 2) + 2, (SEQAN_DEFAULT_QUALITY << 2) + 3, Dna5QValueN_ + }; + target.value = table[source.value]; +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna5Q & target, Dna const & source) +{ + assign(target, (DnaQ) source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna Type; +}; + +inline void assign(Dna & target, Dna5Q const & source) +{ + assign(target, (Dna5)source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5 & target, DnaQ const & source) +{ + assign(target, (Dna5Q)source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5Q & target, uint8_t c_source) +{ + assign(target, (Dna5)c_source); +} + +template <> +struct CompareTypeImpl +{ + typedef Dna5 Type; +}; + +inline void assign(Dna5Q & target, char c_source) +{ + assign(target, (Dna5)c_source); +} + +template <> +struct CompareTypeImpl +{ + typedef Iupac Type; +}; + +inline void assign(Dna5Q & target, Iupac const & source) +{ + assign(target, (Dna5)source); +} + +template <> +struct CompareTypeImpl +{ + typedef Iupac Type; +}; + +inline void assign(Iupac & target, Dna5Q const & source) +{ + assign(target, (Dna5)source); +} + +inline void +assign(Dna5Q & target, Dna5Q const & source) +{ + target.value = source.value; +} + +template +inline void +assign(Dna5Q & target, TSource const & source) +{ + assign(target, (Dna5)source); +} + +// int64_t + +inline void +assign(int64_t & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(int64_t & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +// uint64_t + +inline void +assign(uint64_t & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(uint64_t & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +// int + +inline void +assign(int & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(int & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +// unsigned int + +inline void +assign(unsigned int & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(unsigned int & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + + +//short + +inline void +assign(short & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(short & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +//unsigned short + +inline void +assign(unsigned short & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(unsigned short & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +// char + +inline void +assign(char & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(char & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +// signed char + +inline void +assign(signed char & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(signed char & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +// unsigned char + +inline void +assign(unsigned char & c_target, + Dna5Q & source) +{ + c_target = Dna5(source); +} + +inline void +assign(unsigned char & c_target, + Dna5Q const & source) +{ + c_target = Dna5(source); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_H_ diff --git a/seqan/basic/alphabet_residue_funcs.h b/seqan/basic/alphabet_residue_funcs.h new file mode 100644 index 0000000..7c11c1d --- /dev/null +++ b/seqan/basic/alphabet_residue_funcs.h @@ -0,0 +1,87 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2013 NVIDIA Corporation +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Enrico Siragusa +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_ + + +namespace seqan { + +// -------------------------------------------------------------------------- +// Dna +// -------------------------------------------------------------------------- + +template +inline unsigned char +_translateCharToDna(unsigned char c) +{ + switch (toUpperValue(c)) + { + case 'C': + return 1; + case 'G': + return 2; + case 'T': + return 3; + default: + return 0; + }; +} + +// -------------------------------------------------------------------------- +// Dna5 +// -------------------------------------------------------------------------- + +template +inline unsigned char +_translateCharToDna5(unsigned char c) +{ + switch (toUpperValue(c)) + { + case 'A': + return 0; + case 'C': + return 1; + case 'G': + return 2; + case 'T': + return 3; + default: + return 4; + }; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_FUNCS_H_ diff --git a/seqan/basic/alphabet_residue_tabs.h b/seqan/basic/alphabet_residue_tabs.h new file mode 100644 index 0000000..ca2f439 --- /dev/null +++ b/seqan/basic/alphabet_residue_tabs.h @@ -0,0 +1,461 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// ========================================================================== +// Conversion tables for residue SimpleType specializations. +// +// Dna and Dna5 share their tables for conversion to char. So do Rna and +// Rna5. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_ + + +namespace seqan { + +// -------------------------------------------------------------------------- +// Dna and Dna5 +// -------------------------------------------------------------------------- + +template +struct TranslateTableDna5ToChar_ +{ + static char const VALUE[5]; +}; + +template +char const TranslateTableDna5ToChar_::VALUE[5] = {'A', 'C', 'G', 'T', 'N'}; + + +template +struct TranslateTableDna5ToIupac_ +{ + static char const VALUE[5]; +}; + +template +char const TranslateTableDna5ToIupac_::VALUE[5] = {0x01, 0x02, 0x04, 0x08, 0x0f}; + +template +struct TranslateTableCharToDna_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableCharToDna_::VALUE[256] = +{ + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //0 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //1 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //2 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //3 + + 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, //4 +// , A, B, C, D, E, D, G, H, I, J, K, L, M, N, O, + + 0, 0, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //5 +// P, Q, R, S, T, U, V, W, X, Y, Z, , , , , + + 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, //6 +// , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, + + 0, 0, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //7 +// p, q, r, s, t, u, v, w, x, y, z, , , , , + + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //8 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //9 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //10 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //11 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //12 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //13 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //14 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 //15 +}; + + +template +struct TranslateTableCharToDna5_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableCharToDna5_::VALUE[256] = +{ + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //0 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //1 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //2 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //3 + + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, //4 +// , A, B, C, D, E, D, G, H, I, J, K, L, M, N, O, + + 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //5 +// P, Q, R, S, T, U, V, W, X, Y, Z, , , , , + + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, //6 +// , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, + + 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //7 +// p, q, r, s, t, u, v, w, x, y, z, , , , , + + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //8 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //9 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //10 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //11 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //12 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //13 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //14 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 //15 +}; + +template +struct TranslateTableByteToDna_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableByteToDna_::VALUE[256] = +{ + 0, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //0 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //1 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //2 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //3 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //4 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //5 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //6 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //7 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //8 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //9 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //10 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //11 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //12 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //13 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, //14 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 //15 +}; + +template +struct TranslateTableByteToDna5_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableByteToDna5_::VALUE[256] = +{ + 0, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //0 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //1 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //2 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //3 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //4 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //5 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //6 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //7 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //8 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //9 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //10 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //11 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //12 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //13 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, //14 + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 //15 +}; + +// -------------------------------------------------------------------------- +// Rna and Rna5 +// -------------------------------------------------------------------------- + +template +struct TranslateTableRna5ToChar_ +{ + static char const VALUE[5]; +}; + +template +char const TranslateTableRna5ToChar_::VALUE[5] = {'A', 'C', 'G', 'U', 'N'}; + +// other tables identical to Dna(5) + +// -------------------------------------------------------------------------- +// Iupac +// -------------------------------------------------------------------------- + +template +struct TranslateTableIupacToChar_ +{ + static char const VALUE[16]; +}; + +template +char const TranslateTableIupacToChar_::VALUE[16] = +{ //TGCA + 'U', //0000=0 = or U + 'A', //0001=1 + 'C', //0010=2 + 'M', //0011=3 AC + 'G', //0100=4 + 'R', //0101=5 AG (purine) + 'S', //0110=6 CG + 'V', //0111=7 non-T + 'T', //1000=8 + 'W', //1001=9 TA + 'Y', //1010=A TC (pyrimidine) + 'H', //1011=B not-G + 'K', //1100=C TG + 'D', //1101=D not-C + 'B', //1110=E non-A + 'N' //1111=F any +}; + +template +struct TranslateTableIupacToDna_ +{ + static char const VALUE[16]; +}; + +template +char const TranslateTableIupacToDna_::VALUE[16] = +{ //TGCA + 3, //0000=0 = or U + 0, //0001=1 + 1, //0010=2 + 0, //0011=3 AC + 2, //0100=4 + 0, //0101=5 AG (purine) + 1, //0110=6 CG + 0, //0111=7 non-T + 3, //1000=8 + 0, //1001=9 TA + 1, //1010=A TC (pyrimidine) + 0, //1011=B not-G + 2, //1100=C TG + 0, //1101=D not-C + 1, //1110=E non-A + 0 //1111=F any +}; + +template +struct TranslateTableIupacToDna5_ +{ + static char const VALUE[16]; +}; + +template +char const TranslateTableIupacToDna5_::VALUE[16] = +{ //TGCA + 3, //0000=0 = or U + 0, //0001=1 + 1, //0010=2 + 4, //0011=3 AC + 2, //0100=4 + 4, //0101=5 AG (purine) + 4, //0110=6 CG + 4, //0111=7 non-T + 3, //1000=8 + 4, //1001=9 TA + 4, //1010=A TC (pyrimidine) + 4, //1011=B not-G + 4, //1100=C TG + 4, //1101=D not-C + 4, //1110=E non-A + 4 //1111=F any +}; + +template +struct TranslateTableCharToIupac_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableCharToIupac_::VALUE[256] = +{ + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + // = + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 15, 15, + // A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, + 15, 1, 14, 2, 13, 15, 15, 4, 11, 15, 15, 12, 15, 3, 15, 15, + // Q, R, S, T, U, V, W, X, Y, Z + 15, 15, 5, 6, 8, 0, 7, 9, 15, 10, 15, 15, 15, 15, 15, 15, + // a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, + 15, 1, 14, 2, 13, 15, 15, 4, 11, 15, 15, 12, 15, 3, 15, 15, + // q, r, s, t, u, v, w, x, y, z + 15, 15, 5, 6, 8, 0, 7, 9, 15, 10, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15 +}; + +template +struct TranslateTableByteToIupac_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableByteToIupac_::VALUE[256] = +{ + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, //0 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //1 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //2 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //3 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //4 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //5 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //6 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //7 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //8 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //9 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //10 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //11 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //12 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //13 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, //14 + 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15 //15 +}; + +// -------------------------------------------------------------------------- +// Amino Acid +// -------------------------------------------------------------------------- + +template +struct TranslateTableAAToChar_ +{ + static char const VALUE[27]; +}; +template +char const TranslateTableAAToChar_::VALUE[27] = +{ + 'A', // Ala Alanine + 'B', // Aspartic Acid, Asparagine + 'C', // Cys Cystine + 'D', // Asp Aspartic Acid + 'E', // Glu Glutamic Acid + 'F', // Phe Phenylalanine + 'G', // Gly Glycine + 'H', // His Histidine + 'I', // Ile Isoleucine + 'J', // Leucine, Isoleucine + 'K', // Lys Lysine + 'L', // Leu Leucine + 'M', // Met Methionine + 'N', // Asn Asparagine + 'O', // Pyl Pyrrolysine + 'P', // Pro Proline + 'Q', // Gln Glutamine + 'R', // Arg Arginine + 'S', // Ser Serine + 'T', // Thr Threonine + 'U', // Selenocystein + 'V', // Val Valine + 'W', // Trp Tryptophan + 'Y', // Tyr Tyrosine + 'Z', // Glutamic Acid, Glutamine + 'X', // Unknown + '*' // Terminator +}; + +template +struct TranslateTableCharToAA_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableCharToAA_::VALUE[256] = +{ + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //0 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //1 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 25, 25, 25, 25, 25, //2 +// * + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //3 + 25, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, //4 +// , A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, + + 15, 16, 17, 18, 19, 20, 21, 22, 25, 23, 24, 25, 25, 25, 25, 25, //5 +// P, Q, R, S, T, U, V, W, X, Y, Z, , , , , , + + 25, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, //6 +// , a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, + + 15, 16, 17, 18, 19, 20, 21, 22, 25, 23, 24, 25, 25, 25, 25, //7 +// p, q, r, s, t, u, v, w, x, y, z, , , , , , + + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //8 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //9 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //10 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //11 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //12 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //13 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //14 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25 //15 +}; + +template +struct TranslateTableByteToAA_ +{ + static char const VALUE[256]; +}; + +template +char const TranslateTableByteToAA_::VALUE[256] = +{ + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, //0 + 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 25, 25, 25, 25, 25, //1 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //2 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //3 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //4 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //5 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //6 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //7 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //8 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //9 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //10 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //11 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //12 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //13 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, //14 + 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25 //15 +}; + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_RESIDUE_TABS_H_ diff --git a/seqan/basic/alphabet_simple_type.h b/seqan/basic/alphabet_simple_type.h new file mode 100644 index 0000000..f4955fc --- /dev/null +++ b/seqan/basic/alphabet_simple_type.h @@ -0,0 +1,1092 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== +// The SimpleType alphabet type is the base class for all residue types. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Class SimpleType +// ---------------------------------------------------------------------------- + +/*! + * @class SimpleType + * @implements FiniteOrderedAlphabetConcept + * @headerfile + * + * @brief Implementation for "simple" types. + * + * @signature template + * class SimpleType; + * + * @tparam TSpec Specialization tag. + * @tparam TValue Type that stores the values of an instance. TValue must be a simple type. + * + * A "simple type" is a C++ type that can be constructed without constructor, destructed without destructor and copied + * without copy constructor or assignment operator. All basic types (like char, int or + * float) are simple. Pointers, references and arrays of simple types are simple. POD types ("plain old data + * types"), that are - simplified spoken - C++-types that already existed in C, are simple too. + * + * Arrays of simple types can be copied very fast by memory manipulation routines, but the default implementation of + * functions like arrayCopyForward and arrayCopy are not optimized for simple types this way. But for classes derived + * from SimpleType, optimized variants of array manipulation functions are applied. + * + * Note that simple types need not to be derived or specialized from SimpleType, but it could be convenient to + * do so. + * + * @see IsSimple + */ + +/*! + * @var TValue SimpleType::value + * @brief The internal value storage of the SimpleType object. + * + * @important Do not modify this value directly. SimpleType implements conversion operators for all numeric types, so + * you can simply assign and cast the SimpleType to all built-in numeric types. + * + * Stores the value of the SimpleType, is of type TValue. Valid values are from 0 to @link + * FiniteOrderedAlphabetConcept#ValueSize @endlink minus one. + */ + +/*! + * @fn SimpleType::SimpleType + * @brief Constructor of SimpleType type. + * + * @signature SimpleType::SimpleType(); + * @signature SimpleType::SimpleType(other); + * @signature template SimpleType::SimpleType(param); + * + * @param[in] other Other SimpleType to copy construct with. + * @param[in] param Any value of type TParam that can be assigned to the SimpleType object. + * + * The default constructor initializes the SimpleType object with the value 0 and the copy constructor copies + * over the value of the SimpleType. + * + * When constructing with a param that is not a SimpleType then param is assigned to the SimpleType + * object, using @link AssignableConcept#assign assign @endlink. This function can be overloaded differently for each + * type. You can expect the following behaviour for all SimpleType objects, however: + * + *
    + *
  • If param is a builtin integer then this value is directly assigned to the @link SimpleType::value value + * @endlink member of the SimpleType object. Note that this can allow an invalid assignment, e.g., when assigning + * 42 to a @link Dna @endlink object.
    • + *
  • If param is a char then this character value is converted to the appropriate value and written + * to the @link SimpleType::value value @endlink member. For example, assigning 'A' or 'a' to + * a SimpleType object assigns 0 to the @link SimpleType::value value @endlink member.
    • + *
+ * + * @section Example + * + * The following example shows construction of a @link Dna @endlink (specialization of SimpleType) object with from + * char and integer values. + * + * @snippet demos/dox/basic/simple_type_construction.cpp simple type construction and assignment + */ + +#pragma pack(push,1) +template +class SimpleType +{ +public: + // ------------------------------------------------------------------------ + // Members; Have to be defined in class. + // ------------------------------------------------------------------------ + + TValue value; + + // ------------------------------------------------------------------------ + // Constructors; Have to be defined in class. + // ------------------------------------------------------------------------ + + // TODO(holtgrew): Do we want default initialization? + + SimpleType() : value(0) + {} + + + SimpleType(SimpleType const & other) + { + assign(*this, other); + } + + // TODO(holtgrew): Do we want an explicit here? + template + + SimpleType(T const & other) + { + assign(*this, other); + } + + // ------------------------------------------------------------------------ + // Assignment Operator; Have to be defined in class. + // ------------------------------------------------------------------------ + + + SimpleType & operator=(SimpleType const & other) + { + assign(*this, other); + return *this; + } + + template + inline SimpleType & + operator=(T const & other) + { + assign(*this, other); + return *this; + } + + // ------------------------------------------------------------------------ + // Conversion Operators; Have to be defined in class. + // ------------------------------------------------------------------------ + + // Class.SimpleType specifies type conversion operators for all built-in + // integer types since there is no way to extend the build-in types with + // copy and assignment constructors in C++. + // + // This cannot be a template since it would conflict to the template + // constructor. + + + operator int64_t() const + { + int64_t c; + assign(c, *this); + return c; + } + + + operator uint64_t() const + { + uint64_t c; + assign(c, *this); + return c; + } + + + operator int() const + { + int c; + assign(c, *this); + return c; + } + + + operator unsigned int() const + { + unsigned int c; + assign(c, *this); + return c; + } + + + operator short() const + { + short c; + assign(c, *this); + return c; + } + + + operator unsigned short() const + { + unsigned short c; + assign(c, *this); + return c; + } + + + operator char() const + { + char c; + assign(c, *this); + return c; + } + + + operator signed char() const + { + signed char c; + assign(c, *this); + return c; + } + + + operator unsigned char() const + { + unsigned char c; + assign(c, *this); + return c; + } +}; +#pragma pack(pop) + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction IsSimple +// ---------------------------------------------------------------------------- + +template +struct IsSimple > +{ + typedef True Type; +}; + +// ---------------------------------------------------------------------------- +// Concept Convertible +// ---------------------------------------------------------------------------- + +template +struct Is< Convertible, TSource> > : + Is< FundamentalConcept > {}; + +template +struct Is< Convertible > > : + Is< FundamentalConcept > {}; + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Rename? SimpleType is no container! + +template +struct Value > +{ + typedef TValue Type; +}; + +template +struct Value const> +{ + typedef TValue const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction MinValue +// ---------------------------------------------------------------------------- + +template +struct MinValue > +{ + static const SimpleType VALUE; +}; + +template +const SimpleType MinValue >::VALUE = SimpleType(0); + +template +inline SimpleType const & +infimumValueImpl(SimpleType *) +{ + return MinValue >::VALUE; +} + +// ---------------------------------------------------------------------------- +// Metafunction MaxValue +// ---------------------------------------------------------------------------- + +template +struct MaxValue > +{ + static const SimpleType VALUE; +}; + +template +const SimpleType MaxValue >::VALUE = SimpleType(((TValue)ValueSize >::VALUE - 1)); + +template +inline SimpleType const & +supremumValueImpl(SimpleType *) +{ + return MaxValue >::VALUE; +} + +// ---------------------------------------------------------------------------- +// Metafunction Spec +// ---------------------------------------------------------------------------- + +template +struct Spec > +{ + typedef TSpec Type; +}; + +template +struct Spec const> +{ + typedef TSpec Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction CompareType +// ---------------------------------------------------------------------------- + +// TODO(doering): muss geprueft werden, ob diese Metafunktion noch ausgeweitet oder aber versteckt wird. +// TODO(holtgrew): Is this at the right place here? Do we need it for all types? +// TODO(holtgrew): CompareType is not symmetric because of class instantiation conflicts. Evaluate these problems and possibly fix them. +// TODO(holtgrew): Is some of the code below redundant, can we lose some copy and paste here? + +template +struct CompareTypeImpl, TRight> +{ + typedef TRight Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// TODO(holtgrew): Why are functions with Proxies defined here? Better in Proxy header? Or externalize? + +// ---------------------------------------------------------------------------- +// Function convertImpl() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Document + +template +inline typename RemoveConst_::Type +convertImpl(Convert const, + SimpleType const & source_) +{ + typename RemoveConst_::Type target_; + assign(target_, source_); + return target_; +} + +// ---------------------------------------------------------------------------- +// Function operator<<() +// ---------------------------------------------------------------------------- + +template +inline TStream & +operator<<(TStream & stream, + SimpleType const & data) +{ + stream << convert(data); + return stream; +} + +// ---------------------------------------------------------------------------- +// Function operator>>() +// ---------------------------------------------------------------------------- + +template +inline TStream & +operator>>(TStream & stream, + SimpleType & data) +{ + char c; + stream >> c; + assign(data, c); + return stream; +} + +// ---------------------------------------------------------------------------- +// Function assign() +// ---------------------------------------------------------------------------- + +template +inline void +assign(SimpleType & target, + SimpleType & source) +{ + target.value = source.value; +} + +template +inline void +assign(SimpleType & target, + SimpleType const & source) +{ + target.value = source.value; +} + +template +inline void +assign(SimpleType & target, + TSource & source) +{ + target.value = source; +} + +template +inline void +assign(SimpleType & target, + TSource const & source) +{ + target.value = source; +} + +// Assign Proxy to SimpleType +// NOTE(doering): Diese Funktionen wurden noetig wegen eines seltsamen VC++-Verhaltens +// TODO(holtgrew): Still necessary with dropped 2003 support? + +template +inline void +assign(SimpleType & target, + Proxy & source) +{ + target.value = getValue(source); +} + +template +inline void +assign(SimpleType & target, + Proxy const & source) +{ + target.value = getValue(source); +} + +//INTEGRAL TYPES +// NOTE(doering): It is not possible to write a single function here since "assign" must be specialized for the first argument at the first place + +template +inline void +assign(int64_t & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(int64_t & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(uint64_t & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(uint64_t & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(int & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(int & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(unsigned int & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(unsigned int & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(short & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(short & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(unsigned short & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(unsigned short & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(char & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(char & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(signed char & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(signed char & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +template +inline void +assign(unsigned char & c_target, + SimpleType & source) +{ + c_target = source.value; +} + +template +inline void +assign(unsigned char & c_target, + SimpleType const & source) +{ + c_target = source.value; +} + +// ---------------------------------------------------------------------------- +// Function operator==() +// ---------------------------------------------------------------------------- + +template +inline bool +operator==(SimpleType const & left_, + TRight const & right_) +{ + typedef SimpleType TLeft; + typedef typename CompareType::Type TCompareType; + return convert(left_) == convert(right_); +} + +template +inline bool +operator==(TLeft const & left_, + SimpleType const & right_) +{ + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) == convert(right_); +} + +template +inline bool +operator==(SimpleType const & left_, + SimpleType const & right_) +{ + typedef SimpleType TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) == convert(right_); +} + +template +inline bool +operator==(SimpleType const & left_, + SimpleType const & right_) +{ + return convert(left_) == convert(right_); +} + +template +inline bool +operator==(Proxy const & left_, + SimpleType const & right_) +{ + typedef Proxy TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) == convert(right_); +} + +template +inline bool +operator==(SimpleType const & left_, + Proxy const & right_) +{ + typedef SimpleType TLeft; + typedef Proxy TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) == convert(right_); +} + +// ---------------------------------------------------------------------------- +// Function operator!=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator!=(SimpleType const & left_, + TRight const & right_) +{ + typedef SimpleType TLeft; + typedef typename CompareType::Type TCompareType; + return convert(left_) != convert(right_); +} + +template +inline bool +operator!=(TLeft const & left_, + SimpleType const & right_) +{ + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) != convert(right_); +} + +template +inline bool +operator!=(SimpleType const & left_, + SimpleType const & right_) +{ + typedef SimpleType TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) != convert(right_); +} + +template +inline bool +operator!=(SimpleType const & left_, + SimpleType const & right_) +{ + return convert(left_) != convert(right_); +} + +template +inline bool +operator!=(Proxy const & left_, + SimpleType const & right_) +{ + typedef Proxy TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) != convert(right_); +} + +template +inline bool +operator!=(SimpleType const & left_, + Proxy const & right_) +{ + typedef SimpleType TLeft; + typedef Proxy TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) != convert(right_); +} + +// ---------------------------------------------------------------------------- +// Function operator<() +// ---------------------------------------------------------------------------- + +template +inline bool +operator<(SimpleType const & left_, + TRight const & right_) +{ + typedef SimpleType TLeft; + typedef typename CompareType::Type TCompareType; + return convert(left_) < convert(right_); +} + +template +inline bool +operator<(TLeft const & left_, + SimpleType const & right_) +{ + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) < convert(right_); +} + +template +inline bool +operator<(SimpleType const & left_, + SimpleType const & right_) +{ + typedef SimpleType TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) < convert(right_); +} + +template +inline bool +operator<(SimpleType const & left_, + SimpleType const & right_) +{ + return convert(left_) < convert(right_); +} + +template +inline bool +operator<(Proxy const & left_, + SimpleType const & right_) +{ + typedef Proxy TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) < convert(right_); +} + +template +inline bool +operator<(SimpleType const & left_, + Proxy const & right_) +{ + typedef SimpleType TLeft; + typedef Proxy TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) < convert(right_); +} + +// ---------------------------------------------------------------------------- +// Function operator<=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator<=(SimpleType const & left_, + TRight const & right_) +{ + typedef SimpleType TLeft; + typedef typename CompareType::Type TCompareType; + return convert(left_) <= convert(right_); +} + +template +inline bool +operator<=(TLeft const & left_, + SimpleType const & right_) +{ + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) <= convert(right_); +} + +template +inline bool +operator<=(SimpleType const & left_, + SimpleType const & right_) +{ + typedef SimpleType TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) <= convert(right_); +} + +template +inline bool +operator<=(SimpleType const & left_, + SimpleType const & right_) +{ + return convert(left_) <= convert(right_); +} + +template +inline bool +operator<=(Proxy const & left_, + SimpleType const & right_) +{ + typedef Proxy TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) <= convert(right_); +} +template +inline bool +operator<=(SimpleType const & left_, + Proxy const & right_) +{ + typedef SimpleType TLeft; + typedef Proxy TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) <= convert(right_); +} + +// ---------------------------------------------------------------------------- +// Function operator>() +// ---------------------------------------------------------------------------- + +template +inline bool +operator>(SimpleType const & left_, + TRight const & right_) +{ + typedef SimpleType TLeft; + typedef typename CompareType::Type TCompareType; + return convert(left_) > convert(right_); +} + +template +inline bool +operator>(TLeft const & left_, + SimpleType const & right_) +{ + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) > convert(right_); +} + +template +inline bool +operator>(SimpleType const & left_, + SimpleType const & right_) +{ + typedef SimpleType TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) > convert(right_); +} + +template +inline bool +operator>(SimpleType const & left_, + SimpleType const & right_) +{ + return convert(left_) > convert(right_); +} + +template +inline bool +operator>(Proxy const & left_, + SimpleType const & right_) +{ + typedef Proxy TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) > convert(right_); +} + +template +inline bool +operator>(SimpleType const & left_, + Proxy const & right_) +{ + typedef SimpleType TLeft; + typedef Proxy TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) > convert(right_); +} + +// ---------------------------------------------------------------------------- +// Function operator>=() +// ---------------------------------------------------------------------------- + +template +inline bool +operator>=(SimpleType const & left_, + TRight const & right_) +{ + typedef SimpleType TLeft; + typedef typename CompareType::Type TCompareType; + return convert(left_) >= convert(right_); +} + +template +inline bool +operator>=(TLeft const & left_, + SimpleType const & right_) +{ + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) >= convert(right_); +} + +template +inline bool +operator>=(SimpleType const & left_, + SimpleType const & right_) +{ + typedef SimpleType TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) >= convert(right_); +} + +template +inline bool +operator>=(SimpleType const & left_, + SimpleType const & right_) +{ + return convert(left_) >= convert(right_); +} + +template +inline bool +operator>=(Proxy const & left_, + SimpleType const & right_) +{ + typedef Proxy TLeft; + typedef SimpleType TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) >= convert(right_); +} +template +inline bool +operator>=(SimpleType const & left_, + Proxy const & right_) +{ + typedef SimpleType TLeft; + typedef Proxy TRight; + typedef typename CompareType::Type TCompareType; + return convert(left_) >= convert(right_); +} + +// ---------------------------------------------------------------------------- +// Function operator++() +// ---------------------------------------------------------------------------- + +template +inline SimpleType & +operator++(SimpleType & me) +{ + ++me.value; + return me; +} + +template +inline SimpleType +operator++(SimpleType & me, int) +{ + SimpleType dummy = me; + ++me.value; + return dummy; +} + +// ---------------------------------------------------------------------------- +// Function operator--() +// ---------------------------------------------------------------------------- + +template +inline SimpleType & +operator--(SimpleType & me) +{ + --me.value; + return me; +} + +template +inline SimpleType +operator--(SimpleType & me, int) +{ + SimpleType dummy = me; + --me.value; + return dummy; +} + +// ---------------------------------------------------------------------------- +// Function operator+() [unary] +// ---------------------------------------------------------------------------- + +template +inline SimpleType +operator+(SimpleType const & v) +{ + return v; +} + +template +inline typename ValueSize >::Type +_internalOrdValue(SimpleType const & c) +{ + return c.value; +} + +template +inline typename ValueSize >::Type +ordValue(SimpleType const & c) +{ + return convert(c); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_SIMPLE_H_ diff --git a/seqan/basic/alphabet_storage.h b/seqan/basic/alphabet_storage.h new file mode 100644 index 0000000..53a5df3 --- /dev/null +++ b/seqan/basic/alphabet_storage.h @@ -0,0 +1,291 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Doering +// Author: Manuel Holtgrewe +// ========================================================================== +// Storage-related alphabet interface part. This means both +// construction type (simple, non-simple) and storage size. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_ + +#include + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +class SimpleType; + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction BitsPerValue +// ---------------------------------------------------------------------------- + +template +struct BitsPerValue +{ + static const unsigned VALUE = sizeof(TValue) * 8; + typedef unsigned Type; +}; + +template +struct BitsPerValue : public BitsPerValue +{}; + +// template +// const unsigned BitsPerValue::VALUE = ; + +// ---------------------------------------------------------------------------- +// Metafunction ValueSize +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Enable default implementation only for integers? Move to adapt builtins? + +template +struct ValueSize +{ + typedef uint64_t Type; + static const Type VALUE = (BitsPerValue::VALUE < 64)? 1ull << (BitsPerValue::VALUE & 63) : 0ull; +}; + +template +struct ValueSize : ValueSize +{}; + +// TODO(holtgrew): Use static assertion to make sure that ValueSize is never called on floating point numbers? Include assertion for int64_t and uint64_t? + +template <> +struct ValueSize +{ + typedef uint64_t Type; + static const Type VALUE = 0; +}; + +template <> +struct ValueSize +{ + typedef uint64_t Type; + static const Type VALUE = 0; +}; + +template <> +struct ValueSize +{ + typedef uint64_t Type; + static const Type VALUE = 0; +}; + +template <> +struct ValueSize +{ + typedef uint64_t Type; + static const Type VALUE = 0; +}; + + +// The internal value size is used for alphabets with piggyback qualities, +// for example Dna5Q. Here, the public value size is 5 but the internal +// value size is 256. + +template +struct InternalValueSize_ + : public ValueSize +{}; + +// ---------------------------------------------------------------------------- +// Metafunction BytesPerValue +// ---------------------------------------------------------------------------- + +/*! + * @mfn BytesPerValue + * @headerfile + * @brief Number of bytes needed to store a value. + * + * @signature BytesPerValue::VALUE + * + * @tparam T The type to query. + * + * @return VALUE The number of bytes to store on T object. + * + * By default, this function returns ceil(BitsPerValue<T>::VALUE). For built-in types, this is the same + * as sizeof(T). + * + * @see FiniteOrderedAlphabetConcept#ValueSize + * @see AlphabetConcept#BitsPerValue + * @see IntegralForValue + */ + +template +struct BytesPerValue +{ + enum { VALUE = (BitsPerValue::VALUE + 7) / 8 }; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IntegralForValue +// ---------------------------------------------------------------------------- + +/*! + * @mfn IntegralForValue + * @headerfile + * @brief Returns an itegral type that provides sufficient space to store a value. + * + * @signature IntegralForValue::Type; + * + * @tparam T The type to query. + * + * @return Type An integral type. + * + * The type is the smallest unsigned integral type that has a size of at least BytesPerValue bytes. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
sizeof(T) in bytesintegral types
1unsigned char
2unsigned short
3unsigned int
4unsigned int
> 4int64_t
+ * + * Note that the returned integral type cannot store T values, if T takes more than 8 bytes, since + * there exists no integral type that provides sufficient space to store types of this size. + * + * @see FiniteOrderedAlphabetConcept#ValueSize + * @see AlphabetConcept#BitsPerValue + * @see BytesPerValue + */ + +template +struct IntegralForValueImpl_ +{ + typedef int64_t Type; +}; + +// TODO(holtgrew): Switch to uint8_t, uint16_t, uint32_t? +template <> +struct IntegralForValueImpl_<1> +{ + typedef unsigned char Type; +}; + +template <> +struct IntegralForValueImpl_<2> +{ + typedef unsigned short Type; +}; + +template <> +struct IntegralForValueImpl_<3> +{ + typedef unsigned int Type; +}; + +template <> +struct IntegralForValueImpl_<4> +{ + typedef unsigned int Type; +}; + +template +struct IntegralForValue : IntegralForValueImpl_::VALUE> +{}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function ordValue() +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Enable only for integers, move to adapt builtins? + +template +inline typename ValueSize::Type +ordValue(TValue const & c) +{ + return convert(static_cast::Type const &>(c)); +} + +// The internal ord value is used for alphabets with piggyback qualities. + +template +inline typename ValueSize::Type +_internalOrdValue(TValue const & c) +{ + return ordValue(c); +} + +// ---------------------------------------------------------------------------- +// Function valueSize() +// ---------------------------------------------------------------------------- + +template +inline typename ValueSize::Type +valueSize() +{ + return +ValueSize::VALUE; +} + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_STORAGE_H_ diff --git a/seqan/basic/array_construct_destruct.h b/seqan/basic/array_construct_destruct.h new file mode 100644 index 0000000..cb83d7a --- /dev/null +++ b/seqan/basic/array_construct_destruct.h @@ -0,0 +1,1272 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Döring +// ========================================================================== +// Functions for destructing and several ways of constructing (e.g. copy, +// move) values or arrays of values. +// ========================================================================== + +// TODO(holtgrew): Order of parameters should be (target1, target2, ..., source1, source2, ...). +// TODO(holtgrew): Can we maybe replace at least part with http://www.cplusplus.com/reference/std/memory/? +// TODO(holtgrew): The metafunction should go into the alphabet submodule, the functions into the sequence/string module. + +#include + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction IsSimple +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This has to go to alphabet sub module, storage section, adaption. + +/*! + * @mfn IsSimple + * @headerfile + * @brief Tests type to be simple. + * + * @signature IsSimple::Type; + * + * @tparam T Type that is tested. + * + * @return Type Either True or False, depending on T being a "POD" type. + * + * A simple type is a type that does not need constructors to be created, a destructor to be destroyed, and copy + * assignment operators or copy constructors to be copied. All POD ("plain old data") types are simple, but some + * non-POD types could be simple too, e.g. some specializations of SimpleType. + * + * @see SimpleType + */ + +template +struct IsSimple_ +{ + typedef False Type; + enum { VALUE = 0 }; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IsSimple +// ---------------------------------------------------------------------------- + +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; + +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; + +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; + +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; +template <> struct IsSimple_ { typedef True Type; }; + +template +struct IsSimple +{ + typedef typename IsSimple_::Type Type; + enum { VALUE = Type::VALUE }; +}; + +// user defined types (re-specializations are allowed here) +template <> struct IsSimple { typedef True Type; }; +template <> struct IsSimple { typedef True Type; }; +template <> struct IsSimple { typedef True Type; }; + +template +struct IsSimple : public IsSimple {}; + +// ---------------------------------------------------------------------------- +// Metafunction Value +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This should probably to into sequence module along with this header. + +template +struct Value +{ + typedef TValue Type; +}; + +template +struct Value +{ + typedef TValue Type; +}; + +// TODO(holtgrew): Is this still a problem with dropped 2003 support of VC++? + +//The next two metafunctions dont work in VC++ due to a compiler bug. +//(the default implementation in common_type.h is called instead) +//work-around: convert arrays to pointers. +template +struct Value +{ + typedef TValue Type; +}; + +template +struct Value +{ + typedef TValue Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Reference +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This should probably to into sequence module along with this header. + +template +struct Reference +{ + typedef TValue & Type; +}; + +template +struct Reference +{ + typedef TValue const & Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function value() for pointers. +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This has to go to iterator module, adaption of pointers to iterators. + +template +inline T & +value(T * me) +{ + return *me; +} + +// ---------------------------------------------------------------------------- +// Function getValue() for pointers. +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): This has to go to iterator module, adaption of pointers to iterators. + +template +inline T & +getValue(T * me) +{ + return value(me); +} + +// TODO(holtgrew): All of the helper structs could be replaced by global functions. + +// TODO(holtgrew): First, the generic versions for iterators are defined. Below are the versions for pointers. + +// ---------------------------------------------------------------------------- +// Function valueConstruct() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn valueConstruct + * @headerfile + * @brief Constructs an object at specified position. + * + * @signature void valueConstruct(iterator [, param [, move_tag]]); + * + * @param[in,out] iterator Pointer or iterator to position where the object should be constructed. + * @param[in] param Parameter that is forwarded to constructor. + * @param[in] moveTag Instance of the move tag. If the tag is specified, it is forwarded to the constructor, + * so the constructed object must support move construction. + * + * The type of the destructed object is the value type of iterator. + */ + +// Helper code for constructing values behind iterators that do not return +// proxies from their value() functions but references. +struct ValueConstructor_ +{ + template + static inline void + construct(TIterator it) + { + typedef typename Value::Type TValue; + typedef typename RemoveConst::Type TNonConstValue; + new( (void*) & value(it) ) TNonConstValue; + } + + template + static inline void + construct(TIterator it, + TParam && param_) + { + typedef typename Value::Type TValue; + typedef typename RemoveConst::Type TNonConstValue; + new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + } +}; + +// Helper code for constructing values behind iterators that return proxies +// from their value() function. +// +// TODO(holtgrew): These implementations are empty and to be overwritten. Should we have dynamic/static asserstions here? +struct ValueConstructorProxy_ +{ + template + static inline void construct(TIterator) {} + + template + static inline void construct(TIterator, TParam &&) {} +}; + +template +inline void +valueConstruct(TIterator it) +{ + typedef typename IfC< + IsSameType< + typename Value::Type &, + typename Reference::Type + >::VALUE, + // THEN + ValueConstructor_, // true, types are equal + // ELSE + ValueConstructorProxy_ // false, types differ -> value() returns a proxy + >::Type TConstructor; + + TConstructor::construct(it); +} + +template +inline void +valueConstruct(TIterator it, + TParam && param_) +{ + typedef typename IfC< + IsSameType< + typename Value::Type &, + typename Reference::Type + >::VALUE, + // THEN + ValueConstructor_, // true, types are equal + // ELSE + ValueConstructorProxy_ // false, types differ -> value() returns a proxy + >::Type TConstructor; + + TConstructor::construct(it, std::forward(param_)); +} + +// ---------------------------------------------------------------------------- +// Function valueDestruct() using iterators +// ---------------------------------------------------------------------------- + +// Helper code for destructing values behind iterators that do not return +// proxies from their value() function but references. +struct ValueDestructor_ +{ + template + static inline void + _destruct(TValue * p) + { + p->~TValue(); + } + + template + static inline void + destruct(TIterator it) + { + _destruct(&value(it)); + } +}; + +// Helper code for destructing values behind iterators that return proxies +// from their value() function. +// +// TODO(holtgrew): These implementations are empty and to be overwritten. Should we have dynamic/static asserstions here? +struct ValueDestructorProxy_ +{ + template + static inline void destruct(TIterator) {} +}; + +/*! + * @fn valueDestruct + * @headerfile + * @brief Destroys an object at specified position. + * + * @signature void valueDestruct(iterator); + * + * @param[in,out] iterator Pointer or iterator to position where the object should be destructed. + * + * The type of the constructed object is the value type of iterator. + */ + +template +inline void +valueDestruct(TIterator it) +{ + typedef typename IfC< + IsSameType< + typename Value::Type &, + typename Reference::Type + >::VALUE, + // THEN + ValueDestructor_, // true, types are equal + // ELSE + ValueDestructorProxy_ // false, types differ -> value() returns a proxy + >::Type TDestructor; + + TDestructor::destruct(it); +} + +// ---------------------------------------------------------------------------- +// Function arrayConstruct() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayConstruct + * @headerfile + * @brief Construct objects in a given memory buffer. + * + * @signature void arrayConstruct(begin, end[, value]); + * + * @param[in] begin Iterator to the begin of the range that is to be constructed. + * @param[in] end Iterator behind the end of the range. + * @param[in] value Argument that is forwarded to the constructor. An appropriate constructor is required. If + * value is not specified, the default constructor is used. + * + * The type of the constructed Objects is the value type of begin and end. + */ + +// NOTE(holtgrew): Of course, it does not make sense to declare this in a move version! + +template +inline void +_arrayConstructDefault(TIterator1 begin_, + TIterator2 end_) +{ + while (begin_ != end_) + { + valueConstruct(begin_); + ++begin_; + } +} + +template +inline void +arrayConstruct(TIterator1 begin_, + TIterator2 end_) +{ + _arrayConstructDefault(begin_, end_); +} + +template +inline void +_arrayConstructDefault(TIterator1 begin_, + TIterator2 end_, + TParam const & param_) +{ + while (begin_ != end_) + { + valueConstruct(begin_, param_); + ++begin_; + } +} + +template +inline void +arrayConstruct(TIterator1 begin_, + TIterator2 end_, + TParam const & param_) +{ + _arrayConstructDefault(begin_, end_, param_); +} + +// ---------------------------------------------------------------------------- +// Function arrayConstructCopy() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayConstructCopy + * @headerfile + * @brief Copy constructs an array of objects into in a given memory buffer. + * + * @signature void arrayConstructCopy(sourceBegin, sourceEnd, target); + * + * @param[in] sourceBegin Iterator to the first element of the source range. + * @param[in] sourceEnd Iterator behind the last element of the source range. sourceEnd should have the same + * type as sourceBegin. + * @param[in] target Pointer to the memory block the new objects will be constructed in. The type of target + * specifies the type of the constructed objects: If T* is the type of target, then + * the function constructs objects of type T. The memory buffer should be large enough to + * store sourceEnd - sourceBegin objects. An appropriate (copy-) constructor that + * constructs an target objects given a source object is required. + */ + +template +inline void +_arrayConstructCopyDefault(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + while (source_begin != source_end) + { + // NOTE(holtgrew): getValue() is used here since value() could return + // a proxy! + valueConstruct(target_begin, getValue(source_begin)); + ++source_begin; + ++target_begin; + } +} + +template +inline void +arrayConstructCopy(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + _arrayConstructCopyDefault(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayConstructMove() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayConstructMove + * @headerfile + * @brief Move constructs an array of objects into in a given memory buffer. + * + * @signature void arrayConstructMove(sourceBegin, sourceEnd, target); + * + * @param[in] sourceEnd Iterator behind the last element of the source range. sourceEnd should have the same + * type as sourceBegin. + * @param[in] sourceBegin Iterator to the first element of the source range. + * @param[in] target Pointer to the memory block the new objects will be constructed in. The type of target + * specifies the type of the constructed objects: If T* is the type of target, then + * the function constructs objects of type T. The memory buffer should be large enough to + * store sourceEnd - sourceBegin objects. An appropriate move constructor that + * constructs an target objects given a source object is required. + */ + +template +inline void +_arrayConstructMoveDefault(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + while (source_begin < source_end) + { + // NOTE(holtgrew): Using value() here, used to be getValue() but + // cannot move from const reference or proxy. + // valueConstruct(target_begin, value(source_begin), Move()); + // TODO(holtgrew): We need a "has move constructor" metafunction to switch between move/copy constructing before we can use the line here. + valueConstruct(target_begin, std::move(*source_begin)); + ++source_begin; + ++target_begin; + } +} + +template +inline void +arrayConstructMove(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + _arrayConstructMoveDefault(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayDestruct() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayDestruct + * @headerfile + * @brief Destroys an array of objects. + * + * @signature void arrayDestruct(begin, end); + * + * @param[in] begin Iterator to the begin of the range that is to be destructed. + * @param[in] end Iterator behind the end of the range. + * + * This function does not deallocates the memory. + */ + +template +inline void +_arrayDestructDefault(TIterator1 begin_, + TIterator2 end_) +{ + while (begin_ != end_) + { + valueDestruct(begin_); + ++begin_; + } +} + +template +inline void +arrayDestruct(TIterator1 begin_, + TIterator2 end_) +{ + _arrayDestructDefault(begin_, end_); +} + +// ---------------------------------------------------------------------------- +// Function arrayFill() using iterators +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): What is the advantage over arrayConstruct() with prototype? + +/*! + * @fn arrayFill + * @headerfile + * @brief Assigns one object to each element of a range. + * + * @signature void arrayFill(begin, end, value[, parallelTag]); + * + * @param[in] begin Iterator to the begin of the range that is to be filled. + * @param[in] end Iterator behind the end of the range. + * @param[in] value Argument that is assigned to all count objects in array. + * @param[in] parallelTag Tag to enable/disable parallelism. Types: Serial, Parallel + * + * All objects target_begin[0] to target_begin[count-1] are set to value. + */ + +// TODO(holtgrew): Redirects to fill_n. What are the exact semantics here? Do the array elements have to be initialized already? fill_n uses assignment, not copy construction! + +template +inline void +arrayFill(TIterator begin_, + TIterator end_, + TValue const & value) +{ + std::fill_n(begin_, end_ - begin_, value); +} + +template +inline void +arrayFill(TIterator begin_, + TIterator end_, + TValue const & value, + Serial) +{ + arrayFill(begin_, end_, value); +} + +// ---------------------------------------------------------------------------- +// Function arrayCopyForward() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayCopyForward + * @headerfile + * @brief Copies a range of objects into another range of objects starting from the first element. + * + * @signature void arrayCopyForward(sourceBegin, sourceEnd, target); + * + * @param[in] sourceEnd Iterator behind the last element of the source array. sourceEnd must have the same type + * as sourceBegin. + * @param[in] sourceBegin Iterator to the first element of the source array. + * @param[in] target Iterator to the first element of the target array. The target capacity should be at least as + * long as the source range. + * + * Be careful if source and target range overlap, because in this case some source elements could be accidently + * overwritten before they are copied. + * + * If there is no need for the source elements to persist, consider to use arrayMoveForward instead to improve + * performance. + */ + +template +inline void +_arrayCopyForwardDefault(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + std::copy(source_begin, source_end, target_begin); +} + +template +inline void +arrayCopyForward(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + _arrayCopyForwardDefault(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayCopyBackward() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayCopyBackward + * @headerfile + * @brief Copies a range of objects into another range of objects starting from the last element. + * + * @signature void arrayCopyBackward(source_begin, source_end, target); + * + * @param[in] sourceBegin Iterator to the first element of the source array. + * @param[in] sourceEnd Iterator behind the last element of the source array. sourceEnd must have the same type + * as source_begin. + * @param[in] target Iterator to the first element of the target array. The target capacity should be at least as + * long as the source range. + * + * Be careful if source and target range overlap, because in this case some source elements could be accidently + * overwritten before they are moved. + * + * If source and target do not overlap, consider to use the function arrayCopyForward instead that is faster in some + * cases. + * + * If there is no need for the source elements to persist, consider to use arrayMoveBackward instead to improve + * performance. + * + * The semantic of this function's argument target differ from the arguments of std::copy_backward. + */ + +template +inline void +_arrayCopyBackwardDefault(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + std::copy_backward(source_begin, source_end, target_begin + (source_end - source_begin)); +} + +template +inline void +arrayCopyBackward(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + _arrayCopyBackwardDefault(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayCopy() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayCopy + * + * @headerfile + * + * @brief Copies a range of objects into another range of objects. + * + * @signature void arrayCopy(sourceBegin, sourceEnd, target); + * + * @param[in] sourceEnd Iterator behind the last element of the source range. sourceEnd must have the same type + * as sourceBegin. + * @param[in] sourceBegin Iterator to the first element of the source range. + * @param[in] target Iterator to the first element of the target range.The target capacity should be at least as long + * as the source range. + * + * If source and target range do not overlap, consider to use arrayCopyForward instead to improve performance. + * + * If there is no need for the source elements to persist, consider to use arrayMoveForward instead to improve + * performance. + */ + +template +inline void arrayCopy(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + if (target_begin <= source_begin) + arrayCopyForward(source_begin, source_end, target_begin); + else + arrayCopyBackward(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayMoveForward() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayMoveForward + * @headerfile + * @brief Moves a range of objects into another range of objects starting from the first element. + * + * @signature void arrayMoveForward(sourceBegin, sourceEnd, target); + * + * @param[in] sourceEnd Iterator behind the last element of the source array. sourceEnd must have the same type + * as sourceBegin. + * @param[in] sourceBegin Iterator to the first element of the source array. + * @param[in] target Iterator to the first element of the target array. The target capacity should be at least as + * long as the source range. + * + * The function possibly clears (but does not destroy) the source elements. If source elements must persist, consider + * to use arrayCopyForward instead. + * + * Be careful if source and target range overlap, because in this case some source elements could be accidently + * overwritten before they are moved. + */ + +template +inline void +_arrayMoveForwardDefault(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + std::move(source_begin, source_end, target_begin); +} + +template +inline void +arrayMoveForward(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + _arrayMoveForwardDefault(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayMoveBackward() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayMoveBackward + * @headerfile + * @brief Moves a range of objects into another range of objects starting from the last element. + * + * @signature void arrayMoveBackward(sourceBegin, sourceEnd, target); + * + * @param[in] sourceEnd Iterator behind the last element of the source array. sourceEnd must have the same type + * as sourceBegin. + * @param[in] sourceBegin Iterator to the first element of the source array. + * @param[in] target Iterator to the first element of the target array.The target capacity should be at least as long + * as the source range. + * + * The function possibly clears (but does not destroy) the source elements. If source elements must persist, consider + * to use arrayCopyBackward instead. + * + * Be careful if source and target range overlap, because in this case some source elements could be accidently + * overwritten before they are moved. + * + * If source and target do not overlap, consider to use the function arrayMoveForward instead that is faster in some + * cases. + * + * The semantic of this function's argument target differ from the arguments of std::copy_backward. + */ + +template +inline void +_arrayMoveBackwardDefault(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + std::move_backward(source_begin, source_end, target_begin + (source_end - source_begin)); +} + +template +inline void +arrayMoveBackward(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + _arrayMoveBackwardDefault(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayMove using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayMove + * @headerfile + * @brief Moves a range of objects into another range of objects. + * + * @signature void arrayMove(sourceBegin, sourceEnd, target); + * + * @param[in] sourceBegin Iterator to the first element of the source range. + * @param[in] sourceEnd Iterator behind the last element of the source range. sourceEnd must have the same type + * as sourceBegin. + * @param[in] target Iterator to the first element of the target range. The target capacity should be at least as + * long as the source range. + * + * The function possibly clears (but does not destroy) the source elements. If source elements must persist, consider + * to use arrayCopy instead. + * + * If source and target range do not overlap, consider to use arrayMoveForward instead to improve performance. + * + * Don't confuse this function with the standard move function that resembles arrayCopy. + */ + +template +inline void +arrayMove(TSource1 source_begin, + TSource2 source_end, + TTarget target_begin) +{ + if (target_begin <= source_begin) + arrayMoveForward(source_begin, source_end, target_begin); + else + arrayMoveBackward(source_begin, source_end, target_begin); +} + +// ---------------------------------------------------------------------------- +// Function arrayClearSpace() using iterators +// ---------------------------------------------------------------------------- + +/*! + * @fn arrayClearSpace + * @headerfile + * @brief Destroys the begin of an array and keeps the rest. + * + * @signature void arrayClearSpace(arrBegin, arrLength, keepFrom, moveTo); + * + * @param[in] arrBegin Pointer to the first element of the array. + * @param[in] keepFrom Offset of the first object that will be kept. + * @param[in] arrLength Length of the array. + * @param[in] moveTo Offset the first kept object will get at the end of the function. + * + * The objects arr[keep_from] to arr[arr_length-1] are moved to the area beginning at positions + * move_to. All objects in arr[0] to arr[keep_from-1] are destroyed. After this function, the + * first move_to positions of the array are free and dont contain objects. + * + * The array must have at least enough space to store arr_length + move_to - keep_from objects. + * + * The objects from arr[0] to arr[array_length-1] have to be initialized/constructed, arrays beyond + * arr[array_length-1] are assumed not to be constructed. If this assumption is violated, memory might leak. + */ + +// TODO(holtgrew): The feature that the range [0, array_begin) is deleted is used nowhere. Can this be removed to simplify behaviour? + +template +void _arrayClearSpaceDefault(TIterator array_begin, + size_t array_length, + size_t keep_from, + size_t move_to) +{ + if (keep_from == array_length) { + // In the simplest case, we only destruct elements. + arrayDestruct(array_begin, array_begin + array_length); + return; + } + + // Otherwise, we will perform the destruction & movement. + SEQAN_ASSERT_LT(keep_from, array_length); + if (keep_from == move_to) { + // Case 1: No movement, just destroy elements. + arrayDestruct(array_begin, array_begin + move_to); + return; + } else if (keep_from < move_to) { + // Case 2: Move to the right. + if (array_length > move_to) { + // Case 2a: Moving right of array_length, i.e. we can move a part + // of the objects and have to move-construct the rest. + size_t middle = array_length - (move_to - keep_from); + arrayConstructMove(array_begin + middle, array_begin + array_length, array_begin + array_length); + arrayMove(array_begin + keep_from, array_begin + middle, array_begin + move_to); + arrayDestruct(array_begin, array_begin + move_to); + } else { + // Case 2b: We have to move-construct all target objects. + arrayConstructMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); + arrayDestruct(array_begin, array_begin + array_length); + } + } else { + // Case 3: Move to the left. + arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); + arrayDestruct(array_begin, array_begin + move_to); + arrayDestruct(array_begin + array_length - (keep_from - move_to), array_begin + array_length); + } +} + +template +void arrayClearSpace(TIterator array_begin, + size_t array_length, + size_t keep_from, + size_t move_to) +{ + _arrayClearSpaceDefault(array_begin, array_length, keep_from, move_to); +} + +// ---------------------------------------------------------------------------- +// Function arrayConstruct() using pointers +// ---------------------------------------------------------------------------- + +template +inline void +_arrayConstructPointer(TIterator, + TIterator, + True) +{ + //nothing to do +} + +template +inline void +_arrayConstructPointer(TIterator begin_, + TIterator end_, + False) +{ + _arrayConstructDefault(begin_, end_); +} + +template +inline void +arrayConstruct(TValue * begin_, + TValue * end_) +{ + _arrayConstructPointer(begin_, end_, typename IsSimple::Type() ); +} + +template +inline void +_arrayConstructPointer(TValue * begin_, + TValue * end_, + TParam const & param_, + True) +{ + arrayFill(begin_, end_, static_cast(param_)); +} + +template +inline void +_arrayConstructPointer(TValue * begin_, + TValue * end_, + TParam const & param_, + False) +{ + _arrayConstructDefault(begin_, end_, param_); +} + +template +inline void +arrayConstruct(TValue * begin_, + TValue * end_, + TParam const & param_) +{ + _arrayConstructPointer(begin_, end_, param_, typename IsSimple::Type()); +} + +// ---------------------------------------------------------------------------- +// Function arrayConstructCopy() using pointers +// ---------------------------------------------------------------------------- + +template +inline void +_arrayConstructCopyPointer(TValueSource * source_begin, + TValueSource * source_end, + TValueTarget * target_begin, + True) +{ + arrayCopyForward(source_begin, source_end, target_begin); +} + +template +inline void +_arrayConstructCopyPointer(TValueSource * source_begin, + TValueSource * source_end, + TValueTarget const* target_begin, + True) +{ + arrayCopyForward(source_begin, source_end, const_cast(target_begin)); +} + +template +inline void +_arrayConstructCopyPointer(TValueSource * source_begin, + TValueSource * source_end, + TValueTarget * target_begin, + False) +{ + _arrayConstructCopyDefault(source_begin, source_end, target_begin); +} +template +inline void +arrayConstructCopy(TValueSource * source_begin, + TValueSource * source_end, + TValueTarget * target_begin) +{ + _arrayConstructCopyPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); +} + +// ---------------------------------------------------------------------------- +// Function arrayConstructMove() using pointers +// ---------------------------------------------------------------------------- + +template +inline void +_arrayConstructMovePointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + True) +{ + arrayMoveForward(source_begin, source_end, target_begin); +} + +template +inline void +_arrayConstructMovePointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + False) +{ + _arrayConstructMoveDefault(source_begin, source_end, target_begin); +} + +template +inline void +arrayConstructMove(TValue * source_begin, + TValue * source_end, + TValue * target_begin) +{ + _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); +} + +// ---------------------------------------------------------------------------- +// Function arrayDestruct() using pointers +// ---------------------------------------------------------------------------- + +template +inline void +_arrayDestructPointer(TValue * /*begin_*/, + TValue * /*end_*/, + True) +{ + //do nothing +} + +template +inline void +_arrayDestructPointer(TValue * begin_, + TValue * end_, + False) +{ + _arrayDestructDefault(begin_, end_); +} + +template +inline void +arrayDestruct(TValue * begin_, + TValue * end_) +{ + _arrayDestructPointer(begin_, end_, typename IsSimple::Type() ); +} + +// ---------------------------------------------------------------------------- +// Function arrayFill() using pointers +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Missing? + +//no specializiation for pointer to simple + +// ---------------------------------------------------------------------------- +// Function arrayCopyBackward() using pointers +// ---------------------------------------------------------------------------- + +template +inline void +_arrayCopyForwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + True) +{ + std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); +} + +template +inline void +_arrayCopyForwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + False) +{ + _arrayCopyForwardDefault(source_begin, source_end, target_begin); +} + +template +inline void +arrayCopyForward(TValue * source_begin, + TValue * source_end, + TValue * target_begin) +{ + _arrayCopyForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); +} + +template +inline void +_arrayCopyBackwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + True) +{ + std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); +} + +template +inline void +_arrayCopyBackwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + False) +{ + _arrayCopyBackwardDefault(source_begin, source_end, target_begin); +} + +template +inline void +arrayCopyBackward(TValue * source_begin, + TValue * source_end, + TValue * target_begin) +{ + _arrayCopyBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); +} + +// ---------------------------------------------------------------------------- +// Function arrayMoveBackward() using pointers +// ---------------------------------------------------------------------------- + +template +inline void +_arrayMoveForwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + True) +{ + std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); +} + +template +inline void +_arrayMoveForwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + False) +{ + _arrayMoveForwardDefault(source_begin, source_end, target_begin); +} + +template +inline void +arrayMoveForward(TValue * source_begin, + TValue * source_end, + TValue * target_begin) +{ + _arrayMoveForwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); +} + +template +inline void +_arrayMoveBackwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + True) +{ + std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); +} +template +inline void +_arrayMoveBackwardPointer(TValue * source_begin, + TValue * source_end, + TValue * target_begin, + False) +{ + _arrayMoveBackwardDefault(source_begin, source_end, target_begin); +} + +template +inline void +arrayMoveBackward(TValue * source_begin, + TValue * source_end, + TValue * target_begin) +{ + _arrayMoveBackwardPointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); +} + +// ---------------------------------------------------------------------------- +// Function arrayClearSpace() using pointers +// ---------------------------------------------------------------------------- + +// clearSpace() on simple type using pointers. +template +inline void +_arrayClearSpacePointer(TValue * array_begin, + size_t array_length, + size_t keep_from, + size_t move_to, + True const & /*isSimple*/) +{ + if (keep_from == move_to) return; + // TODO(holtgrew): arrayCopy is more appropriate here since we are dealing with the IsSimple case. + arrayMove(array_begin + keep_from, array_begin + array_length, array_begin + move_to); +} + +// clearSpace() on non-simple type using pointers. +template +inline void +_arrayClearSpacePointer(TValue * array_begin, + size_t array_length, + size_t keep_from, + size_t move_to, + False const & /*isSimple*/) +{ + _arrayClearSpaceDefault(array_begin, array_length, keep_from, move_to); +} + +template +void arrayClearSpace(TValue * array_begin, + size_t array_length, + size_t keep_from, + size_t move_to) +{ + _arrayClearSpacePointer(array_begin, array_length, keep_from, move_to, typename IsSimple::Type()); +} + + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ARRAY_CONSTRUCT_DESTRUCT_H_ diff --git a/seqan/basic/basic_aggregate.h b/seqan/basic/basic_aggregate.h new file mode 100644 index 0000000..e0998f7 --- /dev/null +++ b/seqan/basic/basic_aggregate.h @@ -0,0 +1,62 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for basic/aggregate submodule. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_ + +// -------------------------------------------------------------------------- +// Prerequisites +// -------------------------------------------------------------------------- + +#include +#include +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +#include +#include +#include +#include +#include +#include +#include +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_AGGREGATE_H_ diff --git a/seqan/basic/basic_allocator.h b/seqan/basic/basic_allocator.h new file mode 100644 index 0000000..1a3f609 --- /dev/null +++ b/seqan/basic/basic_allocator.h @@ -0,0 +1,64 @@ +// ========================================================================== +// basic_allocator.h +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for basic/allocator submodule. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// The allocator interface definitions. +#include + +// The allocator specializations. +#include +#include +#include +#include + +// Adaption from SeqAn allocator to STL allocator. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALLOCATOR_H_ diff --git a/seqan/basic/basic_alphabet.h b/seqan/basic/basic_alphabet.h new file mode 100644 index 0000000..91da52a --- /dev/null +++ b/seqan/basic/basic_alphabet.h @@ -0,0 +1,98 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for the basic/alphabet sub module. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// The first, more generic part of this sub module contains concepts, and the +// necessary metafunction and function prototypes as well as some forward and +// default implementations. + +// The alphabet concepts. +#include + +// Alphabet math functions / metafunctions forwards and default +// implementations. +#include + +// Adaptions for builtin C++ types to the alphabet concepts. +// TODO(holtgrew): Move into second part? +#include + +// Alphabets from Bioinformatics application - gapped unknown values. +#include + +// Alphabet with qualities metafunction and function forwards and default +// implementations +#include + +// Forward declarations and default implementations for storage related +// aspects of alphabets. +#include + +// The second part contains basic alphabets, namely the SimpleType class with +// the specialization for the biological data types, such as Dna, Rna, and +// Amino Acid. Furthermore, it contains a character storing profile entries. + +// The SimpleType class. +#include + +// Conversion tables for the biological SimpleType specializations. +#include + +// Conversion functions for the biological SimpleType specializations. +#include + +// The actual biological SimpleType specializations. +#include + +// The profile character implementation. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ALPHABET_H_ diff --git a/seqan/basic/basic_concept.h b/seqan/basic/basic_concept.h new file mode 100644 index 0000000..5fb0376 --- /dev/null +++ b/seqan/basic/basic_concept.h @@ -0,0 +1,67 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for sub module basic_concept. +// +// This sub module contains the SeqAn Concept Checking library (ported from +// Boost Concept Checking Library) and fundamental concepts (based both on +// Boost concepts and ConceptC++ concepts). +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_ + +// -------------------------------------------------------------------------- +// Prerequisites +// -------------------------------------------------------------------------- + +#include +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// Minimal subset of the boost preprocessor library, required for concept +// checknig library port. +#include + +// SeqAn Concept Checking Library (ported from Boost). +#include + +// Fundamental concepts such as Assignable. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONCEPT_H_ diff --git a/seqan/basic/basic_container.h b/seqan/basic/basic_container.h new file mode 100644 index 0000000..d8f8bf0 --- /dev/null +++ b/seqan/basic/basic_container.h @@ -0,0 +1,59 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for the basic_container submodule. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// PropertyMap concept. +#include + +// Container concept. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_CONTAINER_H_ diff --git a/seqan/basic/basic_debug.h b/seqan/basic/basic_debug.h new file mode 100644 index 0000000..3b0aefe --- /dev/null +++ b/seqan/basic/basic_debug.h @@ -0,0 +1,60 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// The submodule basic/debug contains supporting codes for debugging, the +// assert macros double for test checks. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_ + +// -------------------------------------------------------------------------- +// Prerequisites +// -------------------------------------------------------------------------- + +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// The debug system with assertions. +#include + +// Test and debug helpers. +#include + +// Code for profiling. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_DEBUG_H_ diff --git a/seqan/basic/basic_device.h b/seqan/basic/basic_device.h new file mode 100644 index 0000000..c20f412 --- /dev/null +++ b/seqan/basic/basic_device.h @@ -0,0 +1,152 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2013 NVIDIA Corporation +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of NVIDIA Corporation nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Enrico Siragusa +// ========================================================================== + +#ifndef SEQAN_BASIC_DEVICE_H +#define SEQAN_BASIC_DEVICE_H + +namespace seqan { + +// ============================================================================ +// Tags +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Execution space tags +// ---------------------------------------------------------------------------- + +struct ExecHost_; +struct ExecDevice_; + +typedef Tag ExecHost; +typedef Tag ExecDevice; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Device +// ---------------------------------------------------------------------------- + +/*! + * @mfn Device + * @headerfile + * @brief Converts a given type into one that lives on a device. + * + * @signature Device::Type; + * @tparam TObject The type to be converted into a device type. + * @return Type The resulting device type. + * + * This metafunction is used to convert host containers into device containers. + * + * @see View + */ + +template +struct Device +{ + typedef TObject Type; +}; + +template +struct Device +{ + typedef typename Device::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IsDevice +// ---------------------------------------------------------------------------- + +/*! + * @mfn IsDevice + * @headerfile + * @brief Tests if a given type is a device type. + * + * @signature IsDevice::Type; + * @tparam TObject The type to be tested for being a device type. + * @return Type @link LogicalValuesTags#True @endlink or @link LogicalValuesTags#False @endlink. + * + * @see Device + */ + +template +struct IsDevice : public False {}; + +template +struct IsDevice : public IsDevice {}; + +// ---------------------------------------------------------------------------- +// Metafunction IfDevice +// ---------------------------------------------------------------------------- + +template +struct IfDevice +{ + typedef typename If, T1, T2>::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction ExecSpace +// ---------------------------------------------------------------------------- + +template +struct ExecSpace +{ + typedef typename If, ExecDevice, ExecHost>::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction ExecSpec +// ---------------------------------------------------------------------------- + +template +struct ExecSpec +{ + typedef typename IfDevice, TSpec>::Type Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction CtaSize +// ---------------------------------------------------------------------------- + +template +struct CtaSize +{ + static const unsigned VALUE = 256; +}; + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_DEVICE_H diff --git a/seqan/basic/basic_exception.h b/seqan/basic/basic_exception.h new file mode 100644 index 0000000..8a5a95a --- /dev/null +++ b/seqan/basic/basic_exception.h @@ -0,0 +1,378 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Enrico Siragusa +// ========================================================================== +// Definition of basic exceptions. +// ========================================================================== + +#ifndef SEQAN_BASIC_BASIC_EXCEPTION_H_ +#define SEQAN_BASIC_BASIC_EXCEPTION_H_ + +// ============================================================================ +// Prerequisites +// ============================================================================ + +#include +#include +#include + +#if !defined(STDLIB_VS) +#include +#endif + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +struct Tag; + +//struct Nothing_; +//typedef Tag Nothing; + +// ============================================================================ +// Macros +// ============================================================================ + +/*! + * @defgroup ExceptionHandling SeqAn Exception Handling + * @brief Macros supporting exception handling on various platforms. + */ + +/*! + * @macro ExceptionHandling#SEQAN_EXCEPTIONS + * @headerfile + * @brief Determines whether exceptions are enabled or not. + * + * @signature #define SEQAN_EXCEPTIONS + * + * @see ExceptionHandling#SEQAN_TRY + * @see ExceptionHandling#SEQAN_CATCH + * @see ExceptionHandling#SEQAN_THROW + * @see Exception + */ + +#define SEQAN_EXCEPTIONS __EXCEPTIONS + +/*! + * @macro ExceptionHandling#SEQAN_TRY + * @headerfile + * @brief Replaces the C++ try keyword. + * + * @signature SEQAN_TRY {} SEQAN_CATCH() {} + * + * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the code inside the try block is always executed. + * + * @see ExceptionHandling#SEQAN_CATCH + * @see ExceptionHandling#SEQAN_THROW + * @see Exception + * + * @section Examples + * + * @code{.cpp} + * + * SEQAN_TRY + * { + * SEQAN_THROW(Exception) + * } + * SEQAN_CATCH(Exception const & e) + * { + * std::cerr << e.what() << std::endl; + * } + * + * @endcode + */ + +/*! + * @macro ExceptionHandling#SEQAN_CATCH + * @headerfile + * @brief Replaces the C++ catch keyword. + * + * @signature SEQAN_TRY {} SEQAN_CATCH() {} + * + * When exceptions are disabled, i.e. SEQAN_EXCEPTIONS is set to false, the code inside the catch block is never executed. + * + * @see ExceptionHandling#SEQAN_TRY + * @see ExceptionHandling#SEQAN_THROW + * @see Exception + * + * @section Examples + * + * See @link ExceptionHandling#SEQAN_TRY @endlink for a full example. + */ + +/*! + * @macro ExceptionHandling#SEQAN_THROW + * @headerfile + * @brief Replaces the C++ throw keyword. + * + * @signature SEQAN_THROW(Exception); + * + * When exceptions are disabled, i.e. AssertMacros#SEQAN_EXCEPTIONS is set to false, the macro turns into SEQAN_FAIL. + * + * @see ExceptionHandling#SEQAN_TRY + * @see ExceptionHandling#SEQAN_CATCH + * @see AssertMacros#SEQAN_FAIL + * @see Exception + * + * @section Examples + * + * See @link ExceptionHandling#SEQAN_TRY @endlink for a full example. + */ + +#ifdef SEQAN_EXCEPTIONS + +#define SEQAN_TRY try +#define SEQAN_CATCH(E) catch(E) +#define SEQAN_THROW(E) throw E +#define SEQAN_RETHROW throw + +#else + +#define SEQAN_TRY if (true) +#define SEQAN_CATCH(E) if (false) +//#define SEQAN_CATCH(E) for (E ; false; ) +#define SEQAN_THROW(E) SEQAN_FAIL(#E) +#define SEQAN_RETHROW + +#endif // #ifdef SEQAN_EXCEPTIONS + +// ============================================================================ +// Exceptions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Basic Exception +// ---------------------------------------------------------------------------- + +/*! + * @class Exception + * @headerfile + * @brief Generic SeqAn exception. + * @signature typedef std::exception Exception; + * + * @fn Exception::Exception + * @brief Constructor. + * + * @signature Exception::Exception(msg); + * @param[in] msg The message as a std::string. + */ + +typedef std::exception Exception; + +// ---------------------------------------------------------------------------- +// Exception BadAlloc +// ---------------------------------------------------------------------------- + +/*! + * @class BadAlloc + * @headerfile + * @brief Generic SeqAn exception. + * @signature typedef std::bad_alloc BadAlloc; + * + * @fn BadAlloc::BadAlloc + * @brief Constructor. + * + * @signature BadAlloc::BadAlloc(msg); + * @param[in] msg The message as a std::string. + */ + +typedef std::bad_alloc BadAlloc; + +// ---------------------------------------------------------------------------- +// Exception BadCast +// ---------------------------------------------------------------------------- + +/*! + * @class BadCast + * @headerfile + * @brief Generic SeqAn exception. + * @signature typedef std::bad_cast BadCast; + * + * @fn BadCast::BadCast + * @brief Constructor. + * + * @signature BadCast::BadCast(msg); + * @param[in] msg The message as a std::string. + */ + +typedef std::bad_cast BadCast; + +// ---------------------------------------------------------------------------- +// Exceptions Bad* +// ---------------------------------------------------------------------------- +// NOTE(esiragusa): These exceptions can be introduced as long as we need them. + +//typedef std::bad_exception BadException; +//typedef std::bad_typeid BadTypeId; +//typedef std::bad_function_call BadFunctionCall; +//typedef std::bad_weak_ptr BadWeakPtr; + +// ---------------------------------------------------------------------------- +// Exception RuntimeError +// ---------------------------------------------------------------------------- + +/*! + * @class RuntimeError + * @headerfile + * @brief Runtime error exception. + * @signature typedef std::runtime_error RuntimeError; + * + * + * @fn RuntimeError::RuntimeError + * @brief Constructor. + * + * @signature RuntimeError::RuntimeError(msg); + * @param[in] msg The message as a std::string. + */ + +typedef std::runtime_error RuntimeError; + +// ---------------------------------------------------------------------------- +// Exception LogicError +// ---------------------------------------------------------------------------- +// NOTE(esiragusa): Always prefer SEQAN_ASSERT to logic error exceptions. + +//typedef std::logic_error LogicError; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction ExceptionMessage +// ---------------------------------------------------------------------------- + +template +struct ExceptionMessage +{ + static const std::string VALUE; +}; + +template +const std::string ExceptionMessage::VALUE; + +// ---------------------------------------------------------------------------- +// Function getExceptionMessage() +// ---------------------------------------------------------------------------- + +template +inline std::string const & +getExceptionMessage(TFunctor const &, TContext const &) +{ + return ExceptionMessage::VALUE; +} + +// ============================================================================ +// Functors +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Functor AssertFunctor +// ---------------------------------------------------------------------------- + +template +struct AssertFunctor +{ + TFunctor func; + + AssertFunctor() {} + + AssertFunctor(TFunctor & func) : + func(func) + {} + + std::string escapeChar(unsigned char val) + { + if (val <= '\r') + { + static const char * const escapeCodes[14] = { + "\\0", "\\1", "\\2", "\\3", "\\4", "\\5", "\\6", "\\a", + "\\b", "\\t", "\\n", "\\v", "\\f", "\\r" }; + return std::string(escapeCodes[val]); + } + else if (' ' <= val && val < 128u) + return std::string() + (char)val; + else + { + char buffer[6]; // 5 + 1, e.g. "\0xff" + trailing zero + snprintf(buffer, 6, "\\%#2x", (unsigned)val); + return std::string(buffer); + } + } + + template + bool operator() (TValue const & val) + { + if (SEQAN_UNLIKELY(!func(val))) + throw TException(std::string("Unexpected character '") + escapeChar(val) + "' found. " + + getExceptionMessage(func, TContext())); + return RETURN_VALUE; + } +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function globalExceptionHandler() +// ---------------------------------------------------------------------------- + +#if defined(SEQAN_EXCEPTIONS) && defined(SEQAN_GLOBAL_EXCEPTION_HANDLER) +// Declare global exception handler. +inline static void globalExceptionHandler() +{ + SEQAN_TRY + { + SEQAN_RETHROW; + } + SEQAN_CATCH(Exception & e) + { + SEQAN_FAIL("Uncaught exception of type %s: %s", toCString(Demangler(e)), e.what()); + } + SEQAN_CATCH(...) + { + SEQAN_FAIL("Uncaught exception of unknown type.\n"); + } +} + +// Install global exception handler. +static const std::terminate_handler SEQAN_UNUSED _globalExceptionHandler = std::set_terminate(globalExceptionHandler); + +#endif // #if defined(SEQAN_EXCEPTIONS) && defined(SEQAN_GLOBAL_EXCEPTION_HANDLER) + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_BASIC_EXCEPTION_H_ diff --git a/seqan/basic/basic_functors.h b/seqan/basic/basic_functors.h new file mode 100644 index 0000000..6633709 --- /dev/null +++ b/seqan/basic/basic_functors.h @@ -0,0 +1,214 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// Author: Enrico Siragusa +// ========================================================================== + +#ifndef SEQAN_BASIC_FUNCTORS_H_ +#define SEQAN_BASIC_FUNCTORS_H_ + +namespace seqan { + +// ============================================================================ +// Functors +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Functor OrFunctor +// ---------------------------------------------------------------------------- + +template +struct OrFunctor +{ + TFunctor1 func1; + TFunctor2 func2; + + OrFunctor() + {} + + OrFunctor(TFunctor1 const &func1, TFunctor2 const &func2): + func1(func1), func2(func2) + {} + + template + bool operator() (TValue const & val) + { + return func1(val) || func2(val); + } + + template + bool operator() (TValue const & val) const + { + return func1(val) || func2(val); + } +}; + +// ---------------------------------------------------------------------------- +// Functor AndFunctor +// ---------------------------------------------------------------------------- + +template +struct AndFunctor +{ + TFunctor1 func1; + TFunctor2 func2; + + AndFunctor() + {} + + AndFunctor(TFunctor1 const &func1, TFunctor2 const &func2): + func1(func1), func2(func2) + {} + + template + bool operator() (TValue const & val) + { + return func1(val) && func2(val); + } + + template + bool operator() (TValue const & val) const + { + return func1(val) && func2(val); + } +}; + +// ---------------------------------------------------------------------------- +// Functor NotFunctor +// ---------------------------------------------------------------------------- + +template +struct NotFunctor +{ + TFunctor func; + + NotFunctor() + {} + + NotFunctor(TFunctor const &func): + func(func) + {} + + template + bool operator() (TValue const & val) + { + return !func(val); + } + + + template + bool operator() (TValue const & val) const + { + return !func(val); + } +}; + +// ---------------------------------------------------------------------------- +// Functor CountDownFunctor +// ---------------------------------------------------------------------------- + +template +struct CountDownFunctor +{ + uint64_t remaining; + TFunctor func; + + CountDownFunctor(uint64_t remaining = REMAINING): + remaining(remaining) + {} + + CountDownFunctor(uint64_t remaining, TFunctor const &func): + remaining(remaining), + func(func) + {} + + template + bool operator() (TValue const & val) + { + if (remaining == 0) + return true; + if (func(val)) + --remaining; + return false; + } + + operator bool() + { + return remaining == 0; + } +}; + +// ---------------------------------------------------------------------------- +// Functor CountFunctor +// ---------------------------------------------------------------------------- + +template +struct CountFunctor +{ + uint64_t count; + TFunctor func; + + CountFunctor() : count(0) + {} + + CountFunctor(TFunctor const & func) : count(0), func(func) + {} + + template + bool operator() (TValue const & val) + { + if (func(val)) + ++count; + return false; + } + + operator uint64_t() const + { + return count; + } +}; + +template +inline void clear(CountFunctor &func) +{ + func.count = 0; +} + +template +inline uint64_t & value(CountFunctor &func) +{ + return func.count; +} + +} // namespace seqan + +#endif // SEQAN_BASIC_FUNCTORS_H_ diff --git a/seqan/basic/basic_fundamental.h b/seqan/basic/basic_fundamental.h new file mode 100644 index 0000000..b60abdc --- /dev/null +++ b/seqan/basic/basic_fundamental.h @@ -0,0 +1,88 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade hader for the submodule basic_fundamental. +// +// This module contains fundamental code such as forward declarations and +// prototypes for common metafunctions like Value<>, functions assign() etc. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_FUNDAMENTAL_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_FUNDAMENTAL_H_ + +// -------------------------------------------------------------------------- +// Prerequisites +// -------------------------------------------------------------------------- + +#include + +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// Macros for deprecating code. +#include + +// Pseudo header with documentation for builtin functions. +#include + +// Common metafunctions such as Value<>. +#include + +// Basic tag-related code. +#include + +// Functions and metafunctions to use contiguous chunks of memory +#include + +// Definition of assign(), set(), move(). +#include + +// Code supporting comparison. +#include + +// Conversion support. +#include + +// TODO(holtgrew): This is not fundamental. Should go into sequence module. +// Construct/destruct functions for arrays. +#include + +// TODO(holtgrew): This is not really fundamental, either. Should go into its own sub module. +// Hosted type. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_HOSTED_TYPE_INTERFACE_H_ diff --git a/seqan/basic/basic_iterator.h b/seqan/basic/basic_iterator.h new file mode 100644 index 0000000..82a1ecc --- /dev/null +++ b/seqan/basic/basic_iterator.h @@ -0,0 +1,92 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for basic_iterator submodule. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include +#include +#include + +#include // TODO(holtgrew): Temporary dependency + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// Iterator interface definition. +#include + +// Iter base class. +#include + +// Iterator concept. +#include + +// PropertyMap concept. +#include + +// Container concept. +#include + +// Counting iterator. +#include + +// Positional iterator. +#include + +// Makes a container out of begin/end iterators +#include + +// Iterator for adapting iterators to Rooted Iterators. +#include + +// Adaption between STL iterators and SeqAn iterators. +#include + +// TODO(holtgrew): Does proxy really belong here? +#include +#include + +// Zip iterator. Requires C++11 +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_ITERATOR_H_ diff --git a/seqan/basic/basic_math.h b/seqan/basic/basic_math.h new file mode 100644 index 0000000..a9473b6 --- /dev/null +++ b/seqan/basic/basic_math.h @@ -0,0 +1,58 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for the basic/math sub module. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include + +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +#include +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_MATH_H_ + diff --git a/seqan/basic/basic_metaprogramming.h b/seqan/basic/basic_metaprogramming.h new file mode 100644 index 0000000..d620dcf --- /dev/null +++ b/seqan/basic/basic_metaprogramming.h @@ -0,0 +1,64 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for the basic/metaprogramming submodule. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_METAPROGRAMMING_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_METAPROGRAMMING_H_ + +#include + +#include + +#include + +// Metaprogramming logical operations. +#include + +// Metaprogramming control structures. +#include + +// Metaprogramming mathematics. +#include + +// Metaprogramming for querying and modifying types. +#include + +// Metaprogramming for type algebra. +#include + +// Metaprogramming for conditional enabling/disabling of code. +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_METAPROGRAMMING_H_ diff --git a/seqan/basic/basic_parallelism.h b/seqan/basic/basic_parallelism.h new file mode 100644 index 0000000..b96c43a --- /dev/null +++ b/seqan/basic/basic_parallelism.h @@ -0,0 +1,76 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// This sub module contains simple, generic support code for parallelism in +// SeqAn. +// +// It mainly defines the macro SEQAN_ENABLE_PARALLELISM. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_ + +/*! + * @macro SEQAN_ENABLE_PARALLELISM + * @headerfile + * @brief Indicates whether parallelism is enabled with value 0/1. + * + * @signature SEQAN_ENABLE_PARALLELISM + * + * By default, set to 1 if _OPENMP is defined and set to 0 otherwise. + * + * @section Examples + * + * If you want to change tihs value then you have to define this value before include any SeqAn header. + * + * @code{.cpp} + * #define SEQAN_ENABLE_PARALLELISM 0 // ALWAYS switch off parallelism! + * + * #include + * + * int main(int argc, char ** argv) + * { + * return 0; + * } + * @endcode + */ + +#if !defined(SEQAN_ENABLE_PARALLELISM) +#if defined(_OPENMP) +#define SEQAN_ENABLE_PARALLELISM 1 +#else // defined(_OPENMP) +#define SEQAN_ENABLE_PARALLELISM 0 +#endif // defined(_OPENMP) +#endif // !defined(SEQAN_ENABLE_PARALLELISM) + +#endif // SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PARALLELISM_H_ diff --git a/seqan/basic/basic_proxy.h b/seqan/basic/basic_proxy.h new file mode 100644 index 0000000..fe6b711 --- /dev/null +++ b/seqan/basic/basic_proxy.h @@ -0,0 +1,59 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Proxy definition. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include +#include + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +// Proxy base class. +#include + +// Implementation of a proxy through an iterator (the latter only needs +// assignValue() and setValue()). +#include + +#endif // SEQAN_INCLUDE_SEQAN_BASIC_BASIC_PROXY_H_ diff --git a/seqan/basic/basic_simd_vector.h b/seqan/basic/basic_simd_vector.h new file mode 100644 index 0000000..40f6e56 --- /dev/null +++ b/seqan/basic/basic_simd_vector.h @@ -0,0 +1,1671 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// René Rahn +// Stefan Budach +// ========================================================================== +// generic SIMD interface for SSE3 / AVX2 +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_SIMD_VECTOR_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_SIMD_VECTOR_H_ + +#include +#include + +// Currently only support the following compilers +#if defined(COMPILER_GCC) || defined(COMPILER_CLANG) || defined(COMPILER_LINTEL) + // Define global macro to check if simd instructions are enabled. + #define SEQAN_SIMD_ENABLED + + // Define maximal size of vector in byte. + #if defined(__AVX2__) + #define SEQAN_SIZEOF_MAX_VECTOR 32 + #elif defined(__SSE4_1__) && defined(__SSE4_2__) + #define SEQAN_SSE4 + #define SEQAN_SIZEOF_MAX_VECTOR 16 + #else // defined(__AVX2__) + #undef SEQAN_SIMD_ENABLED // Disable simd if instruction set is not supported. + #endif // defined(__AVX2__) +#endif // defined(COMPILER_GCC) || defined(COMPILER_CLANG) || defined(COMPILER_LINTEL) + +#ifdef SEQAN_SIMD_ENABLED // Include header with intrinsics. + #include +#endif // SEQAN_SIMD_ENABLED + +namespace seqan { + +#ifdef COMPILER_LINTEL +#include +#define SEQAN_VECTOR_CAST_(T, v) static_cast::type>(v) +#define SEQAN_VECTOR_CAST_LVALUE_(T, v) static_cast(v) +#else +#define SEQAN_VECTOR_CAST_(T, v) reinterpret_cast(v) +#define SEQAN_VECTOR_CAST_LVALUE_(T, v) reinterpret_cast(v) +#endif + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Useful Macros +// ============================================================================ + +#define SEQAN_DEFINE_SIMD_VECTOR_GETVALUE_(TSimdVector) \ +template \ +inline typename Value::Type \ +getValue(TSimdVector &vector, TPosition pos) \ +{ \ +/* \ + typedef typename Value::Type TValue; \ + TValue val = (SEQAN_VECTOR_CAST_(TValue*, &vector))[pos]; \ + return val; \ +*/ \ + return vector[pos]; \ +} + +#define SEQAN_DEFINE_SIMD_VECTOR_VALUE_(TSimdVector) \ +template \ +inline typename Value::Type \ +value(TSimdVector &vector, TPosition pos) \ +{ \ + return getValue(vector, pos); \ +} + +#define SEQAN_DEFINE_SIMD_VECTOR_ASSIGNVALUE_(TSimdVector) \ +template \ +inline void \ +assignValue(TSimdVector &vector, TPosition pos, TValue2 value) \ +{ \ +/* \ + typedef typename Value::Type TValue; \ + (SEQAN_VECTOR_CAST_(TValue*, &vector))[pos] = value; \ +*/ \ + vector[pos] = value; \ +} + +// define a concept and its models +// they allow us to define generic vector functions +SEQAN_CONCEPT(SimdVectorConcept, (T)) {}; + +// Only include following code if simd instructions are enabled. +#ifdef SEQAN_SIMD_ENABLED + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// a metafunction returning the biggest supported SIMD vector +template +struct SimdVector; + +// internal struct to specialize for vector parameters +// VEC_SIZE = Vector size := sizeof(vec) +// LENGTH = number of elements := VEC_SIZE / sizeof(InnerValue::Type) +template +struct SimdParams_ {}; + +template +struct ScaleParam_ +{}; + +// internal struct to specialize for matrix parameters +template +struct SimdMatrixParams_ {}; + +#define SEQAN_DEFINE_SIMD_VECTOR_(TSimdVector, TValue, SIZEOF_VECTOR) \ + typedef TValue TSimdVector __attribute__ ((__vector_size__(SIZEOF_VECTOR))); \ + template <> struct SimdVector { typedef TSimdVector Type; }; \ + template <> struct Value { typedef TValue Type; }; \ + template <> struct Value: public Value {}; \ + template <> struct LENGTH { enum { VALUE = SIZEOF_VECTOR / sizeof(TValue) }; }; \ + template <> struct LENGTH: public LENGTH {}; \ + SEQAN_DEFINE_SIMD_VECTOR_GETVALUE_(TSimdVector) \ + SEQAN_DEFINE_SIMD_VECTOR_GETVALUE_(TSimdVector const) \ + SEQAN_DEFINE_SIMD_VECTOR_VALUE_(TSimdVector) \ + SEQAN_DEFINE_SIMD_VECTOR_VALUE_(TSimdVector const) \ + SEQAN_DEFINE_SIMD_VECTOR_ASSIGNVALUE_(TSimdVector) \ + template <> \ + SEQAN_CONCEPT_IMPL((TSimdVector), (SimdVectorConcept)); \ + template <> \ + SEQAN_CONCEPT_IMPL((TSimdVector const), (SimdVectorConcept)); + +#ifdef __AVX2__ +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector32Char, char, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector32SChar, signed char, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector32UChar, unsigned char, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16Short, short, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16UShort, unsigned short, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Int, int, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8UInt, unsigned int, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Int64, int64_t, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4UInt64, uint64_t, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Float, float, 32) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Double, double, 32) +#endif // __AVX2__ + +#ifdef SEQAN_SSE4 +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Char, char, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8SChar, signed char, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8UChar, unsigned char, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Short, short, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4UShort, unsigned short, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Int, int, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2UInt, unsigned int, 8) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Float, float, 8) + +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16Char, char, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16SChar, signed char, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector16UChar, unsigned char, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8Short, short, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector8UShort, unsigned short, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Int, int, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4UInt, unsigned int, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Int64, int64_t, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2UInt64, uint64_t, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector4Float, float, 16) +SEQAN_DEFINE_SIMD_VECTOR_(SimdVector2Double, double, 16) +#endif // SEQAN_SSE4 + +// ============================================================================ +// Functions +// ============================================================================ + +// ============================================================================ +// AVX/AVX2 wrappers (256bit vectors) +// ============================================================================ + +#ifdef __AVX2__ + +// -------------------------------------------------------------------------- +// _fillVector (256bit) +// -------------------------------------------------------------------------- + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<32, 32>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set1_epi8(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<32, 16>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set1_epi16(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<32, 8>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set1_epi32(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<32, 4>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set1_epi64x(std::get<0>(x)); } +template + inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<32, 8>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set1_ps(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<32, 4>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set1_pd(std::get<0>(x)); } + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & values, std::index_sequence const &, SimdParams_<32, 32>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set_epi8(std::get(values)...); +} + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & values, std::index_sequence const &, SimdParams_<32, 16>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set_epi16(std::get(values)...); +} +template +inline void _fillVector(TSimdVector &vector, std::tuple const & values, std::index_sequence const &, SimdParams_<32, 8>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set_epi32(std::get(values)...); +} + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & values, std::index_sequence const &, SimdParams_<32, 4>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_set_epi64x(std::get(values)...); +} + +// -------------------------------------------------------------------------- +// _clearVector (256bit) +// -------------------------------------------------------------------------- + +template +inline void _clearVector(TSimdVector &vector, SimdParams_<32, L>) { SEQAN_VECTOR_CAST_LVALUE_(__m256i&, vector) = _mm256_setzero_si256(); } +template +inline void _clearVector(TSimdVector &vector, SimdParams_<32, 8>) { SEQAN_VECTOR_CAST_LVALUE_(__m256&, vector) = _mm256_setzero_ps(); } +template +inline void _clearVector(TSimdVector &vector, SimdParams_<32, 4>) { SEQAN_VECTOR_CAST_LVALUE_(__m256d&, vector) = _mm256_setzero_pd(); } + +// -------------------------------------------------------------------------- +// _createVector (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _createVector(TValue x, SimdParams_<32, 32>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_set1_epi8(x)); } +template +inline TSimdVector _createVector(TValue x, SimdParams_<32, 16>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_set1_epi16(x)); } +template +inline TSimdVector _createVector(TValue x, SimdParams_<32, 8>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_set1_epi32(x)); } +template +inline TSimdVector _createVector(TValue x, SimdParams_< 32, 4>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_set1_epi64x(x)); } +template +inline TSimdVector _createVector(float x, SimdParams_<32, 8>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_set1_ps(x)); } +template +inline TSimdVector _createVector(double x, SimdParams_<32, 4>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_set1_pd(x)); } + +// -------------------------------------------------------------------------- +// _cmpEq (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpeq_epi8(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpeq_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpeq_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpeq_epi64(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +// -------------------------------------------------------------------------- +// _cmpGt (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpgt_epi8(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpgt_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpgt_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_cmpgt_epi64(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseOr (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseOr(TSimdVector &a, TSimdVector &b, SimdParams_<32, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_or_si256(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseAnd (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseAnd(TSimdVector &a, TSimdVector &b, SimdParams_<32, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_and_si256(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _bitwiseAnd(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_and_ps(SEQAN_VECTOR_CAST_(const __m256&, a), + SEQAN_VECTOR_CAST_(const __m256&, b))); +} + +template +inline TSimdVector _bitwiseAnd(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_and_pd(SEQAN_VECTOR_CAST_(const __m256d&, a), + SEQAN_VECTOR_CAST_(const __m256d&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseAndNot (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseAndNot(TSimdVector &a, TSimdVector &b, SimdParams_<32, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_andnot_si256(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseNot (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_cmpeq_epi8(SEQAN_VECTOR_CAST_(const __m256i&, a), _mm256_setzero_si256())); +} + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_cmpeq_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), _mm256_setzero_si256())); +} + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_cmpeq_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), _mm256_setzero_si256())); + +} +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_cmpeq_epi64(SEQAN_VECTOR_CAST_(const __m256i&, a), _mm256_setzero_si256())); +} + +// -------------------------------------------------------------------------- +// _divide (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<32, 32>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_div_epi8(a, _mm256_set1_epi8(b))); } + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<32, 16>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_div_epi16(a, _mm256_set1_epi16(b))); } + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<32, 8>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_div_epi32(a, _mm256_set1_epi32(b))); } + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<32, 4>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_div_epi64(a, _mm256_set1_epi64x(b))); } + +// -------------------------------------------------------------------------- +// _add (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_add_epi8(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_add_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_add_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_add_epi64(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +// -------------------------------------------------------------------------- +// _sub (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_sub_epi8(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_sub_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_sub_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_sub_epi64(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +// -------------------------------------------------------------------------- +// _mult (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &b, SimdParams_<32, 32>) +{ + SEQAN_ASSERT_FAIL("AVX2 intrinsics for multiplying 8 bit values not implemented!"); + return a; +} + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &b, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_mullo_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_mullo_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + SEQAN_ASSERT_FAIL("AVX2 intrinsics for multiplying 64 bit values not implemented!"); + return a; +} + +// -------------------------------------------------------------------------- +// _max (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_max_epi8(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_max_epi16(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_max_epi32(SEQAN_VECTOR_CAST_(const __m256i&, a), + SEQAN_VECTOR_CAST_(const __m256i&, b))); +} + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<32, 4>) +{ + SEQAN_ASSERT_FAIL("AVX2 intrinsics for max on 64 bit values not implemented!"); + return a; +} + +// -------------------------------------------------------------------------- +// _blend (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _blend(TSimdVector const &a, TSimdVector const &b, TSimdVectorMask const &mask, SimdParams_<32, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm256_blendv_epi8(SEQAN_VECTOR_CAST_(const __m256i &, a), + SEQAN_VECTOR_CAST_(const __m256i &, b), + SEQAN_VECTOR_CAST_(const __m256i &, mask))); +} + +// -------------------------------------------------------------------------- +// _storeu (256bit) +// -------------------------------------------------------------------------- + +template +inline void _storeu(T * memAddr, TSimdVector &vec, SimdParams_<32, L>) +{ + _mm256_storeu_si256((__m256i*)memAddr, SEQAN_VECTOR_CAST_(const __m256i&, vec)); +} + +// ---------------------------------------------------------------------------- +// Function _load() 256bit +// ---------------------------------------------------------------------------- + +template +inline TSimdVector _load(T const * memAddr, SimdParams_<32, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_load_si256((__m256i const *) memAddr)); +} + +// -------------------------------------------------------------------------- +// _shuffleVector (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector1 +_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<32, 32>, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector1, _mm256_shuffle_epi8(SEQAN_VECTOR_CAST_(const __m256i &, vector), + SEQAN_VECTOR_CAST_(const __m256i &, indices))); +} +template +inline TSimdVector1 +_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<32, 16>, SimdParams_<16, 16>) +{ + // copy 2nd 64bit word to 3rd, compute 2*idx + __m256i idx = _mm256_slli_epi16(_mm256_permute4x64_epi64(_mm256_castsi128_si256(SEQAN_VECTOR_CAST_(const __m128i &, indices)), 0x50), 1); + + // interleave with 2*idx+1 and call shuffle + return SEQAN_VECTOR_CAST_(TSimdVector1, _mm256_shuffle_epi8(SEQAN_VECTOR_CAST_(const __m256i &, vector), + _mm256_unpacklo_epi8(idx, _mm256_add_epi8(idx, _mm256_set1_epi8(1))))); +} + +// -------------------------------------------------------------------------- +// _shiftRightLogical (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 32>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_srli_epi16(SEQAN_VECTOR_CAST_(const __m256i &, vector), imm) & _mm256_set1_epi8(0xff >> imm)); +} +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_srli_epi16(SEQAN_VECTOR_CAST_(const __m256i &, vector), imm)); +} +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_srli_epi32(SEQAN_VECTOR_CAST_(const __m256i &, vector), imm)); +} +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<32, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_srli_epi64(SEQAN_VECTOR_CAST_(const __m256i &, vector), imm)); +} + +// -------------------------------------------------------------------------- +// _gather (256bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _gather(TValue const * memAddr, + TSimdVector const & idx, + std::integral_constant const & /*scale*/, + SimdParams_<32, 16>) +{ + // 1. Unpack low idx values and interleave with 0 and gather from memAddr. + // 2. Unpack high idx values and interleave with 0, than gather from memAddr. + // 3. Merge 2 8x32 vectors into 1x16 vector by signed saturation. This operation reverts the interleave by the unpack operations above. + return SEQAN_VECTOR_CAST_(TSimdVector, _mm256_packs_epi32(_mm256_i32gather_epi32(static_cast(memAddr), _mm256_unpacklo_epi16(SEQAN_VECTOR_CAST_(__m256i const &, idx), _mm256_set1_epi16(0)), SCALE), + _mm256_i32gather_epi32(static_cast(memAddr), _mm256_unpackhi_epi16(SEQAN_VECTOR_CAST_(__m256i const &, idx), _mm256_set1_epi16(0)), SCALE))); +} + +// -------------------------------------------------------------------------- +// _transposeMatrix (256bit) +// -------------------------------------------------------------------------- + +// emulate missing _mm256_unpacklo_epi128/_mm256_unpackhi_epi128 instructions +inline __m256i _mm256_unpacklo_epi128(__m256i const &a, __m256i const &b) +{ + return _mm256_permute2x128_si256(a, b, 0x20); +// return _mm256_inserti128_si256(a, _mm256_extracti128_si256(b, 0), 1); +} + +inline __m256i _mm256_unpackhi_epi128(__m256i const &a, __m256i const &b) +{ + return _mm256_permute2x128_si256(a, b, 0x31); +// return _mm256_inserti128_si256(b, _mm256_extracti128_si256(a, 1), 0); +} + +template +inline void +_transposeMatrix(TSimdVector matrix[], SimdMatrixParams_<32, 32, 8>) +{ + // we need a look-up table to reverse the lowest 4 bits + // in order to place the permute the transposed rows + static const unsigned char bitRev[] = { 0, 8, 4,12, 2,10, 6,14, 1, 9, 5,13, 3,11, 7,15, + 16,24,20,28,18,26,22,30,17,25,21,29,19,27,23,31}; + + // transpose a 32x32 byte matrix + __m256i tmp1[32]; + for (int i = 0; i < 16; ++i) + { + tmp1[i] = _mm256_unpacklo_epi8(SEQAN_VECTOR_CAST_(const __m256i &, matrix[2*i]), SEQAN_VECTOR_CAST_(const __m256i &, matrix[2*i+1])); + tmp1[i+16] = _mm256_unpackhi_epi8(SEQAN_VECTOR_CAST_(const __m256i &, matrix[2*i]), SEQAN_VECTOR_CAST_(const __m256i &, matrix[2*i+1])); + } + __m256i tmp2[32]; + for (int i = 0; i < 16; ++i) + { + tmp2[i] = _mm256_unpacklo_epi16(tmp1[2*i], tmp1[2*i+1]); + tmp2[i+16] = _mm256_unpackhi_epi16(tmp1[2*i], tmp1[2*i+1]); + } + for (int i = 0; i < 16; ++i) + { + tmp1[i] = _mm256_unpacklo_epi32(tmp2[2*i], tmp2[2*i+1]); + tmp1[i+16] = _mm256_unpackhi_epi32(tmp2[2*i], tmp2[2*i+1]); + } + for (int i = 0; i < 16; ++i) + { + tmp2[i] = _mm256_unpacklo_epi64(tmp1[2*i], tmp1[2*i+1]); + tmp2[i+16] = _mm256_unpackhi_epi64(tmp1[2*i], tmp1[2*i+1]); + } + for (int i = 0; i < 16; ++i) + { + matrix[bitRev[i]] = SEQAN_VECTOR_CAST_(TSimdVector, _mm256_unpacklo_epi128(tmp2[2*i],tmp2[2*i+1])); + matrix[bitRev[i+16]] = SEQAN_VECTOR_CAST_(TSimdVector, _mm256_unpackhi_epi128(tmp2[2*i],tmp2[2*i+1])); + } +} + +// -------------------------------------------------------------------------- +// Function _testAllZeros (256bit) +// -------------------------------------------------------------------------- + +template +SEQAN_FUNC_ENABLE_IF(Is >, int) +inline _testAllZeros(TSimdVector const &vector, TSimdVector const &mask, SimdParams_<32>) +{ + return _mm256_testz_si256(SEQAN_VECTOR_CAST_(const __m256i &, vector), + SEQAN_VECTOR_CAST_(const __m256i &, mask)); +} + +// -------------------------------------------------------------------------- +// Function _testAllOnes (256bit) +// -------------------------------------------------------------------------- + +template +inline int _testAllOnes(TSimdVector const &vector, SimdParams_<32>) +{ + __m256i vec = SEQAN_VECTOR_CAST_(const __m256i &, vector); + return _mm256_testc_si256(vec, _mm256_cmpeq_epi32(vec, vec)); +} + +#endif // #ifdef __AVX2__ + +// ============================================================================ +// SSE3 wrappers (128bit vectors) +// ============================================================================ + +#ifdef SEQAN_SSE4 + +// -------------------------------------------------------------------------- +// _fillVector (128bit) +// -------------------------------------------------------------------------- + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<16, 16>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set1_epi8(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<16, 8>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set1_epi16(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<16, 4>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set1_epi32(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<16, 2>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set1_epi64x(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<16, 4>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set1_ps(std::get<0>(x)); } +template +inline void _fillVector(TSimdVector &vector, std::tuple const & x, std::index_sequence<0> const &, SimdParams_<16, 2>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set1_pd(std::get<0>(x)); } + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & args, std::index_sequence const &, SimdParams_<16, 16>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set_epi8(std::get(args)...); +} + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & args, std::index_sequence const &, SimdParams_<16, 8>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set_epi16(std::get(args)...); +} + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & args, std::index_sequence const &, SimdParams_<16, 4>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set_epi32(std::get(args)...); +} + +template +inline void _fillVector(TSimdVector &vector, std::tuple const & args, std::index_sequence const &, SimdParams_<16, 2>) +{ + SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_set_epi64x(std::get(args)...); +} + +// -------------------------------------------------------------------------- +// _clearVector (128bit) +// -------------------------------------------------------------------------- + +template +inline void _clearVector(TSimdVector &vector, SimdParams_<16, L>) { SEQAN_VECTOR_CAST_LVALUE_(__m128i&, vector) = _mm_setzero_si128(); } +template +inline void _clearVector(TSimdVector &vector, SimdParams_<16, 4>) { SEQAN_VECTOR_CAST_LVALUE_(__m128&, vector) = _mm_setzero_ps(); } +template +inline void _clearVector(TSimdVector &vector, SimdParams_<16, 2>) { SEQAN_VECTOR_CAST_LVALUE_(__m128d&, vector) = _mm_setzero_pd(); } + +// -------------------------------------------------------------------------- +// _createVector (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _createVector(TValue x, SimdParams_<16, 16>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_set1_epi8(x)); } +template +inline TSimdVector _createVector(TValue x, SimdParams_<16, 8>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_set1_epi16(x)); } +template +inline TSimdVector _createVector(TValue x, SimdParams_<16, 4>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_set1_epi32(x)); } +template +inline TSimdVector _createVector(TValue x, SimdParams_<16, 2>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_set1_epi64x(x)); } +template +inline TSimdVector _createVector(float x, SimdParams_<16, 4>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_set1_ps(x)); } +template +inline TSimdVector _createVector(double x, SimdParams_<16, 2>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_set1_pd(x)); } + +// -------------------------------------------------------------------------- +// cmpEq (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _cmpEq(TSimdVector &a, TSimdVector &b, SimdParams_<16, 2>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi64(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _cmpGt (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpgt_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpgt_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpgt_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _cmpGt(TSimdVector &a, TSimdVector &b, SimdParams_<16, 2>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpgt_epi64(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseOr (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseOr(TSimdVector &a, TSimdVector &b, SimdParams_<16, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_or_si128(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseAnd (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseAnd(TSimdVector &a, TSimdVector &b, SimdParams_<16, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_and_si128(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseAndNot (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseAndNot(TSimdVector &a, TSimdVector &b, SimdParams_<16, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_andnot_si128(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _bitwiseNot (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + _mm_setzero_si128())); +} + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + _mm_setzero_si128())); +} + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + _mm_setzero_si128())); +} + +template +inline TSimdVector _bitwiseNot(TSimdVector &a, SimdParams_<16, 2>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_cmpeq_epi64(SEQAN_VECTOR_CAST_(const __m128i&, a), + _mm_setzero_si128())); +} + +// -------------------------------------------------------------------------- +// _divide (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<16, 16>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_div_epi8(a, _mm_set1_epi8(b))); } + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<16, 8>){ return SEQAN_VECTOR_CAST_(TSimdVector, _mm_div_epi16(a, _mm_set1_epi16(b))); } + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<16, 4>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_div_epi32(a, _mm_set1_epi32(b))); } + +template +inline TSimdVector _divide(TSimdVector &a, int b, SimdParams_<16, 2>) { return SEQAN_VECTOR_CAST_(TSimdVector, _mm_div_epi64(a, _mm_set1_epi64x(b))); } + +// -------------------------------------------------------------------------- +// _add (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_add_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_add_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_add_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _add(TSimdVector &a, TSimdVector &b, SimdParams_<16, 2>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_add_epi64(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _sub (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_sub_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_sub_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_sub_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _sub(TSimdVector &a, TSimdVector &b, SimdParams_<16, 2>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_sub_epi64(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _mult (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &/*b*/, SimdParams_<16, 16>) +{ + SEQAN_ASSERT_FAIL("SSE intrinsics for multiplying 8 bit values not implemented!"); + return a; +} + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &b, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_mullo_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &b, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_mullo_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _mult(TSimdVector &a, TSimdVector &/*b*/, SimdParams_<16, 2>) +{ + SEQAN_ASSERT_FAIL("SSE intrinsics for multiplying 64 bit values not implemented!"); + return a; +} + +// -------------------------------------------------------------------------- +// _max (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_max_epi16(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_max_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +template +inline TSimdVector _max(TSimdVector &a, TSimdVector &b, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_max_epi32(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b))); +} + +// -------------------------------------------------------------------------- +// _blend (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _blend(TSimdVector const &a, TSimdVector const &b, TSimdVectorMask const &mask, SimdParams_<16, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, + _mm_blendv_epi8(SEQAN_VECTOR_CAST_(const __m128i&, a), + SEQAN_VECTOR_CAST_(const __m128i&, b), + SEQAN_VECTOR_CAST_(const __m128i&, mask))); +} + +// -------------------------------------------------------------------------- +// _storeu (128bit) +// -------------------------------------------------------------------------- + +template +inline void _storeu(T * memAddr, TSimdVector &vec, SimdParams_<16, L>) +{ + _mm_storeu_si128((__m128i*)memAddr, reinterpret_cast(vec)); +} + +// ---------------------------------------------------------------------------- +// Function _load() 128bit +// ---------------------------------------------------------------------------- + +template +inline TSimdVector _load(T const * memAddr, SimdParams_<16, L>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm_load_si128((__m128i const *) memAddr)); +} + +// -------------------------------------------------------------------------- +// _shuffleVector (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector1 +_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<16, 16>, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector1, _mm_shuffle_epi8(SEQAN_VECTOR_CAST_(const __m128i &, vector), + SEQAN_VECTOR_CAST_(const __m128i &, indices))); +} + +template +inline TSimdVector1 +_shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices, SimdParams_<16, 8>, SimdParams_<8, 8>) +{ +#if SEQAN_IS_32_BIT + __m128i idx = _mm_slli_epi16(_mm_unpacklo_epi32(_mm_cvtsi32_si128(reinterpret_cast(indices)), + _mm_cvtsi32_si128(reinterpret_cast(indices) >> 32)), 1); +#else + __m128i idx = _mm_slli_epi16(_mm_cvtsi64_si128(reinterpret_cast(indices)), 1); +#endif // SEQAN_IS_32_BIT + return SEQAN_VECTOR_CAST_(TSimdVector1, _mm_shuffle_epi8(SEQAN_VECTOR_CAST_(const __m128i &, vector), + _mm_unpacklo_epi8(idx, _mm_add_epi8(idx, _mm_set1_epi8(1))))); +} + +// -------------------------------------------------------------------------- +// _shiftRightLogical (128bit) +// -------------------------------------------------------------------------- + +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 16>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm_srli_epi16(SEQAN_VECTOR_CAST_(const __m128i &, vector), imm) & _mm_set1_epi8(0xff >> imm)); +} +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 8>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm_srli_epi16(SEQAN_VECTOR_CAST_(const __m128i &, vector), imm)); +} +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 4>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm_srli_epi32(SEQAN_VECTOR_CAST_(const __m128i &, vector), imm)); +} +template +inline TSimdVector _shiftRightLogical(TSimdVector const &vector, const int imm, SimdParams_<16, 2>) +{ + return SEQAN_VECTOR_CAST_(TSimdVector, _mm_srli_epi64(SEQAN_VECTOR_CAST_(const __m128i &, vector), imm)); +} + +// -------------------------------------------------------------------------- +// _transposeMatrix (128bit) +// -------------------------------------------------------------------------- + +template +inline void +_transposeMatrix(TSimdVector matrix[], SimdMatrixParams_<8, 8, 8>) +{ + // we need a look-up table to reverse the lowest 4 bits + // in order to place the permute the transposed rows + static const unsigned char bitRev[] = {0,4,2,6,1,5,3,7}; + + // transpose a 8x8 byte matrix + __m64 tmp1[8]; + for (int i = 0; i < 4; ++i) + { + tmp1[i] = _mm_unpacklo_pi8(SEQAN_VECTOR_CAST_(const __m64 &, matrix[2*i]), SEQAN_VECTOR_CAST_(const __m64 &, matrix[2*i+1])); + tmp1[i+4] = _mm_unpackhi_pi8(SEQAN_VECTOR_CAST_(const __m64 &, matrix[2*i]), SEQAN_VECTOR_CAST_(const __m64 &, matrix[2*i+1])); + } + __m64 tmp2[8]; + for (int i = 0; i < 4; ++i) + { + tmp2[i] = _mm_unpacklo_pi16(tmp1[2*i], tmp1[2*i+1]); + tmp2[i+4] = _mm_unpackhi_pi16(tmp1[2*i], tmp1[2*i+1]); + } + for (int i = 0; i < 4; ++i) + { + matrix[bitRev[i]] = SEQAN_VECTOR_CAST_(TSimdVector, _mm_unpacklo_pi32(tmp2[2*i], tmp2[2*i+1])); + matrix[bitRev[i+4]] = SEQAN_VECTOR_CAST_(TSimdVector, _mm_unpackhi_pi32(tmp2[2*i], tmp2[2*i+1])); + } +} + +template +inline void +_transposeMatrix(TSimdVector matrix[], SimdMatrixParams_<16, 16, 8>) +{ + // we need a look-up table to reverse the lowest 4 bits + // in order to place the permute the transposed rows + static const unsigned char bitRev[] = {0,8,4,12,2,10,6,14,1,9,5,13,3,11,7,15}; + + // transpose a 16x16 byte matrix + // + // matrix = + // A0 A1 A2 ... Ae Af + // B0 B1 B2 ... Be Bf + // ... + // P0 P1 P2 ... Pe Pf + __m128i tmp1[16]; + for (int i = 0; i < 8; ++i) + { + tmp1[i] = _mm_unpacklo_epi8(SEQAN_VECTOR_CAST_(const __m128i &, matrix[2*i]), SEQAN_VECTOR_CAST_(const __m128i &, matrix[2*i+1])); + tmp1[i+8] = _mm_unpackhi_epi8(SEQAN_VECTOR_CAST_(const __m128i &, matrix[2*i]), SEQAN_VECTOR_CAST_(const __m128i &, matrix[2*i+1])); + } + // tmp1[0] = A0 B0 A1 B1 ... A7 B7 + // tmp1[1] = C0 D0 C1 D1 ... C7 D7 + // ... + // tmp1[7] = O0 P0 O1 P1 ... O7 P7 + // tmp1[8] = A8 B8 A9 B9 ... Af Bf + // ... + // tmp1[15] = O8 P8 O9 P9 ... Of Pf + __m128i tmp2[16]; + for (int i = 0; i < 8; ++i) + { + tmp2[i] = _mm_unpacklo_epi16(tmp1[2*i], tmp1[2*i+1]); + tmp2[i+8] = _mm_unpackhi_epi16(tmp1[2*i], tmp1[2*i+1]); + } + // tmp2[0] = A0 B0 C0 D0 ... A3 B3 C3 D3 + // tmp2[1] = E0 F0 G0 H0 ... E3 F3 G3 H3 + // ... + // tmp2[3] = M0 N0 O0 P0 ... M3 N3 O3 P3 + // tmp2[4] = A8 B8 C8 D8 ... Ab Bb Cb Db + // ... + // tmp2[7] = M8 N8 O8 P8 ... Mb Nb Ob Pb + // tmp2[8] = A4 B4 C4 D4 ... A7 B7 C7 D7 + // .. + // tmp2[12] = Ac Bc Cc Dc ... Af Bf Cf Df + // ... + // tmp2[15] = Mc Nc Oc Pc ... Mf Nf Of Pf + for (int i = 0; i < 8; ++i) + { + tmp1[i] = _mm_unpacklo_epi32(tmp2[2*i], tmp2[2*i+1]); + tmp1[i+8] = _mm_unpackhi_epi32(tmp2[2*i], tmp2[2*i+1]); + } + // tmp1[0] = A0 B0 .... H0 A1 B1 .... H1 + // tmp1[1] = I0 J0 .... P0 I1 J1 .... P1 + // ... + // tmp1[4] = A0 B0 .... H0 A1 B1 .... H1 + // tmp1[1] = I0 J0 .... P0 I1 J1 .... P1 + for (int i = 0; i < 8; ++i) + { + matrix[bitRev[i]] = SEQAN_VECTOR_CAST_(TSimdVector, _mm_unpacklo_epi64(tmp1[2*i], tmp1[2*i+1])); + matrix[bitRev[i+8]] = SEQAN_VECTOR_CAST_(TSimdVector, _mm_unpackhi_epi64(tmp1[2*i], tmp1[2*i+1])); + } +} + +// -------------------------------------------------------------------------- +// Function _testAllZeros (128bit) +// -------------------------------------------------------------------------- + +template +SEQAN_FUNC_ENABLE_IF(Is >, int) +inline _testAllZeros(TSimdVector const &vector, TSimdVector const &mask, SimdParams_<16>) +{ + return _mm_testz_si128(vector, mask); +} + +// -------------------------------------------------------------------------- +// Function _testAllOnes (128bit) +// -------------------------------------------------------------------------- + +template +inline +SEQAN_FUNC_ENABLE_IF(Is >, int) +_testAllOnes(TSimdVector const &vector, SimdParams_<16>) +{ + return _mm_test_all_ones(SEQAN_VECTOR_CAST_(const __m128i &, vector)); +} +#endif // #ifdef SEQAN_SSE4 + +// ============================================================================ +// +// INTERFACE FUNCTIONS +// - these should be used in the actual code, they will call one of the wrapper +// functions defined above based on the vector type +// +// ============================================================================ + +// -------------------------------------------------------------------------- +// Function transpose() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +transpose(TSimdVector matrix[ROWS]) +{ + typedef typename Value::Type TValue; + _transposeMatrix(matrix, SimdMatrixParams_::VALUE, BitsPerValue::VALUE>()); +} + +// -------------------------------------------------------------------------- +// Function clearVector() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +clearVector(TSimdVector &vector) +{ + typedef typename Value::Type TValue; + _clearVector(vector, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function createVector() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +createVector(TValue x) +{ + typedef typename Value::Type TIVal; + return _createVector(x, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function fillVector() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +fillVector(TSimdVector &vector, TValue const... args) +{ + typedef typename Value::Type TIVal; + _fillVector(vector, std::make_tuple(args...), + std::make_index_sequence{}, + SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function cmpEq() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +cmpEq (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _cmpEq(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator==() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator == (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _cmpEq(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operatorGt() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +cmpGt (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _cmpGt(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator>() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator > (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _cmpGt(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function max() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +max(TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _max(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator|() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator | (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _bitwiseOr(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator|=() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector &) +operator |= (TSimdVector &a, TSimdVector const &b) +{ + a = a | b; + return a; +} + +// -------------------------------------------------------------------------- +// Function operator&() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator & (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _bitwiseAnd(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator&=() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector &) +operator &= (TSimdVector &a, TSimdVector const &b) +{ + a = a & b; + return a; +} + +// -------------------------------------------------------------------------- +// Function operator~() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator ~ (TSimdVector const &a) +{ + typedef typename Value::Type TValue; + return _bitwiseNot(a, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator+() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator + (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _add(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator-() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator - (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _sub(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator*() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator * (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _mult(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function operator/() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +operator/ (TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _div(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function andNot +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +andNot(TSimdVector const &a, TSimdVector const &b) +{ + typedef typename Value::Type TValue; + return _bitwiseAndNot(a, b, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function shuffleVector() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector1) +shuffleVector(TSimdVector1 const &vector, TSimdVector2 const &indices) +{ + typedef typename Value::Type TValue1; + typedef typename Value::Type TValue2; + return _shuffleVector( + vector, + indices, + SimdParams_(), + SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function shiftRightLogical() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +shiftRightLogical(TSimdVector const &vector, const int imm) +{ + typedef typename Value::Type TValue; + return _shiftRightLogical(vector, imm, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function blend() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +blend(TSimdVector const &a, TSimdVector const &b, TSimdVectorMask const & mask) +{ + typedef typename Value::Type TValue; + return _blend(a, b, mask, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function storeu() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +storeu(T * memAddr, TSimdVector const &vec) +{ + typedef typename Value::Type TValue; + _storeu(memAddr, vec, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function load() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +load(T const * memAddr) +{ + typedef typename Value::Type TValue; + return _load(memAddr, SimdParams_()); +} + +// -------------------------------------------------------------------------- +// Function gather() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSimdVector) +gather(TValue const * memAddr, TSimdVector const & idx) +{ + typedef typename Value::Type TInnerValue; + return _gather(memAddr, idx, std::integral_constant(), SimdParams_()); +} + +#endif // SEQAN_SIMD_ENABLED + +// NOTE(rmaerker): Make this function available, also if SIMD is not enabled. +template +inline SEQAN_FUNC_DISABLE_IF(Is >, TSimdVector) +createVector(TValue x) +{ + return x; +} + +// -------------------------------------------------------------------------- +// Function print() +// -------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, std::ostream &) +print(std::ostream &stream, TSimdVector const &vector) +{ + stream << '<'; + for (int i = 0; i < LENGTH::VALUE; ++i) + stream << '\t' << vector[i]; + stream << "\t>\n"; + return stream; +} + +} // namespace seqan + +#endif // SEQAN_INCLUDE_SEQAN_BASIC_SIMD_VECTOR_H_ diff --git a/seqan/basic/basic_smart_pointer.h b/seqan/basic/basic_smart_pointer.h new file mode 100644 index 0000000..deca95f --- /dev/null +++ b/seqan/basic/basic_smart_pointer.h @@ -0,0 +1,59 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Facade header for the basic/smart_pointer sub module. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_ + +// -------------------------------------------------------------------------- +// Dependencies +// -------------------------------------------------------------------------- + +#include +#include +#include // TODO(holtgrew): Drop dependency, only for pointer holder which does not work anyway. +#include // TODO(holtgrew): Really required? Deprecated header? + +// -------------------------------------------------------------------------- +// Sub Module Headers +// -------------------------------------------------------------------------- + +#include +#include +#include + +#include + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_SMART_POINTER_H_ diff --git a/seqan/basic/basic_stream.h b/seqan/basic/basic_stream.h new file mode 100644 index 0000000..e03dca2 --- /dev/null +++ b/seqan/basic/basic_stream.h @@ -0,0 +1,1303 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// ========================================================================== +// Basic definitions for the stream module. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_STREAM_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BASIC_STREAM_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +template +struct StreamIterator; + +template +inline void writeValue(std::basic_ostream &ostream, TValue2 val); + +template +inline void writeValue(std::ostreambuf_iterator &iter, TValue2 val); + +template +inline void writeValue(Iter > &iter, TValue val); + +template +inline bool atEnd(std::istreambuf_iterator const &it); + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename Size::Type) +length(TContainer const & me); + +template +inline void +appendValue(TContainer && me, TSource && source); + +/*! + * @macro SEQAN_HAS_ZLIB + * @headerfile + * @brief Defined as 0 or 1, depending on zlib being available. + * + * @signature #define SEQAN_HAS_ZLIB 0 // or 1 + */ + +/*! + * @macro SEQAN_HAS_BZIP2 + * @headerfile + * @brief Defined as 0 or 1, depending on bzlib being available. + * + * @signature #define SEQAN_HAS_BZIP 0 // or 1 + */ + +// ============================================================================ +// Tags +// ============================================================================ + +// ============================================================================ +// Concepts +// ============================================================================ + +// -------------------------------------------------------------------------- +// Concept StreamConcept +// -------------------------------------------------------------------------- + +/*! + * @concept StreamConcept + * @headerfile + * + * @brief Base concept for streams. + * + * @signature concept StreamConcept; + */ + +/*! + * @mfn StreamConcept#Value + * @brief Metafunction for retrieving the value type of a stream. + * + * @signature Value::Type; + * + * @tparam TStream The stream type to query for its value type. + * @return Type The resulting value type. + */ + +/*! + * @mfn StreamConcept#Size + * @brief Metafunction for retrieving the type of a stream. + * + * @signature Size::Type; + * + * @tparam TStream The stream type to query for its size type. + * @return Type The resulting size type. + */ + +/*! + * @mfn StreamConcept#Position + * @brief Metafunction for retrieving the position type of a stream. + * + * @signature Position::Type; + * + * @tparam TStream The stream type to query for its position type. + * @return Type The resulting position type. + */ + +/*! + * @fn StreamConcept#position + * @brief Return current stream position. + * + * @signature TPosition position(stream); + * + * @param[in] stream The stream to query. + * @return TPosition Current position in stream, see @link StreamConcept#Position Position @endlink. + */ + +/*! + * @fn StreamConcept#setPosition + * @brief Set stream position. + * + * @signature void setPosition(stream, pos); + * + * @param[in,out] stream The stream to update + * @param[in] pos The positoin to set. + */ + +/*! + * @fn StreamConcept#atEnd + * @brief Return whether stream is at the end. + * + * @signature bool atEnd(stream); + * + * @param[in] stream The stream to check. + * @return bool true if the file at EOF, false otherwise. + */ + +SEQAN_CONCEPT(StreamConcept, (TStream)) +{}; + +// -------------------------------------------------------------------------- +// Concept InputStreamConcept +// -------------------------------------------------------------------------- + +/*! + * @concept InputStreamConcept Input StreamConcept + * @extends StreamConcept + * @headerfile + * + * @signature concept InputStreamConcept : StreamConcept; + * + * @brief Concept for input streams (for reading). + */ + +SEQAN_CONCEPT_REFINE(InputStreamConcept, (TStream), (StreamConcept)) +{ + typedef typename Value::Type TValue; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + + SEQAN_CONCEPT_ASSERT((SignedIntegerConcept)); + + SEQAN_CONCEPT_USAGE(InputStreamConcept) + {} +}; + +// -------------------------------------------------------------------------- +// Concept OutputStreamConcept +// -------------------------------------------------------------------------- + +/*! + * @concept OutputStreamConcept Output StreamConcept + * @extends StreamConcept + * @headerfile + * + * @signature concept OutputStreamConcept : StreamConcept; + * + * @brief Concept for output streams (for writing). + */ + +SEQAN_CONCEPT_REFINE(OutputStreamConcept, (TStream), (StreamConcept)) +{ + typedef typename Value::Type TValue; + typedef typename Size::Type TSize; + typedef typename Position::Type TPosition; + + SEQAN_CONCEPT_ASSERT((SignedIntegerConcept)); + + SEQAN_CONCEPT_USAGE(OutputStreamConcept) + {} +}; + +// -------------------------------------------------------------------------- +// Concept BidirectionalStreamConcept +// -------------------------------------------------------------------------- + +/*! + * @concept BidirectionalStreamConcept Bidirectional StreamConcept + * @extends StreamConcept + * @headerfile + * + * @signature concept BidirectionalStreamConcept : StreamConcept; + * + * @brief Concept for bidirectional streams (both for reading and writing). + */ + +SEQAN_CONCEPT_REFINE(BidirectionalStreamConcept, (TStream), (InputStreamConcept)(OutputStreamConcept)) +{}; + +// ============================================================================ +// Classes +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Struct FormattedNumber +// ---------------------------------------------------------------------------- + +/*! + * @class FormattedNumber + * @implements NumberConcept + * @headerfile + * + * @brief Helper class for storing a numeric value together with a + * printf format string. + * + * @signature template + * struct FormattedNumber; + * + * @tparam The numeric value type. + */ + +template +struct FormattedNumber +{ + char const * format; + TValue value; + + /*! + * @fn FormattedNumber::FormattedNumber + * @brief Constructor. + * + * @signature FormattedNumber::FormattedNumber(format, value); + * + * @param[in] format A char const * for the format string. + * @param[in] value The TValue to store. + * + * The constructed FormattedNumber object store the format pointer "as is". This means that you are + * responsible for keeping this pointer valid until the object is deconstructed. Passing in a C string literal + * (as in FormattedNumber<double>("%.2f", 1.234) is fine. + */ + + FormattedNumber(char const * format, TValue const & value) : + format(format), value(value) + {} + + operator TValue() const + { + return value; + } +}; + +template +struct Is< NumberConcept< FormattedNumber > > : + Is< NumberConcept > {}; + +// ============================================================================ +// Exceptions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Exception ParseError +// ---------------------------------------------------------------------------- + +/*! + * @class ParseError + * @extends RuntimeError + * @headerfile + * + * @brief Exception class for parser errors. + * + * @signature struct ParseError : RuntimeError; + */ + +struct ParseError : RuntimeError +{ + /*! + * @fn ParseError::ParseError + * @headerfile + * + * @brief Constructor. + * + * @signature ParseError::ParseError(message); + * + * @param[in] message The error message to use, std::string or char const * . + */ + + template + ParseError(TString const & message) : + RuntimeError(message) + {} +}; + +// ---------------------------------------------------------------------------- +// Exception UnexpectedEnd +// ---------------------------------------------------------------------------- + +/*! + * @class UnexpectedEnd + * @extends ParseError + * @headerfile + * + * @brief Exception class for "unexpected end of input" errors. + * + * @signature struct UnexpectedEnd : RuntimeError; + */ + +struct UnexpectedEnd : ParseError +{ + /*! + * @fn UnexpectedEnd::UnexpectedEnd + * @headerfile + * + * @brief Default constructor, makes the object use a default message. + * + * @signature UnexpectedEnd::UnexpectedEnd(); + */ + + UnexpectedEnd() : + ParseError("Unexpected end of input.") + {} +}; + +// ---------------------------------------------------------------------------- +// Exception EmptyFieldError +// ---------------------------------------------------------------------------- + +/*! + * @class EmptyFieldError + * @extends ParseError + * @headerfile + * + * @brief Exception class for "empty field" errors. + * + * @signature struct EmptyFieldError : RuntimeError; + */ + +struct EmptyFieldError : ParseError +{ + /*! + * @fn EmptyFieldError::EmptyFieldError + * @headerfile + * + * @brief Construct the exception with fieldName + " field was empty.". + * + * @signature EmptyFieldEror::EmptyFieldError(fieldName); + * + * @param[in] fieldName The field name to use for the message, std::string. + */ + + EmptyFieldError(std::string fieldName): + ParseError(fieldName + " field was empty.") + {} +}; + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction Iterator +// ---------------------------------------------------------------------------- + +/*! + * @mfn StreamConcept#DirectionIterator + * @brief Return the direction iterator for the given direction. + * + * @signature DirectionIterator::Type; + * + * @tparam TStream The stream to query for its direction iterator. + * @return Type The resulting direction iterator. + */ + +/*! + * @mfn ContainerConcept#DirectionIterator + * @brief Return the direction iterator for the given direction. + * + * @signature DirectionIterator::Type; + * + * @tparam TContainer The container to query for its direction iterator. + * @return Type The resulting direction iterator. + */ + +template +struct DirectionIterator : + If >, + Iter >, + typename Iterator::Type> +{}; + +// -------------------------------------------------------------------------- +// Metafunction BasicStream +// -------------------------------------------------------------------------- + +/*! + * @mfn BasicStream + * @headerfile + * @brief Return the stream type to read or write values. + * + * @signature BasicStream::Type; + * + * @tparam TValue The value type of the stream. + * @tparam TDirection The direction of the stream, one of the @link DirectionTags @endlink. + * @tparam TTraits The traits to use for the values, defaults to std::char_traits<TValue>. + * + */ + +template > +struct BasicStream : + If< + IsSameType, + std::basic_istream, + typename If< + IsSameType, + std::basic_ostream, + std::basic_iostream + >::Type + > +{}; + +// -------------------------------------------------------------------------- +// Metafunction IosOpenMode +// -------------------------------------------------------------------------- + +/*! + * @mfn IosOpenMode + * @headerfile + * @brief Return the std::ios open mode for a direction. + * + * @signature IosOpenMode::Type; + * + * @tparam TDirection The direction to query for the open mode, one of the @link DirectionTags @endlink. + * @tparam TDummy Implementation detail, defaults to void and is ignored. + * @return Type The resulting open mode of type const int. + */ + +template +struct IosOpenMode; + + +template +struct IosOpenMode +{ + static const int VALUE; +}; + +template +struct IosOpenMode +{ + static const int VALUE; +}; + +template +struct IosOpenMode +{ + static const int VALUE; +}; + +template +const int IosOpenMode::VALUE = std::ios::in | std::ios::binary; + +template +const int IosOpenMode::VALUE = std::ios::out | std::ios::binary; + +template +const int IosOpenMode::VALUE = std::ios::in | std::ios::out | std::ios::binary; + + +// -------------------------------------------------------------------------- +// Metafunction MagicHeader +// -------------------------------------------------------------------------- + +/*! + * @mfn MagicHeader + * @headerfile + * @brief Returns the magic header for a file format tag. + * + * The magic header is used for recognizing files from the first few bytes. + * + * @signature MagicHeader::VALUE; + * + * @tparam TTag The file format tag to use for the query. + * @tparam TDummy Implementation detail, defaults to void and is ignored. + * @return VALUE The magic header string, of type char const *. + * + * This metafunction must be implemented in the modules implementing the file I/O. The metafunction is predefined when + * TTag is @link Nothing @endlink. In this case, VALUE is NULL. + */ + +template +struct MagicHeader; + +template +struct MagicHeader +{ + static char const * VALUE; +}; + +template +char const * MagicHeader::VALUE = NULL; + +// -------------------------------------------------------------------------- +// Metafunction FileExtensions +// -------------------------------------------------------------------------- + +/*! + * @mfn FileExtensions + * @headerfile + * @brief Returns an array of file format extension strings for file foramt tag. + * + * @signature FileExtensions::VALUE; + * + * @tparam TTag The file format tag to use for the query. + * @tparam TDummy Implementation detail, defaults to void and is ignored. + * @return VALUE The array of file format extension, of type char const *[]. + * + * This metafunction must be implemented in the modules implementing the file I/O. The metafunction is predefined when + * TTag is @link Nothing @endlink. In this case, VALUE is {""}. + */ + +template +struct FileExtensions; + +template +struct FileExtensions +{ + static char const * VALUE[1]; +}; + +template +char const * FileExtensions::VALUE[1] = +{ + "" // default output extension +}; + +// ---------------------------------------------------------------------------- +// Metafunction IntegerFormatString_ +// ---------------------------------------------------------------------------- +// Return the format string for numbers. + +template +struct IntegerFormatString_; + + +template +struct IntegerFormatString_ : + IntegerFormatString_ {}; + + +template +struct IntegerFormatString_ +{ + static const char VALUE[]; + typedef short Type; +}; +template +const char IntegerFormatString_::VALUE[] = "%hi"; + + +template +struct IntegerFormatString_ +{ + static const char VALUE[]; + typedef unsigned short Type; +}; +template +const char IntegerFormatString_::VALUE[] = "%hu"; + + +template +struct IntegerFormatString_ +{ + static const char VALUE[]; + typedef int Type; +}; +template +const char IntegerFormatString_::VALUE[] = "%i"; + + +template +struct IntegerFormatString_ +{ + static const char VALUE[]; + typedef unsigned Type; +}; +template +const char IntegerFormatString_::VALUE[] = "%u"; + + +// helper for the case: typedef long int64_t; +template +struct LongFormatString_; + +template +struct LongFormatString_ +{ + static const char VALUE[]; + typedef long Type; +}; +template +const char LongFormatString_::VALUE[] = "%li"; + +template +struct LongFormatString_ +{ + static const char VALUE[]; + typedef unsigned long Type; +}; +template +const char LongFormatString_::VALUE[] = "%lu"; + +// helper for the case: typedef long long int64_t; +template +struct Int64FormatString_; + +template +struct Int64FormatString_ +{ + static const char VALUE[]; + typedef int64_t Type; +}; +template +const char Int64FormatString_::VALUE[] = "%lli"; + +template +struct Int64FormatString_ +{ + static const char VALUE[]; + typedef uint64_t Type; +}; +template +const char Int64FormatString_::VALUE[] = "%llu"; + + +template +struct IntegerFormatString_ : + If, + LongFormatString_, + Int64FormatString_ >::Type {}; + + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function writeValue() [ContainerConcept] +// ---------------------------------------------------------------------------- + +/*! + * @fn ContainerConcept#writeValue + * @brief Write a value at the end of a container. + * + * @signature void writeValue(container, val); + * + * @param[in,out] container to append to. + * @param[in] val The value to append. + * + * @see ContainerConcept#appendValue + */ + +// resizable containers +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +writeValue(TSequence &cont, TValue val) +{ + appendValue(cont, val); +} + +// ---------------------------------------------------------------------------- +// Function writeValue() [Range] +// ---------------------------------------------------------------------------- + +/*! + * @fn Range#writeValue + * @brief Write a value to a @link Range @endlink. + * + * @signature void writeValue(range, val); + * + * val will be assigned to the first element of the range. Then, the beginning of the range will be advanced + * by one. + * + * @param[in,out] range to append to. + * @param[in] val The value to append. + */ + +// Range +template +inline void +writeValue(Range &range, TValue val) +{ + assignValue(range.begin, val); + ++range.begin; +} + +// ---------------------------------------------------------------------------- +// Function writeValue() [Iter] +// ---------------------------------------------------------------------------- + +/*! + * @fn OutputIteratorConcept#writeValue + * @brief Write a single value to a container by dereferencing its iterator. + * + * @signature void writeValue(iter, val); + * + * @param[in,out] iter The iterator to use for dereferenced writing. + * @param[in] val The value to write into the container. + * + * If the host of iter is a @link ContainerConcept @endlink then container is resized to make space for the + * item. + */ + +// resizable containers +template +inline SEQAN_FUNC_ENABLE_IF(Is >, void) +writeValue(Iter & iter, TValue val) +{ + typedef Iter TIter; + + TSequence &cont = container(iter); + typename Position::Type pos = position(iter); + typename Size::Type len = length(cont); + + if (pos < len) + { + assignValue(iter, val); + ++iter; + } + else + { + if (pos > len) + resize(cont, pos - 1); + appendValue(cont, val); + setPosition(iter, pos + 1); + } +} + +// non-resizable containers +template +inline SEQAN_FUNC_DISABLE_IF(Is >, void) +writeValue(Iter & iter, TValue val) +{ + SEQAN_ASSERT_LT(position(iter), length(container(iter))); + + assignValue(iter, val); + ++iter; +} + +// ---------------------------------------------------------------------------- +// Function writeValue() [pointer] +// ---------------------------------------------------------------------------- + +///*! +// * @fn ContainerConcept#writeValue +// * @brief Write a value by dereferencing a pointer and incrementing its position by one. +// * +// * @signature void writeValue(pointer, val); +// * +// * @param[in,out] iter The pointer to dereference, usually a char *. +// * @param[in] val The value to write to the dereferenced pointer. +// * +// * This function is equivalent to *iter++ = val. +// */ + +template +inline void +writeValue(TTargetValue * & iter, TValue val) +{ + *iter++ = val; +} + +// ---------------------------------------------------------------------------- +// Function _write(); Element-wise +// ---------------------------------------------------------------------------- + +template +inline void _write(TTarget &target, TFwdIterator &iter, TSize n, TIChunk, TOChunk) +{ + for (; n > (TSize)0; --n, ++iter) + writeValue(target, getValue(iter)); +} + +// ---------------------------------------------------------------------------- +// Function _write(); Chunked +// ---------------------------------------------------------------------------- + +template +inline void _write(TTarget &target, TFwdIterator &iter, TSize n, Range *, Range *) +{ + typedef Nothing* TNoChunking; + typedef typename Size::Type TTargetSize; + + Range ichunk; + Range ochunk; + + while (n != (TSize)0) + { + getChunk(ichunk, iter, Input()); + getChunk(ochunk, target, Output()); + + TTargetSize minChunkSize = std::min((TTargetSize)length(ichunk), (TTargetSize)length(ochunk)); + + if (SEQAN_UNLIKELY(minChunkSize == 0u)) + { + reserveChunk(target, n, Output()); + reserveChunk(iter, n, Input()); + getChunk(ochunk, target, Output()); + getChunk(ichunk, iter, Input()); + minChunkSize = std::min((TTargetSize)length(ichunk), (TTargetSize)length(ochunk)); + if (SEQAN_UNLIKELY(minChunkSize == 0u)) + { + _write(target, iter, n, TNoChunking(), TNoChunking()); + return; + } + } + + if (minChunkSize > (TTargetSize)n) + minChunkSize = (TTargetSize)n; + + arrayCopyForward(ichunk.begin, ichunk.begin + minChunkSize, ochunk.begin); + + iter += minChunkSize; // advance input iterator + advanceChunk(target, minChunkSize); + n -= minChunkSize; + } +} + +// chunked, target is pointer (e.g. readRawPod) +template +inline SEQAN_FUNC_DISABLE_IF(IsSameType::Type, Nothing>, void) +write(TOValue *ptr, TFwdIterator &iter, TSize n) +{ + typedef Nothing* TNoChunking; + typedef typename Size::Type TSourceSize; + typedef typename Chunk::Type TIChunk; + + TIChunk ichunk; + + while (n != (TSize)0) + { + getChunk(ichunk, iter, Input()); + TSourceSize chunkSize = length(ichunk); + + if (SEQAN_UNLIKELY(chunkSize == 0u)) + { + reserveChunk(iter, n, Input()); + getChunk(ichunk, iter, Input()); + TSourceSize chunkSize = length(ichunk); + if (SEQAN_UNLIKELY(chunkSize == 0u)) + { + _write(ptr, iter, n, TNoChunking(), TNoChunking()); + return; + } + } + + if (chunkSize > (TSourceSize)n) + chunkSize = (TSourceSize)n; + + arrayCopyForward(ichunk.begin, ichunk.begin + chunkSize, ptr); + + iter += chunkSize; // advance input iterator + ptr += chunkSize; + n -= chunkSize; + } +} + +// non-chunked fallback +template +inline SEQAN_FUNC_ENABLE_IF(And< IsSameType::Type, Nothing>, + Is::Type, TIValue> > >, void) +write(TTarget &target, TIValue *ptr, TSize n) +{ + _write(target, ptr, n, Nothing(), Nothing()); +} + +// ostream shortcut, source is pointer (e.g. readRawPod) +template +inline SEQAN_FUNC_ENABLE_IF(Is< OutputStreamConcept >, void) +write(TTarget &target, const char *ptr, TSize n) +{ + target.write(ptr, n); +} + +// ostream shortcut, source is pointer (e.g. readRawPod) +template +inline SEQAN_FUNC_ENABLE_IF(Is< OutputStreamConcept >, void) +write(TTarget &target, char *ptr, TSize n) +{ + target.write(ptr, n); +} + +// chunked, source is pointer (e.g. readRawPod) +template +inline SEQAN_FUNC_ENABLE_IF(And< Not::Type, Nothing> >, + Is::Type, TIValue> > >, void) +write(TTarget &target, TIValue *ptr, TSize n) +{ + typedef Nothing* TNoChunking; + typedef typename Size::Type TTargetSize; + typedef typename Chunk::Type TOChunk; + + TOChunk ochunk; + + while (n != (TSize)0) + { + getChunk(ochunk, target, Output()); + TTargetSize chunkSize = length(ochunk); + + if (SEQAN_UNLIKELY(chunkSize == 0u)) + { + reserveChunk(target, n, Output()); + getChunk(ochunk, target, Output()); + chunkSize = length(ochunk); + if (SEQAN_UNLIKELY(chunkSize == 0u)) + { + _write(target, ptr, n, TNoChunking(), TNoChunking()); + return; + } + } + + if (chunkSize > (TTargetSize)n) + chunkSize = (TTargetSize)n; + + arrayCopyForward(ptr, ptr + chunkSize, ochunk.begin); + + ptr += chunkSize; // advance input iterator + advanceChunk(target, chunkSize); + n -= chunkSize; + } +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< Is >, + Is > >, void) +write(TOValue * &optr, TIValue *iptr, TSize n) +{ + std::memcpy(optr, iptr, n); + optr += n; +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< Is >, + Is > >, void) +write(TOValue * optr, TIValue * &iptr, TSize n) +{ + std::memcpy(optr, iptr, n); + iptr += n; +} + +// ---------------------------------------------------------------------------- +// Function write(TValue *) +// ---------------------------------------------------------------------------- +// NOTE(esiragusa): should it be defined for Streams and Containers? + +//template +//inline SEQAN_FUNC_ENABLE_IF(Or >, Is > >, void) +//write(TTarget &target, TValue *ptr, TSize n) +//{ +// typedef Range TRange; +// typedef typename Iterator::Type TIterator; +// typedef typename Chunk::Type* TIChunk; +// typedef typename Chunk::Type* TOChunk; +// +// TRange range(ptr, ptr + n); +// TIterator iter = begin(range, Rooted()); +// _write(target, iter, n, TIChunk(), TOChunk()); +//} + +// ---------------------------------------------------------------------------- +// Function write(Iterator) +// ---------------------------------------------------------------------------- + +/*! + * @fn ContainerConcept#write + * @brief Write to a container. + * + * @signature void write(container, iter, n); + * + * @param[in,out] container The container to append to. + * @param[in,out] iter The @link ForwardIteratorConcept forward iterator @endlink to take the values from. + * @param[in] n Number of elements to write from iter. + * + * This function reads n values from iter and appends them to the back of container. + */ + +//TODO(singer): Enable this! +template +//inline SEQAN_FUNC_ENABLE_IF(Or >, Is > >, void) +inline SEQAN_FUNC_ENABLE_IF(And< Is >, + Is::Type, + typename Value::Type> > >, void) +write(TTarget &target, TFwdIterator &iter, TSize n) +{ + typedef typename Chunk::Type* TIChunk; + typedef typename Chunk::Type* TOChunk; + + _write(target, iter, n, TIChunk(), TOChunk()); +} + +// write for more complex values (defer to write of iterator value) +// used for Strings of Pairs +template +//inline SEQAN_FUNC_ENABLE_IF(Or >, Is > >, void) +inline SEQAN_FUNC_ENABLE_IF(And< + Is >, + Not< Is::Type, + typename Value::Type> > > >, void) +write(TTarget &target, TFwdIterator &iter, TSize n) +{ + for (; n > (TSize)0; --n, ++iter) + { + write(target, *iter); + writeValue(target, ' '); + } +} + +// ---------------------------------------------------------------------------- +// Function write(TContainer) but not container of container +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(And< Not >, + And< Is >, + Not::Type> > > > >, void) +write(TTarget &target, TContainer &cont) +{ + typename DirectionIterator::Type iter = directionIterator(cont, Input()); + write(target, iter, length(cont)); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< IsContiguous, + And< Is >, + Not::Type> > > > >, void) +write(TTarget &target, TContainer &cont) +{ + typename Iterator::Type iter = begin(cont, Standard()); + write(target, iter, length(cont)); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< Not >, + And< Is >, + Not::Type> > > > >, void) +write(TTarget &target, TContainer const &cont) +{ + typename DirectionIterator::Type iter = directionIterator(cont, Input()); + write(target, iter, length(cont)); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< IsContiguous, + And< Is >, + Not::Type> > > > >, void) +write(TTarget &target, TContainer const &cont) +{ + typename Iterator::Type iter = begin(cont, Standard()); + write(target, iter, length(cont)); +} + +template +inline void +write(TTarget &target, TValue * ptr) +{ + write(target, ptr, length(ptr)); +} + +// ---------------------------------------------------------------------------- +// Function appendNumber() +// ---------------------------------------------------------------------------- +// Generic version for integers. + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, typename Size::Type) +appendNumber(TTarget & target, TInteger i) +{ + typedef IntegerFormatString_ >::Type, + sizeof(TInteger)> TInt; + + // 1 byte has at most 3 decimal digits (plus 2 for '-' and the NULL character) + char buffer[sizeof(TInteger) * 3 + 2]; + size_t len = snprintf(buffer, sizeof(buffer), + TInt::VALUE, static_cast(i)); + char *bufPtr = buffer; + write(target, bufPtr, len); + return len; +} + +// ---------------------------------------------------------------------------- +// Function appendNumber(bool) +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +appendNumber(TTarget & target, bool source) +{ + writeValue(target, '0' + source); + return 1; +} + +// ---------------------------------------------------------------------------- +// Function appendNumber(float) +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +appendNumber(TTarget & target, float source) +{ + char buffer[32]; + size_t len = snprintf(buffer, sizeof(buffer), "%g", source); + write(target, (char *)buffer, len); + return len; +} + +// ---------------------------------------------------------------------------- +// Function appendNumber(double) +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +appendNumber(TTarget & target, double source) +{ + char buffer[32]; + size_t len = snprintf(buffer, sizeof(buffer), "%g", source); + write(target, (char *)buffer, len); + return len; +} + +// ---------------------------------------------------------------------------- +// Function appendNumber(double) +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +appendNumber(TTarget & target, FormattedNumber const & source) +{ + char buffer[100]; + size_t len = snprintf(buffer, sizeof(buffer), source.format, source.value); + write(target, (char *)buffer, len); + return len; +} + +template +inline FormattedNumber +formattedNumber(const char *format, TValue const & val) +{ + return FormattedNumber(format, val); +} + +// ---------------------------------------------------------------------------- +// Function appendRawPod() +// ---------------------------------------------------------------------------- + +template +inline void +appendRawPod(TTarget & target, TValue const & val) +{ + write(target, (unsigned char*)&val, sizeof(TValue)); +} + +template +inline void +appendRawPod(TTargetValue * &ptr, TValue const & val) +{ + *reinterpret_cast(ptr)++ = val; +} + +// ---------------------------------------------------------------------------- +// Function write(TNumber); write fundamental type +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(And< Is::Type, TValue> >, + Is > >, void) +write(TTarget &target, TValue &number) +{ + if (sizeof(TValue) == 1) + writeValue(target, number); // write chars as chars + else + appendNumber(target, number); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< Is::Type, TValue> >, + Is > >, void) +write(TTarget &target, TValue const &number) +{ + if (sizeof(TValue) == 1) + writeValue(target, number); // write chars as chars + else + appendNumber(target, number); +} + +// ---------------------------------------------------------------------------- +// Function write(TNumber); write non-fundamental, convertible type +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(And< Is::Type, TValue> >, + Not > > >, void) +write(TTarget &target, TValue &number) +{ + writeValue(target, number); +} + +template +inline SEQAN_FUNC_ENABLE_IF(And< Is::Type, TValue const> >, + Not > > >, void) +write(TTarget &target, TValue const &number) +{ + writeValue(target, number); +} + +// ---------------------------------------------------------------------------- +// Function read(Iterator) +// ---------------------------------------------------------------------------- + +template +inline SEQAN_FUNC_ENABLE_IF(Is >, TSize) +read(TTarget &target, TFwdIterator &iter, TSize n) +{ + TSize i; + for (i = 0; !atEnd(iter) && i < n; ++i, ++iter) + writeValue(target, value(iter)); + return i; +} + +// ---------------------------------------------------------------------------- +// Function read(TContainer) +// ---------------------------------------------------------------------------- + +template +inline typename Size::Type +read(TTarget &target, TContainer &cont) +{ + typename DirectionIterator::Type iter = directionIterator(cont, Input()); + return read(target, iter, length(cont)); +} + +// ---------------------------------------------------------------------------- +// operator<< +// ---------------------------------------------------------------------------- + +template +inline TStream & +operator<<(TStream & target, + Range const & source) +{ + typename DirectionIterator::Type it = directionIterator(target, Output()); + write(it, source); + return target; +} + +template +inline TStream & +operator<<(TStream & target, + FormattedNumber const & source) +{ + typename DirectionIterator::Type it = directionIterator(target, Output()); + write(it, source); + return target; +} + +} // namespace seqean + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BASIC_STREAM_H_ diff --git a/seqan/basic/basic_tangle.h b/seqan/basic/basic_tangle.h new file mode 100644 index 0000000..4190559 --- /dev/null +++ b/seqan/basic/basic_tangle.h @@ -0,0 +1,166 @@ +// ========================================================================== +// basic_tangle.h +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== + +// TODO(holtgrew): This header contains code that does not clearly belongs somewhere else. + +#ifndef INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_ +#define INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_ + +namespace seqan { + +// TODO(holtgrew): Remove this define. +#define seqan seqan + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// TODO(holtgrew): Remove auto-sequence! +template +struct Iterator, Standard> +{ + typedef SimpleType * Type; +// typedef Iter, SimpleIterator> * Type; +}; + +template +struct Iterator const, Standard> +{ + typedef SimpleType const * Type; +// typedef Iter const, SimpleIterator> * Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Key +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Is this part of some adaption? + +template +struct Key > +{ + typedef TKey Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction Cargo +// ---------------------------------------------------------------------------- + +// TODO(holtgrew): Is this part of some adaption? + +template +struct Cargo > +{ + typedef TCargo Type; +}; + + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function assignQualities() +// ---------------------------------------------------------------------------- + +/*! + * @fn assignQualities + * @headerfile + * @brief Assign quality values between strings. + * + * @signature void assignQualities(target, source); + * + * @param[out] target Target string, can be a String of DnaQ or Dna5Q characters. + * @param[in] source Source string. Can be a String of int or char. + * + * @section Remarks + * + * The target is resized to the length of source. This function calls assignQualityValue for all entries of + * target and source, look at the documentation of assignQualityValue on how the values of + * source are interpreted. + * + * Note that qualities are expected to be in PHRED scale. + * + * @see AlphabetWithQualitiesConcept#assignQualityValue + */ + +template +inline void +_assignQualities(TDest &dst, TSource const &src, True) +{ + typedef typename Iterator::Type TDestIter; + typedef typename Iterator::Type TSourceIter; + + if (length(dst) < length(src)) + resize(dst, length(src)); + + TDestIter itDst = begin(dst, Standard()); + TSourceIter itSrcEnd = end(src, Standard()); + + for (TSourceIter itSrc = begin(src, Standard()); itSrc != itSrcEnd; ++itDst, ++itSrc) + assignQualityValue(*itDst, *itSrc); +} + +template +inline void +_assignQualities(TDest &, TSource const &, False) +{} + +// TODO(holtgrew): Uncomment, place somewhere that knows both iterators and assignQualityValue, maybe in module sequence? +template +inline void +assignQualities(TDest &dst, TSource const &src) +{ + typedef typename Value::Type TValue; + _assignQualities(dst, src, typename Or, IsSameType >::Type()); +} + +template +inline T +unknownValueImpl(T *) +{ + return 'N'; +} + +} // namespace seqan + +#endif // #ifndef INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_ diff --git a/seqan/basic/basic_type.h b/seqan/basic/basic_type.h new file mode 100644 index 0000000..1039a24 --- /dev/null +++ b/seqan/basic/basic_type.h @@ -0,0 +1,543 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// Copyright (c) 2013 NVIDIA Corporation +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Andreas Gogol-Döring +// ========================================================================== +// Definition of basic Metafunctions. +// ========================================================================== + +// TODO(holtgrew): Rename to "shared metafunctions.h"? +// TODO(holtgrew): This could use some cleanup. + +#ifndef SEQAN_BASIC_BASIC_TYPE_H_ +#define SEQAN_BASIC_BASIC_TYPE_H_ + +#include + +namespace seqan { + +////////////////////////////////////////////////////////////////////////////// + +// TODO(holtgrew): Remove default implementation. +// SEQREV: elements-are-containers should not have a default implementation + +template +struct Value +{ + typedef T Type; +}; + +template +struct Value +{ + typedef T const Type; +}; + +//____________________________________________________________________________ + + +// TODO(holtgrew): Remove default implementation. +template +struct GetValue +{ + typedef typename Value::Type const & Type; +}; + +template +struct GetValue: + public GetValue +{ +}; + +//____________________________________________________________________________ + +// TODO(holtgrew): Remove default implementation. +template +struct Reference +{ + typedef typename Value::Type & Type; +}; + +template +struct Reference +{ + typedef typename Value::Type const & Type; +}; + +//____________________________________________________________________________ + + +// TODO(holtgrew): Remove default implementation. +template +struct Size +{ + typedef size_t Type; +}; + +template +struct Size: + Size +{ +}; + +//____________________________________________________________________________ + + + +// TODO(holtgrew): Remove default implementation. +template +struct Difference +{ + typedef ptrdiff_t Type; +}; + +template +struct Difference: + Difference +{ +}; + +//____________________________________________________________________________ + + +// TODO(holtgrew): Remove default implementation. +template +struct Position +{ + typedef typename Size::Type Type; +}; + +template +struct Position: + Position +{ +}; + +//____________________________________________________________________________ + +// SEQREV: elements-are-containers should not have a default implementation, if a type has no host, do not return self + +template +struct Host +{ + typedef T Type; +}; + +//____________________________________________________________________________ + +//____________________________________________________________________________ + +/*! + * @mfn Cargo + * @headerfile + * @brief Type of additional data stored in an object. + * + * @signature Cargo::Type; + * + * @tparam T Type for which the cargo tpye is queried. + * + * @return Type The cargo type of T. + * + * The definition of Cargo allows the addition of user-specified data into existing data structures. + */ + +// TODO(holtgrew): Should this have a default implementation? + +template +struct Cargo { + typedef Nothing Type; +}; +template +struct Cargo { + typedef typename Cargo::Type const Type; +}; + +//____________________________________________________________________________ + +/*! + * @mfn VertexDescriptor + * @headerfile + * @brief Type of an object that represents a vertex descriptor. + * + * @signature VertexDescriptor::Type; + * + * @tparam T The graph type to query. + * + * @return Type The resulting vertex descriptor type. + */ + +// TODO(holtgrew): Should this have a default implementation? For all graphs -- OK but for all types? + +template +struct VertexDescriptor { + typedef void* Type; +}; +template +struct VertexDescriptor: + public VertexDescriptor {}; + + +//____________________________________________________________________________ + +/*! + * @mfn Id + * @headerfile + * @brief Type of an object that represents an id. + * + * @signature Id::Type + * + * @tparam T The type to query for its id type. + * + * @return Type The resulting identifier type. + */ + +// TODO(holtgrew): Should this have a default implementation? + +template +struct Id { + typedef unsigned int Type; +}; + +template +struct Id : Id {}; + +//____________________________________________________________________________ + +/*! + * @mfn Key + * @headerfile + * @brief Key type of a key to cargo mapping. + * + * @signature Key::Type; + * + * @tparam T Type for which a key type is determined. + * + * @return Type The key type. + */ + +// TODO(holtgrew): Should this have a default implementation? + +template< typename T > +struct Key +{ + typedef T Type; +}; + +template +struct Key: + Key {}; + +//____________________________________________________________________________ + +template +struct Object; + +template +struct Object: + Object {}; + + +//____________________________________________________________________________ + +// TODO(holtgrew): Move to alignments? +// TODO(holtgrew): Is this default implementation what we want? + +template < typename TSpec = void > +struct Source +{ + typedef TSpec Type; +}; + +template +struct Source: + Source +{ +}; + + +//____________________________________________________________________________ + +/*! + * @mfn IsLightWeight + * @headerfile + * @brief Determines whether an object can efficiently be passed by copy. + * + * @signature IsLightWeight::Type; + * + * @tparam T The type to query. + * + * @return Type Either True or False. True if the object can efficiently be copied. + */ + +template +struct IsLightWeight: + False {}; + +//____________________________________________________________________________ + +// TODO(holtgrew): Really required? + +template +struct Parameter_ +{ + typedef T & Type; +}; + +template +struct Parameter_ +{ + typedef T const & Type; +}; + +template +struct Parameter_ +{ + typedef T * Type; +}; + +template +struct Parameter_ +{ + typedef T const * Type; +}; + +template +struct Parameter_ +{ + typedef T * Type; +}; + +template +struct Parameter_ +{ + typedef T const * Type; +}; + +// TODO(holtgrew): Really required? + +template +typename Parameter_::Type +inline _toParameter(T * _object) +{ + return * _object; +} + +template +typename Parameter_::Type +inline _toParameter(T & _object) +{ + return _object; +} + +template +typename Parameter_::Type +inline _toParameter(T const & _object) +{ + return _object; +} + +//____________________________________________________________________________ + +/*! + * @mfn Member + * @headerfile + * @brief Type of a member of an object. + * + * @signature Member::Type; + * @tparam TObject The object holding the member. + * @tparam TSpec A tag to identify the object's member. + * @return Type The resulting object's member type. + * + * This metafunction is used to control the type of a member of a given object. It works analogously to @link Fibre @endlink. + * For instance, it is used to change the relationship between two objects from aggregation to composition and vice versa. + * + * @see Fibre + */ + +template +struct Member; + +template +struct Member : + Member {}; + +//____________________________________________________________________________ + +// TODO(holtgrew): Really required? + +template +struct Pointer_ +{ + typedef T * Type; +}; + +template +struct Pointer_ +{ + typedef T * Type; +}; +template +struct Pointer_ +{ + typedef T * Type; +}; + +template +struct Pointer_ +{ + typedef T * Type; +}; + +//non const version of Pointer_ for return values + +template +struct NonConstPointer_: + Pointer_ +{ +}; +template +struct NonConstPointer_ +{ + typedef T * Type; +}; + +// TODO(holtgrew): Really required? + +template +inline typename NonConstPointer_::Type +_toPointer(T & _object) +{ + return & _object; +} +template +inline typename NonConstPointer_::Type +_toPointer(T const & _object) +{ + return & _object; +} + +template +inline typename NonConstPointer_::Type +_toPointer(T * _object) +{ + return _object; +} + +// -------------------------------------------------------------------------- +// Function _referenceCast() +// -------------------------------------------------------------------------- + +// explicitly give desired dereferenced type as first argument, +// e.g. _dereference(int*) or _dereference &>(Segment<..> &) +template +inline T +_referenceCast(typename RemoveReference::Type & ptr) +{ + return ptr; +} + +template +inline SEQAN_FUNC_DISABLE_IF(IsSameType::Type>, T) +_referenceCast(typename RemoveReference::Type * ptr) +{ + return *ptr; +} + +template +inline SEQAN_FUNC_DISABLE_IF(IsSameType::Type>, T) +_referenceCast(typename RemovePointer::Type & ptr) +{ + return &ptr; +} + + +//____________________________________________________________________________ + +/*! + * @mfn LENGTH + * @brief Number of elements in a fixed-size container/vector. + * + * @signature LENGTH::VALUE; + * + * @tparam T The type to query for its length. + * + * @return VALUE The length of T. + */ + +// SEQREV: elements-are-containers should probably not have a default implementation +// TODO(holtgrew): Rather switch to static const unsigned VALUE = ? + +template +struct LENGTH +{ + enum { VALUE = 1 }; +}; + +template +struct LENGTH: + LENGTH +{ +}; + +/*! + * @mfn WEIGHT + * @brief Number of relevant positions in a shape. + * + * @signature WEIGHT::VALUE; + * + * @tparam T The Shape type to query. + * @return VALUE The number of relevant positions in a shape. + */ + +// TODO(holtgrew): Should probably go to wherever shapes are defined. + +template +struct WEIGHT: + LENGTH +{ +}; +template +struct WEIGHT: + WEIGHT +{ +}; + +////////////////////////////////////////////////////////////////////////////// + +//Iterator: see basic_iterator.h + +////////////////////////////////////////////////////////////////////////////// + + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_BASIC_TYPE_H_ diff --git a/seqan/basic/basic_view.h b/seqan/basic/basic_view.h new file mode 100644 index 0000000..debdcfc --- /dev/null +++ b/seqan/basic/basic_view.h @@ -0,0 +1,190 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2013 NVIDIA Corporation +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of NVIDIA Corporation nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Enrico Siragusa +// ========================================================================== + +#ifndef SEQAN_BASIC_VIEW_H +#define SEQAN_BASIC_VIEW_H + +namespace seqan { + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Metafunction View +// ---------------------------------------------------------------------------- + +/*! + * @mfn View + * @headerfile + * @brief Converts a given type into its view type. + * + * @signature View::Type; + * + * @tparam TObject The type to be converted into a view type. + * @return Type The resulting view type. + * + * This metafunction is used to convert device containers into views of device containers. + * Subsequently, the view of a device container can be safely passed to and used in device space. + * On the host, a view of a @link String @endlink is equivalent to an @link SegmentableConcept#Infix @endlink of the complete string. + * @link RemoveView @endlink is the inverse of this metafunction. + * + * @see RemoveView + * @see Device + * @see SegmentableConcept#Infix + */ + +template +struct View +{ + typedef TObject Type; +}; + +template +struct View +{ + typedef typename View::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction RemoveView +// ---------------------------------------------------------------------------- + +/*! + * @mfn RemoveView + * @headerfile + * @brief Converts a given view type into its original type. + * + * @signature RemoveView::Type; + * + * @tparam TObject The view type to be converted into its original type. + * @return Type The resulting original type. + * + * @link View @endlink is the inverse of this metafunction. + * + * @see View + */ + +template +struct RemoveView +{ + typedef TObject Type; +}; + +template +struct RemoveView +{ + typedef typename RemoveView::Type const Type; +}; + +// ---------------------------------------------------------------------------- +// Metafunction IsView +// ---------------------------------------------------------------------------- + +/*! + * @mfn IsView + * @headerfile + * @brief Tests if a given type is a view type. + * + * @signature IsView::Type; + * + * @tparam TObject The type to be tested for being a view type. + * @return Type @link LogicalValuesTags#True @endlink or @link LogicalValuesTags#False @endlink. + * + * @see View + * @see RemoveView + */ + +template +struct IsView : public False {}; + +template +struct IsView : public IsView {}; + +// ---------------------------------------------------------------------------- +// Metafunction IfView +// ---------------------------------------------------------------------------- + +template +struct IfView +{ + typedef typename If, T1, T2>::Type Type; +}; + +// ============================================================================ +// Functions +// ============================================================================ + +// ---------------------------------------------------------------------------- +// Function view() +// ---------------------------------------------------------------------------- + +/*! + * @fn TView view + * @headerfile + * @brief Returns the view of a given object. + * + * @signature TView view(object); + * + * @param[in] object A generic object. + * @return TView The @link View @endlink type of the given object. + * + * @see View + * @see IsView + */ + +template +inline typename View::Type +view(TObject & object) +{ + return typename View::Type(object); +} + +template +inline typename View::Type +view(TObject const & object) +{ + return typename View::Type(object); +} + +template +inline typename View::Type +view(TObject * object) +{ + return typename View::Type(value(object)); +} + +} // namespace seqan + +#endif // #ifndef SEQAN_BASIC_VIEW_H diff --git a/seqan/basic/boost_preprocessor_subset.h b/seqan/basic/boost_preprocessor_subset.h new file mode 100644 index 0000000..634568a --- /dev/null +++ b/seqan/basic/boost_preprocessor_subset.h @@ -0,0 +1,4850 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Taken from Boost preprocessors library, Boost version 1.47. We extracted +// the minimal subset (header-wise) for supporting the concepts. +// +// There is currently no plan to incorporate more of Boost into SeqAn and +// thus this can be seen as a quick hack to get BCCL's nice syntax. It is +// probably a bad idea to repeat this. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_ + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/tuple/rem.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_TUPLE_REM_HPP +// # define SEQAN_PREPROCESSOR_TUPLE_REM_HPP +# +// # include +# +# /* SEQAN_PP_TUPLE_REM */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_TUPLE_REM(size) SEQAN_PP_TUPLE_REM_I(size) +// # else +// # define SEQAN_PP_TUPLE_REM(size) SEQAN_PP_TUPLE_REM_OO((size)) +// # define SEQAN_PP_TUPLE_REM_OO(par) SEQAN_PP_TUPLE_REM_I ## par +// # endif +# +# define SEQAN_PP_TUPLE_REM_I(size) SEQAN_PP_TUPLE_REM_ ## size +# +# define SEQAN_PP_TUPLE_REM_0() +# define SEQAN_PP_TUPLE_REM_1(a) a +# define SEQAN_PP_TUPLE_REM_2(a, b) a, b +# define SEQAN_PP_TUPLE_REM_3(a, b, c) a, b, c +# define SEQAN_PP_TUPLE_REM_4(a, b, c, d) a, b, c, d +# define SEQAN_PP_TUPLE_REM_5(a, b, c, d, e) a, b, c, d, e +# define SEQAN_PP_TUPLE_REM_6(a, b, c, d, e, f) a, b, c, d, e, f +# define SEQAN_PP_TUPLE_REM_7(a, b, c, d, e, f, g) a, b, c, d, e, f, g +# define SEQAN_PP_TUPLE_REM_8(a, b, c, d, e, f, g, h) a, b, c, d, e, f, g, h +# define SEQAN_PP_TUPLE_REM_9(a, b, c, d, e, f, g, h, i) a, b, c, d, e, f, g, h, i +# define SEQAN_PP_TUPLE_REM_10(a, b, c, d, e, f, g, h, i, j) a, b, c, d, e, f, g, h, i, j +# define SEQAN_PP_TUPLE_REM_11(a, b, c, d, e, f, g, h, i, j, k) a, b, c, d, e, f, g, h, i, j, k +# define SEQAN_PP_TUPLE_REM_12(a, b, c, d, e, f, g, h, i, j, k, l) a, b, c, d, e, f, g, h, i, j, k, l +# define SEQAN_PP_TUPLE_REM_13(a, b, c, d, e, f, g, h, i, j, k, l, m) a, b, c, d, e, f, g, h, i, j, k, l, m +# define SEQAN_PP_TUPLE_REM_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n) a, b, c, d, e, f, g, h, i, j, k, l, m, n +# define SEQAN_PP_TUPLE_REM_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o +# define SEQAN_PP_TUPLE_REM_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p +# define SEQAN_PP_TUPLE_REM_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q +# define SEQAN_PP_TUPLE_REM_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r +# define SEQAN_PP_TUPLE_REM_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s +# define SEQAN_PP_TUPLE_REM_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t +# define SEQAN_PP_TUPLE_REM_21(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u +# define SEQAN_PP_TUPLE_REM_22(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v +# define SEQAN_PP_TUPLE_REM_23(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w +# define SEQAN_PP_TUPLE_REM_24(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x +# define SEQAN_PP_TUPLE_REM_25(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y +# +# /* SEQAN_PP_TUPLE_REM_CTOR */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_TUPLE_REM_CTOR(size, tuple) SEQAN_PP_TUPLE_REM_CTOR_I(SEQAN_PP_TUPLE_REM(size), tuple) +// # else +// # define SEQAN_PP_TUPLE_REM_CTOR(size, tuple) SEQAN_PP_TUPLE_REM_CTOR_D(size, tuple) +// # define SEQAN_PP_TUPLE_REM_CTOR_D(size, tuple) SEQAN_PP_TUPLE_REM_CTOR_I(SEQAN_PP_TUPLE_REM(size), tuple) +// # endif +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_TUPLE_REM_CTOR_I(ext, tuple) ext tuple +// # else +// # define SEQAN_PP_TUPLE_REM_CTOR_I(ext, tuple) SEQAN_PP_TUPLE_REM_CTOR_OO((ext, tuple)) +// # define SEQAN_PP_TUPLE_REM_CTOR_OO(par) SEQAN_PP_TUPLE_REM_CTOR_II ## par +// # define SEQAN_PP_TUPLE_REM_CTOR_II(ext, tuple) ext ## tuple +// # endif +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/tuple/elem.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_TUPLE_ELEM_HPP +// # define SEQAN_PREPROCESSOR_TUPLE_ELEM_HPP +# +// # include +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_TUPLE_ELEM(size, index, tuple) SEQAN_PP_TUPLE_ELEM_I(size, index, tuple) +// # else +// # define SEQAN_PP_TUPLE_ELEM(size, index, tuple) SEQAN_PP_TUPLE_ELEM_OO((size, index, tuple)) +// # define SEQAN_PP_TUPLE_ELEM_OO(par) SEQAN_PP_TUPLE_ELEM_I ## par +// # endif +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +// # define SEQAN_PP_TUPLE_ELEM_I(s, i, t) SEQAN_PP_TUPLE_ELEM_ ## s ## _ ## i ## t +#ifdef STDLIB_VS // # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +# define SEQAN_PP_TUPLE_ELEM_I(s, i, t) SEQAN_PP_TUPLE_ELEM_II(SEQAN_PP_TUPLE_ELEM_ ## s ## _ ## i t) +# define SEQAN_PP_TUPLE_ELEM_II(res) res +#else // #ifdef STDLIB_VS +# define SEQAN_PP_TUPLE_ELEM_I(s, i, t) SEQAN_PP_TUPLE_ELEM_ ## s ## _ ## i t +#endif // #ifdef STDLIB_VS +# +# define SEQAN_PP_TUPLE_ELEM_1_0(a) a +# +# define SEQAN_PP_TUPLE_ELEM_2_0(a, b) a +# define SEQAN_PP_TUPLE_ELEM_2_1(a, b) b +# +# define SEQAN_PP_TUPLE_ELEM_3_0(a, b, c) a +# define SEQAN_PP_TUPLE_ELEM_3_1(a, b, c) b +# define SEQAN_PP_TUPLE_ELEM_3_2(a, b, c) c +# +# define SEQAN_PP_TUPLE_ELEM_4_0(a, b, c, d) a +# define SEQAN_PP_TUPLE_ELEM_4_1(a, b, c, d) b +# define SEQAN_PP_TUPLE_ELEM_4_2(a, b, c, d) c +# define SEQAN_PP_TUPLE_ELEM_4_3(a, b, c, d) d +# +# define SEQAN_PP_TUPLE_ELEM_5_0(a, b, c, d, e) a +# define SEQAN_PP_TUPLE_ELEM_5_1(a, b, c, d, e) b +# define SEQAN_PP_TUPLE_ELEM_5_2(a, b, c, d, e) c +# define SEQAN_PP_TUPLE_ELEM_5_3(a, b, c, d, e) d +# define SEQAN_PP_TUPLE_ELEM_5_4(a, b, c, d, e) e +# +# define SEQAN_PP_TUPLE_ELEM_6_0(a, b, c, d, e, f) a +# define SEQAN_PP_TUPLE_ELEM_6_1(a, b, c, d, e, f) b +# define SEQAN_PP_TUPLE_ELEM_6_2(a, b, c, d, e, f) c +# define SEQAN_PP_TUPLE_ELEM_6_3(a, b, c, d, e, f) d +# define SEQAN_PP_TUPLE_ELEM_6_4(a, b, c, d, e, f) e +# define SEQAN_PP_TUPLE_ELEM_6_5(a, b, c, d, e, f) f +# +# define SEQAN_PP_TUPLE_ELEM_7_0(a, b, c, d, e, f, g) a +# define SEQAN_PP_TUPLE_ELEM_7_1(a, b, c, d, e, f, g) b +# define SEQAN_PP_TUPLE_ELEM_7_2(a, b, c, d, e, f, g) c +# define SEQAN_PP_TUPLE_ELEM_7_3(a, b, c, d, e, f, g) d +# define SEQAN_PP_TUPLE_ELEM_7_4(a, b, c, d, e, f, g) e +# define SEQAN_PP_TUPLE_ELEM_7_5(a, b, c, d, e, f, g) f +# define SEQAN_PP_TUPLE_ELEM_7_6(a, b, c, d, e, f, g) g +# +# define SEQAN_PP_TUPLE_ELEM_8_0(a, b, c, d, e, f, g, h) a +# define SEQAN_PP_TUPLE_ELEM_8_1(a, b, c, d, e, f, g, h) b +# define SEQAN_PP_TUPLE_ELEM_8_2(a, b, c, d, e, f, g, h) c +# define SEQAN_PP_TUPLE_ELEM_8_3(a, b, c, d, e, f, g, h) d +# define SEQAN_PP_TUPLE_ELEM_8_4(a, b, c, d, e, f, g, h) e +# define SEQAN_PP_TUPLE_ELEM_8_5(a, b, c, d, e, f, g, h) f +# define SEQAN_PP_TUPLE_ELEM_8_6(a, b, c, d, e, f, g, h) g +# define SEQAN_PP_TUPLE_ELEM_8_7(a, b, c, d, e, f, g, h) h +# +# define SEQAN_PP_TUPLE_ELEM_9_0(a, b, c, d, e, f, g, h, i) a +# define SEQAN_PP_TUPLE_ELEM_9_1(a, b, c, d, e, f, g, h, i) b +# define SEQAN_PP_TUPLE_ELEM_9_2(a, b, c, d, e, f, g, h, i) c +# define SEQAN_PP_TUPLE_ELEM_9_3(a, b, c, d, e, f, g, h, i) d +# define SEQAN_PP_TUPLE_ELEM_9_4(a, b, c, d, e, f, g, h, i) e +# define SEQAN_PP_TUPLE_ELEM_9_5(a, b, c, d, e, f, g, h, i) f +# define SEQAN_PP_TUPLE_ELEM_9_6(a, b, c, d, e, f, g, h, i) g +# define SEQAN_PP_TUPLE_ELEM_9_7(a, b, c, d, e, f, g, h, i) h +# define SEQAN_PP_TUPLE_ELEM_9_8(a, b, c, d, e, f, g, h, i) i +# +# define SEQAN_PP_TUPLE_ELEM_10_0(a, b, c, d, e, f, g, h, i, j) a +# define SEQAN_PP_TUPLE_ELEM_10_1(a, b, c, d, e, f, g, h, i, j) b +# define SEQAN_PP_TUPLE_ELEM_10_2(a, b, c, d, e, f, g, h, i, j) c +# define SEQAN_PP_TUPLE_ELEM_10_3(a, b, c, d, e, f, g, h, i, j) d +# define SEQAN_PP_TUPLE_ELEM_10_4(a, b, c, d, e, f, g, h, i, j) e +# define SEQAN_PP_TUPLE_ELEM_10_5(a, b, c, d, e, f, g, h, i, j) f +# define SEQAN_PP_TUPLE_ELEM_10_6(a, b, c, d, e, f, g, h, i, j) g +# define SEQAN_PP_TUPLE_ELEM_10_7(a, b, c, d, e, f, g, h, i, j) h +# define SEQAN_PP_TUPLE_ELEM_10_8(a, b, c, d, e, f, g, h, i, j) i +# define SEQAN_PP_TUPLE_ELEM_10_9(a, b, c, d, e, f, g, h, i, j) j +# +# define SEQAN_PP_TUPLE_ELEM_11_0(a, b, c, d, e, f, g, h, i, j, k) a +# define SEQAN_PP_TUPLE_ELEM_11_1(a, b, c, d, e, f, g, h, i, j, k) b +# define SEQAN_PP_TUPLE_ELEM_11_2(a, b, c, d, e, f, g, h, i, j, k) c +# define SEQAN_PP_TUPLE_ELEM_11_3(a, b, c, d, e, f, g, h, i, j, k) d +# define SEQAN_PP_TUPLE_ELEM_11_4(a, b, c, d, e, f, g, h, i, j, k) e +# define SEQAN_PP_TUPLE_ELEM_11_5(a, b, c, d, e, f, g, h, i, j, k) f +# define SEQAN_PP_TUPLE_ELEM_11_6(a, b, c, d, e, f, g, h, i, j, k) g +# define SEQAN_PP_TUPLE_ELEM_11_7(a, b, c, d, e, f, g, h, i, j, k) h +# define SEQAN_PP_TUPLE_ELEM_11_8(a, b, c, d, e, f, g, h, i, j, k) i +# define SEQAN_PP_TUPLE_ELEM_11_9(a, b, c, d, e, f, g, h, i, j, k) j +# define SEQAN_PP_TUPLE_ELEM_11_10(a, b, c, d, e, f, g, h, i, j, k) k +# +# define SEQAN_PP_TUPLE_ELEM_12_0(a, b, c, d, e, f, g, h, i, j, k, l) a +# define SEQAN_PP_TUPLE_ELEM_12_1(a, b, c, d, e, f, g, h, i, j, k, l) b +# define SEQAN_PP_TUPLE_ELEM_12_2(a, b, c, d, e, f, g, h, i, j, k, l) c +# define SEQAN_PP_TUPLE_ELEM_12_3(a, b, c, d, e, f, g, h, i, j, k, l) d +# define SEQAN_PP_TUPLE_ELEM_12_4(a, b, c, d, e, f, g, h, i, j, k, l) e +# define SEQAN_PP_TUPLE_ELEM_12_5(a, b, c, d, e, f, g, h, i, j, k, l) f +# define SEQAN_PP_TUPLE_ELEM_12_6(a, b, c, d, e, f, g, h, i, j, k, l) g +# define SEQAN_PP_TUPLE_ELEM_12_7(a, b, c, d, e, f, g, h, i, j, k, l) h +# define SEQAN_PP_TUPLE_ELEM_12_8(a, b, c, d, e, f, g, h, i, j, k, l) i +# define SEQAN_PP_TUPLE_ELEM_12_9(a, b, c, d, e, f, g, h, i, j, k, l) j +# define SEQAN_PP_TUPLE_ELEM_12_10(a, b, c, d, e, f, g, h, i, j, k, l) k +# define SEQAN_PP_TUPLE_ELEM_12_11(a, b, c, d, e, f, g, h, i, j, k, l) l +# +# define SEQAN_PP_TUPLE_ELEM_13_0(a, b, c, d, e, f, g, h, i, j, k, l, m) a +# define SEQAN_PP_TUPLE_ELEM_13_1(a, b, c, d, e, f, g, h, i, j, k, l, m) b +# define SEQAN_PP_TUPLE_ELEM_13_2(a, b, c, d, e, f, g, h, i, j, k, l, m) c +# define SEQAN_PP_TUPLE_ELEM_13_3(a, b, c, d, e, f, g, h, i, j, k, l, m) d +# define SEQAN_PP_TUPLE_ELEM_13_4(a, b, c, d, e, f, g, h, i, j, k, l, m) e +# define SEQAN_PP_TUPLE_ELEM_13_5(a, b, c, d, e, f, g, h, i, j, k, l, m) f +# define SEQAN_PP_TUPLE_ELEM_13_6(a, b, c, d, e, f, g, h, i, j, k, l, m) g +# define SEQAN_PP_TUPLE_ELEM_13_7(a, b, c, d, e, f, g, h, i, j, k, l, m) h +# define SEQAN_PP_TUPLE_ELEM_13_8(a, b, c, d, e, f, g, h, i, j, k, l, m) i +# define SEQAN_PP_TUPLE_ELEM_13_9(a, b, c, d, e, f, g, h, i, j, k, l, m) j +# define SEQAN_PP_TUPLE_ELEM_13_10(a, b, c, d, e, f, g, h, i, j, k, l, m) k +# define SEQAN_PP_TUPLE_ELEM_13_11(a, b, c, d, e, f, g, h, i, j, k, l, m) l +# define SEQAN_PP_TUPLE_ELEM_13_12(a, b, c, d, e, f, g, h, i, j, k, l, m) m +# +# define SEQAN_PP_TUPLE_ELEM_14_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n) a +# define SEQAN_PP_TUPLE_ELEM_14_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n) b +# define SEQAN_PP_TUPLE_ELEM_14_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n) c +# define SEQAN_PP_TUPLE_ELEM_14_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n) d +# define SEQAN_PP_TUPLE_ELEM_14_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n) e +# define SEQAN_PP_TUPLE_ELEM_14_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n) f +# define SEQAN_PP_TUPLE_ELEM_14_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n) g +# define SEQAN_PP_TUPLE_ELEM_14_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n) h +# define SEQAN_PP_TUPLE_ELEM_14_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n) i +# define SEQAN_PP_TUPLE_ELEM_14_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n) j +# define SEQAN_PP_TUPLE_ELEM_14_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n) k +# define SEQAN_PP_TUPLE_ELEM_14_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n) l +# define SEQAN_PP_TUPLE_ELEM_14_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n) m +# define SEQAN_PP_TUPLE_ELEM_14_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n) n +# +# define SEQAN_PP_TUPLE_ELEM_15_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) a +# define SEQAN_PP_TUPLE_ELEM_15_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) b +# define SEQAN_PP_TUPLE_ELEM_15_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) c +# define SEQAN_PP_TUPLE_ELEM_15_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) d +# define SEQAN_PP_TUPLE_ELEM_15_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) e +# define SEQAN_PP_TUPLE_ELEM_15_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) f +# define SEQAN_PP_TUPLE_ELEM_15_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) g +# define SEQAN_PP_TUPLE_ELEM_15_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) h +# define SEQAN_PP_TUPLE_ELEM_15_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) i +# define SEQAN_PP_TUPLE_ELEM_15_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) j +# define SEQAN_PP_TUPLE_ELEM_15_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) k +# define SEQAN_PP_TUPLE_ELEM_15_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) l +# define SEQAN_PP_TUPLE_ELEM_15_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) m +# define SEQAN_PP_TUPLE_ELEM_15_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) n +# define SEQAN_PP_TUPLE_ELEM_15_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) o +# +# define SEQAN_PP_TUPLE_ELEM_16_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) a +# define SEQAN_PP_TUPLE_ELEM_16_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) b +# define SEQAN_PP_TUPLE_ELEM_16_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) c +# define SEQAN_PP_TUPLE_ELEM_16_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) d +# define SEQAN_PP_TUPLE_ELEM_16_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) e +# define SEQAN_PP_TUPLE_ELEM_16_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) f +# define SEQAN_PP_TUPLE_ELEM_16_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) g +# define SEQAN_PP_TUPLE_ELEM_16_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) h +# define SEQAN_PP_TUPLE_ELEM_16_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) i +# define SEQAN_PP_TUPLE_ELEM_16_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) j +# define SEQAN_PP_TUPLE_ELEM_16_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) k +# define SEQAN_PP_TUPLE_ELEM_16_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) l +# define SEQAN_PP_TUPLE_ELEM_16_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) m +# define SEQAN_PP_TUPLE_ELEM_16_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) n +# define SEQAN_PP_TUPLE_ELEM_16_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) o +# define SEQAN_PP_TUPLE_ELEM_16_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) p +# +# define SEQAN_PP_TUPLE_ELEM_17_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) a +# define SEQAN_PP_TUPLE_ELEM_17_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) b +# define SEQAN_PP_TUPLE_ELEM_17_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) c +# define SEQAN_PP_TUPLE_ELEM_17_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) d +# define SEQAN_PP_TUPLE_ELEM_17_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) e +# define SEQAN_PP_TUPLE_ELEM_17_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) f +# define SEQAN_PP_TUPLE_ELEM_17_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) g +# define SEQAN_PP_TUPLE_ELEM_17_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) h +# define SEQAN_PP_TUPLE_ELEM_17_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) i +# define SEQAN_PP_TUPLE_ELEM_17_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) j +# define SEQAN_PP_TUPLE_ELEM_17_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) k +# define SEQAN_PP_TUPLE_ELEM_17_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) l +# define SEQAN_PP_TUPLE_ELEM_17_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) m +# define SEQAN_PP_TUPLE_ELEM_17_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) n +# define SEQAN_PP_TUPLE_ELEM_17_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) o +# define SEQAN_PP_TUPLE_ELEM_17_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) p +# define SEQAN_PP_TUPLE_ELEM_17_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) q +# +# define SEQAN_PP_TUPLE_ELEM_18_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) a +# define SEQAN_PP_TUPLE_ELEM_18_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) b +# define SEQAN_PP_TUPLE_ELEM_18_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) c +# define SEQAN_PP_TUPLE_ELEM_18_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) d +# define SEQAN_PP_TUPLE_ELEM_18_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) e +# define SEQAN_PP_TUPLE_ELEM_18_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) f +# define SEQAN_PP_TUPLE_ELEM_18_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) g +# define SEQAN_PP_TUPLE_ELEM_18_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) h +# define SEQAN_PP_TUPLE_ELEM_18_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) i +# define SEQAN_PP_TUPLE_ELEM_18_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) j +# define SEQAN_PP_TUPLE_ELEM_18_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) k +# define SEQAN_PP_TUPLE_ELEM_18_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) l +# define SEQAN_PP_TUPLE_ELEM_18_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) m +# define SEQAN_PP_TUPLE_ELEM_18_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) n +# define SEQAN_PP_TUPLE_ELEM_18_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) o +# define SEQAN_PP_TUPLE_ELEM_18_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) p +# define SEQAN_PP_TUPLE_ELEM_18_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) q +# define SEQAN_PP_TUPLE_ELEM_18_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) r +# +# define SEQAN_PP_TUPLE_ELEM_19_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) a +# define SEQAN_PP_TUPLE_ELEM_19_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) b +# define SEQAN_PP_TUPLE_ELEM_19_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) c +# define SEQAN_PP_TUPLE_ELEM_19_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) d +# define SEQAN_PP_TUPLE_ELEM_19_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) e +# define SEQAN_PP_TUPLE_ELEM_19_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) f +# define SEQAN_PP_TUPLE_ELEM_19_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) g +# define SEQAN_PP_TUPLE_ELEM_19_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) h +# define SEQAN_PP_TUPLE_ELEM_19_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) i +# define SEQAN_PP_TUPLE_ELEM_19_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) j +# define SEQAN_PP_TUPLE_ELEM_19_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) k +# define SEQAN_PP_TUPLE_ELEM_19_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) l +# define SEQAN_PP_TUPLE_ELEM_19_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) m +# define SEQAN_PP_TUPLE_ELEM_19_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) n +# define SEQAN_PP_TUPLE_ELEM_19_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) o +# define SEQAN_PP_TUPLE_ELEM_19_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) p +# define SEQAN_PP_TUPLE_ELEM_19_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) q +# define SEQAN_PP_TUPLE_ELEM_19_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) r +# define SEQAN_PP_TUPLE_ELEM_19_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) s +# +# define SEQAN_PP_TUPLE_ELEM_20_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) a +# define SEQAN_PP_TUPLE_ELEM_20_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) b +# define SEQAN_PP_TUPLE_ELEM_20_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) c +# define SEQAN_PP_TUPLE_ELEM_20_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) d +# define SEQAN_PP_TUPLE_ELEM_20_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) e +# define SEQAN_PP_TUPLE_ELEM_20_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) f +# define SEQAN_PP_TUPLE_ELEM_20_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) g +# define SEQAN_PP_TUPLE_ELEM_20_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) h +# define SEQAN_PP_TUPLE_ELEM_20_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) i +# define SEQAN_PP_TUPLE_ELEM_20_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) j +# define SEQAN_PP_TUPLE_ELEM_20_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) k +# define SEQAN_PP_TUPLE_ELEM_20_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) l +# define SEQAN_PP_TUPLE_ELEM_20_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) m +# define SEQAN_PP_TUPLE_ELEM_20_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) n +# define SEQAN_PP_TUPLE_ELEM_20_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) o +# define SEQAN_PP_TUPLE_ELEM_20_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) p +# define SEQAN_PP_TUPLE_ELEM_20_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) q +# define SEQAN_PP_TUPLE_ELEM_20_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) r +# define SEQAN_PP_TUPLE_ELEM_20_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) s +# define SEQAN_PP_TUPLE_ELEM_20_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) t +# +# define SEQAN_PP_TUPLE_ELEM_21_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) a +# define SEQAN_PP_TUPLE_ELEM_21_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) b +# define SEQAN_PP_TUPLE_ELEM_21_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) c +# define SEQAN_PP_TUPLE_ELEM_21_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) d +# define SEQAN_PP_TUPLE_ELEM_21_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) e +# define SEQAN_PP_TUPLE_ELEM_21_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) f +# define SEQAN_PP_TUPLE_ELEM_21_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) g +# define SEQAN_PP_TUPLE_ELEM_21_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) h +# define SEQAN_PP_TUPLE_ELEM_21_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) i +# define SEQAN_PP_TUPLE_ELEM_21_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) j +# define SEQAN_PP_TUPLE_ELEM_21_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) k +# define SEQAN_PP_TUPLE_ELEM_21_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) l +# define SEQAN_PP_TUPLE_ELEM_21_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) m +# define SEQAN_PP_TUPLE_ELEM_21_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) n +# define SEQAN_PP_TUPLE_ELEM_21_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) o +# define SEQAN_PP_TUPLE_ELEM_21_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) p +# define SEQAN_PP_TUPLE_ELEM_21_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) q +# define SEQAN_PP_TUPLE_ELEM_21_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) r +# define SEQAN_PP_TUPLE_ELEM_21_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) s +# define SEQAN_PP_TUPLE_ELEM_21_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) t +# define SEQAN_PP_TUPLE_ELEM_21_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) u +# +# define SEQAN_PP_TUPLE_ELEM_22_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) a +# define SEQAN_PP_TUPLE_ELEM_22_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) b +# define SEQAN_PP_TUPLE_ELEM_22_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) c +# define SEQAN_PP_TUPLE_ELEM_22_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) d +# define SEQAN_PP_TUPLE_ELEM_22_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) e +# define SEQAN_PP_TUPLE_ELEM_22_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) f +# define SEQAN_PP_TUPLE_ELEM_22_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) g +# define SEQAN_PP_TUPLE_ELEM_22_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) h +# define SEQAN_PP_TUPLE_ELEM_22_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) i +# define SEQAN_PP_TUPLE_ELEM_22_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) j +# define SEQAN_PP_TUPLE_ELEM_22_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) k +# define SEQAN_PP_TUPLE_ELEM_22_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) l +# define SEQAN_PP_TUPLE_ELEM_22_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) m +# define SEQAN_PP_TUPLE_ELEM_22_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) n +# define SEQAN_PP_TUPLE_ELEM_22_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) o +# define SEQAN_PP_TUPLE_ELEM_22_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) p +# define SEQAN_PP_TUPLE_ELEM_22_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) q +# define SEQAN_PP_TUPLE_ELEM_22_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) r +# define SEQAN_PP_TUPLE_ELEM_22_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) s +# define SEQAN_PP_TUPLE_ELEM_22_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) t +# define SEQAN_PP_TUPLE_ELEM_22_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) u +# define SEQAN_PP_TUPLE_ELEM_22_21(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) v +# +# define SEQAN_PP_TUPLE_ELEM_23_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) a +# define SEQAN_PP_TUPLE_ELEM_23_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) b +# define SEQAN_PP_TUPLE_ELEM_23_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) c +# define SEQAN_PP_TUPLE_ELEM_23_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) d +# define SEQAN_PP_TUPLE_ELEM_23_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) e +# define SEQAN_PP_TUPLE_ELEM_23_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) f +# define SEQAN_PP_TUPLE_ELEM_23_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) g +# define SEQAN_PP_TUPLE_ELEM_23_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) h +# define SEQAN_PP_TUPLE_ELEM_23_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) i +# define SEQAN_PP_TUPLE_ELEM_23_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) j +# define SEQAN_PP_TUPLE_ELEM_23_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) k +# define SEQAN_PP_TUPLE_ELEM_23_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) l +# define SEQAN_PP_TUPLE_ELEM_23_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) m +# define SEQAN_PP_TUPLE_ELEM_23_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) n +# define SEQAN_PP_TUPLE_ELEM_23_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) o +# define SEQAN_PP_TUPLE_ELEM_23_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) p +# define SEQAN_PP_TUPLE_ELEM_23_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) q +# define SEQAN_PP_TUPLE_ELEM_23_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) r +# define SEQAN_PP_TUPLE_ELEM_23_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) s +# define SEQAN_PP_TUPLE_ELEM_23_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) t +# define SEQAN_PP_TUPLE_ELEM_23_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) u +# define SEQAN_PP_TUPLE_ELEM_23_21(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) v +# define SEQAN_PP_TUPLE_ELEM_23_22(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) w +# +# define SEQAN_PP_TUPLE_ELEM_24_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) a +# define SEQAN_PP_TUPLE_ELEM_24_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) b +# define SEQAN_PP_TUPLE_ELEM_24_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) c +# define SEQAN_PP_TUPLE_ELEM_24_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) d +# define SEQAN_PP_TUPLE_ELEM_24_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) e +# define SEQAN_PP_TUPLE_ELEM_24_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) f +# define SEQAN_PP_TUPLE_ELEM_24_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) g +# define SEQAN_PP_TUPLE_ELEM_24_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) h +# define SEQAN_PP_TUPLE_ELEM_24_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) i +# define SEQAN_PP_TUPLE_ELEM_24_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) j +# define SEQAN_PP_TUPLE_ELEM_24_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) k +# define SEQAN_PP_TUPLE_ELEM_24_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) l +# define SEQAN_PP_TUPLE_ELEM_24_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) m +# define SEQAN_PP_TUPLE_ELEM_24_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) n +# define SEQAN_PP_TUPLE_ELEM_24_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) o +# define SEQAN_PP_TUPLE_ELEM_24_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) p +# define SEQAN_PP_TUPLE_ELEM_24_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) q +# define SEQAN_PP_TUPLE_ELEM_24_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) r +# define SEQAN_PP_TUPLE_ELEM_24_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) s +# define SEQAN_PP_TUPLE_ELEM_24_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) t +# define SEQAN_PP_TUPLE_ELEM_24_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) u +# define SEQAN_PP_TUPLE_ELEM_24_21(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) v +# define SEQAN_PP_TUPLE_ELEM_24_22(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) w +# define SEQAN_PP_TUPLE_ELEM_24_23(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) x +# +# define SEQAN_PP_TUPLE_ELEM_25_0(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) a +# define SEQAN_PP_TUPLE_ELEM_25_1(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) b +# define SEQAN_PP_TUPLE_ELEM_25_2(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) c +# define SEQAN_PP_TUPLE_ELEM_25_3(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) d +# define SEQAN_PP_TUPLE_ELEM_25_4(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) e +# define SEQAN_PP_TUPLE_ELEM_25_5(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) f +# define SEQAN_PP_TUPLE_ELEM_25_6(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) g +# define SEQAN_PP_TUPLE_ELEM_25_7(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) h +# define SEQAN_PP_TUPLE_ELEM_25_8(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) i +# define SEQAN_PP_TUPLE_ELEM_25_9(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) j +# define SEQAN_PP_TUPLE_ELEM_25_10(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) k +# define SEQAN_PP_TUPLE_ELEM_25_11(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) l +# define SEQAN_PP_TUPLE_ELEM_25_12(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) m +# define SEQAN_PP_TUPLE_ELEM_25_13(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) n +# define SEQAN_PP_TUPLE_ELEM_25_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) o +# define SEQAN_PP_TUPLE_ELEM_25_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) p +# define SEQAN_PP_TUPLE_ELEM_25_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) q +# define SEQAN_PP_TUPLE_ELEM_25_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) r +# define SEQAN_PP_TUPLE_ELEM_25_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) s +# define SEQAN_PP_TUPLE_ELEM_25_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) t +# define SEQAN_PP_TUPLE_ELEM_25_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) u +# define SEQAN_PP_TUPLE_ELEM_25_21(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) v +# define SEQAN_PP_TUPLE_ELEM_25_22(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) w +# define SEQAN_PP_TUPLE_ELEM_25_23(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) x +# define SEQAN_PP_TUPLE_ELEM_25_24(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) y + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/seq/size.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_SEQ_SIZE_HPP +// # define SEQAN_PREPROCESSOR_SEQ_SIZE_HPP +# +// # include +// # include +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +// # define SEQAN_PP_SEQ_SIZE(seq) SEQAN_PP_SEQ_SIZE_I((seq)) +// # define SEQAN_PP_SEQ_SIZE_I(par) SEQAN_PP_SEQ_SIZE_II ## par +// # define SEQAN_PP_SEQ_SIZE_II(seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_SIZE_, SEQAN_PP_SEQ_SIZE_0 ## seq) +// # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() || SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +#ifdef STDLIB_VS +# define SEQAN_PP_SEQ_SIZE(seq) SEQAN_PP_SEQ_SIZE_I(seq) +# define SEQAN_PP_SEQ_SIZE_I(seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_SIZE_, SEQAN_PP_SEQ_SIZE_0 seq) +#else // #ifdef STDLIB_VS +// # elif defined(__IBMC__) || defined(__IBMCPP__) +// # define SEQAN_PP_SEQ_SIZE(seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_SIZE_, SEQAN_PP_CAT(SEQAN_PP_SEQ_SIZE_0, seq)) +// # else +# define SEQAN_PP_SEQ_SIZE(seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_SIZE_, SEQAN_PP_SEQ_SIZE_0 seq) +#endif // #ifdef STDLIB_VS + +# define SEQAN_PP_SEQ_SIZE_0(_) SEQAN_PP_SEQ_SIZE_1 +# define SEQAN_PP_SEQ_SIZE_1(_) SEQAN_PP_SEQ_SIZE_2 +# define SEQAN_PP_SEQ_SIZE_2(_) SEQAN_PP_SEQ_SIZE_3 +# define SEQAN_PP_SEQ_SIZE_3(_) SEQAN_PP_SEQ_SIZE_4 +# define SEQAN_PP_SEQ_SIZE_4(_) SEQAN_PP_SEQ_SIZE_5 +# define SEQAN_PP_SEQ_SIZE_5(_) SEQAN_PP_SEQ_SIZE_6 +# define SEQAN_PP_SEQ_SIZE_6(_) SEQAN_PP_SEQ_SIZE_7 +# define SEQAN_PP_SEQ_SIZE_7(_) SEQAN_PP_SEQ_SIZE_8 +# define SEQAN_PP_SEQ_SIZE_8(_) SEQAN_PP_SEQ_SIZE_9 +# define SEQAN_PP_SEQ_SIZE_9(_) SEQAN_PP_SEQ_SIZE_10 +# define SEQAN_PP_SEQ_SIZE_10(_) SEQAN_PP_SEQ_SIZE_11 +# define SEQAN_PP_SEQ_SIZE_11(_) SEQAN_PP_SEQ_SIZE_12 +# define SEQAN_PP_SEQ_SIZE_12(_) SEQAN_PP_SEQ_SIZE_13 +# define SEQAN_PP_SEQ_SIZE_13(_) SEQAN_PP_SEQ_SIZE_14 +# define SEQAN_PP_SEQ_SIZE_14(_) SEQAN_PP_SEQ_SIZE_15 +# define SEQAN_PP_SEQ_SIZE_15(_) SEQAN_PP_SEQ_SIZE_16 +# define SEQAN_PP_SEQ_SIZE_16(_) SEQAN_PP_SEQ_SIZE_17 +# define SEQAN_PP_SEQ_SIZE_17(_) SEQAN_PP_SEQ_SIZE_18 +# define SEQAN_PP_SEQ_SIZE_18(_) SEQAN_PP_SEQ_SIZE_19 +# define SEQAN_PP_SEQ_SIZE_19(_) SEQAN_PP_SEQ_SIZE_20 +# define SEQAN_PP_SEQ_SIZE_20(_) SEQAN_PP_SEQ_SIZE_21 +# define SEQAN_PP_SEQ_SIZE_21(_) SEQAN_PP_SEQ_SIZE_22 +# define SEQAN_PP_SEQ_SIZE_22(_) SEQAN_PP_SEQ_SIZE_23 +# define SEQAN_PP_SEQ_SIZE_23(_) SEQAN_PP_SEQ_SIZE_24 +# define SEQAN_PP_SEQ_SIZE_24(_) SEQAN_PP_SEQ_SIZE_25 +# define SEQAN_PP_SEQ_SIZE_25(_) SEQAN_PP_SEQ_SIZE_26 +# define SEQAN_PP_SEQ_SIZE_26(_) SEQAN_PP_SEQ_SIZE_27 +# define SEQAN_PP_SEQ_SIZE_27(_) SEQAN_PP_SEQ_SIZE_28 +# define SEQAN_PP_SEQ_SIZE_28(_) SEQAN_PP_SEQ_SIZE_29 +# define SEQAN_PP_SEQ_SIZE_29(_) SEQAN_PP_SEQ_SIZE_30 +# define SEQAN_PP_SEQ_SIZE_30(_) SEQAN_PP_SEQ_SIZE_31 +# define SEQAN_PP_SEQ_SIZE_31(_) SEQAN_PP_SEQ_SIZE_32 +# define SEQAN_PP_SEQ_SIZE_32(_) SEQAN_PP_SEQ_SIZE_33 +# define SEQAN_PP_SEQ_SIZE_33(_) SEQAN_PP_SEQ_SIZE_34 +# define SEQAN_PP_SEQ_SIZE_34(_) SEQAN_PP_SEQ_SIZE_35 +# define SEQAN_PP_SEQ_SIZE_35(_) SEQAN_PP_SEQ_SIZE_36 +# define SEQAN_PP_SEQ_SIZE_36(_) SEQAN_PP_SEQ_SIZE_37 +# define SEQAN_PP_SEQ_SIZE_37(_) SEQAN_PP_SEQ_SIZE_38 +# define SEQAN_PP_SEQ_SIZE_38(_) SEQAN_PP_SEQ_SIZE_39 +# define SEQAN_PP_SEQ_SIZE_39(_) SEQAN_PP_SEQ_SIZE_40 +# define SEQAN_PP_SEQ_SIZE_40(_) SEQAN_PP_SEQ_SIZE_41 +# define SEQAN_PP_SEQ_SIZE_41(_) SEQAN_PP_SEQ_SIZE_42 +# define SEQAN_PP_SEQ_SIZE_42(_) SEQAN_PP_SEQ_SIZE_43 +# define SEQAN_PP_SEQ_SIZE_43(_) SEQAN_PP_SEQ_SIZE_44 +# define SEQAN_PP_SEQ_SIZE_44(_) SEQAN_PP_SEQ_SIZE_45 +# define SEQAN_PP_SEQ_SIZE_45(_) SEQAN_PP_SEQ_SIZE_46 +# define SEQAN_PP_SEQ_SIZE_46(_) SEQAN_PP_SEQ_SIZE_47 +# define SEQAN_PP_SEQ_SIZE_47(_) SEQAN_PP_SEQ_SIZE_48 +# define SEQAN_PP_SEQ_SIZE_48(_) SEQAN_PP_SEQ_SIZE_49 +# define SEQAN_PP_SEQ_SIZE_49(_) SEQAN_PP_SEQ_SIZE_50 +# define SEQAN_PP_SEQ_SIZE_50(_) SEQAN_PP_SEQ_SIZE_51 +# define SEQAN_PP_SEQ_SIZE_51(_) SEQAN_PP_SEQ_SIZE_52 +# define SEQAN_PP_SEQ_SIZE_52(_) SEQAN_PP_SEQ_SIZE_53 +# define SEQAN_PP_SEQ_SIZE_53(_) SEQAN_PP_SEQ_SIZE_54 +# define SEQAN_PP_SEQ_SIZE_54(_) SEQAN_PP_SEQ_SIZE_55 +# define SEQAN_PP_SEQ_SIZE_55(_) SEQAN_PP_SEQ_SIZE_56 +# define SEQAN_PP_SEQ_SIZE_56(_) SEQAN_PP_SEQ_SIZE_57 +# define SEQAN_PP_SEQ_SIZE_57(_) SEQAN_PP_SEQ_SIZE_58 +# define SEQAN_PP_SEQ_SIZE_58(_) SEQAN_PP_SEQ_SIZE_59 +# define SEQAN_PP_SEQ_SIZE_59(_) SEQAN_PP_SEQ_SIZE_60 +# define SEQAN_PP_SEQ_SIZE_60(_) SEQAN_PP_SEQ_SIZE_61 +# define SEQAN_PP_SEQ_SIZE_61(_) SEQAN_PP_SEQ_SIZE_62 +# define SEQAN_PP_SEQ_SIZE_62(_) SEQAN_PP_SEQ_SIZE_63 +# define SEQAN_PP_SEQ_SIZE_63(_) SEQAN_PP_SEQ_SIZE_64 +# define SEQAN_PP_SEQ_SIZE_64(_) SEQAN_PP_SEQ_SIZE_65 +# define SEQAN_PP_SEQ_SIZE_65(_) SEQAN_PP_SEQ_SIZE_66 +# define SEQAN_PP_SEQ_SIZE_66(_) SEQAN_PP_SEQ_SIZE_67 +# define SEQAN_PP_SEQ_SIZE_67(_) SEQAN_PP_SEQ_SIZE_68 +# define SEQAN_PP_SEQ_SIZE_68(_) SEQAN_PP_SEQ_SIZE_69 +# define SEQAN_PP_SEQ_SIZE_69(_) SEQAN_PP_SEQ_SIZE_70 +# define SEQAN_PP_SEQ_SIZE_70(_) SEQAN_PP_SEQ_SIZE_71 +# define SEQAN_PP_SEQ_SIZE_71(_) SEQAN_PP_SEQ_SIZE_72 +# define SEQAN_PP_SEQ_SIZE_72(_) SEQAN_PP_SEQ_SIZE_73 +# define SEQAN_PP_SEQ_SIZE_73(_) SEQAN_PP_SEQ_SIZE_74 +# define SEQAN_PP_SEQ_SIZE_74(_) SEQAN_PP_SEQ_SIZE_75 +# define SEQAN_PP_SEQ_SIZE_75(_) SEQAN_PP_SEQ_SIZE_76 +# define SEQAN_PP_SEQ_SIZE_76(_) SEQAN_PP_SEQ_SIZE_77 +# define SEQAN_PP_SEQ_SIZE_77(_) SEQAN_PP_SEQ_SIZE_78 +# define SEQAN_PP_SEQ_SIZE_78(_) SEQAN_PP_SEQ_SIZE_79 +# define SEQAN_PP_SEQ_SIZE_79(_) SEQAN_PP_SEQ_SIZE_80 +# define SEQAN_PP_SEQ_SIZE_80(_) SEQAN_PP_SEQ_SIZE_81 +# define SEQAN_PP_SEQ_SIZE_81(_) SEQAN_PP_SEQ_SIZE_82 +# define SEQAN_PP_SEQ_SIZE_82(_) SEQAN_PP_SEQ_SIZE_83 +# define SEQAN_PP_SEQ_SIZE_83(_) SEQAN_PP_SEQ_SIZE_84 +# define SEQAN_PP_SEQ_SIZE_84(_) SEQAN_PP_SEQ_SIZE_85 +# define SEQAN_PP_SEQ_SIZE_85(_) SEQAN_PP_SEQ_SIZE_86 +# define SEQAN_PP_SEQ_SIZE_86(_) SEQAN_PP_SEQ_SIZE_87 +# define SEQAN_PP_SEQ_SIZE_87(_) SEQAN_PP_SEQ_SIZE_88 +# define SEQAN_PP_SEQ_SIZE_88(_) SEQAN_PP_SEQ_SIZE_89 +# define SEQAN_PP_SEQ_SIZE_89(_) SEQAN_PP_SEQ_SIZE_90 +# define SEQAN_PP_SEQ_SIZE_90(_) SEQAN_PP_SEQ_SIZE_91 +# define SEQAN_PP_SEQ_SIZE_91(_) SEQAN_PP_SEQ_SIZE_92 +# define SEQAN_PP_SEQ_SIZE_92(_) SEQAN_PP_SEQ_SIZE_93 +# define SEQAN_PP_SEQ_SIZE_93(_) SEQAN_PP_SEQ_SIZE_94 +# define SEQAN_PP_SEQ_SIZE_94(_) SEQAN_PP_SEQ_SIZE_95 +# define SEQAN_PP_SEQ_SIZE_95(_) SEQAN_PP_SEQ_SIZE_96 +# define SEQAN_PP_SEQ_SIZE_96(_) SEQAN_PP_SEQ_SIZE_97 +# define SEQAN_PP_SEQ_SIZE_97(_) SEQAN_PP_SEQ_SIZE_98 +# define SEQAN_PP_SEQ_SIZE_98(_) SEQAN_PP_SEQ_SIZE_99 +# define SEQAN_PP_SEQ_SIZE_99(_) SEQAN_PP_SEQ_SIZE_100 +# define SEQAN_PP_SEQ_SIZE_100(_) SEQAN_PP_SEQ_SIZE_101 +# define SEQAN_PP_SEQ_SIZE_101(_) SEQAN_PP_SEQ_SIZE_102 +# define SEQAN_PP_SEQ_SIZE_102(_) SEQAN_PP_SEQ_SIZE_103 +# define SEQAN_PP_SEQ_SIZE_103(_) SEQAN_PP_SEQ_SIZE_104 +# define SEQAN_PP_SEQ_SIZE_104(_) SEQAN_PP_SEQ_SIZE_105 +# define SEQAN_PP_SEQ_SIZE_105(_) SEQAN_PP_SEQ_SIZE_106 +# define SEQAN_PP_SEQ_SIZE_106(_) SEQAN_PP_SEQ_SIZE_107 +# define SEQAN_PP_SEQ_SIZE_107(_) SEQAN_PP_SEQ_SIZE_108 +# define SEQAN_PP_SEQ_SIZE_108(_) SEQAN_PP_SEQ_SIZE_109 +# define SEQAN_PP_SEQ_SIZE_109(_) SEQAN_PP_SEQ_SIZE_110 +# define SEQAN_PP_SEQ_SIZE_110(_) SEQAN_PP_SEQ_SIZE_111 +# define SEQAN_PP_SEQ_SIZE_111(_) SEQAN_PP_SEQ_SIZE_112 +# define SEQAN_PP_SEQ_SIZE_112(_) SEQAN_PP_SEQ_SIZE_113 +# define SEQAN_PP_SEQ_SIZE_113(_) SEQAN_PP_SEQ_SIZE_114 +# define SEQAN_PP_SEQ_SIZE_114(_) SEQAN_PP_SEQ_SIZE_115 +# define SEQAN_PP_SEQ_SIZE_115(_) SEQAN_PP_SEQ_SIZE_116 +# define SEQAN_PP_SEQ_SIZE_116(_) SEQAN_PP_SEQ_SIZE_117 +# define SEQAN_PP_SEQ_SIZE_117(_) SEQAN_PP_SEQ_SIZE_118 +# define SEQAN_PP_SEQ_SIZE_118(_) SEQAN_PP_SEQ_SIZE_119 +# define SEQAN_PP_SEQ_SIZE_119(_) SEQAN_PP_SEQ_SIZE_120 +# define SEQAN_PP_SEQ_SIZE_120(_) SEQAN_PP_SEQ_SIZE_121 +# define SEQAN_PP_SEQ_SIZE_121(_) SEQAN_PP_SEQ_SIZE_122 +# define SEQAN_PP_SEQ_SIZE_122(_) SEQAN_PP_SEQ_SIZE_123 +# define SEQAN_PP_SEQ_SIZE_123(_) SEQAN_PP_SEQ_SIZE_124 +# define SEQAN_PP_SEQ_SIZE_124(_) SEQAN_PP_SEQ_SIZE_125 +# define SEQAN_PP_SEQ_SIZE_125(_) SEQAN_PP_SEQ_SIZE_126 +# define SEQAN_PP_SEQ_SIZE_126(_) SEQAN_PP_SEQ_SIZE_127 +# define SEQAN_PP_SEQ_SIZE_127(_) SEQAN_PP_SEQ_SIZE_128 +# define SEQAN_PP_SEQ_SIZE_128(_) SEQAN_PP_SEQ_SIZE_129 +# define SEQAN_PP_SEQ_SIZE_129(_) SEQAN_PP_SEQ_SIZE_130 +# define SEQAN_PP_SEQ_SIZE_130(_) SEQAN_PP_SEQ_SIZE_131 +# define SEQAN_PP_SEQ_SIZE_131(_) SEQAN_PP_SEQ_SIZE_132 +# define SEQAN_PP_SEQ_SIZE_132(_) SEQAN_PP_SEQ_SIZE_133 +# define SEQAN_PP_SEQ_SIZE_133(_) SEQAN_PP_SEQ_SIZE_134 +# define SEQAN_PP_SEQ_SIZE_134(_) SEQAN_PP_SEQ_SIZE_135 +# define SEQAN_PP_SEQ_SIZE_135(_) SEQAN_PP_SEQ_SIZE_136 +# define SEQAN_PP_SEQ_SIZE_136(_) SEQAN_PP_SEQ_SIZE_137 +# define SEQAN_PP_SEQ_SIZE_137(_) SEQAN_PP_SEQ_SIZE_138 +# define SEQAN_PP_SEQ_SIZE_138(_) SEQAN_PP_SEQ_SIZE_139 +# define SEQAN_PP_SEQ_SIZE_139(_) SEQAN_PP_SEQ_SIZE_140 +# define SEQAN_PP_SEQ_SIZE_140(_) SEQAN_PP_SEQ_SIZE_141 +# define SEQAN_PP_SEQ_SIZE_141(_) SEQAN_PP_SEQ_SIZE_142 +# define SEQAN_PP_SEQ_SIZE_142(_) SEQAN_PP_SEQ_SIZE_143 +# define SEQAN_PP_SEQ_SIZE_143(_) SEQAN_PP_SEQ_SIZE_144 +# define SEQAN_PP_SEQ_SIZE_144(_) SEQAN_PP_SEQ_SIZE_145 +# define SEQAN_PP_SEQ_SIZE_145(_) SEQAN_PP_SEQ_SIZE_146 +# define SEQAN_PP_SEQ_SIZE_146(_) SEQAN_PP_SEQ_SIZE_147 +# define SEQAN_PP_SEQ_SIZE_147(_) SEQAN_PP_SEQ_SIZE_148 +# define SEQAN_PP_SEQ_SIZE_148(_) SEQAN_PP_SEQ_SIZE_149 +# define SEQAN_PP_SEQ_SIZE_149(_) SEQAN_PP_SEQ_SIZE_150 +# define SEQAN_PP_SEQ_SIZE_150(_) SEQAN_PP_SEQ_SIZE_151 +# define SEQAN_PP_SEQ_SIZE_151(_) SEQAN_PP_SEQ_SIZE_152 +# define SEQAN_PP_SEQ_SIZE_152(_) SEQAN_PP_SEQ_SIZE_153 +# define SEQAN_PP_SEQ_SIZE_153(_) SEQAN_PP_SEQ_SIZE_154 +# define SEQAN_PP_SEQ_SIZE_154(_) SEQAN_PP_SEQ_SIZE_155 +# define SEQAN_PP_SEQ_SIZE_155(_) SEQAN_PP_SEQ_SIZE_156 +# define SEQAN_PP_SEQ_SIZE_156(_) SEQAN_PP_SEQ_SIZE_157 +# define SEQAN_PP_SEQ_SIZE_157(_) SEQAN_PP_SEQ_SIZE_158 +# define SEQAN_PP_SEQ_SIZE_158(_) SEQAN_PP_SEQ_SIZE_159 +# define SEQAN_PP_SEQ_SIZE_159(_) SEQAN_PP_SEQ_SIZE_160 +# define SEQAN_PP_SEQ_SIZE_160(_) SEQAN_PP_SEQ_SIZE_161 +# define SEQAN_PP_SEQ_SIZE_161(_) SEQAN_PP_SEQ_SIZE_162 +# define SEQAN_PP_SEQ_SIZE_162(_) SEQAN_PP_SEQ_SIZE_163 +# define SEQAN_PP_SEQ_SIZE_163(_) SEQAN_PP_SEQ_SIZE_164 +# define SEQAN_PP_SEQ_SIZE_164(_) SEQAN_PP_SEQ_SIZE_165 +# define SEQAN_PP_SEQ_SIZE_165(_) SEQAN_PP_SEQ_SIZE_166 +# define SEQAN_PP_SEQ_SIZE_166(_) SEQAN_PP_SEQ_SIZE_167 +# define SEQAN_PP_SEQ_SIZE_167(_) SEQAN_PP_SEQ_SIZE_168 +# define SEQAN_PP_SEQ_SIZE_168(_) SEQAN_PP_SEQ_SIZE_169 +# define SEQAN_PP_SEQ_SIZE_169(_) SEQAN_PP_SEQ_SIZE_170 +# define SEQAN_PP_SEQ_SIZE_170(_) SEQAN_PP_SEQ_SIZE_171 +# define SEQAN_PP_SEQ_SIZE_171(_) SEQAN_PP_SEQ_SIZE_172 +# define SEQAN_PP_SEQ_SIZE_172(_) SEQAN_PP_SEQ_SIZE_173 +# define SEQAN_PP_SEQ_SIZE_173(_) SEQAN_PP_SEQ_SIZE_174 +# define SEQAN_PP_SEQ_SIZE_174(_) SEQAN_PP_SEQ_SIZE_175 +# define SEQAN_PP_SEQ_SIZE_175(_) SEQAN_PP_SEQ_SIZE_176 +# define SEQAN_PP_SEQ_SIZE_176(_) SEQAN_PP_SEQ_SIZE_177 +# define SEQAN_PP_SEQ_SIZE_177(_) SEQAN_PP_SEQ_SIZE_178 +# define SEQAN_PP_SEQ_SIZE_178(_) SEQAN_PP_SEQ_SIZE_179 +# define SEQAN_PP_SEQ_SIZE_179(_) SEQAN_PP_SEQ_SIZE_180 +# define SEQAN_PP_SEQ_SIZE_180(_) SEQAN_PP_SEQ_SIZE_181 +# define SEQAN_PP_SEQ_SIZE_181(_) SEQAN_PP_SEQ_SIZE_182 +# define SEQAN_PP_SEQ_SIZE_182(_) SEQAN_PP_SEQ_SIZE_183 +# define SEQAN_PP_SEQ_SIZE_183(_) SEQAN_PP_SEQ_SIZE_184 +# define SEQAN_PP_SEQ_SIZE_184(_) SEQAN_PP_SEQ_SIZE_185 +# define SEQAN_PP_SEQ_SIZE_185(_) SEQAN_PP_SEQ_SIZE_186 +# define SEQAN_PP_SEQ_SIZE_186(_) SEQAN_PP_SEQ_SIZE_187 +# define SEQAN_PP_SEQ_SIZE_187(_) SEQAN_PP_SEQ_SIZE_188 +# define SEQAN_PP_SEQ_SIZE_188(_) SEQAN_PP_SEQ_SIZE_189 +# define SEQAN_PP_SEQ_SIZE_189(_) SEQAN_PP_SEQ_SIZE_190 +# define SEQAN_PP_SEQ_SIZE_190(_) SEQAN_PP_SEQ_SIZE_191 +# define SEQAN_PP_SEQ_SIZE_191(_) SEQAN_PP_SEQ_SIZE_192 +# define SEQAN_PP_SEQ_SIZE_192(_) SEQAN_PP_SEQ_SIZE_193 +# define SEQAN_PP_SEQ_SIZE_193(_) SEQAN_PP_SEQ_SIZE_194 +# define SEQAN_PP_SEQ_SIZE_194(_) SEQAN_PP_SEQ_SIZE_195 +# define SEQAN_PP_SEQ_SIZE_195(_) SEQAN_PP_SEQ_SIZE_196 +# define SEQAN_PP_SEQ_SIZE_196(_) SEQAN_PP_SEQ_SIZE_197 +# define SEQAN_PP_SEQ_SIZE_197(_) SEQAN_PP_SEQ_SIZE_198 +# define SEQAN_PP_SEQ_SIZE_198(_) SEQAN_PP_SEQ_SIZE_199 +# define SEQAN_PP_SEQ_SIZE_199(_) SEQAN_PP_SEQ_SIZE_200 +# define SEQAN_PP_SEQ_SIZE_200(_) SEQAN_PP_SEQ_SIZE_201 +# define SEQAN_PP_SEQ_SIZE_201(_) SEQAN_PP_SEQ_SIZE_202 +# define SEQAN_PP_SEQ_SIZE_202(_) SEQAN_PP_SEQ_SIZE_203 +# define SEQAN_PP_SEQ_SIZE_203(_) SEQAN_PP_SEQ_SIZE_204 +# define SEQAN_PP_SEQ_SIZE_204(_) SEQAN_PP_SEQ_SIZE_205 +# define SEQAN_PP_SEQ_SIZE_205(_) SEQAN_PP_SEQ_SIZE_206 +# define SEQAN_PP_SEQ_SIZE_206(_) SEQAN_PP_SEQ_SIZE_207 +# define SEQAN_PP_SEQ_SIZE_207(_) SEQAN_PP_SEQ_SIZE_208 +# define SEQAN_PP_SEQ_SIZE_208(_) SEQAN_PP_SEQ_SIZE_209 +# define SEQAN_PP_SEQ_SIZE_209(_) SEQAN_PP_SEQ_SIZE_210 +# define SEQAN_PP_SEQ_SIZE_210(_) SEQAN_PP_SEQ_SIZE_211 +# define SEQAN_PP_SEQ_SIZE_211(_) SEQAN_PP_SEQ_SIZE_212 +# define SEQAN_PP_SEQ_SIZE_212(_) SEQAN_PP_SEQ_SIZE_213 +# define SEQAN_PP_SEQ_SIZE_213(_) SEQAN_PP_SEQ_SIZE_214 +# define SEQAN_PP_SEQ_SIZE_214(_) SEQAN_PP_SEQ_SIZE_215 +# define SEQAN_PP_SEQ_SIZE_215(_) SEQAN_PP_SEQ_SIZE_216 +# define SEQAN_PP_SEQ_SIZE_216(_) SEQAN_PP_SEQ_SIZE_217 +# define SEQAN_PP_SEQ_SIZE_217(_) SEQAN_PP_SEQ_SIZE_218 +# define SEQAN_PP_SEQ_SIZE_218(_) SEQAN_PP_SEQ_SIZE_219 +# define SEQAN_PP_SEQ_SIZE_219(_) SEQAN_PP_SEQ_SIZE_220 +# define SEQAN_PP_SEQ_SIZE_220(_) SEQAN_PP_SEQ_SIZE_221 +# define SEQAN_PP_SEQ_SIZE_221(_) SEQAN_PP_SEQ_SIZE_222 +# define SEQAN_PP_SEQ_SIZE_222(_) SEQAN_PP_SEQ_SIZE_223 +# define SEQAN_PP_SEQ_SIZE_223(_) SEQAN_PP_SEQ_SIZE_224 +# define SEQAN_PP_SEQ_SIZE_224(_) SEQAN_PP_SEQ_SIZE_225 +# define SEQAN_PP_SEQ_SIZE_225(_) SEQAN_PP_SEQ_SIZE_226 +# define SEQAN_PP_SEQ_SIZE_226(_) SEQAN_PP_SEQ_SIZE_227 +# define SEQAN_PP_SEQ_SIZE_227(_) SEQAN_PP_SEQ_SIZE_228 +# define SEQAN_PP_SEQ_SIZE_228(_) SEQAN_PP_SEQ_SIZE_229 +# define SEQAN_PP_SEQ_SIZE_229(_) SEQAN_PP_SEQ_SIZE_230 +# define SEQAN_PP_SEQ_SIZE_230(_) SEQAN_PP_SEQ_SIZE_231 +# define SEQAN_PP_SEQ_SIZE_231(_) SEQAN_PP_SEQ_SIZE_232 +# define SEQAN_PP_SEQ_SIZE_232(_) SEQAN_PP_SEQ_SIZE_233 +# define SEQAN_PP_SEQ_SIZE_233(_) SEQAN_PP_SEQ_SIZE_234 +# define SEQAN_PP_SEQ_SIZE_234(_) SEQAN_PP_SEQ_SIZE_235 +# define SEQAN_PP_SEQ_SIZE_235(_) SEQAN_PP_SEQ_SIZE_236 +# define SEQAN_PP_SEQ_SIZE_236(_) SEQAN_PP_SEQ_SIZE_237 +# define SEQAN_PP_SEQ_SIZE_237(_) SEQAN_PP_SEQ_SIZE_238 +# define SEQAN_PP_SEQ_SIZE_238(_) SEQAN_PP_SEQ_SIZE_239 +# define SEQAN_PP_SEQ_SIZE_239(_) SEQAN_PP_SEQ_SIZE_240 +# define SEQAN_PP_SEQ_SIZE_240(_) SEQAN_PP_SEQ_SIZE_241 +# define SEQAN_PP_SEQ_SIZE_241(_) SEQAN_PP_SEQ_SIZE_242 +# define SEQAN_PP_SEQ_SIZE_242(_) SEQAN_PP_SEQ_SIZE_243 +# define SEQAN_PP_SEQ_SIZE_243(_) SEQAN_PP_SEQ_SIZE_244 +# define SEQAN_PP_SEQ_SIZE_244(_) SEQAN_PP_SEQ_SIZE_245 +# define SEQAN_PP_SEQ_SIZE_245(_) SEQAN_PP_SEQ_SIZE_246 +# define SEQAN_PP_SEQ_SIZE_246(_) SEQAN_PP_SEQ_SIZE_247 +# define SEQAN_PP_SEQ_SIZE_247(_) SEQAN_PP_SEQ_SIZE_248 +# define SEQAN_PP_SEQ_SIZE_248(_) SEQAN_PP_SEQ_SIZE_249 +# define SEQAN_PP_SEQ_SIZE_249(_) SEQAN_PP_SEQ_SIZE_250 +# define SEQAN_PP_SEQ_SIZE_250(_) SEQAN_PP_SEQ_SIZE_251 +# define SEQAN_PP_SEQ_SIZE_251(_) SEQAN_PP_SEQ_SIZE_252 +# define SEQAN_PP_SEQ_SIZE_252(_) SEQAN_PP_SEQ_SIZE_253 +# define SEQAN_PP_SEQ_SIZE_253(_) SEQAN_PP_SEQ_SIZE_254 +# define SEQAN_PP_SEQ_SIZE_254(_) SEQAN_PP_SEQ_SIZE_255 +# define SEQAN_PP_SEQ_SIZE_255(_) SEQAN_PP_SEQ_SIZE_256 +# define SEQAN_PP_SEQ_SIZE_256(_) SEQAN_PP_SEQ_SIZE_257 +# +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_0 0 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_1 1 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_2 2 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_3 3 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_4 4 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_5 5 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_6 6 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_7 7 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_8 8 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_9 9 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_10 10 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_11 11 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_12 12 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_13 13 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_14 14 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_15 15 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_16 16 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_17 17 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_18 18 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_19 19 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_20 20 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_21 21 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_22 22 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_23 23 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_24 24 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_25 25 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_26 26 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_27 27 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_28 28 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_29 29 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_30 30 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_31 31 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_32 32 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_33 33 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_34 34 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_35 35 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_36 36 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_37 37 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_38 38 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_39 39 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_40 40 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_41 41 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_42 42 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_43 43 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_44 44 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_45 45 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_46 46 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_47 47 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_48 48 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_49 49 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_50 50 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_51 51 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_52 52 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_53 53 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_54 54 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_55 55 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_56 56 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_57 57 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_58 58 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_59 59 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_60 60 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_61 61 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_62 62 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_63 63 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_64 64 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_65 65 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_66 66 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_67 67 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_68 68 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_69 69 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_70 70 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_71 71 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_72 72 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_73 73 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_74 74 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_75 75 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_76 76 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_77 77 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_78 78 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_79 79 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_80 80 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_81 81 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_82 82 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_83 83 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_84 84 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_85 85 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_86 86 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_87 87 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_88 88 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_89 89 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_90 90 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_91 91 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_92 92 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_93 93 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_94 94 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_95 95 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_96 96 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_97 97 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_98 98 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_99 99 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_100 100 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_101 101 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_102 102 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_103 103 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_104 104 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_105 105 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_106 106 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_107 107 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_108 108 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_109 109 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_110 110 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_111 111 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_112 112 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_113 113 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_114 114 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_115 115 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_116 116 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_117 117 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_118 118 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_119 119 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_120 120 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_121 121 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_122 122 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_123 123 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_124 124 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_125 125 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_126 126 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_127 127 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_128 128 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_129 129 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_130 130 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_131 131 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_132 132 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_133 133 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_134 134 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_135 135 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_136 136 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_137 137 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_138 138 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_139 139 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_140 140 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_141 141 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_142 142 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_143 143 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_144 144 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_145 145 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_146 146 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_147 147 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_148 148 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_149 149 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_150 150 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_151 151 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_152 152 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_153 153 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_154 154 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_155 155 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_156 156 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_157 157 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_158 158 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_159 159 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_160 160 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_161 161 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_162 162 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_163 163 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_164 164 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_165 165 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_166 166 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_167 167 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_168 168 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_169 169 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_170 170 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_171 171 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_172 172 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_173 173 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_174 174 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_175 175 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_176 176 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_177 177 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_178 178 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_179 179 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_180 180 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_181 181 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_182 182 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_183 183 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_184 184 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_185 185 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_186 186 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_187 187 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_188 188 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_189 189 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_190 190 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_191 191 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_192 192 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_193 193 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_194 194 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_195 195 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_196 196 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_197 197 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_198 198 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_199 199 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_200 200 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_201 201 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_202 202 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_203 203 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_204 204 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_205 205 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_206 206 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_207 207 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_208 208 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_209 209 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_210 210 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_211 211 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_212 212 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_213 213 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_214 214 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_215 215 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_216 216 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_217 217 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_218 218 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_219 219 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_220 220 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_221 221 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_222 222 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_223 223 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_224 224 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_225 225 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_226 226 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_227 227 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_228 228 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_229 229 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_230 230 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_231 231 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_232 232 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_233 233 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_234 234 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_235 235 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_236 236 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_237 237 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_238 238 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_239 239 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_240 240 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_241 241 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_242 242 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_243 243 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_244 244 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_245 245 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_246 246 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_247 247 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_248 248 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_249 249 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_250 250 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_251 251 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_252 252 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_253 253 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_254 254 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_255 255 +# define SEQAN_PP_SEQ_SIZE_SEQAN_PP_SEQ_SIZE_256 256 + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/cat.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_CAT_HPP +// # define SEQAN_PREPROCESSOR_CAT_HPP +# +// # include +# +# /* SEQAN_PP_CAT */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_CAT(a, b) SEQAN_PP_CAT_I(a, b) +// # else +// # define SEQAN_PP_CAT(a, b) SEQAN_PP_CAT_OO((a, b)) +// # define SEQAN_PP_CAT_OO(par) SEQAN_PP_CAT_I ## par +// # endif +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +#ifndef STDLIB_VS +# define SEQAN_PP_CAT_I(a, b) a ## b +#else // #ifndef STDLIB_VS +# define SEQAN_PP_CAT_I(a, b) SEQAN_PP_CAT_II(a ## b) +# define SEQAN_PP_CAT_II(res) res +#endif // #ifndef STDLIB_VS +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/seq/enum.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_SEQ_ENUM_HPP +//# define SEQAN_PREPROCESSOR_SEQ_ENUM_HPP +# +//# include +//# include +//# include +# +# /* SEQAN_PP_SEQ_ENUM */ +# +//# if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_SEQ_ENUM(seq) SEQAN_PP_SEQ_ENUM_I(seq) +# define SEQAN_PP_SEQ_ENUM_I(seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_ENUM_, SEQAN_PP_SEQ_SIZE(seq)) seq +//# elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +//# define SEQAN_PP_SEQ_ENUM(seq) SEQAN_PP_SEQ_ENUM_I(SEQAN_PP_SEQ_SIZE(seq), seq) +//# define SEQAN_PP_SEQ_ENUM_I(size, seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_ENUM_, size) seq +//# else +//# define SEQAN_PP_SEQ_ENUM(seq) SEQAN_PP_CAT(SEQAN_PP_SEQ_ENUM_, SEQAN_PP_SEQ_SIZE(seq)) seq +//# endif +# +# define SEQAN_PP_SEQ_ENUM_1(x) x +# define SEQAN_PP_SEQ_ENUM_2(x) x, SEQAN_PP_SEQ_ENUM_1 +# define SEQAN_PP_SEQ_ENUM_3(x) x, SEQAN_PP_SEQ_ENUM_2 +# define SEQAN_PP_SEQ_ENUM_4(x) x, SEQAN_PP_SEQ_ENUM_3 +# define SEQAN_PP_SEQ_ENUM_5(x) x, SEQAN_PP_SEQ_ENUM_4 +# define SEQAN_PP_SEQ_ENUM_6(x) x, SEQAN_PP_SEQ_ENUM_5 +# define SEQAN_PP_SEQ_ENUM_7(x) x, SEQAN_PP_SEQ_ENUM_6 +# define SEQAN_PP_SEQ_ENUM_8(x) x, SEQAN_PP_SEQ_ENUM_7 +# define SEQAN_PP_SEQ_ENUM_9(x) x, SEQAN_PP_SEQ_ENUM_8 +# define SEQAN_PP_SEQ_ENUM_10(x) x, SEQAN_PP_SEQ_ENUM_9 +# define SEQAN_PP_SEQ_ENUM_11(x) x, SEQAN_PP_SEQ_ENUM_10 +# define SEQAN_PP_SEQ_ENUM_12(x) x, SEQAN_PP_SEQ_ENUM_11 +# define SEQAN_PP_SEQ_ENUM_13(x) x, SEQAN_PP_SEQ_ENUM_12 +# define SEQAN_PP_SEQ_ENUM_14(x) x, SEQAN_PP_SEQ_ENUM_13 +# define SEQAN_PP_SEQ_ENUM_15(x) x, SEQAN_PP_SEQ_ENUM_14 +# define SEQAN_PP_SEQ_ENUM_16(x) x, SEQAN_PP_SEQ_ENUM_15 +# define SEQAN_PP_SEQ_ENUM_17(x) x, SEQAN_PP_SEQ_ENUM_16 +# define SEQAN_PP_SEQ_ENUM_18(x) x, SEQAN_PP_SEQ_ENUM_17 +# define SEQAN_PP_SEQ_ENUM_19(x) x, SEQAN_PP_SEQ_ENUM_18 +# define SEQAN_PP_SEQ_ENUM_20(x) x, SEQAN_PP_SEQ_ENUM_19 +# define SEQAN_PP_SEQ_ENUM_21(x) x, SEQAN_PP_SEQ_ENUM_20 +# define SEQAN_PP_SEQ_ENUM_22(x) x, SEQAN_PP_SEQ_ENUM_21 +# define SEQAN_PP_SEQ_ENUM_23(x) x, SEQAN_PP_SEQ_ENUM_22 +# define SEQAN_PP_SEQ_ENUM_24(x) x, SEQAN_PP_SEQ_ENUM_23 +# define SEQAN_PP_SEQ_ENUM_25(x) x, SEQAN_PP_SEQ_ENUM_24 +# define SEQAN_PP_SEQ_ENUM_26(x) x, SEQAN_PP_SEQ_ENUM_25 +# define SEQAN_PP_SEQ_ENUM_27(x) x, SEQAN_PP_SEQ_ENUM_26 +# define SEQAN_PP_SEQ_ENUM_28(x) x, SEQAN_PP_SEQ_ENUM_27 +# define SEQAN_PP_SEQ_ENUM_29(x) x, SEQAN_PP_SEQ_ENUM_28 +# define SEQAN_PP_SEQ_ENUM_30(x) x, SEQAN_PP_SEQ_ENUM_29 +# define SEQAN_PP_SEQ_ENUM_31(x) x, SEQAN_PP_SEQ_ENUM_30 +# define SEQAN_PP_SEQ_ENUM_32(x) x, SEQAN_PP_SEQ_ENUM_31 +# define SEQAN_PP_SEQ_ENUM_33(x) x, SEQAN_PP_SEQ_ENUM_32 +# define SEQAN_PP_SEQ_ENUM_34(x) x, SEQAN_PP_SEQ_ENUM_33 +# define SEQAN_PP_SEQ_ENUM_35(x) x, SEQAN_PP_SEQ_ENUM_34 +# define SEQAN_PP_SEQ_ENUM_36(x) x, SEQAN_PP_SEQ_ENUM_35 +# define SEQAN_PP_SEQ_ENUM_37(x) x, SEQAN_PP_SEQ_ENUM_36 +# define SEQAN_PP_SEQ_ENUM_38(x) x, SEQAN_PP_SEQ_ENUM_37 +# define SEQAN_PP_SEQ_ENUM_39(x) x, SEQAN_PP_SEQ_ENUM_38 +# define SEQAN_PP_SEQ_ENUM_40(x) x, SEQAN_PP_SEQ_ENUM_39 +# define SEQAN_PP_SEQ_ENUM_41(x) x, SEQAN_PP_SEQ_ENUM_40 +# define SEQAN_PP_SEQ_ENUM_42(x) x, SEQAN_PP_SEQ_ENUM_41 +# define SEQAN_PP_SEQ_ENUM_43(x) x, SEQAN_PP_SEQ_ENUM_42 +# define SEQAN_PP_SEQ_ENUM_44(x) x, SEQAN_PP_SEQ_ENUM_43 +# define SEQAN_PP_SEQ_ENUM_45(x) x, SEQAN_PP_SEQ_ENUM_44 +# define SEQAN_PP_SEQ_ENUM_46(x) x, SEQAN_PP_SEQ_ENUM_45 +# define SEQAN_PP_SEQ_ENUM_47(x) x, SEQAN_PP_SEQ_ENUM_46 +# define SEQAN_PP_SEQ_ENUM_48(x) x, SEQAN_PP_SEQ_ENUM_47 +# define SEQAN_PP_SEQ_ENUM_49(x) x, SEQAN_PP_SEQ_ENUM_48 +# define SEQAN_PP_SEQ_ENUM_50(x) x, SEQAN_PP_SEQ_ENUM_49 +# define SEQAN_PP_SEQ_ENUM_51(x) x, SEQAN_PP_SEQ_ENUM_50 +# define SEQAN_PP_SEQ_ENUM_52(x) x, SEQAN_PP_SEQ_ENUM_51 +# define SEQAN_PP_SEQ_ENUM_53(x) x, SEQAN_PP_SEQ_ENUM_52 +# define SEQAN_PP_SEQ_ENUM_54(x) x, SEQAN_PP_SEQ_ENUM_53 +# define SEQAN_PP_SEQ_ENUM_55(x) x, SEQAN_PP_SEQ_ENUM_54 +# define SEQAN_PP_SEQ_ENUM_56(x) x, SEQAN_PP_SEQ_ENUM_55 +# define SEQAN_PP_SEQ_ENUM_57(x) x, SEQAN_PP_SEQ_ENUM_56 +# define SEQAN_PP_SEQ_ENUM_58(x) x, SEQAN_PP_SEQ_ENUM_57 +# define SEQAN_PP_SEQ_ENUM_59(x) x, SEQAN_PP_SEQ_ENUM_58 +# define SEQAN_PP_SEQ_ENUM_60(x) x, SEQAN_PP_SEQ_ENUM_59 +# define SEQAN_PP_SEQ_ENUM_61(x) x, SEQAN_PP_SEQ_ENUM_60 +# define SEQAN_PP_SEQ_ENUM_62(x) x, SEQAN_PP_SEQ_ENUM_61 +# define SEQAN_PP_SEQ_ENUM_63(x) x, SEQAN_PP_SEQ_ENUM_62 +# define SEQAN_PP_SEQ_ENUM_64(x) x, SEQAN_PP_SEQ_ENUM_63 +# define SEQAN_PP_SEQ_ENUM_65(x) x, SEQAN_PP_SEQ_ENUM_64 +# define SEQAN_PP_SEQ_ENUM_66(x) x, SEQAN_PP_SEQ_ENUM_65 +# define SEQAN_PP_SEQ_ENUM_67(x) x, SEQAN_PP_SEQ_ENUM_66 +# define SEQAN_PP_SEQ_ENUM_68(x) x, SEQAN_PP_SEQ_ENUM_67 +# define SEQAN_PP_SEQ_ENUM_69(x) x, SEQAN_PP_SEQ_ENUM_68 +# define SEQAN_PP_SEQ_ENUM_70(x) x, SEQAN_PP_SEQ_ENUM_69 +# define SEQAN_PP_SEQ_ENUM_71(x) x, SEQAN_PP_SEQ_ENUM_70 +# define SEQAN_PP_SEQ_ENUM_72(x) x, SEQAN_PP_SEQ_ENUM_71 +# define SEQAN_PP_SEQ_ENUM_73(x) x, SEQAN_PP_SEQ_ENUM_72 +# define SEQAN_PP_SEQ_ENUM_74(x) x, SEQAN_PP_SEQ_ENUM_73 +# define SEQAN_PP_SEQ_ENUM_75(x) x, SEQAN_PP_SEQ_ENUM_74 +# define SEQAN_PP_SEQ_ENUM_76(x) x, SEQAN_PP_SEQ_ENUM_75 +# define SEQAN_PP_SEQ_ENUM_77(x) x, SEQAN_PP_SEQ_ENUM_76 +# define SEQAN_PP_SEQ_ENUM_78(x) x, SEQAN_PP_SEQ_ENUM_77 +# define SEQAN_PP_SEQ_ENUM_79(x) x, SEQAN_PP_SEQ_ENUM_78 +# define SEQAN_PP_SEQ_ENUM_80(x) x, SEQAN_PP_SEQ_ENUM_79 +# define SEQAN_PP_SEQ_ENUM_81(x) x, SEQAN_PP_SEQ_ENUM_80 +# define SEQAN_PP_SEQ_ENUM_82(x) x, SEQAN_PP_SEQ_ENUM_81 +# define SEQAN_PP_SEQ_ENUM_83(x) x, SEQAN_PP_SEQ_ENUM_82 +# define SEQAN_PP_SEQ_ENUM_84(x) x, SEQAN_PP_SEQ_ENUM_83 +# define SEQAN_PP_SEQ_ENUM_85(x) x, SEQAN_PP_SEQ_ENUM_84 +# define SEQAN_PP_SEQ_ENUM_86(x) x, SEQAN_PP_SEQ_ENUM_85 +# define SEQAN_PP_SEQ_ENUM_87(x) x, SEQAN_PP_SEQ_ENUM_86 +# define SEQAN_PP_SEQ_ENUM_88(x) x, SEQAN_PP_SEQ_ENUM_87 +# define SEQAN_PP_SEQ_ENUM_89(x) x, SEQAN_PP_SEQ_ENUM_88 +# define SEQAN_PP_SEQ_ENUM_90(x) x, SEQAN_PP_SEQ_ENUM_89 +# define SEQAN_PP_SEQ_ENUM_91(x) x, SEQAN_PP_SEQ_ENUM_90 +# define SEQAN_PP_SEQ_ENUM_92(x) x, SEQAN_PP_SEQ_ENUM_91 +# define SEQAN_PP_SEQ_ENUM_93(x) x, SEQAN_PP_SEQ_ENUM_92 +# define SEQAN_PP_SEQ_ENUM_94(x) x, SEQAN_PP_SEQ_ENUM_93 +# define SEQAN_PP_SEQ_ENUM_95(x) x, SEQAN_PP_SEQ_ENUM_94 +# define SEQAN_PP_SEQ_ENUM_96(x) x, SEQAN_PP_SEQ_ENUM_95 +# define SEQAN_PP_SEQ_ENUM_97(x) x, SEQAN_PP_SEQ_ENUM_96 +# define SEQAN_PP_SEQ_ENUM_98(x) x, SEQAN_PP_SEQ_ENUM_97 +# define SEQAN_PP_SEQ_ENUM_99(x) x, SEQAN_PP_SEQ_ENUM_98 +# define SEQAN_PP_SEQ_ENUM_100(x) x, SEQAN_PP_SEQ_ENUM_99 +# define SEQAN_PP_SEQ_ENUM_101(x) x, SEQAN_PP_SEQ_ENUM_100 +# define SEQAN_PP_SEQ_ENUM_102(x) x, SEQAN_PP_SEQ_ENUM_101 +# define SEQAN_PP_SEQ_ENUM_103(x) x, SEQAN_PP_SEQ_ENUM_102 +# define SEQAN_PP_SEQ_ENUM_104(x) x, SEQAN_PP_SEQ_ENUM_103 +# define SEQAN_PP_SEQ_ENUM_105(x) x, SEQAN_PP_SEQ_ENUM_104 +# define SEQAN_PP_SEQ_ENUM_106(x) x, SEQAN_PP_SEQ_ENUM_105 +# define SEQAN_PP_SEQ_ENUM_107(x) x, SEQAN_PP_SEQ_ENUM_106 +# define SEQAN_PP_SEQ_ENUM_108(x) x, SEQAN_PP_SEQ_ENUM_107 +# define SEQAN_PP_SEQ_ENUM_109(x) x, SEQAN_PP_SEQ_ENUM_108 +# define SEQAN_PP_SEQ_ENUM_110(x) x, SEQAN_PP_SEQ_ENUM_109 +# define SEQAN_PP_SEQ_ENUM_111(x) x, SEQAN_PP_SEQ_ENUM_110 +# define SEQAN_PP_SEQ_ENUM_112(x) x, SEQAN_PP_SEQ_ENUM_111 +# define SEQAN_PP_SEQ_ENUM_113(x) x, SEQAN_PP_SEQ_ENUM_112 +# define SEQAN_PP_SEQ_ENUM_114(x) x, SEQAN_PP_SEQ_ENUM_113 +# define SEQAN_PP_SEQ_ENUM_115(x) x, SEQAN_PP_SEQ_ENUM_114 +# define SEQAN_PP_SEQ_ENUM_116(x) x, SEQAN_PP_SEQ_ENUM_115 +# define SEQAN_PP_SEQ_ENUM_117(x) x, SEQAN_PP_SEQ_ENUM_116 +# define SEQAN_PP_SEQ_ENUM_118(x) x, SEQAN_PP_SEQ_ENUM_117 +# define SEQAN_PP_SEQ_ENUM_119(x) x, SEQAN_PP_SEQ_ENUM_118 +# define SEQAN_PP_SEQ_ENUM_120(x) x, SEQAN_PP_SEQ_ENUM_119 +# define SEQAN_PP_SEQ_ENUM_121(x) x, SEQAN_PP_SEQ_ENUM_120 +# define SEQAN_PP_SEQ_ENUM_122(x) x, SEQAN_PP_SEQ_ENUM_121 +# define SEQAN_PP_SEQ_ENUM_123(x) x, SEQAN_PP_SEQ_ENUM_122 +# define SEQAN_PP_SEQ_ENUM_124(x) x, SEQAN_PP_SEQ_ENUM_123 +# define SEQAN_PP_SEQ_ENUM_125(x) x, SEQAN_PP_SEQ_ENUM_124 +# define SEQAN_PP_SEQ_ENUM_126(x) x, SEQAN_PP_SEQ_ENUM_125 +# define SEQAN_PP_SEQ_ENUM_127(x) x, SEQAN_PP_SEQ_ENUM_126 +# define SEQAN_PP_SEQ_ENUM_128(x) x, SEQAN_PP_SEQ_ENUM_127 +# define SEQAN_PP_SEQ_ENUM_129(x) x, SEQAN_PP_SEQ_ENUM_128 +# define SEQAN_PP_SEQ_ENUM_130(x) x, SEQAN_PP_SEQ_ENUM_129 +# define SEQAN_PP_SEQ_ENUM_131(x) x, SEQAN_PP_SEQ_ENUM_130 +# define SEQAN_PP_SEQ_ENUM_132(x) x, SEQAN_PP_SEQ_ENUM_131 +# define SEQAN_PP_SEQ_ENUM_133(x) x, SEQAN_PP_SEQ_ENUM_132 +# define SEQAN_PP_SEQ_ENUM_134(x) x, SEQAN_PP_SEQ_ENUM_133 +# define SEQAN_PP_SEQ_ENUM_135(x) x, SEQAN_PP_SEQ_ENUM_134 +# define SEQAN_PP_SEQ_ENUM_136(x) x, SEQAN_PP_SEQ_ENUM_135 +# define SEQAN_PP_SEQ_ENUM_137(x) x, SEQAN_PP_SEQ_ENUM_136 +# define SEQAN_PP_SEQ_ENUM_138(x) x, SEQAN_PP_SEQ_ENUM_137 +# define SEQAN_PP_SEQ_ENUM_139(x) x, SEQAN_PP_SEQ_ENUM_138 +# define SEQAN_PP_SEQ_ENUM_140(x) x, SEQAN_PP_SEQ_ENUM_139 +# define SEQAN_PP_SEQ_ENUM_141(x) x, SEQAN_PP_SEQ_ENUM_140 +# define SEQAN_PP_SEQ_ENUM_142(x) x, SEQAN_PP_SEQ_ENUM_141 +# define SEQAN_PP_SEQ_ENUM_143(x) x, SEQAN_PP_SEQ_ENUM_142 +# define SEQAN_PP_SEQ_ENUM_144(x) x, SEQAN_PP_SEQ_ENUM_143 +# define SEQAN_PP_SEQ_ENUM_145(x) x, SEQAN_PP_SEQ_ENUM_144 +# define SEQAN_PP_SEQ_ENUM_146(x) x, SEQAN_PP_SEQ_ENUM_145 +# define SEQAN_PP_SEQ_ENUM_147(x) x, SEQAN_PP_SEQ_ENUM_146 +# define SEQAN_PP_SEQ_ENUM_148(x) x, SEQAN_PP_SEQ_ENUM_147 +# define SEQAN_PP_SEQ_ENUM_149(x) x, SEQAN_PP_SEQ_ENUM_148 +# define SEQAN_PP_SEQ_ENUM_150(x) x, SEQAN_PP_SEQ_ENUM_149 +# define SEQAN_PP_SEQ_ENUM_151(x) x, SEQAN_PP_SEQ_ENUM_150 +# define SEQAN_PP_SEQ_ENUM_152(x) x, SEQAN_PP_SEQ_ENUM_151 +# define SEQAN_PP_SEQ_ENUM_153(x) x, SEQAN_PP_SEQ_ENUM_152 +# define SEQAN_PP_SEQ_ENUM_154(x) x, SEQAN_PP_SEQ_ENUM_153 +# define SEQAN_PP_SEQ_ENUM_155(x) x, SEQAN_PP_SEQ_ENUM_154 +# define SEQAN_PP_SEQ_ENUM_156(x) x, SEQAN_PP_SEQ_ENUM_155 +# define SEQAN_PP_SEQ_ENUM_157(x) x, SEQAN_PP_SEQ_ENUM_156 +# define SEQAN_PP_SEQ_ENUM_158(x) x, SEQAN_PP_SEQ_ENUM_157 +# define SEQAN_PP_SEQ_ENUM_159(x) x, SEQAN_PP_SEQ_ENUM_158 +# define SEQAN_PP_SEQ_ENUM_160(x) x, SEQAN_PP_SEQ_ENUM_159 +# define SEQAN_PP_SEQ_ENUM_161(x) x, SEQAN_PP_SEQ_ENUM_160 +# define SEQAN_PP_SEQ_ENUM_162(x) x, SEQAN_PP_SEQ_ENUM_161 +# define SEQAN_PP_SEQ_ENUM_163(x) x, SEQAN_PP_SEQ_ENUM_162 +# define SEQAN_PP_SEQ_ENUM_164(x) x, SEQAN_PP_SEQ_ENUM_163 +# define SEQAN_PP_SEQ_ENUM_165(x) x, SEQAN_PP_SEQ_ENUM_164 +# define SEQAN_PP_SEQ_ENUM_166(x) x, SEQAN_PP_SEQ_ENUM_165 +# define SEQAN_PP_SEQ_ENUM_167(x) x, SEQAN_PP_SEQ_ENUM_166 +# define SEQAN_PP_SEQ_ENUM_168(x) x, SEQAN_PP_SEQ_ENUM_167 +# define SEQAN_PP_SEQ_ENUM_169(x) x, SEQAN_PP_SEQ_ENUM_168 +# define SEQAN_PP_SEQ_ENUM_170(x) x, SEQAN_PP_SEQ_ENUM_169 +# define SEQAN_PP_SEQ_ENUM_171(x) x, SEQAN_PP_SEQ_ENUM_170 +# define SEQAN_PP_SEQ_ENUM_172(x) x, SEQAN_PP_SEQ_ENUM_171 +# define SEQAN_PP_SEQ_ENUM_173(x) x, SEQAN_PP_SEQ_ENUM_172 +# define SEQAN_PP_SEQ_ENUM_174(x) x, SEQAN_PP_SEQ_ENUM_173 +# define SEQAN_PP_SEQ_ENUM_175(x) x, SEQAN_PP_SEQ_ENUM_174 +# define SEQAN_PP_SEQ_ENUM_176(x) x, SEQAN_PP_SEQ_ENUM_175 +# define SEQAN_PP_SEQ_ENUM_177(x) x, SEQAN_PP_SEQ_ENUM_176 +# define SEQAN_PP_SEQ_ENUM_178(x) x, SEQAN_PP_SEQ_ENUM_177 +# define SEQAN_PP_SEQ_ENUM_179(x) x, SEQAN_PP_SEQ_ENUM_178 +# define SEQAN_PP_SEQ_ENUM_180(x) x, SEQAN_PP_SEQ_ENUM_179 +# define SEQAN_PP_SEQ_ENUM_181(x) x, SEQAN_PP_SEQ_ENUM_180 +# define SEQAN_PP_SEQ_ENUM_182(x) x, SEQAN_PP_SEQ_ENUM_181 +# define SEQAN_PP_SEQ_ENUM_183(x) x, SEQAN_PP_SEQ_ENUM_182 +# define SEQAN_PP_SEQ_ENUM_184(x) x, SEQAN_PP_SEQ_ENUM_183 +# define SEQAN_PP_SEQ_ENUM_185(x) x, SEQAN_PP_SEQ_ENUM_184 +# define SEQAN_PP_SEQ_ENUM_186(x) x, SEQAN_PP_SEQ_ENUM_185 +# define SEQAN_PP_SEQ_ENUM_187(x) x, SEQAN_PP_SEQ_ENUM_186 +# define SEQAN_PP_SEQ_ENUM_188(x) x, SEQAN_PP_SEQ_ENUM_187 +# define SEQAN_PP_SEQ_ENUM_189(x) x, SEQAN_PP_SEQ_ENUM_188 +# define SEQAN_PP_SEQ_ENUM_190(x) x, SEQAN_PP_SEQ_ENUM_189 +# define SEQAN_PP_SEQ_ENUM_191(x) x, SEQAN_PP_SEQ_ENUM_190 +# define SEQAN_PP_SEQ_ENUM_192(x) x, SEQAN_PP_SEQ_ENUM_191 +# define SEQAN_PP_SEQ_ENUM_193(x) x, SEQAN_PP_SEQ_ENUM_192 +# define SEQAN_PP_SEQ_ENUM_194(x) x, SEQAN_PP_SEQ_ENUM_193 +# define SEQAN_PP_SEQ_ENUM_195(x) x, SEQAN_PP_SEQ_ENUM_194 +# define SEQAN_PP_SEQ_ENUM_196(x) x, SEQAN_PP_SEQ_ENUM_195 +# define SEQAN_PP_SEQ_ENUM_197(x) x, SEQAN_PP_SEQ_ENUM_196 +# define SEQAN_PP_SEQ_ENUM_198(x) x, SEQAN_PP_SEQ_ENUM_197 +# define SEQAN_PP_SEQ_ENUM_199(x) x, SEQAN_PP_SEQ_ENUM_198 +# define SEQAN_PP_SEQ_ENUM_200(x) x, SEQAN_PP_SEQ_ENUM_199 +# define SEQAN_PP_SEQ_ENUM_201(x) x, SEQAN_PP_SEQ_ENUM_200 +# define SEQAN_PP_SEQ_ENUM_202(x) x, SEQAN_PP_SEQ_ENUM_201 +# define SEQAN_PP_SEQ_ENUM_203(x) x, SEQAN_PP_SEQ_ENUM_202 +# define SEQAN_PP_SEQ_ENUM_204(x) x, SEQAN_PP_SEQ_ENUM_203 +# define SEQAN_PP_SEQ_ENUM_205(x) x, SEQAN_PP_SEQ_ENUM_204 +# define SEQAN_PP_SEQ_ENUM_206(x) x, SEQAN_PP_SEQ_ENUM_205 +# define SEQAN_PP_SEQ_ENUM_207(x) x, SEQAN_PP_SEQ_ENUM_206 +# define SEQAN_PP_SEQ_ENUM_208(x) x, SEQAN_PP_SEQ_ENUM_207 +# define SEQAN_PP_SEQ_ENUM_209(x) x, SEQAN_PP_SEQ_ENUM_208 +# define SEQAN_PP_SEQ_ENUM_210(x) x, SEQAN_PP_SEQ_ENUM_209 +# define SEQAN_PP_SEQ_ENUM_211(x) x, SEQAN_PP_SEQ_ENUM_210 +# define SEQAN_PP_SEQ_ENUM_212(x) x, SEQAN_PP_SEQ_ENUM_211 +# define SEQAN_PP_SEQ_ENUM_213(x) x, SEQAN_PP_SEQ_ENUM_212 +# define SEQAN_PP_SEQ_ENUM_214(x) x, SEQAN_PP_SEQ_ENUM_213 +# define SEQAN_PP_SEQ_ENUM_215(x) x, SEQAN_PP_SEQ_ENUM_214 +# define SEQAN_PP_SEQ_ENUM_216(x) x, SEQAN_PP_SEQ_ENUM_215 +# define SEQAN_PP_SEQ_ENUM_217(x) x, SEQAN_PP_SEQ_ENUM_216 +# define SEQAN_PP_SEQ_ENUM_218(x) x, SEQAN_PP_SEQ_ENUM_217 +# define SEQAN_PP_SEQ_ENUM_219(x) x, SEQAN_PP_SEQ_ENUM_218 +# define SEQAN_PP_SEQ_ENUM_220(x) x, SEQAN_PP_SEQ_ENUM_219 +# define SEQAN_PP_SEQ_ENUM_221(x) x, SEQAN_PP_SEQ_ENUM_220 +# define SEQAN_PP_SEQ_ENUM_222(x) x, SEQAN_PP_SEQ_ENUM_221 +# define SEQAN_PP_SEQ_ENUM_223(x) x, SEQAN_PP_SEQ_ENUM_222 +# define SEQAN_PP_SEQ_ENUM_224(x) x, SEQAN_PP_SEQ_ENUM_223 +# define SEQAN_PP_SEQ_ENUM_225(x) x, SEQAN_PP_SEQ_ENUM_224 +# define SEQAN_PP_SEQ_ENUM_226(x) x, SEQAN_PP_SEQ_ENUM_225 +# define SEQAN_PP_SEQ_ENUM_227(x) x, SEQAN_PP_SEQ_ENUM_226 +# define SEQAN_PP_SEQ_ENUM_228(x) x, SEQAN_PP_SEQ_ENUM_227 +# define SEQAN_PP_SEQ_ENUM_229(x) x, SEQAN_PP_SEQ_ENUM_228 +# define SEQAN_PP_SEQ_ENUM_230(x) x, SEQAN_PP_SEQ_ENUM_229 +# define SEQAN_PP_SEQ_ENUM_231(x) x, SEQAN_PP_SEQ_ENUM_230 +# define SEQAN_PP_SEQ_ENUM_232(x) x, SEQAN_PP_SEQ_ENUM_231 +# define SEQAN_PP_SEQ_ENUM_233(x) x, SEQAN_PP_SEQ_ENUM_232 +# define SEQAN_PP_SEQ_ENUM_234(x) x, SEQAN_PP_SEQ_ENUM_233 +# define SEQAN_PP_SEQ_ENUM_235(x) x, SEQAN_PP_SEQ_ENUM_234 +# define SEQAN_PP_SEQ_ENUM_236(x) x, SEQAN_PP_SEQ_ENUM_235 +# define SEQAN_PP_SEQ_ENUM_237(x) x, SEQAN_PP_SEQ_ENUM_236 +# define SEQAN_PP_SEQ_ENUM_238(x) x, SEQAN_PP_SEQ_ENUM_237 +# define SEQAN_PP_SEQ_ENUM_239(x) x, SEQAN_PP_SEQ_ENUM_238 +# define SEQAN_PP_SEQ_ENUM_240(x) x, SEQAN_PP_SEQ_ENUM_239 +# define SEQAN_PP_SEQ_ENUM_241(x) x, SEQAN_PP_SEQ_ENUM_240 +# define SEQAN_PP_SEQ_ENUM_242(x) x, SEQAN_PP_SEQ_ENUM_241 +# define SEQAN_PP_SEQ_ENUM_243(x) x, SEQAN_PP_SEQ_ENUM_242 +# define SEQAN_PP_SEQ_ENUM_244(x) x, SEQAN_PP_SEQ_ENUM_243 +# define SEQAN_PP_SEQ_ENUM_245(x) x, SEQAN_PP_SEQ_ENUM_244 +# define SEQAN_PP_SEQ_ENUM_246(x) x, SEQAN_PP_SEQ_ENUM_245 +# define SEQAN_PP_SEQ_ENUM_247(x) x, SEQAN_PP_SEQ_ENUM_246 +# define SEQAN_PP_SEQ_ENUM_248(x) x, SEQAN_PP_SEQ_ENUM_247 +# define SEQAN_PP_SEQ_ENUM_249(x) x, SEQAN_PP_SEQ_ENUM_248 +# define SEQAN_PP_SEQ_ENUM_250(x) x, SEQAN_PP_SEQ_ENUM_249 +# define SEQAN_PP_SEQ_ENUM_251(x) x, SEQAN_PP_SEQ_ENUM_250 +# define SEQAN_PP_SEQ_ENUM_252(x) x, SEQAN_PP_SEQ_ENUM_251 +# define SEQAN_PP_SEQ_ENUM_253(x) x, SEQAN_PP_SEQ_ENUM_252 +# define SEQAN_PP_SEQ_ENUM_254(x) x, SEQAN_PP_SEQ_ENUM_253 +# define SEQAN_PP_SEQ_ENUM_255(x) x, SEQAN_PP_SEQ_ENUM_254 +# define SEQAN_PP_SEQ_ENUM_256(x) x, SEQAN_PP_SEQ_ENUM_255 +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/tuple/eat.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_TUPLE_EAT_HPP +// # define SEQAN_PREPROCESSOR_TUPLE_EAT_HPP +# +// # include +# +# /* SEQAN_PP_TUPLE_EAT */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_TUPLE_EAT(size) SEQAN_PP_TUPLE_EAT_I(size) +// # else +// # define SEQAN_PP_TUPLE_EAT(size) SEQAN_PP_TUPLE_EAT_OO((size)) +// # define SEQAN_PP_TUPLE_EAT_OO(par) SEQAN_PP_TUPLE_EAT_I ## par +// # endif +# +# define SEQAN_PP_TUPLE_EAT_I(size) SEQAN_PP_TUPLE_EAT_ ## size +# +# define SEQAN_PP_TUPLE_EAT_0() +# define SEQAN_PP_TUPLE_EAT_1(a) +# define SEQAN_PP_TUPLE_EAT_2(a, b) +# define SEQAN_PP_TUPLE_EAT_3(a, b, c) +# define SEQAN_PP_TUPLE_EAT_4(a, b, c, d) +# define SEQAN_PP_TUPLE_EAT_5(a, b, c, d, e) +# define SEQAN_PP_TUPLE_EAT_6(a, b, c, d, e, f) +# define SEQAN_PP_TUPLE_EAT_7(a, b, c, d, e, f, g) +# define SEQAN_PP_TUPLE_EAT_8(a, b, c, d, e, f, g, h) +# define SEQAN_PP_TUPLE_EAT_9(a, b, c, d, e, f, g, h, i) +# define SEQAN_PP_TUPLE_EAT_10(a, b, c, d, e, f, g, h, i, j) +# define SEQAN_PP_TUPLE_EAT_11(a, b, c, d, e, f, g, h, i, j, k) +# define SEQAN_PP_TUPLE_EAT_12(a, b, c, d, e, f, g, h, i, j, k, l) +# define SEQAN_PP_TUPLE_EAT_13(a, b, c, d, e, f, g, h, i, j, k, l, m) +# define SEQAN_PP_TUPLE_EAT_14(a, b, c, d, e, f, g, h, i, j, k, l, m, n) +# define SEQAN_PP_TUPLE_EAT_15(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o) +# define SEQAN_PP_TUPLE_EAT_16(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p) +# define SEQAN_PP_TUPLE_EAT_17(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q) +# define SEQAN_PP_TUPLE_EAT_18(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r) +# define SEQAN_PP_TUPLE_EAT_19(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s) +# define SEQAN_PP_TUPLE_EAT_20(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t) +# define SEQAN_PP_TUPLE_EAT_21(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u) +# define SEQAN_PP_TUPLE_EAT_22(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v) +# define SEQAN_PP_TUPLE_EAT_23(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w) +# define SEQAN_PP_TUPLE_EAT_24(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x) +# define SEQAN_PP_TUPLE_EAT_25(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y) +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/repetition/detail/for.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_REPETITION_DETAIL_FOR_HPP +// # define SEQAN_PREPROCESSOR_REPETITION_DETAIL_FOR_HPP +// # +// # include +// # include +// # include +// # include +# +# define SEQAN_PP_FOR_1(s, p, o, m) SEQAN_PP_FOR_1_C(SEQAN_PP_BOOL(p(2, s)), s, p, o, m) +# define SEQAN_PP_FOR_2(s, p, o, m) SEQAN_PP_FOR_2_C(SEQAN_PP_BOOL(p(3, s)), s, p, o, m) +# define SEQAN_PP_FOR_3(s, p, o, m) SEQAN_PP_FOR_3_C(SEQAN_PP_BOOL(p(4, s)), s, p, o, m) +# define SEQAN_PP_FOR_4(s, p, o, m) SEQAN_PP_FOR_4_C(SEQAN_PP_BOOL(p(5, s)), s, p, o, m) +# define SEQAN_PP_FOR_5(s, p, o, m) SEQAN_PP_FOR_5_C(SEQAN_PP_BOOL(p(6, s)), s, p, o, m) +# define SEQAN_PP_FOR_6(s, p, o, m) SEQAN_PP_FOR_6_C(SEQAN_PP_BOOL(p(7, s)), s, p, o, m) +# define SEQAN_PP_FOR_7(s, p, o, m) SEQAN_PP_FOR_7_C(SEQAN_PP_BOOL(p(8, s)), s, p, o, m) +# define SEQAN_PP_FOR_8(s, p, o, m) SEQAN_PP_FOR_8_C(SEQAN_PP_BOOL(p(9, s)), s, p, o, m) +# define SEQAN_PP_FOR_9(s, p, o, m) SEQAN_PP_FOR_9_C(SEQAN_PP_BOOL(p(10, s)), s, p, o, m) +# define SEQAN_PP_FOR_10(s, p, o, m) SEQAN_PP_FOR_10_C(SEQAN_PP_BOOL(p(11, s)), s, p, o, m) +# define SEQAN_PP_FOR_11(s, p, o, m) SEQAN_PP_FOR_11_C(SEQAN_PP_BOOL(p(12, s)), s, p, o, m) +# define SEQAN_PP_FOR_12(s, p, o, m) SEQAN_PP_FOR_12_C(SEQAN_PP_BOOL(p(13, s)), s, p, o, m) +# define SEQAN_PP_FOR_13(s, p, o, m) SEQAN_PP_FOR_13_C(SEQAN_PP_BOOL(p(14, s)), s, p, o, m) +# define SEQAN_PP_FOR_14(s, p, o, m) SEQAN_PP_FOR_14_C(SEQAN_PP_BOOL(p(15, s)), s, p, o, m) +# define SEQAN_PP_FOR_15(s, p, o, m) SEQAN_PP_FOR_15_C(SEQAN_PP_BOOL(p(16, s)), s, p, o, m) +# define SEQAN_PP_FOR_16(s, p, o, m) SEQAN_PP_FOR_16_C(SEQAN_PP_BOOL(p(17, s)), s, p, o, m) +# define SEQAN_PP_FOR_17(s, p, o, m) SEQAN_PP_FOR_17_C(SEQAN_PP_BOOL(p(18, s)), s, p, o, m) +# define SEQAN_PP_FOR_18(s, p, o, m) SEQAN_PP_FOR_18_C(SEQAN_PP_BOOL(p(19, s)), s, p, o, m) +# define SEQAN_PP_FOR_19(s, p, o, m) SEQAN_PP_FOR_19_C(SEQAN_PP_BOOL(p(20, s)), s, p, o, m) +# define SEQAN_PP_FOR_20(s, p, o, m) SEQAN_PP_FOR_20_C(SEQAN_PP_BOOL(p(21, s)), s, p, o, m) +# define SEQAN_PP_FOR_21(s, p, o, m) SEQAN_PP_FOR_21_C(SEQAN_PP_BOOL(p(22, s)), s, p, o, m) +# define SEQAN_PP_FOR_22(s, p, o, m) SEQAN_PP_FOR_22_C(SEQAN_PP_BOOL(p(23, s)), s, p, o, m) +# define SEQAN_PP_FOR_23(s, p, o, m) SEQAN_PP_FOR_23_C(SEQAN_PP_BOOL(p(24, s)), s, p, o, m) +# define SEQAN_PP_FOR_24(s, p, o, m) SEQAN_PP_FOR_24_C(SEQAN_PP_BOOL(p(25, s)), s, p, o, m) +# define SEQAN_PP_FOR_25(s, p, o, m) SEQAN_PP_FOR_25_C(SEQAN_PP_BOOL(p(26, s)), s, p, o, m) +# define SEQAN_PP_FOR_26(s, p, o, m) SEQAN_PP_FOR_26_C(SEQAN_PP_BOOL(p(27, s)), s, p, o, m) +# define SEQAN_PP_FOR_27(s, p, o, m) SEQAN_PP_FOR_27_C(SEQAN_PP_BOOL(p(28, s)), s, p, o, m) +# define SEQAN_PP_FOR_28(s, p, o, m) SEQAN_PP_FOR_28_C(SEQAN_PP_BOOL(p(29, s)), s, p, o, m) +# define SEQAN_PP_FOR_29(s, p, o, m) SEQAN_PP_FOR_29_C(SEQAN_PP_BOOL(p(30, s)), s, p, o, m) +# define SEQAN_PP_FOR_30(s, p, o, m) SEQAN_PP_FOR_30_C(SEQAN_PP_BOOL(p(31, s)), s, p, o, m) +# define SEQAN_PP_FOR_31(s, p, o, m) SEQAN_PP_FOR_31_C(SEQAN_PP_BOOL(p(32, s)), s, p, o, m) +# define SEQAN_PP_FOR_32(s, p, o, m) SEQAN_PP_FOR_32_C(SEQAN_PP_BOOL(p(33, s)), s, p, o, m) +# define SEQAN_PP_FOR_33(s, p, o, m) SEQAN_PP_FOR_33_C(SEQAN_PP_BOOL(p(34, s)), s, p, o, m) +# define SEQAN_PP_FOR_34(s, p, o, m) SEQAN_PP_FOR_34_C(SEQAN_PP_BOOL(p(35, s)), s, p, o, m) +# define SEQAN_PP_FOR_35(s, p, o, m) SEQAN_PP_FOR_35_C(SEQAN_PP_BOOL(p(36, s)), s, p, o, m) +# define SEQAN_PP_FOR_36(s, p, o, m) SEQAN_PP_FOR_36_C(SEQAN_PP_BOOL(p(37, s)), s, p, o, m) +# define SEQAN_PP_FOR_37(s, p, o, m) SEQAN_PP_FOR_37_C(SEQAN_PP_BOOL(p(38, s)), s, p, o, m) +# define SEQAN_PP_FOR_38(s, p, o, m) SEQAN_PP_FOR_38_C(SEQAN_PP_BOOL(p(39, s)), s, p, o, m) +# define SEQAN_PP_FOR_39(s, p, o, m) SEQAN_PP_FOR_39_C(SEQAN_PP_BOOL(p(40, s)), s, p, o, m) +# define SEQAN_PP_FOR_40(s, p, o, m) SEQAN_PP_FOR_40_C(SEQAN_PP_BOOL(p(41, s)), s, p, o, m) +# define SEQAN_PP_FOR_41(s, p, o, m) SEQAN_PP_FOR_41_C(SEQAN_PP_BOOL(p(42, s)), s, p, o, m) +# define SEQAN_PP_FOR_42(s, p, o, m) SEQAN_PP_FOR_42_C(SEQAN_PP_BOOL(p(43, s)), s, p, o, m) +# define SEQAN_PP_FOR_43(s, p, o, m) SEQAN_PP_FOR_43_C(SEQAN_PP_BOOL(p(44, s)), s, p, o, m) +# define SEQAN_PP_FOR_44(s, p, o, m) SEQAN_PP_FOR_44_C(SEQAN_PP_BOOL(p(45, s)), s, p, o, m) +# define SEQAN_PP_FOR_45(s, p, o, m) SEQAN_PP_FOR_45_C(SEQAN_PP_BOOL(p(46, s)), s, p, o, m) +# define SEQAN_PP_FOR_46(s, p, o, m) SEQAN_PP_FOR_46_C(SEQAN_PP_BOOL(p(47, s)), s, p, o, m) +# define SEQAN_PP_FOR_47(s, p, o, m) SEQAN_PP_FOR_47_C(SEQAN_PP_BOOL(p(48, s)), s, p, o, m) +# define SEQAN_PP_FOR_48(s, p, o, m) SEQAN_PP_FOR_48_C(SEQAN_PP_BOOL(p(49, s)), s, p, o, m) +# define SEQAN_PP_FOR_49(s, p, o, m) SEQAN_PP_FOR_49_C(SEQAN_PP_BOOL(p(50, s)), s, p, o, m) +# define SEQAN_PP_FOR_50(s, p, o, m) SEQAN_PP_FOR_50_C(SEQAN_PP_BOOL(p(51, s)), s, p, o, m) +# define SEQAN_PP_FOR_51(s, p, o, m) SEQAN_PP_FOR_51_C(SEQAN_PP_BOOL(p(52, s)), s, p, o, m) +# define SEQAN_PP_FOR_52(s, p, o, m) SEQAN_PP_FOR_52_C(SEQAN_PP_BOOL(p(53, s)), s, p, o, m) +# define SEQAN_PP_FOR_53(s, p, o, m) SEQAN_PP_FOR_53_C(SEQAN_PP_BOOL(p(54, s)), s, p, o, m) +# define SEQAN_PP_FOR_54(s, p, o, m) SEQAN_PP_FOR_54_C(SEQAN_PP_BOOL(p(55, s)), s, p, o, m) +# define SEQAN_PP_FOR_55(s, p, o, m) SEQAN_PP_FOR_55_C(SEQAN_PP_BOOL(p(56, s)), s, p, o, m) +# define SEQAN_PP_FOR_56(s, p, o, m) SEQAN_PP_FOR_56_C(SEQAN_PP_BOOL(p(57, s)), s, p, o, m) +# define SEQAN_PP_FOR_57(s, p, o, m) SEQAN_PP_FOR_57_C(SEQAN_PP_BOOL(p(58, s)), s, p, o, m) +# define SEQAN_PP_FOR_58(s, p, o, m) SEQAN_PP_FOR_58_C(SEQAN_PP_BOOL(p(59, s)), s, p, o, m) +# define SEQAN_PP_FOR_59(s, p, o, m) SEQAN_PP_FOR_59_C(SEQAN_PP_BOOL(p(60, s)), s, p, o, m) +# define SEQAN_PP_FOR_60(s, p, o, m) SEQAN_PP_FOR_60_C(SEQAN_PP_BOOL(p(61, s)), s, p, o, m) +# define SEQAN_PP_FOR_61(s, p, o, m) SEQAN_PP_FOR_61_C(SEQAN_PP_BOOL(p(62, s)), s, p, o, m) +# define SEQAN_PP_FOR_62(s, p, o, m) SEQAN_PP_FOR_62_C(SEQAN_PP_BOOL(p(63, s)), s, p, o, m) +# define SEQAN_PP_FOR_63(s, p, o, m) SEQAN_PP_FOR_63_C(SEQAN_PP_BOOL(p(64, s)), s, p, o, m) +# define SEQAN_PP_FOR_64(s, p, o, m) SEQAN_PP_FOR_64_C(SEQAN_PP_BOOL(p(65, s)), s, p, o, m) +# define SEQAN_PP_FOR_65(s, p, o, m) SEQAN_PP_FOR_65_C(SEQAN_PP_BOOL(p(66, s)), s, p, o, m) +# define SEQAN_PP_FOR_66(s, p, o, m) SEQAN_PP_FOR_66_C(SEQAN_PP_BOOL(p(67, s)), s, p, o, m) +# define SEQAN_PP_FOR_67(s, p, o, m) SEQAN_PP_FOR_67_C(SEQAN_PP_BOOL(p(68, s)), s, p, o, m) +# define SEQAN_PP_FOR_68(s, p, o, m) SEQAN_PP_FOR_68_C(SEQAN_PP_BOOL(p(69, s)), s, p, o, m) +# define SEQAN_PP_FOR_69(s, p, o, m) SEQAN_PP_FOR_69_C(SEQAN_PP_BOOL(p(70, s)), s, p, o, m) +# define SEQAN_PP_FOR_70(s, p, o, m) SEQAN_PP_FOR_70_C(SEQAN_PP_BOOL(p(71, s)), s, p, o, m) +# define SEQAN_PP_FOR_71(s, p, o, m) SEQAN_PP_FOR_71_C(SEQAN_PP_BOOL(p(72, s)), s, p, o, m) +# define SEQAN_PP_FOR_72(s, p, o, m) SEQAN_PP_FOR_72_C(SEQAN_PP_BOOL(p(73, s)), s, p, o, m) +# define SEQAN_PP_FOR_73(s, p, o, m) SEQAN_PP_FOR_73_C(SEQAN_PP_BOOL(p(74, s)), s, p, o, m) +# define SEQAN_PP_FOR_74(s, p, o, m) SEQAN_PP_FOR_74_C(SEQAN_PP_BOOL(p(75, s)), s, p, o, m) +# define SEQAN_PP_FOR_75(s, p, o, m) SEQAN_PP_FOR_75_C(SEQAN_PP_BOOL(p(76, s)), s, p, o, m) +# define SEQAN_PP_FOR_76(s, p, o, m) SEQAN_PP_FOR_76_C(SEQAN_PP_BOOL(p(77, s)), s, p, o, m) +# define SEQAN_PP_FOR_77(s, p, o, m) SEQAN_PP_FOR_77_C(SEQAN_PP_BOOL(p(78, s)), s, p, o, m) +# define SEQAN_PP_FOR_78(s, p, o, m) SEQAN_PP_FOR_78_C(SEQAN_PP_BOOL(p(79, s)), s, p, o, m) +# define SEQAN_PP_FOR_79(s, p, o, m) SEQAN_PP_FOR_79_C(SEQAN_PP_BOOL(p(80, s)), s, p, o, m) +# define SEQAN_PP_FOR_80(s, p, o, m) SEQAN_PP_FOR_80_C(SEQAN_PP_BOOL(p(81, s)), s, p, o, m) +# define SEQAN_PP_FOR_81(s, p, o, m) SEQAN_PP_FOR_81_C(SEQAN_PP_BOOL(p(82, s)), s, p, o, m) +# define SEQAN_PP_FOR_82(s, p, o, m) SEQAN_PP_FOR_82_C(SEQAN_PP_BOOL(p(83, s)), s, p, o, m) +# define SEQAN_PP_FOR_83(s, p, o, m) SEQAN_PP_FOR_83_C(SEQAN_PP_BOOL(p(84, s)), s, p, o, m) +# define SEQAN_PP_FOR_84(s, p, o, m) SEQAN_PP_FOR_84_C(SEQAN_PP_BOOL(p(85, s)), s, p, o, m) +# define SEQAN_PP_FOR_85(s, p, o, m) SEQAN_PP_FOR_85_C(SEQAN_PP_BOOL(p(86, s)), s, p, o, m) +# define SEQAN_PP_FOR_86(s, p, o, m) SEQAN_PP_FOR_86_C(SEQAN_PP_BOOL(p(87, s)), s, p, o, m) +# define SEQAN_PP_FOR_87(s, p, o, m) SEQAN_PP_FOR_87_C(SEQAN_PP_BOOL(p(88, s)), s, p, o, m) +# define SEQAN_PP_FOR_88(s, p, o, m) SEQAN_PP_FOR_88_C(SEQAN_PP_BOOL(p(89, s)), s, p, o, m) +# define SEQAN_PP_FOR_89(s, p, o, m) SEQAN_PP_FOR_89_C(SEQAN_PP_BOOL(p(90, s)), s, p, o, m) +# define SEQAN_PP_FOR_90(s, p, o, m) SEQAN_PP_FOR_90_C(SEQAN_PP_BOOL(p(91, s)), s, p, o, m) +# define SEQAN_PP_FOR_91(s, p, o, m) SEQAN_PP_FOR_91_C(SEQAN_PP_BOOL(p(92, s)), s, p, o, m) +# define SEQAN_PP_FOR_92(s, p, o, m) SEQAN_PP_FOR_92_C(SEQAN_PP_BOOL(p(93, s)), s, p, o, m) +# define SEQAN_PP_FOR_93(s, p, o, m) SEQAN_PP_FOR_93_C(SEQAN_PP_BOOL(p(94, s)), s, p, o, m) +# define SEQAN_PP_FOR_94(s, p, o, m) SEQAN_PP_FOR_94_C(SEQAN_PP_BOOL(p(95, s)), s, p, o, m) +# define SEQAN_PP_FOR_95(s, p, o, m) SEQAN_PP_FOR_95_C(SEQAN_PP_BOOL(p(96, s)), s, p, o, m) +# define SEQAN_PP_FOR_96(s, p, o, m) SEQAN_PP_FOR_96_C(SEQAN_PP_BOOL(p(97, s)), s, p, o, m) +# define SEQAN_PP_FOR_97(s, p, o, m) SEQAN_PP_FOR_97_C(SEQAN_PP_BOOL(p(98, s)), s, p, o, m) +# define SEQAN_PP_FOR_98(s, p, o, m) SEQAN_PP_FOR_98_C(SEQAN_PP_BOOL(p(99, s)), s, p, o, m) +# define SEQAN_PP_FOR_99(s, p, o, m) SEQAN_PP_FOR_99_C(SEQAN_PP_BOOL(p(100, s)), s, p, o, m) +# define SEQAN_PP_FOR_100(s, p, o, m) SEQAN_PP_FOR_100_C(SEQAN_PP_BOOL(p(101, s)), s, p, o, m) +# define SEQAN_PP_FOR_101(s, p, o, m) SEQAN_PP_FOR_101_C(SEQAN_PP_BOOL(p(102, s)), s, p, o, m) +# define SEQAN_PP_FOR_102(s, p, o, m) SEQAN_PP_FOR_102_C(SEQAN_PP_BOOL(p(103, s)), s, p, o, m) +# define SEQAN_PP_FOR_103(s, p, o, m) SEQAN_PP_FOR_103_C(SEQAN_PP_BOOL(p(104, s)), s, p, o, m) +# define SEQAN_PP_FOR_104(s, p, o, m) SEQAN_PP_FOR_104_C(SEQAN_PP_BOOL(p(105, s)), s, p, o, m) +# define SEQAN_PP_FOR_105(s, p, o, m) SEQAN_PP_FOR_105_C(SEQAN_PP_BOOL(p(106, s)), s, p, o, m) +# define SEQAN_PP_FOR_106(s, p, o, m) SEQAN_PP_FOR_106_C(SEQAN_PP_BOOL(p(107, s)), s, p, o, m) +# define SEQAN_PP_FOR_107(s, p, o, m) SEQAN_PP_FOR_107_C(SEQAN_PP_BOOL(p(108, s)), s, p, o, m) +# define SEQAN_PP_FOR_108(s, p, o, m) SEQAN_PP_FOR_108_C(SEQAN_PP_BOOL(p(109, s)), s, p, o, m) +# define SEQAN_PP_FOR_109(s, p, o, m) SEQAN_PP_FOR_109_C(SEQAN_PP_BOOL(p(110, s)), s, p, o, m) +# define SEQAN_PP_FOR_110(s, p, o, m) SEQAN_PP_FOR_110_C(SEQAN_PP_BOOL(p(111, s)), s, p, o, m) +# define SEQAN_PP_FOR_111(s, p, o, m) SEQAN_PP_FOR_111_C(SEQAN_PP_BOOL(p(112, s)), s, p, o, m) +# define SEQAN_PP_FOR_112(s, p, o, m) SEQAN_PP_FOR_112_C(SEQAN_PP_BOOL(p(113, s)), s, p, o, m) +# define SEQAN_PP_FOR_113(s, p, o, m) SEQAN_PP_FOR_113_C(SEQAN_PP_BOOL(p(114, s)), s, p, o, m) +# define SEQAN_PP_FOR_114(s, p, o, m) SEQAN_PP_FOR_114_C(SEQAN_PP_BOOL(p(115, s)), s, p, o, m) +# define SEQAN_PP_FOR_115(s, p, o, m) SEQAN_PP_FOR_115_C(SEQAN_PP_BOOL(p(116, s)), s, p, o, m) +# define SEQAN_PP_FOR_116(s, p, o, m) SEQAN_PP_FOR_116_C(SEQAN_PP_BOOL(p(117, s)), s, p, o, m) +# define SEQAN_PP_FOR_117(s, p, o, m) SEQAN_PP_FOR_117_C(SEQAN_PP_BOOL(p(118, s)), s, p, o, m) +# define SEQAN_PP_FOR_118(s, p, o, m) SEQAN_PP_FOR_118_C(SEQAN_PP_BOOL(p(119, s)), s, p, o, m) +# define SEQAN_PP_FOR_119(s, p, o, m) SEQAN_PP_FOR_119_C(SEQAN_PP_BOOL(p(120, s)), s, p, o, m) +# define SEQAN_PP_FOR_120(s, p, o, m) SEQAN_PP_FOR_120_C(SEQAN_PP_BOOL(p(121, s)), s, p, o, m) +# define SEQAN_PP_FOR_121(s, p, o, m) SEQAN_PP_FOR_121_C(SEQAN_PP_BOOL(p(122, s)), s, p, o, m) +# define SEQAN_PP_FOR_122(s, p, o, m) SEQAN_PP_FOR_122_C(SEQAN_PP_BOOL(p(123, s)), s, p, o, m) +# define SEQAN_PP_FOR_123(s, p, o, m) SEQAN_PP_FOR_123_C(SEQAN_PP_BOOL(p(124, s)), s, p, o, m) +# define SEQAN_PP_FOR_124(s, p, o, m) SEQAN_PP_FOR_124_C(SEQAN_PP_BOOL(p(125, s)), s, p, o, m) +# define SEQAN_PP_FOR_125(s, p, o, m) SEQAN_PP_FOR_125_C(SEQAN_PP_BOOL(p(126, s)), s, p, o, m) +# define SEQAN_PP_FOR_126(s, p, o, m) SEQAN_PP_FOR_126_C(SEQAN_PP_BOOL(p(127, s)), s, p, o, m) +# define SEQAN_PP_FOR_127(s, p, o, m) SEQAN_PP_FOR_127_C(SEQAN_PP_BOOL(p(128, s)), s, p, o, m) +# define SEQAN_PP_FOR_128(s, p, o, m) SEQAN_PP_FOR_128_C(SEQAN_PP_BOOL(p(129, s)), s, p, o, m) +# define SEQAN_PP_FOR_129(s, p, o, m) SEQAN_PP_FOR_129_C(SEQAN_PP_BOOL(p(130, s)), s, p, o, m) +# define SEQAN_PP_FOR_130(s, p, o, m) SEQAN_PP_FOR_130_C(SEQAN_PP_BOOL(p(131, s)), s, p, o, m) +# define SEQAN_PP_FOR_131(s, p, o, m) SEQAN_PP_FOR_131_C(SEQAN_PP_BOOL(p(132, s)), s, p, o, m) +# define SEQAN_PP_FOR_132(s, p, o, m) SEQAN_PP_FOR_132_C(SEQAN_PP_BOOL(p(133, s)), s, p, o, m) +# define SEQAN_PP_FOR_133(s, p, o, m) SEQAN_PP_FOR_133_C(SEQAN_PP_BOOL(p(134, s)), s, p, o, m) +# define SEQAN_PP_FOR_134(s, p, o, m) SEQAN_PP_FOR_134_C(SEQAN_PP_BOOL(p(135, s)), s, p, o, m) +# define SEQAN_PP_FOR_135(s, p, o, m) SEQAN_PP_FOR_135_C(SEQAN_PP_BOOL(p(136, s)), s, p, o, m) +# define SEQAN_PP_FOR_136(s, p, o, m) SEQAN_PP_FOR_136_C(SEQAN_PP_BOOL(p(137, s)), s, p, o, m) +# define SEQAN_PP_FOR_137(s, p, o, m) SEQAN_PP_FOR_137_C(SEQAN_PP_BOOL(p(138, s)), s, p, o, m) +# define SEQAN_PP_FOR_138(s, p, o, m) SEQAN_PP_FOR_138_C(SEQAN_PP_BOOL(p(139, s)), s, p, o, m) +# define SEQAN_PP_FOR_139(s, p, o, m) SEQAN_PP_FOR_139_C(SEQAN_PP_BOOL(p(140, s)), s, p, o, m) +# define SEQAN_PP_FOR_140(s, p, o, m) SEQAN_PP_FOR_140_C(SEQAN_PP_BOOL(p(141, s)), s, p, o, m) +# define SEQAN_PP_FOR_141(s, p, o, m) SEQAN_PP_FOR_141_C(SEQAN_PP_BOOL(p(142, s)), s, p, o, m) +# define SEQAN_PP_FOR_142(s, p, o, m) SEQAN_PP_FOR_142_C(SEQAN_PP_BOOL(p(143, s)), s, p, o, m) +# define SEQAN_PP_FOR_143(s, p, o, m) SEQAN_PP_FOR_143_C(SEQAN_PP_BOOL(p(144, s)), s, p, o, m) +# define SEQAN_PP_FOR_144(s, p, o, m) SEQAN_PP_FOR_144_C(SEQAN_PP_BOOL(p(145, s)), s, p, o, m) +# define SEQAN_PP_FOR_145(s, p, o, m) SEQAN_PP_FOR_145_C(SEQAN_PP_BOOL(p(146, s)), s, p, o, m) +# define SEQAN_PP_FOR_146(s, p, o, m) SEQAN_PP_FOR_146_C(SEQAN_PP_BOOL(p(147, s)), s, p, o, m) +# define SEQAN_PP_FOR_147(s, p, o, m) SEQAN_PP_FOR_147_C(SEQAN_PP_BOOL(p(148, s)), s, p, o, m) +# define SEQAN_PP_FOR_148(s, p, o, m) SEQAN_PP_FOR_148_C(SEQAN_PP_BOOL(p(149, s)), s, p, o, m) +# define SEQAN_PP_FOR_149(s, p, o, m) SEQAN_PP_FOR_149_C(SEQAN_PP_BOOL(p(150, s)), s, p, o, m) +# define SEQAN_PP_FOR_150(s, p, o, m) SEQAN_PP_FOR_150_C(SEQAN_PP_BOOL(p(151, s)), s, p, o, m) +# define SEQAN_PP_FOR_151(s, p, o, m) SEQAN_PP_FOR_151_C(SEQAN_PP_BOOL(p(152, s)), s, p, o, m) +# define SEQAN_PP_FOR_152(s, p, o, m) SEQAN_PP_FOR_152_C(SEQAN_PP_BOOL(p(153, s)), s, p, o, m) +# define SEQAN_PP_FOR_153(s, p, o, m) SEQAN_PP_FOR_153_C(SEQAN_PP_BOOL(p(154, s)), s, p, o, m) +# define SEQAN_PP_FOR_154(s, p, o, m) SEQAN_PP_FOR_154_C(SEQAN_PP_BOOL(p(155, s)), s, p, o, m) +# define SEQAN_PP_FOR_155(s, p, o, m) SEQAN_PP_FOR_155_C(SEQAN_PP_BOOL(p(156, s)), s, p, o, m) +# define SEQAN_PP_FOR_156(s, p, o, m) SEQAN_PP_FOR_156_C(SEQAN_PP_BOOL(p(157, s)), s, p, o, m) +# define SEQAN_PP_FOR_157(s, p, o, m) SEQAN_PP_FOR_157_C(SEQAN_PP_BOOL(p(158, s)), s, p, o, m) +# define SEQAN_PP_FOR_158(s, p, o, m) SEQAN_PP_FOR_158_C(SEQAN_PP_BOOL(p(159, s)), s, p, o, m) +# define SEQAN_PP_FOR_159(s, p, o, m) SEQAN_PP_FOR_159_C(SEQAN_PP_BOOL(p(160, s)), s, p, o, m) +# define SEQAN_PP_FOR_160(s, p, o, m) SEQAN_PP_FOR_160_C(SEQAN_PP_BOOL(p(161, s)), s, p, o, m) +# define SEQAN_PP_FOR_161(s, p, o, m) SEQAN_PP_FOR_161_C(SEQAN_PP_BOOL(p(162, s)), s, p, o, m) +# define SEQAN_PP_FOR_162(s, p, o, m) SEQAN_PP_FOR_162_C(SEQAN_PP_BOOL(p(163, s)), s, p, o, m) +# define SEQAN_PP_FOR_163(s, p, o, m) SEQAN_PP_FOR_163_C(SEQAN_PP_BOOL(p(164, s)), s, p, o, m) +# define SEQAN_PP_FOR_164(s, p, o, m) SEQAN_PP_FOR_164_C(SEQAN_PP_BOOL(p(165, s)), s, p, o, m) +# define SEQAN_PP_FOR_165(s, p, o, m) SEQAN_PP_FOR_165_C(SEQAN_PP_BOOL(p(166, s)), s, p, o, m) +# define SEQAN_PP_FOR_166(s, p, o, m) SEQAN_PP_FOR_166_C(SEQAN_PP_BOOL(p(167, s)), s, p, o, m) +# define SEQAN_PP_FOR_167(s, p, o, m) SEQAN_PP_FOR_167_C(SEQAN_PP_BOOL(p(168, s)), s, p, o, m) +# define SEQAN_PP_FOR_168(s, p, o, m) SEQAN_PP_FOR_168_C(SEQAN_PP_BOOL(p(169, s)), s, p, o, m) +# define SEQAN_PP_FOR_169(s, p, o, m) SEQAN_PP_FOR_169_C(SEQAN_PP_BOOL(p(170, s)), s, p, o, m) +# define SEQAN_PP_FOR_170(s, p, o, m) SEQAN_PP_FOR_170_C(SEQAN_PP_BOOL(p(171, s)), s, p, o, m) +# define SEQAN_PP_FOR_171(s, p, o, m) SEQAN_PP_FOR_171_C(SEQAN_PP_BOOL(p(172, s)), s, p, o, m) +# define SEQAN_PP_FOR_172(s, p, o, m) SEQAN_PP_FOR_172_C(SEQAN_PP_BOOL(p(173, s)), s, p, o, m) +# define SEQAN_PP_FOR_173(s, p, o, m) SEQAN_PP_FOR_173_C(SEQAN_PP_BOOL(p(174, s)), s, p, o, m) +# define SEQAN_PP_FOR_174(s, p, o, m) SEQAN_PP_FOR_174_C(SEQAN_PP_BOOL(p(175, s)), s, p, o, m) +# define SEQAN_PP_FOR_175(s, p, o, m) SEQAN_PP_FOR_175_C(SEQAN_PP_BOOL(p(176, s)), s, p, o, m) +# define SEQAN_PP_FOR_176(s, p, o, m) SEQAN_PP_FOR_176_C(SEQAN_PP_BOOL(p(177, s)), s, p, o, m) +# define SEQAN_PP_FOR_177(s, p, o, m) SEQAN_PP_FOR_177_C(SEQAN_PP_BOOL(p(178, s)), s, p, o, m) +# define SEQAN_PP_FOR_178(s, p, o, m) SEQAN_PP_FOR_178_C(SEQAN_PP_BOOL(p(179, s)), s, p, o, m) +# define SEQAN_PP_FOR_179(s, p, o, m) SEQAN_PP_FOR_179_C(SEQAN_PP_BOOL(p(180, s)), s, p, o, m) +# define SEQAN_PP_FOR_180(s, p, o, m) SEQAN_PP_FOR_180_C(SEQAN_PP_BOOL(p(181, s)), s, p, o, m) +# define SEQAN_PP_FOR_181(s, p, o, m) SEQAN_PP_FOR_181_C(SEQAN_PP_BOOL(p(182, s)), s, p, o, m) +# define SEQAN_PP_FOR_182(s, p, o, m) SEQAN_PP_FOR_182_C(SEQAN_PP_BOOL(p(183, s)), s, p, o, m) +# define SEQAN_PP_FOR_183(s, p, o, m) SEQAN_PP_FOR_183_C(SEQAN_PP_BOOL(p(184, s)), s, p, o, m) +# define SEQAN_PP_FOR_184(s, p, o, m) SEQAN_PP_FOR_184_C(SEQAN_PP_BOOL(p(185, s)), s, p, o, m) +# define SEQAN_PP_FOR_185(s, p, o, m) SEQAN_PP_FOR_185_C(SEQAN_PP_BOOL(p(186, s)), s, p, o, m) +# define SEQAN_PP_FOR_186(s, p, o, m) SEQAN_PP_FOR_186_C(SEQAN_PP_BOOL(p(187, s)), s, p, o, m) +# define SEQAN_PP_FOR_187(s, p, o, m) SEQAN_PP_FOR_187_C(SEQAN_PP_BOOL(p(188, s)), s, p, o, m) +# define SEQAN_PP_FOR_188(s, p, o, m) SEQAN_PP_FOR_188_C(SEQAN_PP_BOOL(p(189, s)), s, p, o, m) +# define SEQAN_PP_FOR_189(s, p, o, m) SEQAN_PP_FOR_189_C(SEQAN_PP_BOOL(p(190, s)), s, p, o, m) +# define SEQAN_PP_FOR_190(s, p, o, m) SEQAN_PP_FOR_190_C(SEQAN_PP_BOOL(p(191, s)), s, p, o, m) +# define SEQAN_PP_FOR_191(s, p, o, m) SEQAN_PP_FOR_191_C(SEQAN_PP_BOOL(p(192, s)), s, p, o, m) +# define SEQAN_PP_FOR_192(s, p, o, m) SEQAN_PP_FOR_192_C(SEQAN_PP_BOOL(p(193, s)), s, p, o, m) +# define SEQAN_PP_FOR_193(s, p, o, m) SEQAN_PP_FOR_193_C(SEQAN_PP_BOOL(p(194, s)), s, p, o, m) +# define SEQAN_PP_FOR_194(s, p, o, m) SEQAN_PP_FOR_194_C(SEQAN_PP_BOOL(p(195, s)), s, p, o, m) +# define SEQAN_PP_FOR_195(s, p, o, m) SEQAN_PP_FOR_195_C(SEQAN_PP_BOOL(p(196, s)), s, p, o, m) +# define SEQAN_PP_FOR_196(s, p, o, m) SEQAN_PP_FOR_196_C(SEQAN_PP_BOOL(p(197, s)), s, p, o, m) +# define SEQAN_PP_FOR_197(s, p, o, m) SEQAN_PP_FOR_197_C(SEQAN_PP_BOOL(p(198, s)), s, p, o, m) +# define SEQAN_PP_FOR_198(s, p, o, m) SEQAN_PP_FOR_198_C(SEQAN_PP_BOOL(p(199, s)), s, p, o, m) +# define SEQAN_PP_FOR_199(s, p, o, m) SEQAN_PP_FOR_199_C(SEQAN_PP_BOOL(p(200, s)), s, p, o, m) +# define SEQAN_PP_FOR_200(s, p, o, m) SEQAN_PP_FOR_200_C(SEQAN_PP_BOOL(p(201, s)), s, p, o, m) +# define SEQAN_PP_FOR_201(s, p, o, m) SEQAN_PP_FOR_201_C(SEQAN_PP_BOOL(p(202, s)), s, p, o, m) +# define SEQAN_PP_FOR_202(s, p, o, m) SEQAN_PP_FOR_202_C(SEQAN_PP_BOOL(p(203, s)), s, p, o, m) +# define SEQAN_PP_FOR_203(s, p, o, m) SEQAN_PP_FOR_203_C(SEQAN_PP_BOOL(p(204, s)), s, p, o, m) +# define SEQAN_PP_FOR_204(s, p, o, m) SEQAN_PP_FOR_204_C(SEQAN_PP_BOOL(p(205, s)), s, p, o, m) +# define SEQAN_PP_FOR_205(s, p, o, m) SEQAN_PP_FOR_205_C(SEQAN_PP_BOOL(p(206, s)), s, p, o, m) +# define SEQAN_PP_FOR_206(s, p, o, m) SEQAN_PP_FOR_206_C(SEQAN_PP_BOOL(p(207, s)), s, p, o, m) +# define SEQAN_PP_FOR_207(s, p, o, m) SEQAN_PP_FOR_207_C(SEQAN_PP_BOOL(p(208, s)), s, p, o, m) +# define SEQAN_PP_FOR_208(s, p, o, m) SEQAN_PP_FOR_208_C(SEQAN_PP_BOOL(p(209, s)), s, p, o, m) +# define SEQAN_PP_FOR_209(s, p, o, m) SEQAN_PP_FOR_209_C(SEQAN_PP_BOOL(p(210, s)), s, p, o, m) +# define SEQAN_PP_FOR_210(s, p, o, m) SEQAN_PP_FOR_210_C(SEQAN_PP_BOOL(p(211, s)), s, p, o, m) +# define SEQAN_PP_FOR_211(s, p, o, m) SEQAN_PP_FOR_211_C(SEQAN_PP_BOOL(p(212, s)), s, p, o, m) +# define SEQAN_PP_FOR_212(s, p, o, m) SEQAN_PP_FOR_212_C(SEQAN_PP_BOOL(p(213, s)), s, p, o, m) +# define SEQAN_PP_FOR_213(s, p, o, m) SEQAN_PP_FOR_213_C(SEQAN_PP_BOOL(p(214, s)), s, p, o, m) +# define SEQAN_PP_FOR_214(s, p, o, m) SEQAN_PP_FOR_214_C(SEQAN_PP_BOOL(p(215, s)), s, p, o, m) +# define SEQAN_PP_FOR_215(s, p, o, m) SEQAN_PP_FOR_215_C(SEQAN_PP_BOOL(p(216, s)), s, p, o, m) +# define SEQAN_PP_FOR_216(s, p, o, m) SEQAN_PP_FOR_216_C(SEQAN_PP_BOOL(p(217, s)), s, p, o, m) +# define SEQAN_PP_FOR_217(s, p, o, m) SEQAN_PP_FOR_217_C(SEQAN_PP_BOOL(p(218, s)), s, p, o, m) +# define SEQAN_PP_FOR_218(s, p, o, m) SEQAN_PP_FOR_218_C(SEQAN_PP_BOOL(p(219, s)), s, p, o, m) +# define SEQAN_PP_FOR_219(s, p, o, m) SEQAN_PP_FOR_219_C(SEQAN_PP_BOOL(p(220, s)), s, p, o, m) +# define SEQAN_PP_FOR_220(s, p, o, m) SEQAN_PP_FOR_220_C(SEQAN_PP_BOOL(p(221, s)), s, p, o, m) +# define SEQAN_PP_FOR_221(s, p, o, m) SEQAN_PP_FOR_221_C(SEQAN_PP_BOOL(p(222, s)), s, p, o, m) +# define SEQAN_PP_FOR_222(s, p, o, m) SEQAN_PP_FOR_222_C(SEQAN_PP_BOOL(p(223, s)), s, p, o, m) +# define SEQAN_PP_FOR_223(s, p, o, m) SEQAN_PP_FOR_223_C(SEQAN_PP_BOOL(p(224, s)), s, p, o, m) +# define SEQAN_PP_FOR_224(s, p, o, m) SEQAN_PP_FOR_224_C(SEQAN_PP_BOOL(p(225, s)), s, p, o, m) +# define SEQAN_PP_FOR_225(s, p, o, m) SEQAN_PP_FOR_225_C(SEQAN_PP_BOOL(p(226, s)), s, p, o, m) +# define SEQAN_PP_FOR_226(s, p, o, m) SEQAN_PP_FOR_226_C(SEQAN_PP_BOOL(p(227, s)), s, p, o, m) +# define SEQAN_PP_FOR_227(s, p, o, m) SEQAN_PP_FOR_227_C(SEQAN_PP_BOOL(p(228, s)), s, p, o, m) +# define SEQAN_PP_FOR_228(s, p, o, m) SEQAN_PP_FOR_228_C(SEQAN_PP_BOOL(p(229, s)), s, p, o, m) +# define SEQAN_PP_FOR_229(s, p, o, m) SEQAN_PP_FOR_229_C(SEQAN_PP_BOOL(p(230, s)), s, p, o, m) +# define SEQAN_PP_FOR_230(s, p, o, m) SEQAN_PP_FOR_230_C(SEQAN_PP_BOOL(p(231, s)), s, p, o, m) +# define SEQAN_PP_FOR_231(s, p, o, m) SEQAN_PP_FOR_231_C(SEQAN_PP_BOOL(p(232, s)), s, p, o, m) +# define SEQAN_PP_FOR_232(s, p, o, m) SEQAN_PP_FOR_232_C(SEQAN_PP_BOOL(p(233, s)), s, p, o, m) +# define SEQAN_PP_FOR_233(s, p, o, m) SEQAN_PP_FOR_233_C(SEQAN_PP_BOOL(p(234, s)), s, p, o, m) +# define SEQAN_PP_FOR_234(s, p, o, m) SEQAN_PP_FOR_234_C(SEQAN_PP_BOOL(p(235, s)), s, p, o, m) +# define SEQAN_PP_FOR_235(s, p, o, m) SEQAN_PP_FOR_235_C(SEQAN_PP_BOOL(p(236, s)), s, p, o, m) +# define SEQAN_PP_FOR_236(s, p, o, m) SEQAN_PP_FOR_236_C(SEQAN_PP_BOOL(p(237, s)), s, p, o, m) +# define SEQAN_PP_FOR_237(s, p, o, m) SEQAN_PP_FOR_237_C(SEQAN_PP_BOOL(p(238, s)), s, p, o, m) +# define SEQAN_PP_FOR_238(s, p, o, m) SEQAN_PP_FOR_238_C(SEQAN_PP_BOOL(p(239, s)), s, p, o, m) +# define SEQAN_PP_FOR_239(s, p, o, m) SEQAN_PP_FOR_239_C(SEQAN_PP_BOOL(p(240, s)), s, p, o, m) +# define SEQAN_PP_FOR_240(s, p, o, m) SEQAN_PP_FOR_240_C(SEQAN_PP_BOOL(p(241, s)), s, p, o, m) +# define SEQAN_PP_FOR_241(s, p, o, m) SEQAN_PP_FOR_241_C(SEQAN_PP_BOOL(p(242, s)), s, p, o, m) +# define SEQAN_PP_FOR_242(s, p, o, m) SEQAN_PP_FOR_242_C(SEQAN_PP_BOOL(p(243, s)), s, p, o, m) +# define SEQAN_PP_FOR_243(s, p, o, m) SEQAN_PP_FOR_243_C(SEQAN_PP_BOOL(p(244, s)), s, p, o, m) +# define SEQAN_PP_FOR_244(s, p, o, m) SEQAN_PP_FOR_244_C(SEQAN_PP_BOOL(p(245, s)), s, p, o, m) +# define SEQAN_PP_FOR_245(s, p, o, m) SEQAN_PP_FOR_245_C(SEQAN_PP_BOOL(p(246, s)), s, p, o, m) +# define SEQAN_PP_FOR_246(s, p, o, m) SEQAN_PP_FOR_246_C(SEQAN_PP_BOOL(p(247, s)), s, p, o, m) +# define SEQAN_PP_FOR_247(s, p, o, m) SEQAN_PP_FOR_247_C(SEQAN_PP_BOOL(p(248, s)), s, p, o, m) +# define SEQAN_PP_FOR_248(s, p, o, m) SEQAN_PP_FOR_248_C(SEQAN_PP_BOOL(p(249, s)), s, p, o, m) +# define SEQAN_PP_FOR_249(s, p, o, m) SEQAN_PP_FOR_249_C(SEQAN_PP_BOOL(p(250, s)), s, p, o, m) +# define SEQAN_PP_FOR_250(s, p, o, m) SEQAN_PP_FOR_250_C(SEQAN_PP_BOOL(p(251, s)), s, p, o, m) +# define SEQAN_PP_FOR_251(s, p, o, m) SEQAN_PP_FOR_251_C(SEQAN_PP_BOOL(p(252, s)), s, p, o, m) +# define SEQAN_PP_FOR_252(s, p, o, m) SEQAN_PP_FOR_252_C(SEQAN_PP_BOOL(p(253, s)), s, p, o, m) +# define SEQAN_PP_FOR_253(s, p, o, m) SEQAN_PP_FOR_253_C(SEQAN_PP_BOOL(p(254, s)), s, p, o, m) +# define SEQAN_PP_FOR_254(s, p, o, m) SEQAN_PP_FOR_254_C(SEQAN_PP_BOOL(p(255, s)), s, p, o, m) +# define SEQAN_PP_FOR_255(s, p, o, m) SEQAN_PP_FOR_255_C(SEQAN_PP_BOOL(p(256, s)), s, p, o, m) +# define SEQAN_PP_FOR_256(s, p, o, m) SEQAN_PP_FOR_256_C(SEQAN_PP_BOOL(p(257, s)), s, p, o, m) +# +# define SEQAN_PP_FOR_1_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(2, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_2, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(2, s), p, o, m) +# define SEQAN_PP_FOR_2_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(3, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_3, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(3, s), p, o, m) +# define SEQAN_PP_FOR_3_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(4, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_4, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(4, s), p, o, m) +# define SEQAN_PP_FOR_4_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(5, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_5, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(5, s), p, o, m) +# define SEQAN_PP_FOR_5_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(6, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_6, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(6, s), p, o, m) +# define SEQAN_PP_FOR_6_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(7, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_7, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(7, s), p, o, m) +# define SEQAN_PP_FOR_7_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(8, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_8, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(8, s), p, o, m) +# define SEQAN_PP_FOR_8_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(9, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_9, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(9, s), p, o, m) +# define SEQAN_PP_FOR_9_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(10, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_10, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(10, s), p, o, m) +# define SEQAN_PP_FOR_10_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(11, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_11, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(11, s), p, o, m) +# define SEQAN_PP_FOR_11_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(12, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_12, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(12, s), p, o, m) +# define SEQAN_PP_FOR_12_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(13, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_13, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(13, s), p, o, m) +# define SEQAN_PP_FOR_13_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(14, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_14, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(14, s), p, o, m) +# define SEQAN_PP_FOR_14_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(15, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_15, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(15, s), p, o, m) +# define SEQAN_PP_FOR_15_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(16, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_16, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(16, s), p, o, m) +# define SEQAN_PP_FOR_16_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(17, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_17, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(17, s), p, o, m) +# define SEQAN_PP_FOR_17_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(18, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_18, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(18, s), p, o, m) +# define SEQAN_PP_FOR_18_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(19, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_19, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(19, s), p, o, m) +# define SEQAN_PP_FOR_19_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(20, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_20, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(20, s), p, o, m) +# define SEQAN_PP_FOR_20_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(21, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_21, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(21, s), p, o, m) +# define SEQAN_PP_FOR_21_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(22, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_22, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(22, s), p, o, m) +# define SEQAN_PP_FOR_22_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(23, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_23, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(23, s), p, o, m) +# define SEQAN_PP_FOR_23_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(24, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_24, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(24, s), p, o, m) +# define SEQAN_PP_FOR_24_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(25, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_25, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(25, s), p, o, m) +# define SEQAN_PP_FOR_25_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(26, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_26, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(26, s), p, o, m) +# define SEQAN_PP_FOR_26_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(27, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_27, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(27, s), p, o, m) +# define SEQAN_PP_FOR_27_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(28, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_28, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(28, s), p, o, m) +# define SEQAN_PP_FOR_28_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(29, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_29, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(29, s), p, o, m) +# define SEQAN_PP_FOR_29_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(30, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_30, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(30, s), p, o, m) +# define SEQAN_PP_FOR_30_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(31, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_31, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(31, s), p, o, m) +# define SEQAN_PP_FOR_31_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(32, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_32, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(32, s), p, o, m) +# define SEQAN_PP_FOR_32_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(33, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_33, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(33, s), p, o, m) +# define SEQAN_PP_FOR_33_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(34, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_34, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(34, s), p, o, m) +# define SEQAN_PP_FOR_34_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(35, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_35, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(35, s), p, o, m) +# define SEQAN_PP_FOR_35_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(36, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_36, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(36, s), p, o, m) +# define SEQAN_PP_FOR_36_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(37, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_37, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(37, s), p, o, m) +# define SEQAN_PP_FOR_37_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(38, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_38, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(38, s), p, o, m) +# define SEQAN_PP_FOR_38_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(39, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_39, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(39, s), p, o, m) +# define SEQAN_PP_FOR_39_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(40, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_40, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(40, s), p, o, m) +# define SEQAN_PP_FOR_40_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(41, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_41, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(41, s), p, o, m) +# define SEQAN_PP_FOR_41_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(42, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_42, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(42, s), p, o, m) +# define SEQAN_PP_FOR_42_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(43, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_43, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(43, s), p, o, m) +# define SEQAN_PP_FOR_43_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(44, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_44, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(44, s), p, o, m) +# define SEQAN_PP_FOR_44_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(45, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_45, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(45, s), p, o, m) +# define SEQAN_PP_FOR_45_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(46, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_46, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(46, s), p, o, m) +# define SEQAN_PP_FOR_46_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(47, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_47, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(47, s), p, o, m) +# define SEQAN_PP_FOR_47_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(48, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_48, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(48, s), p, o, m) +# define SEQAN_PP_FOR_48_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(49, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_49, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(49, s), p, o, m) +# define SEQAN_PP_FOR_49_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(50, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_50, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(50, s), p, o, m) +# define SEQAN_PP_FOR_50_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(51, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_51, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(51, s), p, o, m) +# define SEQAN_PP_FOR_51_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(52, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_52, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(52, s), p, o, m) +# define SEQAN_PP_FOR_52_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(53, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_53, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(53, s), p, o, m) +# define SEQAN_PP_FOR_53_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(54, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_54, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(54, s), p, o, m) +# define SEQAN_PP_FOR_54_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(55, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_55, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(55, s), p, o, m) +# define SEQAN_PP_FOR_55_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(56, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_56, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(56, s), p, o, m) +# define SEQAN_PP_FOR_56_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(57, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_57, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(57, s), p, o, m) +# define SEQAN_PP_FOR_57_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(58, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_58, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(58, s), p, o, m) +# define SEQAN_PP_FOR_58_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(59, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_59, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(59, s), p, o, m) +# define SEQAN_PP_FOR_59_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(60, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_60, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(60, s), p, o, m) +# define SEQAN_PP_FOR_60_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(61, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_61, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(61, s), p, o, m) +# define SEQAN_PP_FOR_61_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(62, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_62, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(62, s), p, o, m) +# define SEQAN_PP_FOR_62_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(63, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_63, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(63, s), p, o, m) +# define SEQAN_PP_FOR_63_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(64, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_64, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(64, s), p, o, m) +# define SEQAN_PP_FOR_64_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(65, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_65, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(65, s), p, o, m) +# define SEQAN_PP_FOR_65_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(66, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_66, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(66, s), p, o, m) +# define SEQAN_PP_FOR_66_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(67, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_67, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(67, s), p, o, m) +# define SEQAN_PP_FOR_67_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(68, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_68, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(68, s), p, o, m) +# define SEQAN_PP_FOR_68_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(69, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_69, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(69, s), p, o, m) +# define SEQAN_PP_FOR_69_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(70, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_70, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(70, s), p, o, m) +# define SEQAN_PP_FOR_70_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(71, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_71, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(71, s), p, o, m) +# define SEQAN_PP_FOR_71_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(72, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_72, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(72, s), p, o, m) +# define SEQAN_PP_FOR_72_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(73, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_73, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(73, s), p, o, m) +# define SEQAN_PP_FOR_73_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(74, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_74, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(74, s), p, o, m) +# define SEQAN_PP_FOR_74_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(75, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_75, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(75, s), p, o, m) +# define SEQAN_PP_FOR_75_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(76, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_76, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(76, s), p, o, m) +# define SEQAN_PP_FOR_76_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(77, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_77, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(77, s), p, o, m) +# define SEQAN_PP_FOR_77_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(78, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_78, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(78, s), p, o, m) +# define SEQAN_PP_FOR_78_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(79, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_79, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(79, s), p, o, m) +# define SEQAN_PP_FOR_79_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(80, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_80, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(80, s), p, o, m) +# define SEQAN_PP_FOR_80_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(81, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_81, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(81, s), p, o, m) +# define SEQAN_PP_FOR_81_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(82, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_82, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(82, s), p, o, m) +# define SEQAN_PP_FOR_82_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(83, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_83, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(83, s), p, o, m) +# define SEQAN_PP_FOR_83_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(84, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_84, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(84, s), p, o, m) +# define SEQAN_PP_FOR_84_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(85, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_85, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(85, s), p, o, m) +# define SEQAN_PP_FOR_85_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(86, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_86, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(86, s), p, o, m) +# define SEQAN_PP_FOR_86_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(87, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_87, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(87, s), p, o, m) +# define SEQAN_PP_FOR_87_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(88, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_88, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(88, s), p, o, m) +# define SEQAN_PP_FOR_88_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(89, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_89, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(89, s), p, o, m) +# define SEQAN_PP_FOR_89_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(90, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_90, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(90, s), p, o, m) +# define SEQAN_PP_FOR_90_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(91, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_91, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(91, s), p, o, m) +# define SEQAN_PP_FOR_91_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(92, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_92, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(92, s), p, o, m) +# define SEQAN_PP_FOR_92_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(93, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_93, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(93, s), p, o, m) +# define SEQAN_PP_FOR_93_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(94, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_94, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(94, s), p, o, m) +# define SEQAN_PP_FOR_94_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(95, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_95, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(95, s), p, o, m) +# define SEQAN_PP_FOR_95_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(96, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_96, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(96, s), p, o, m) +# define SEQAN_PP_FOR_96_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(97, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_97, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(97, s), p, o, m) +# define SEQAN_PP_FOR_97_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(98, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_98, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(98, s), p, o, m) +# define SEQAN_PP_FOR_98_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(99, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_99, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(99, s), p, o, m) +# define SEQAN_PP_FOR_99_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(100, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_100, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(100, s), p, o, m) +# define SEQAN_PP_FOR_100_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(101, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_101, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(101, s), p, o, m) +# define SEQAN_PP_FOR_101_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(102, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_102, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(102, s), p, o, m) +# define SEQAN_PP_FOR_102_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(103, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_103, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(103, s), p, o, m) +# define SEQAN_PP_FOR_103_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(104, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_104, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(104, s), p, o, m) +# define SEQAN_PP_FOR_104_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(105, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_105, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(105, s), p, o, m) +# define SEQAN_PP_FOR_105_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(106, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_106, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(106, s), p, o, m) +# define SEQAN_PP_FOR_106_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(107, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_107, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(107, s), p, o, m) +# define SEQAN_PP_FOR_107_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(108, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_108, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(108, s), p, o, m) +# define SEQAN_PP_FOR_108_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(109, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_109, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(109, s), p, o, m) +# define SEQAN_PP_FOR_109_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(110, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_110, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(110, s), p, o, m) +# define SEQAN_PP_FOR_110_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(111, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_111, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(111, s), p, o, m) +# define SEQAN_PP_FOR_111_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(112, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_112, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(112, s), p, o, m) +# define SEQAN_PP_FOR_112_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(113, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_113, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(113, s), p, o, m) +# define SEQAN_PP_FOR_113_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(114, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_114, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(114, s), p, o, m) +# define SEQAN_PP_FOR_114_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(115, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_115, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(115, s), p, o, m) +# define SEQAN_PP_FOR_115_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(116, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_116, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(116, s), p, o, m) +# define SEQAN_PP_FOR_116_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(117, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_117, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(117, s), p, o, m) +# define SEQAN_PP_FOR_117_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(118, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_118, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(118, s), p, o, m) +# define SEQAN_PP_FOR_118_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(119, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_119, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(119, s), p, o, m) +# define SEQAN_PP_FOR_119_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(120, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_120, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(120, s), p, o, m) +# define SEQAN_PP_FOR_120_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(121, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_121, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(121, s), p, o, m) +# define SEQAN_PP_FOR_121_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(122, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_122, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(122, s), p, o, m) +# define SEQAN_PP_FOR_122_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(123, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_123, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(123, s), p, o, m) +# define SEQAN_PP_FOR_123_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(124, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_124, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(124, s), p, o, m) +# define SEQAN_PP_FOR_124_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(125, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_125, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(125, s), p, o, m) +# define SEQAN_PP_FOR_125_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(126, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_126, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(126, s), p, o, m) +# define SEQAN_PP_FOR_126_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(127, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_127, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(127, s), p, o, m) +# define SEQAN_PP_FOR_127_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(128, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_128, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(128, s), p, o, m) +# define SEQAN_PP_FOR_128_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(129, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_129, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(129, s), p, o, m) +# define SEQAN_PP_FOR_129_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(130, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_130, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(130, s), p, o, m) +# define SEQAN_PP_FOR_130_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(131, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_131, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(131, s), p, o, m) +# define SEQAN_PP_FOR_131_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(132, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_132, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(132, s), p, o, m) +# define SEQAN_PP_FOR_132_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(133, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_133, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(133, s), p, o, m) +# define SEQAN_PP_FOR_133_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(134, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_134, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(134, s), p, o, m) +# define SEQAN_PP_FOR_134_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(135, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_135, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(135, s), p, o, m) +# define SEQAN_PP_FOR_135_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(136, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_136, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(136, s), p, o, m) +# define SEQAN_PP_FOR_136_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(137, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_137, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(137, s), p, o, m) +# define SEQAN_PP_FOR_137_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(138, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_138, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(138, s), p, o, m) +# define SEQAN_PP_FOR_138_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(139, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_139, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(139, s), p, o, m) +# define SEQAN_PP_FOR_139_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(140, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_140, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(140, s), p, o, m) +# define SEQAN_PP_FOR_140_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(141, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_141, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(141, s), p, o, m) +# define SEQAN_PP_FOR_141_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(142, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_142, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(142, s), p, o, m) +# define SEQAN_PP_FOR_142_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(143, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_143, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(143, s), p, o, m) +# define SEQAN_PP_FOR_143_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(144, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_144, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(144, s), p, o, m) +# define SEQAN_PP_FOR_144_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(145, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_145, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(145, s), p, o, m) +# define SEQAN_PP_FOR_145_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(146, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_146, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(146, s), p, o, m) +# define SEQAN_PP_FOR_146_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(147, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_147, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(147, s), p, o, m) +# define SEQAN_PP_FOR_147_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(148, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_148, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(148, s), p, o, m) +# define SEQAN_PP_FOR_148_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(149, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_149, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(149, s), p, o, m) +# define SEQAN_PP_FOR_149_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(150, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_150, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(150, s), p, o, m) +# define SEQAN_PP_FOR_150_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(151, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_151, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(151, s), p, o, m) +# define SEQAN_PP_FOR_151_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(152, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_152, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(152, s), p, o, m) +# define SEQAN_PP_FOR_152_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(153, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_153, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(153, s), p, o, m) +# define SEQAN_PP_FOR_153_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(154, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_154, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(154, s), p, o, m) +# define SEQAN_PP_FOR_154_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(155, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_155, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(155, s), p, o, m) +# define SEQAN_PP_FOR_155_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(156, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_156, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(156, s), p, o, m) +# define SEQAN_PP_FOR_156_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(157, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_157, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(157, s), p, o, m) +# define SEQAN_PP_FOR_157_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(158, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_158, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(158, s), p, o, m) +# define SEQAN_PP_FOR_158_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(159, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_159, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(159, s), p, o, m) +# define SEQAN_PP_FOR_159_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(160, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_160, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(160, s), p, o, m) +# define SEQAN_PP_FOR_160_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(161, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_161, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(161, s), p, o, m) +# define SEQAN_PP_FOR_161_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(162, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_162, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(162, s), p, o, m) +# define SEQAN_PP_FOR_162_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(163, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_163, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(163, s), p, o, m) +# define SEQAN_PP_FOR_163_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(164, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_164, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(164, s), p, o, m) +# define SEQAN_PP_FOR_164_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(165, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_165, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(165, s), p, o, m) +# define SEQAN_PP_FOR_165_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(166, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_166, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(166, s), p, o, m) +# define SEQAN_PP_FOR_166_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(167, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_167, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(167, s), p, o, m) +# define SEQAN_PP_FOR_167_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(168, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_168, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(168, s), p, o, m) +# define SEQAN_PP_FOR_168_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(169, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_169, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(169, s), p, o, m) +# define SEQAN_PP_FOR_169_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(170, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_170, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(170, s), p, o, m) +# define SEQAN_PP_FOR_170_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(171, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_171, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(171, s), p, o, m) +# define SEQAN_PP_FOR_171_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(172, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_172, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(172, s), p, o, m) +# define SEQAN_PP_FOR_172_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(173, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_173, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(173, s), p, o, m) +# define SEQAN_PP_FOR_173_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(174, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_174, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(174, s), p, o, m) +# define SEQAN_PP_FOR_174_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(175, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_175, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(175, s), p, o, m) +# define SEQAN_PP_FOR_175_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(176, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_176, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(176, s), p, o, m) +# define SEQAN_PP_FOR_176_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(177, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_177, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(177, s), p, o, m) +# define SEQAN_PP_FOR_177_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(178, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_178, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(178, s), p, o, m) +# define SEQAN_PP_FOR_178_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(179, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_179, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(179, s), p, o, m) +# define SEQAN_PP_FOR_179_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(180, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_180, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(180, s), p, o, m) +# define SEQAN_PP_FOR_180_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(181, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_181, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(181, s), p, o, m) +# define SEQAN_PP_FOR_181_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(182, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_182, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(182, s), p, o, m) +# define SEQAN_PP_FOR_182_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(183, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_183, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(183, s), p, o, m) +# define SEQAN_PP_FOR_183_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(184, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_184, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(184, s), p, o, m) +# define SEQAN_PP_FOR_184_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(185, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_185, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(185, s), p, o, m) +# define SEQAN_PP_FOR_185_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(186, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_186, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(186, s), p, o, m) +# define SEQAN_PP_FOR_186_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(187, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_187, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(187, s), p, o, m) +# define SEQAN_PP_FOR_187_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(188, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_188, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(188, s), p, o, m) +# define SEQAN_PP_FOR_188_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(189, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_189, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(189, s), p, o, m) +# define SEQAN_PP_FOR_189_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(190, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_190, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(190, s), p, o, m) +# define SEQAN_PP_FOR_190_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(191, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_191, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(191, s), p, o, m) +# define SEQAN_PP_FOR_191_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(192, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_192, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(192, s), p, o, m) +# define SEQAN_PP_FOR_192_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(193, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_193, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(193, s), p, o, m) +# define SEQAN_PP_FOR_193_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(194, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_194, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(194, s), p, o, m) +# define SEQAN_PP_FOR_194_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(195, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_195, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(195, s), p, o, m) +# define SEQAN_PP_FOR_195_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(196, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_196, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(196, s), p, o, m) +# define SEQAN_PP_FOR_196_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(197, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_197, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(197, s), p, o, m) +# define SEQAN_PP_FOR_197_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(198, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_198, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(198, s), p, o, m) +# define SEQAN_PP_FOR_198_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(199, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_199, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(199, s), p, o, m) +# define SEQAN_PP_FOR_199_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(200, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_200, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(200, s), p, o, m) +# define SEQAN_PP_FOR_200_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(201, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_201, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(201, s), p, o, m) +# define SEQAN_PP_FOR_201_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(202, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_202, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(202, s), p, o, m) +# define SEQAN_PP_FOR_202_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(203, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_203, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(203, s), p, o, m) +# define SEQAN_PP_FOR_203_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(204, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_204, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(204, s), p, o, m) +# define SEQAN_PP_FOR_204_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(205, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_205, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(205, s), p, o, m) +# define SEQAN_PP_FOR_205_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(206, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_206, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(206, s), p, o, m) +# define SEQAN_PP_FOR_206_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(207, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_207, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(207, s), p, o, m) +# define SEQAN_PP_FOR_207_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(208, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_208, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(208, s), p, o, m) +# define SEQAN_PP_FOR_208_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(209, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_209, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(209, s), p, o, m) +# define SEQAN_PP_FOR_209_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(210, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_210, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(210, s), p, o, m) +# define SEQAN_PP_FOR_210_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(211, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_211, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(211, s), p, o, m) +# define SEQAN_PP_FOR_211_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(212, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_212, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(212, s), p, o, m) +# define SEQAN_PP_FOR_212_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(213, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_213, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(213, s), p, o, m) +# define SEQAN_PP_FOR_213_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(214, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_214, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(214, s), p, o, m) +# define SEQAN_PP_FOR_214_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(215, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_215, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(215, s), p, o, m) +# define SEQAN_PP_FOR_215_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(216, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_216, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(216, s), p, o, m) +# define SEQAN_PP_FOR_216_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(217, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_217, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(217, s), p, o, m) +# define SEQAN_PP_FOR_217_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(218, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_218, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(218, s), p, o, m) +# define SEQAN_PP_FOR_218_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(219, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_219, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(219, s), p, o, m) +# define SEQAN_PP_FOR_219_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(220, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_220, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(220, s), p, o, m) +# define SEQAN_PP_FOR_220_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(221, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_221, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(221, s), p, o, m) +# define SEQAN_PP_FOR_221_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(222, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_222, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(222, s), p, o, m) +# define SEQAN_PP_FOR_222_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(223, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_223, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(223, s), p, o, m) +# define SEQAN_PP_FOR_223_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(224, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_224, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(224, s), p, o, m) +# define SEQAN_PP_FOR_224_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(225, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_225, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(225, s), p, o, m) +# define SEQAN_PP_FOR_225_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(226, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_226, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(226, s), p, o, m) +# define SEQAN_PP_FOR_226_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(227, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_227, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(227, s), p, o, m) +# define SEQAN_PP_FOR_227_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(228, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_228, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(228, s), p, o, m) +# define SEQAN_PP_FOR_228_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(229, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_229, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(229, s), p, o, m) +# define SEQAN_PP_FOR_229_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(230, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_230, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(230, s), p, o, m) +# define SEQAN_PP_FOR_230_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(231, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_231, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(231, s), p, o, m) +# define SEQAN_PP_FOR_231_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(232, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_232, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(232, s), p, o, m) +# define SEQAN_PP_FOR_232_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(233, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_233, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(233, s), p, o, m) +# define SEQAN_PP_FOR_233_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(234, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_234, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(234, s), p, o, m) +# define SEQAN_PP_FOR_234_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(235, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_235, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(235, s), p, o, m) +# define SEQAN_PP_FOR_235_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(236, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_236, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(236, s), p, o, m) +# define SEQAN_PP_FOR_236_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(237, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_237, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(237, s), p, o, m) +# define SEQAN_PP_FOR_237_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(238, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_238, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(238, s), p, o, m) +# define SEQAN_PP_FOR_238_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(239, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_239, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(239, s), p, o, m) +# define SEQAN_PP_FOR_239_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(240, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_240, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(240, s), p, o, m) +# define SEQAN_PP_FOR_240_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(241, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_241, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(241, s), p, o, m) +# define SEQAN_PP_FOR_241_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(242, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_242, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(242, s), p, o, m) +# define SEQAN_PP_FOR_242_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(243, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_243, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(243, s), p, o, m) +# define SEQAN_PP_FOR_243_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(244, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_244, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(244, s), p, o, m) +# define SEQAN_PP_FOR_244_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(245, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_245, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(245, s), p, o, m) +# define SEQAN_PP_FOR_245_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(246, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_246, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(246, s), p, o, m) +# define SEQAN_PP_FOR_246_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(247, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_247, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(247, s), p, o, m) +# define SEQAN_PP_FOR_247_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(248, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_248, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(248, s), p, o, m) +# define SEQAN_PP_FOR_248_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(249, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_249, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(249, s), p, o, m) +# define SEQAN_PP_FOR_249_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(250, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_250, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(250, s), p, o, m) +# define SEQAN_PP_FOR_250_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(251, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_251, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(251, s), p, o, m) +# define SEQAN_PP_FOR_251_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(252, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_252, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(252, s), p, o, m) +# define SEQAN_PP_FOR_252_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(253, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_253, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(253, s), p, o, m) +# define SEQAN_PP_FOR_253_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(254, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_254, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(254, s), p, o, m) +# define SEQAN_PP_FOR_254_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(255, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_255, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(255, s), p, o, m) +# define SEQAN_PP_FOR_255_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(256, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_256, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(256, s), p, o, m) +# define SEQAN_PP_FOR_256_C(c, s, p, o, m) SEQAN_PP_IIF(c, m, SEQAN_PP_TUPLE_EAT_2)(257, s) SEQAN_PP_IIF(c, SEQAN_PP_FOR_257, SEQAN_PP_TUPLE_EAT_4)(SEQAN_PP_EXPR_IIF(c, o)(257, s), p, o, m) + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/detail/auto_rec.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # include +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_DMC() +// # include +// # else +# +// # ifndef SEQAN_PREPROCESSOR_DETAIL_AUTO_REC_HPP +// # define SEQAN_PREPROCESSOR_DETAIL_AUTO_REC_HPP +# +// # include +# +# /* SEQAN_PP_AUTO_REC */ +# +# define SEQAN_PP_AUTO_REC(pred, n) SEQAN_PP_NODE_ENTRY_ ## n(pred) +# +# define SEQAN_PP_NODE_ENTRY_256(p) SEQAN_PP_NODE_128(p)(p)(p)(p)(p)(p)(p)(p) +# define SEQAN_PP_NODE_ENTRY_128(p) SEQAN_PP_NODE_64(p)(p)(p)(p)(p)(p)(p) +# define SEQAN_PP_NODE_ENTRY_64(p) SEQAN_PP_NODE_32(p)(p)(p)(p)(p)(p) +# define SEQAN_PP_NODE_ENTRY_32(p) SEQAN_PP_NODE_16(p)(p)(p)(p)(p) +# define SEQAN_PP_NODE_ENTRY_16(p) SEQAN_PP_NODE_8(p)(p)(p)(p) +# define SEQAN_PP_NODE_ENTRY_8(p) SEQAN_PP_NODE_4(p)(p)(p) +# define SEQAN_PP_NODE_ENTRY_4(p) SEQAN_PP_NODE_2(p)(p) +# define SEQAN_PP_NODE_ENTRY_2(p) SEQAN_PP_NODE_1(p) +# +# define SEQAN_PP_NODE_128(p) SEQAN_PP_IIF(p(128), SEQAN_PP_NODE_64, SEQAN_PP_NODE_192) +# define SEQAN_PP_NODE_64(p) SEQAN_PP_IIF(p(64), SEQAN_PP_NODE_32, SEQAN_PP_NODE_96) +# define SEQAN_PP_NODE_32(p) SEQAN_PP_IIF(p(32), SEQAN_PP_NODE_16, SEQAN_PP_NODE_48) +# define SEQAN_PP_NODE_16(p) SEQAN_PP_IIF(p(16), SEQAN_PP_NODE_8, SEQAN_PP_NODE_24) +# define SEQAN_PP_NODE_8(p) SEQAN_PP_IIF(p(8), SEQAN_PP_NODE_4, SEQAN_PP_NODE_12) +# define SEQAN_PP_NODE_4(p) SEQAN_PP_IIF(p(4), SEQAN_PP_NODE_2, SEQAN_PP_NODE_6) +# define SEQAN_PP_NODE_2(p) SEQAN_PP_IIF(p(2), SEQAN_PP_NODE_1, SEQAN_PP_NODE_3) +# define SEQAN_PP_NODE_1(p) SEQAN_PP_IIF(p(1), 1, 2) +# define SEQAN_PP_NODE_3(p) SEQAN_PP_IIF(p(3), 3, 4) +# define SEQAN_PP_NODE_6(p) SEQAN_PP_IIF(p(6), SEQAN_PP_NODE_5, SEQAN_PP_NODE_7) +# define SEQAN_PP_NODE_5(p) SEQAN_PP_IIF(p(5), 5, 6) +# define SEQAN_PP_NODE_7(p) SEQAN_PP_IIF(p(7), 7, 8) +# define SEQAN_PP_NODE_12(p) SEQAN_PP_IIF(p(12), SEQAN_PP_NODE_10, SEQAN_PP_NODE_14) +# define SEQAN_PP_NODE_10(p) SEQAN_PP_IIF(p(10), SEQAN_PP_NODE_9, SEQAN_PP_NODE_11) +# define SEQAN_PP_NODE_9(p) SEQAN_PP_IIF(p(9), 9, 10) +# define SEQAN_PP_NODE_11(p) SEQAN_PP_IIF(p(11), 11, 12) +# define SEQAN_PP_NODE_14(p) SEQAN_PP_IIF(p(14), SEQAN_PP_NODE_13, SEQAN_PP_NODE_15) +# define SEQAN_PP_NODE_13(p) SEQAN_PP_IIF(p(13), 13, 14) +# define SEQAN_PP_NODE_15(p) SEQAN_PP_IIF(p(15), 15, 16) +# define SEQAN_PP_NODE_24(p) SEQAN_PP_IIF(p(24), SEQAN_PP_NODE_20, SEQAN_PP_NODE_28) +# define SEQAN_PP_NODE_20(p) SEQAN_PP_IIF(p(20), SEQAN_PP_NODE_18, SEQAN_PP_NODE_22) +# define SEQAN_PP_NODE_18(p) SEQAN_PP_IIF(p(18), SEQAN_PP_NODE_17, SEQAN_PP_NODE_19) +# define SEQAN_PP_NODE_17(p) SEQAN_PP_IIF(p(17), 17, 18) +# define SEQAN_PP_NODE_19(p) SEQAN_PP_IIF(p(19), 19, 20) +# define SEQAN_PP_NODE_22(p) SEQAN_PP_IIF(p(22), SEQAN_PP_NODE_21, SEQAN_PP_NODE_23) +# define SEQAN_PP_NODE_21(p) SEQAN_PP_IIF(p(21), 21, 22) +# define SEQAN_PP_NODE_23(p) SEQAN_PP_IIF(p(23), 23, 24) +# define SEQAN_PP_NODE_28(p) SEQAN_PP_IIF(p(28), SEQAN_PP_NODE_26, SEQAN_PP_NODE_30) +# define SEQAN_PP_NODE_26(p) SEQAN_PP_IIF(p(26), SEQAN_PP_NODE_25, SEQAN_PP_NODE_27) +# define SEQAN_PP_NODE_25(p) SEQAN_PP_IIF(p(25), 25, 26) +# define SEQAN_PP_NODE_27(p) SEQAN_PP_IIF(p(27), 27, 28) +# define SEQAN_PP_NODE_30(p) SEQAN_PP_IIF(p(30), SEQAN_PP_NODE_29, SEQAN_PP_NODE_31) +# define SEQAN_PP_NODE_29(p) SEQAN_PP_IIF(p(29), 29, 30) +# define SEQAN_PP_NODE_31(p) SEQAN_PP_IIF(p(31), 31, 32) +# define SEQAN_PP_NODE_48(p) SEQAN_PP_IIF(p(48), SEQAN_PP_NODE_40, SEQAN_PP_NODE_56) +# define SEQAN_PP_NODE_40(p) SEQAN_PP_IIF(p(40), SEQAN_PP_NODE_36, SEQAN_PP_NODE_44) +# define SEQAN_PP_NODE_36(p) SEQAN_PP_IIF(p(36), SEQAN_PP_NODE_34, SEQAN_PP_NODE_38) +# define SEQAN_PP_NODE_34(p) SEQAN_PP_IIF(p(34), SEQAN_PP_NODE_33, SEQAN_PP_NODE_35) +# define SEQAN_PP_NODE_33(p) SEQAN_PP_IIF(p(33), 33, 34) +# define SEQAN_PP_NODE_35(p) SEQAN_PP_IIF(p(35), 35, 36) +# define SEQAN_PP_NODE_38(p) SEQAN_PP_IIF(p(38), SEQAN_PP_NODE_37, SEQAN_PP_NODE_39) +# define SEQAN_PP_NODE_37(p) SEQAN_PP_IIF(p(37), 37, 38) +# define SEQAN_PP_NODE_39(p) SEQAN_PP_IIF(p(39), 39, 40) +# define SEQAN_PP_NODE_44(p) SEQAN_PP_IIF(p(44), SEQAN_PP_NODE_42, SEQAN_PP_NODE_46) +# define SEQAN_PP_NODE_42(p) SEQAN_PP_IIF(p(42), SEQAN_PP_NODE_41, SEQAN_PP_NODE_43) +# define SEQAN_PP_NODE_41(p) SEQAN_PP_IIF(p(41), 41, 42) +# define SEQAN_PP_NODE_43(p) SEQAN_PP_IIF(p(43), 43, 44) +# define SEQAN_PP_NODE_46(p) SEQAN_PP_IIF(p(46), SEQAN_PP_NODE_45, SEQAN_PP_NODE_47) +# define SEQAN_PP_NODE_45(p) SEQAN_PP_IIF(p(45), 45, 46) +# define SEQAN_PP_NODE_47(p) SEQAN_PP_IIF(p(47), 47, 48) +# define SEQAN_PP_NODE_56(p) SEQAN_PP_IIF(p(56), SEQAN_PP_NODE_52, SEQAN_PP_NODE_60) +# define SEQAN_PP_NODE_52(p) SEQAN_PP_IIF(p(52), SEQAN_PP_NODE_50, SEQAN_PP_NODE_54) +# define SEQAN_PP_NODE_50(p) SEQAN_PP_IIF(p(50), SEQAN_PP_NODE_49, SEQAN_PP_NODE_51) +# define SEQAN_PP_NODE_49(p) SEQAN_PP_IIF(p(49), 49, 50) +# define SEQAN_PP_NODE_51(p) SEQAN_PP_IIF(p(51), 51, 52) +# define SEQAN_PP_NODE_54(p) SEQAN_PP_IIF(p(54), SEQAN_PP_NODE_53, SEQAN_PP_NODE_55) +# define SEQAN_PP_NODE_53(p) SEQAN_PP_IIF(p(53), 53, 54) +# define SEQAN_PP_NODE_55(p) SEQAN_PP_IIF(p(55), 55, 56) +# define SEQAN_PP_NODE_60(p) SEQAN_PP_IIF(p(60), SEQAN_PP_NODE_58, SEQAN_PP_NODE_62) +# define SEQAN_PP_NODE_58(p) SEQAN_PP_IIF(p(58), SEQAN_PP_NODE_57, SEQAN_PP_NODE_59) +# define SEQAN_PP_NODE_57(p) SEQAN_PP_IIF(p(57), 57, 58) +# define SEQAN_PP_NODE_59(p) SEQAN_PP_IIF(p(59), 59, 60) +# define SEQAN_PP_NODE_62(p) SEQAN_PP_IIF(p(62), SEQAN_PP_NODE_61, SEQAN_PP_NODE_63) +# define SEQAN_PP_NODE_61(p) SEQAN_PP_IIF(p(61), 61, 62) +# define SEQAN_PP_NODE_63(p) SEQAN_PP_IIF(p(63), 63, 64) +# define SEQAN_PP_NODE_96(p) SEQAN_PP_IIF(p(96), SEQAN_PP_NODE_80, SEQAN_PP_NODE_112) +# define SEQAN_PP_NODE_80(p) SEQAN_PP_IIF(p(80), SEQAN_PP_NODE_72, SEQAN_PP_NODE_88) +# define SEQAN_PP_NODE_72(p) SEQAN_PP_IIF(p(72), SEQAN_PP_NODE_68, SEQAN_PP_NODE_76) +# define SEQAN_PP_NODE_68(p) SEQAN_PP_IIF(p(68), SEQAN_PP_NODE_66, SEQAN_PP_NODE_70) +# define SEQAN_PP_NODE_66(p) SEQAN_PP_IIF(p(66), SEQAN_PP_NODE_65, SEQAN_PP_NODE_67) +# define SEQAN_PP_NODE_65(p) SEQAN_PP_IIF(p(65), 65, 66) +# define SEQAN_PP_NODE_67(p) SEQAN_PP_IIF(p(67), 67, 68) +# define SEQAN_PP_NODE_70(p) SEQAN_PP_IIF(p(70), SEQAN_PP_NODE_69, SEQAN_PP_NODE_71) +# define SEQAN_PP_NODE_69(p) SEQAN_PP_IIF(p(69), 69, 70) +# define SEQAN_PP_NODE_71(p) SEQAN_PP_IIF(p(71), 71, 72) +# define SEQAN_PP_NODE_76(p) SEQAN_PP_IIF(p(76), SEQAN_PP_NODE_74, SEQAN_PP_NODE_78) +# define SEQAN_PP_NODE_74(p) SEQAN_PP_IIF(p(74), SEQAN_PP_NODE_73, SEQAN_PP_NODE_75) +# define SEQAN_PP_NODE_73(p) SEQAN_PP_IIF(p(73), 73, 74) +# define SEQAN_PP_NODE_75(p) SEQAN_PP_IIF(p(75), 75, 76) +# define SEQAN_PP_NODE_78(p) SEQAN_PP_IIF(p(78), SEQAN_PP_NODE_77, SEQAN_PP_NODE_79) +# define SEQAN_PP_NODE_77(p) SEQAN_PP_IIF(p(77), 77, 78) +# define SEQAN_PP_NODE_79(p) SEQAN_PP_IIF(p(79), 79, 80) +# define SEQAN_PP_NODE_88(p) SEQAN_PP_IIF(p(88), SEQAN_PP_NODE_84, SEQAN_PP_NODE_92) +# define SEQAN_PP_NODE_84(p) SEQAN_PP_IIF(p(84), SEQAN_PP_NODE_82, SEQAN_PP_NODE_86) +# define SEQAN_PP_NODE_82(p) SEQAN_PP_IIF(p(82), SEQAN_PP_NODE_81, SEQAN_PP_NODE_83) +# define SEQAN_PP_NODE_81(p) SEQAN_PP_IIF(p(81), 81, 82) +# define SEQAN_PP_NODE_83(p) SEQAN_PP_IIF(p(83), 83, 84) +# define SEQAN_PP_NODE_86(p) SEQAN_PP_IIF(p(86), SEQAN_PP_NODE_85, SEQAN_PP_NODE_87) +# define SEQAN_PP_NODE_85(p) SEQAN_PP_IIF(p(85), 85, 86) +# define SEQAN_PP_NODE_87(p) SEQAN_PP_IIF(p(87), 87, 88) +# define SEQAN_PP_NODE_92(p) SEQAN_PP_IIF(p(92), SEQAN_PP_NODE_90, SEQAN_PP_NODE_94) +# define SEQAN_PP_NODE_90(p) SEQAN_PP_IIF(p(90), SEQAN_PP_NODE_89, SEQAN_PP_NODE_91) +# define SEQAN_PP_NODE_89(p) SEQAN_PP_IIF(p(89), 89, 90) +# define SEQAN_PP_NODE_91(p) SEQAN_PP_IIF(p(91), 91, 92) +# define SEQAN_PP_NODE_94(p) SEQAN_PP_IIF(p(94), SEQAN_PP_NODE_93, SEQAN_PP_NODE_95) +# define SEQAN_PP_NODE_93(p) SEQAN_PP_IIF(p(93), 93, 94) +# define SEQAN_PP_NODE_95(p) SEQAN_PP_IIF(p(95), 95, 96) +# define SEQAN_PP_NODE_112(p) SEQAN_PP_IIF(p(112), SEQAN_PP_NODE_104, SEQAN_PP_NODE_120) +# define SEQAN_PP_NODE_104(p) SEQAN_PP_IIF(p(104), SEQAN_PP_NODE_100, SEQAN_PP_NODE_108) +# define SEQAN_PP_NODE_100(p) SEQAN_PP_IIF(p(100), SEQAN_PP_NODE_98, SEQAN_PP_NODE_102) +# define SEQAN_PP_NODE_98(p) SEQAN_PP_IIF(p(98), SEQAN_PP_NODE_97, SEQAN_PP_NODE_99) +# define SEQAN_PP_NODE_97(p) SEQAN_PP_IIF(p(97), 97, 98) +# define SEQAN_PP_NODE_99(p) SEQAN_PP_IIF(p(99), 99, 100) +# define SEQAN_PP_NODE_102(p) SEQAN_PP_IIF(p(102), SEQAN_PP_NODE_101, SEQAN_PP_NODE_103) +# define SEQAN_PP_NODE_101(p) SEQAN_PP_IIF(p(101), 101, 102) +# define SEQAN_PP_NODE_103(p) SEQAN_PP_IIF(p(103), 103, 104) +# define SEQAN_PP_NODE_108(p) SEQAN_PP_IIF(p(108), SEQAN_PP_NODE_106, SEQAN_PP_NODE_110) +# define SEQAN_PP_NODE_106(p) SEQAN_PP_IIF(p(106), SEQAN_PP_NODE_105, SEQAN_PP_NODE_107) +# define SEQAN_PP_NODE_105(p) SEQAN_PP_IIF(p(105), 105, 106) +# define SEQAN_PP_NODE_107(p) SEQAN_PP_IIF(p(107), 107, 108) +# define SEQAN_PP_NODE_110(p) SEQAN_PP_IIF(p(110), SEQAN_PP_NODE_109, SEQAN_PP_NODE_111) +# define SEQAN_PP_NODE_109(p) SEQAN_PP_IIF(p(109), 109, 110) +# define SEQAN_PP_NODE_111(p) SEQAN_PP_IIF(p(111), 111, 112) +# define SEQAN_PP_NODE_120(p) SEQAN_PP_IIF(p(120), SEQAN_PP_NODE_116, SEQAN_PP_NODE_124) +# define SEQAN_PP_NODE_116(p) SEQAN_PP_IIF(p(116), SEQAN_PP_NODE_114, SEQAN_PP_NODE_118) +# define SEQAN_PP_NODE_114(p) SEQAN_PP_IIF(p(114), SEQAN_PP_NODE_113, SEQAN_PP_NODE_115) +# define SEQAN_PP_NODE_113(p) SEQAN_PP_IIF(p(113), 113, 114) +# define SEQAN_PP_NODE_115(p) SEQAN_PP_IIF(p(115), 115, 116) +# define SEQAN_PP_NODE_118(p) SEQAN_PP_IIF(p(118), SEQAN_PP_NODE_117, SEQAN_PP_NODE_119) +# define SEQAN_PP_NODE_117(p) SEQAN_PP_IIF(p(117), 117, 118) +# define SEQAN_PP_NODE_119(p) SEQAN_PP_IIF(p(119), 119, 120) +# define SEQAN_PP_NODE_124(p) SEQAN_PP_IIF(p(124), SEQAN_PP_NODE_122, SEQAN_PP_NODE_126) +# define SEQAN_PP_NODE_122(p) SEQAN_PP_IIF(p(122), SEQAN_PP_NODE_121, SEQAN_PP_NODE_123) +# define SEQAN_PP_NODE_121(p) SEQAN_PP_IIF(p(121), 121, 122) +# define SEQAN_PP_NODE_123(p) SEQAN_PP_IIF(p(123), 123, 124) +# define SEQAN_PP_NODE_126(p) SEQAN_PP_IIF(p(126), SEQAN_PP_NODE_125, SEQAN_PP_NODE_127) +# define SEQAN_PP_NODE_125(p) SEQAN_PP_IIF(p(125), 125, 126) +# define SEQAN_PP_NODE_127(p) SEQAN_PP_IIF(p(127), 127, 128) +# define SEQAN_PP_NODE_192(p) SEQAN_PP_IIF(p(192), SEQAN_PP_NODE_160, SEQAN_PP_NODE_224) +# define SEQAN_PP_NODE_160(p) SEQAN_PP_IIF(p(160), SEQAN_PP_NODE_144, SEQAN_PP_NODE_176) +# define SEQAN_PP_NODE_144(p) SEQAN_PP_IIF(p(144), SEQAN_PP_NODE_136, SEQAN_PP_NODE_152) +# define SEQAN_PP_NODE_136(p) SEQAN_PP_IIF(p(136), SEQAN_PP_NODE_132, SEQAN_PP_NODE_140) +# define SEQAN_PP_NODE_132(p) SEQAN_PP_IIF(p(132), SEQAN_PP_NODE_130, SEQAN_PP_NODE_134) +# define SEQAN_PP_NODE_130(p) SEQAN_PP_IIF(p(130), SEQAN_PP_NODE_129, SEQAN_PP_NODE_131) +# define SEQAN_PP_NODE_129(p) SEQAN_PP_IIF(p(129), 129, 130) +# define SEQAN_PP_NODE_131(p) SEQAN_PP_IIF(p(131), 131, 132) +# define SEQAN_PP_NODE_134(p) SEQAN_PP_IIF(p(134), SEQAN_PP_NODE_133, SEQAN_PP_NODE_135) +# define SEQAN_PP_NODE_133(p) SEQAN_PP_IIF(p(133), 133, 134) +# define SEQAN_PP_NODE_135(p) SEQAN_PP_IIF(p(135), 135, 136) +# define SEQAN_PP_NODE_140(p) SEQAN_PP_IIF(p(140), SEQAN_PP_NODE_138, SEQAN_PP_NODE_142) +# define SEQAN_PP_NODE_138(p) SEQAN_PP_IIF(p(138), SEQAN_PP_NODE_137, SEQAN_PP_NODE_139) +# define SEQAN_PP_NODE_137(p) SEQAN_PP_IIF(p(137), 137, 138) +# define SEQAN_PP_NODE_139(p) SEQAN_PP_IIF(p(139), 139, 140) +# define SEQAN_PP_NODE_142(p) SEQAN_PP_IIF(p(142), SEQAN_PP_NODE_141, SEQAN_PP_NODE_143) +# define SEQAN_PP_NODE_141(p) SEQAN_PP_IIF(p(141), 141, 142) +# define SEQAN_PP_NODE_143(p) SEQAN_PP_IIF(p(143), 143, 144) +# define SEQAN_PP_NODE_152(p) SEQAN_PP_IIF(p(152), SEQAN_PP_NODE_148, SEQAN_PP_NODE_156) +# define SEQAN_PP_NODE_148(p) SEQAN_PP_IIF(p(148), SEQAN_PP_NODE_146, SEQAN_PP_NODE_150) +# define SEQAN_PP_NODE_146(p) SEQAN_PP_IIF(p(146), SEQAN_PP_NODE_145, SEQAN_PP_NODE_147) +# define SEQAN_PP_NODE_145(p) SEQAN_PP_IIF(p(145), 145, 146) +# define SEQAN_PP_NODE_147(p) SEQAN_PP_IIF(p(147), 147, 148) +# define SEQAN_PP_NODE_150(p) SEQAN_PP_IIF(p(150), SEQAN_PP_NODE_149, SEQAN_PP_NODE_151) +# define SEQAN_PP_NODE_149(p) SEQAN_PP_IIF(p(149), 149, 150) +# define SEQAN_PP_NODE_151(p) SEQAN_PP_IIF(p(151), 151, 152) +# define SEQAN_PP_NODE_156(p) SEQAN_PP_IIF(p(156), SEQAN_PP_NODE_154, SEQAN_PP_NODE_158) +# define SEQAN_PP_NODE_154(p) SEQAN_PP_IIF(p(154), SEQAN_PP_NODE_153, SEQAN_PP_NODE_155) +# define SEQAN_PP_NODE_153(p) SEQAN_PP_IIF(p(153), 153, 154) +# define SEQAN_PP_NODE_155(p) SEQAN_PP_IIF(p(155), 155, 156) +# define SEQAN_PP_NODE_158(p) SEQAN_PP_IIF(p(158), SEQAN_PP_NODE_157, SEQAN_PP_NODE_159) +# define SEQAN_PP_NODE_157(p) SEQAN_PP_IIF(p(157), 157, 158) +# define SEQAN_PP_NODE_159(p) SEQAN_PP_IIF(p(159), 159, 160) +# define SEQAN_PP_NODE_176(p) SEQAN_PP_IIF(p(176), SEQAN_PP_NODE_168, SEQAN_PP_NODE_184) +# define SEQAN_PP_NODE_168(p) SEQAN_PP_IIF(p(168), SEQAN_PP_NODE_164, SEQAN_PP_NODE_172) +# define SEQAN_PP_NODE_164(p) SEQAN_PP_IIF(p(164), SEQAN_PP_NODE_162, SEQAN_PP_NODE_166) +# define SEQAN_PP_NODE_162(p) SEQAN_PP_IIF(p(162), SEQAN_PP_NODE_161, SEQAN_PP_NODE_163) +# define SEQAN_PP_NODE_161(p) SEQAN_PP_IIF(p(161), 161, 162) +# define SEQAN_PP_NODE_163(p) SEQAN_PP_IIF(p(163), 163, 164) +# define SEQAN_PP_NODE_166(p) SEQAN_PP_IIF(p(166), SEQAN_PP_NODE_165, SEQAN_PP_NODE_167) +# define SEQAN_PP_NODE_165(p) SEQAN_PP_IIF(p(165), 165, 166) +# define SEQAN_PP_NODE_167(p) SEQAN_PP_IIF(p(167), 167, 168) +# define SEQAN_PP_NODE_172(p) SEQAN_PP_IIF(p(172), SEQAN_PP_NODE_170, SEQAN_PP_NODE_174) +# define SEQAN_PP_NODE_170(p) SEQAN_PP_IIF(p(170), SEQAN_PP_NODE_169, SEQAN_PP_NODE_171) +# define SEQAN_PP_NODE_169(p) SEQAN_PP_IIF(p(169), 169, 170) +# define SEQAN_PP_NODE_171(p) SEQAN_PP_IIF(p(171), 171, 172) +# define SEQAN_PP_NODE_174(p) SEQAN_PP_IIF(p(174), SEQAN_PP_NODE_173, SEQAN_PP_NODE_175) +# define SEQAN_PP_NODE_173(p) SEQAN_PP_IIF(p(173), 173, 174) +# define SEQAN_PP_NODE_175(p) SEQAN_PP_IIF(p(175), 175, 176) +# define SEQAN_PP_NODE_184(p) SEQAN_PP_IIF(p(184), SEQAN_PP_NODE_180, SEQAN_PP_NODE_188) +# define SEQAN_PP_NODE_180(p) SEQAN_PP_IIF(p(180), SEQAN_PP_NODE_178, SEQAN_PP_NODE_182) +# define SEQAN_PP_NODE_178(p) SEQAN_PP_IIF(p(178), SEQAN_PP_NODE_177, SEQAN_PP_NODE_179) +# define SEQAN_PP_NODE_177(p) SEQAN_PP_IIF(p(177), 177, 178) +# define SEQAN_PP_NODE_179(p) SEQAN_PP_IIF(p(179), 179, 180) +# define SEQAN_PP_NODE_182(p) SEQAN_PP_IIF(p(182), SEQAN_PP_NODE_181, SEQAN_PP_NODE_183) +# define SEQAN_PP_NODE_181(p) SEQAN_PP_IIF(p(181), 181, 182) +# define SEQAN_PP_NODE_183(p) SEQAN_PP_IIF(p(183), 183, 184) +# define SEQAN_PP_NODE_188(p) SEQAN_PP_IIF(p(188), SEQAN_PP_NODE_186, SEQAN_PP_NODE_190) +# define SEQAN_PP_NODE_186(p) SEQAN_PP_IIF(p(186), SEQAN_PP_NODE_185, SEQAN_PP_NODE_187) +# define SEQAN_PP_NODE_185(p) SEQAN_PP_IIF(p(185), 185, 186) +# define SEQAN_PP_NODE_187(p) SEQAN_PP_IIF(p(187), 187, 188) +# define SEQAN_PP_NODE_190(p) SEQAN_PP_IIF(p(190), SEQAN_PP_NODE_189, SEQAN_PP_NODE_191) +# define SEQAN_PP_NODE_189(p) SEQAN_PP_IIF(p(189), 189, 190) +# define SEQAN_PP_NODE_191(p) SEQAN_PP_IIF(p(191), 191, 192) +# define SEQAN_PP_NODE_224(p) SEQAN_PP_IIF(p(224), SEQAN_PP_NODE_208, SEQAN_PP_NODE_240) +# define SEQAN_PP_NODE_208(p) SEQAN_PP_IIF(p(208), SEQAN_PP_NODE_200, SEQAN_PP_NODE_216) +# define SEQAN_PP_NODE_200(p) SEQAN_PP_IIF(p(200), SEQAN_PP_NODE_196, SEQAN_PP_NODE_204) +# define SEQAN_PP_NODE_196(p) SEQAN_PP_IIF(p(196), SEQAN_PP_NODE_194, SEQAN_PP_NODE_198) +# define SEQAN_PP_NODE_194(p) SEQAN_PP_IIF(p(194), SEQAN_PP_NODE_193, SEQAN_PP_NODE_195) +# define SEQAN_PP_NODE_193(p) SEQAN_PP_IIF(p(193), 193, 194) +# define SEQAN_PP_NODE_195(p) SEQAN_PP_IIF(p(195), 195, 196) +# define SEQAN_PP_NODE_198(p) SEQAN_PP_IIF(p(198), SEQAN_PP_NODE_197, SEQAN_PP_NODE_199) +# define SEQAN_PP_NODE_197(p) SEQAN_PP_IIF(p(197), 197, 198) +# define SEQAN_PP_NODE_199(p) SEQAN_PP_IIF(p(199), 199, 200) +# define SEQAN_PP_NODE_204(p) SEQAN_PP_IIF(p(204), SEQAN_PP_NODE_202, SEQAN_PP_NODE_206) +# define SEQAN_PP_NODE_202(p) SEQAN_PP_IIF(p(202), SEQAN_PP_NODE_201, SEQAN_PP_NODE_203) +# define SEQAN_PP_NODE_201(p) SEQAN_PP_IIF(p(201), 201, 202) +# define SEQAN_PP_NODE_203(p) SEQAN_PP_IIF(p(203), 203, 204) +# define SEQAN_PP_NODE_206(p) SEQAN_PP_IIF(p(206), SEQAN_PP_NODE_205, SEQAN_PP_NODE_207) +# define SEQAN_PP_NODE_205(p) SEQAN_PP_IIF(p(205), 205, 206) +# define SEQAN_PP_NODE_207(p) SEQAN_PP_IIF(p(207), 207, 208) +# define SEQAN_PP_NODE_216(p) SEQAN_PP_IIF(p(216), SEQAN_PP_NODE_212, SEQAN_PP_NODE_220) +# define SEQAN_PP_NODE_212(p) SEQAN_PP_IIF(p(212), SEQAN_PP_NODE_210, SEQAN_PP_NODE_214) +# define SEQAN_PP_NODE_210(p) SEQAN_PP_IIF(p(210), SEQAN_PP_NODE_209, SEQAN_PP_NODE_211) +# define SEQAN_PP_NODE_209(p) SEQAN_PP_IIF(p(209), 209, 210) +# define SEQAN_PP_NODE_211(p) SEQAN_PP_IIF(p(211), 211, 212) +# define SEQAN_PP_NODE_214(p) SEQAN_PP_IIF(p(214), SEQAN_PP_NODE_213, SEQAN_PP_NODE_215) +# define SEQAN_PP_NODE_213(p) SEQAN_PP_IIF(p(213), 213, 214) +# define SEQAN_PP_NODE_215(p) SEQAN_PP_IIF(p(215), 215, 216) +# define SEQAN_PP_NODE_220(p) SEQAN_PP_IIF(p(220), SEQAN_PP_NODE_218, SEQAN_PP_NODE_222) +# define SEQAN_PP_NODE_218(p) SEQAN_PP_IIF(p(218), SEQAN_PP_NODE_217, SEQAN_PP_NODE_219) +# define SEQAN_PP_NODE_217(p) SEQAN_PP_IIF(p(217), 217, 218) +# define SEQAN_PP_NODE_219(p) SEQAN_PP_IIF(p(219), 219, 220) +# define SEQAN_PP_NODE_222(p) SEQAN_PP_IIF(p(222), SEQAN_PP_NODE_221, SEQAN_PP_NODE_223) +# define SEQAN_PP_NODE_221(p) SEQAN_PP_IIF(p(221), 221, 222) +# define SEQAN_PP_NODE_223(p) SEQAN_PP_IIF(p(223), 223, 224) +# define SEQAN_PP_NODE_240(p) SEQAN_PP_IIF(p(240), SEQAN_PP_NODE_232, SEQAN_PP_NODE_248) +# define SEQAN_PP_NODE_232(p) SEQAN_PP_IIF(p(232), SEQAN_PP_NODE_228, SEQAN_PP_NODE_236) +# define SEQAN_PP_NODE_228(p) SEQAN_PP_IIF(p(228), SEQAN_PP_NODE_226, SEQAN_PP_NODE_230) +# define SEQAN_PP_NODE_226(p) SEQAN_PP_IIF(p(226), SEQAN_PP_NODE_225, SEQAN_PP_NODE_227) +# define SEQAN_PP_NODE_225(p) SEQAN_PP_IIF(p(225), 225, 226) +# define SEQAN_PP_NODE_227(p) SEQAN_PP_IIF(p(227), 227, 228) +# define SEQAN_PP_NODE_230(p) SEQAN_PP_IIF(p(230), SEQAN_PP_NODE_229, SEQAN_PP_NODE_231) +# define SEQAN_PP_NODE_229(p) SEQAN_PP_IIF(p(229), 229, 230) +# define SEQAN_PP_NODE_231(p) SEQAN_PP_IIF(p(231), 231, 232) +# define SEQAN_PP_NODE_236(p) SEQAN_PP_IIF(p(236), SEQAN_PP_NODE_234, SEQAN_PP_NODE_238) +# define SEQAN_PP_NODE_234(p) SEQAN_PP_IIF(p(234), SEQAN_PP_NODE_233, SEQAN_PP_NODE_235) +# define SEQAN_PP_NODE_233(p) SEQAN_PP_IIF(p(233), 233, 234) +# define SEQAN_PP_NODE_235(p) SEQAN_PP_IIF(p(235), 235, 236) +# define SEQAN_PP_NODE_238(p) SEQAN_PP_IIF(p(238), SEQAN_PP_NODE_237, SEQAN_PP_NODE_239) +# define SEQAN_PP_NODE_237(p) SEQAN_PP_IIF(p(237), 237, 238) +# define SEQAN_PP_NODE_239(p) SEQAN_PP_IIF(p(239), 239, 240) +# define SEQAN_PP_NODE_248(p) SEQAN_PP_IIF(p(248), SEQAN_PP_NODE_244, SEQAN_PP_NODE_252) +# define SEQAN_PP_NODE_244(p) SEQAN_PP_IIF(p(244), SEQAN_PP_NODE_242, SEQAN_PP_NODE_246) +# define SEQAN_PP_NODE_242(p) SEQAN_PP_IIF(p(242), SEQAN_PP_NODE_241, SEQAN_PP_NODE_243) +# define SEQAN_PP_NODE_241(p) SEQAN_PP_IIF(p(241), 241, 242) +# define SEQAN_PP_NODE_243(p) SEQAN_PP_IIF(p(243), 243, 244) +# define SEQAN_PP_NODE_246(p) SEQAN_PP_IIF(p(246), SEQAN_PP_NODE_245, SEQAN_PP_NODE_247) +# define SEQAN_PP_NODE_245(p) SEQAN_PP_IIF(p(245), 245, 246) +# define SEQAN_PP_NODE_247(p) SEQAN_PP_IIF(p(247), 247, 248) +# define SEQAN_PP_NODE_252(p) SEQAN_PP_IIF(p(252), SEQAN_PP_NODE_250, SEQAN_PP_NODE_254) +# define SEQAN_PP_NODE_250(p) SEQAN_PP_IIF(p(250), SEQAN_PP_NODE_249, SEQAN_PP_NODE_251) +# define SEQAN_PP_NODE_249(p) SEQAN_PP_IIF(p(249), 249, 250) +# define SEQAN_PP_NODE_251(p) SEQAN_PP_IIF(p(251), 251, 252) +# define SEQAN_PP_NODE_254(p) SEQAN_PP_IIF(p(254), SEQAN_PP_NODE_253, SEQAN_PP_NODE_255) +# define SEQAN_PP_NODE_253(p) SEQAN_PP_IIF(p(253), 253, 254) +# define SEQAN_PP_NODE_255(p) SEQAN_PP_IIF(p(255), 255, 256) + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/logical/bool.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_LOGICAL_BOOL_HPP +// # define SEQAN_PREPROCESSOR_LOGICAL_BOOL_HPP +# +// # include +# +# /* SEQAN_PP_BOOL */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_BOOL(x) SEQAN_PP_BOOL_I(x) +// # else +// # define SEQAN_PP_BOOL(x) SEQAN_PP_BOOL_OO((x)) +// # define SEQAN_PP_BOOL_OO(par) SEQAN_PP_BOOL_I ## par +// # endif +# +# define SEQAN_PP_BOOL_I(x) SEQAN_PP_BOOL_ ## x +# +# define SEQAN_PP_BOOL_0 0 +# define SEQAN_PP_BOOL_1 1 +# define SEQAN_PP_BOOL_2 1 +# define SEQAN_PP_BOOL_3 1 +# define SEQAN_PP_BOOL_4 1 +# define SEQAN_PP_BOOL_5 1 +# define SEQAN_PP_BOOL_6 1 +# define SEQAN_PP_BOOL_7 1 +# define SEQAN_PP_BOOL_8 1 +# define SEQAN_PP_BOOL_9 1 +# define SEQAN_PP_BOOL_10 1 +# define SEQAN_PP_BOOL_11 1 +# define SEQAN_PP_BOOL_12 1 +# define SEQAN_PP_BOOL_13 1 +# define SEQAN_PP_BOOL_14 1 +# define SEQAN_PP_BOOL_15 1 +# define SEQAN_PP_BOOL_16 1 +# define SEQAN_PP_BOOL_17 1 +# define SEQAN_PP_BOOL_18 1 +# define SEQAN_PP_BOOL_19 1 +# define SEQAN_PP_BOOL_20 1 +# define SEQAN_PP_BOOL_21 1 +# define SEQAN_PP_BOOL_22 1 +# define SEQAN_PP_BOOL_23 1 +# define SEQAN_PP_BOOL_24 1 +# define SEQAN_PP_BOOL_25 1 +# define SEQAN_PP_BOOL_26 1 +# define SEQAN_PP_BOOL_27 1 +# define SEQAN_PP_BOOL_28 1 +# define SEQAN_PP_BOOL_29 1 +# define SEQAN_PP_BOOL_30 1 +# define SEQAN_PP_BOOL_31 1 +# define SEQAN_PP_BOOL_32 1 +# define SEQAN_PP_BOOL_33 1 +# define SEQAN_PP_BOOL_34 1 +# define SEQAN_PP_BOOL_35 1 +# define SEQAN_PP_BOOL_36 1 +# define SEQAN_PP_BOOL_37 1 +# define SEQAN_PP_BOOL_38 1 +# define SEQAN_PP_BOOL_39 1 +# define SEQAN_PP_BOOL_40 1 +# define SEQAN_PP_BOOL_41 1 +# define SEQAN_PP_BOOL_42 1 +# define SEQAN_PP_BOOL_43 1 +# define SEQAN_PP_BOOL_44 1 +# define SEQAN_PP_BOOL_45 1 +# define SEQAN_PP_BOOL_46 1 +# define SEQAN_PP_BOOL_47 1 +# define SEQAN_PP_BOOL_48 1 +# define SEQAN_PP_BOOL_49 1 +# define SEQAN_PP_BOOL_50 1 +# define SEQAN_PP_BOOL_51 1 +# define SEQAN_PP_BOOL_52 1 +# define SEQAN_PP_BOOL_53 1 +# define SEQAN_PP_BOOL_54 1 +# define SEQAN_PP_BOOL_55 1 +# define SEQAN_PP_BOOL_56 1 +# define SEQAN_PP_BOOL_57 1 +# define SEQAN_PP_BOOL_58 1 +# define SEQAN_PP_BOOL_59 1 +# define SEQAN_PP_BOOL_60 1 +# define SEQAN_PP_BOOL_61 1 +# define SEQAN_PP_BOOL_62 1 +# define SEQAN_PP_BOOL_63 1 +# define SEQAN_PP_BOOL_64 1 +# define SEQAN_PP_BOOL_65 1 +# define SEQAN_PP_BOOL_66 1 +# define SEQAN_PP_BOOL_67 1 +# define SEQAN_PP_BOOL_68 1 +# define SEQAN_PP_BOOL_69 1 +# define SEQAN_PP_BOOL_70 1 +# define SEQAN_PP_BOOL_71 1 +# define SEQAN_PP_BOOL_72 1 +# define SEQAN_PP_BOOL_73 1 +# define SEQAN_PP_BOOL_74 1 +# define SEQAN_PP_BOOL_75 1 +# define SEQAN_PP_BOOL_76 1 +# define SEQAN_PP_BOOL_77 1 +# define SEQAN_PP_BOOL_78 1 +# define SEQAN_PP_BOOL_79 1 +# define SEQAN_PP_BOOL_80 1 +# define SEQAN_PP_BOOL_81 1 +# define SEQAN_PP_BOOL_82 1 +# define SEQAN_PP_BOOL_83 1 +# define SEQAN_PP_BOOL_84 1 +# define SEQAN_PP_BOOL_85 1 +# define SEQAN_PP_BOOL_86 1 +# define SEQAN_PP_BOOL_87 1 +# define SEQAN_PP_BOOL_88 1 +# define SEQAN_PP_BOOL_89 1 +# define SEQAN_PP_BOOL_90 1 +# define SEQAN_PP_BOOL_91 1 +# define SEQAN_PP_BOOL_92 1 +# define SEQAN_PP_BOOL_93 1 +# define SEQAN_PP_BOOL_94 1 +# define SEQAN_PP_BOOL_95 1 +# define SEQAN_PP_BOOL_96 1 +# define SEQAN_PP_BOOL_97 1 +# define SEQAN_PP_BOOL_98 1 +# define SEQAN_PP_BOOL_99 1 +# define SEQAN_PP_BOOL_100 1 +# define SEQAN_PP_BOOL_101 1 +# define SEQAN_PP_BOOL_102 1 +# define SEQAN_PP_BOOL_103 1 +# define SEQAN_PP_BOOL_104 1 +# define SEQAN_PP_BOOL_105 1 +# define SEQAN_PP_BOOL_106 1 +# define SEQAN_PP_BOOL_107 1 +# define SEQAN_PP_BOOL_108 1 +# define SEQAN_PP_BOOL_109 1 +# define SEQAN_PP_BOOL_110 1 +# define SEQAN_PP_BOOL_111 1 +# define SEQAN_PP_BOOL_112 1 +# define SEQAN_PP_BOOL_113 1 +# define SEQAN_PP_BOOL_114 1 +# define SEQAN_PP_BOOL_115 1 +# define SEQAN_PP_BOOL_116 1 +# define SEQAN_PP_BOOL_117 1 +# define SEQAN_PP_BOOL_118 1 +# define SEQAN_PP_BOOL_119 1 +# define SEQAN_PP_BOOL_120 1 +# define SEQAN_PP_BOOL_121 1 +# define SEQAN_PP_BOOL_122 1 +# define SEQAN_PP_BOOL_123 1 +# define SEQAN_PP_BOOL_124 1 +# define SEQAN_PP_BOOL_125 1 +# define SEQAN_PP_BOOL_126 1 +# define SEQAN_PP_BOOL_127 1 +# define SEQAN_PP_BOOL_128 1 +# define SEQAN_PP_BOOL_129 1 +# define SEQAN_PP_BOOL_130 1 +# define SEQAN_PP_BOOL_131 1 +# define SEQAN_PP_BOOL_132 1 +# define SEQAN_PP_BOOL_133 1 +# define SEQAN_PP_BOOL_134 1 +# define SEQAN_PP_BOOL_135 1 +# define SEQAN_PP_BOOL_136 1 +# define SEQAN_PP_BOOL_137 1 +# define SEQAN_PP_BOOL_138 1 +# define SEQAN_PP_BOOL_139 1 +# define SEQAN_PP_BOOL_140 1 +# define SEQAN_PP_BOOL_141 1 +# define SEQAN_PP_BOOL_142 1 +# define SEQAN_PP_BOOL_143 1 +# define SEQAN_PP_BOOL_144 1 +# define SEQAN_PP_BOOL_145 1 +# define SEQAN_PP_BOOL_146 1 +# define SEQAN_PP_BOOL_147 1 +# define SEQAN_PP_BOOL_148 1 +# define SEQAN_PP_BOOL_149 1 +# define SEQAN_PP_BOOL_150 1 +# define SEQAN_PP_BOOL_151 1 +# define SEQAN_PP_BOOL_152 1 +# define SEQAN_PP_BOOL_153 1 +# define SEQAN_PP_BOOL_154 1 +# define SEQAN_PP_BOOL_155 1 +# define SEQAN_PP_BOOL_156 1 +# define SEQAN_PP_BOOL_157 1 +# define SEQAN_PP_BOOL_158 1 +# define SEQAN_PP_BOOL_159 1 +# define SEQAN_PP_BOOL_160 1 +# define SEQAN_PP_BOOL_161 1 +# define SEQAN_PP_BOOL_162 1 +# define SEQAN_PP_BOOL_163 1 +# define SEQAN_PP_BOOL_164 1 +# define SEQAN_PP_BOOL_165 1 +# define SEQAN_PP_BOOL_166 1 +# define SEQAN_PP_BOOL_167 1 +# define SEQAN_PP_BOOL_168 1 +# define SEQAN_PP_BOOL_169 1 +# define SEQAN_PP_BOOL_170 1 +# define SEQAN_PP_BOOL_171 1 +# define SEQAN_PP_BOOL_172 1 +# define SEQAN_PP_BOOL_173 1 +# define SEQAN_PP_BOOL_174 1 +# define SEQAN_PP_BOOL_175 1 +# define SEQAN_PP_BOOL_176 1 +# define SEQAN_PP_BOOL_177 1 +# define SEQAN_PP_BOOL_178 1 +# define SEQAN_PP_BOOL_179 1 +# define SEQAN_PP_BOOL_180 1 +# define SEQAN_PP_BOOL_181 1 +# define SEQAN_PP_BOOL_182 1 +# define SEQAN_PP_BOOL_183 1 +# define SEQAN_PP_BOOL_184 1 +# define SEQAN_PP_BOOL_185 1 +# define SEQAN_PP_BOOL_186 1 +# define SEQAN_PP_BOOL_187 1 +# define SEQAN_PP_BOOL_188 1 +# define SEQAN_PP_BOOL_189 1 +# define SEQAN_PP_BOOL_190 1 +# define SEQAN_PP_BOOL_191 1 +# define SEQAN_PP_BOOL_192 1 +# define SEQAN_PP_BOOL_193 1 +# define SEQAN_PP_BOOL_194 1 +# define SEQAN_PP_BOOL_195 1 +# define SEQAN_PP_BOOL_196 1 +# define SEQAN_PP_BOOL_197 1 +# define SEQAN_PP_BOOL_198 1 +# define SEQAN_PP_BOOL_199 1 +# define SEQAN_PP_BOOL_200 1 +# define SEQAN_PP_BOOL_201 1 +# define SEQAN_PP_BOOL_202 1 +# define SEQAN_PP_BOOL_203 1 +# define SEQAN_PP_BOOL_204 1 +# define SEQAN_PP_BOOL_205 1 +# define SEQAN_PP_BOOL_206 1 +# define SEQAN_PP_BOOL_207 1 +# define SEQAN_PP_BOOL_208 1 +# define SEQAN_PP_BOOL_209 1 +# define SEQAN_PP_BOOL_210 1 +# define SEQAN_PP_BOOL_211 1 +# define SEQAN_PP_BOOL_212 1 +# define SEQAN_PP_BOOL_213 1 +# define SEQAN_PP_BOOL_214 1 +# define SEQAN_PP_BOOL_215 1 +# define SEQAN_PP_BOOL_216 1 +# define SEQAN_PP_BOOL_217 1 +# define SEQAN_PP_BOOL_218 1 +# define SEQAN_PP_BOOL_219 1 +# define SEQAN_PP_BOOL_220 1 +# define SEQAN_PP_BOOL_221 1 +# define SEQAN_PP_BOOL_222 1 +# define SEQAN_PP_BOOL_223 1 +# define SEQAN_PP_BOOL_224 1 +# define SEQAN_PP_BOOL_225 1 +# define SEQAN_PP_BOOL_226 1 +# define SEQAN_PP_BOOL_227 1 +# define SEQAN_PP_BOOL_228 1 +# define SEQAN_PP_BOOL_229 1 +# define SEQAN_PP_BOOL_230 1 +# define SEQAN_PP_BOOL_231 1 +# define SEQAN_PP_BOOL_232 1 +# define SEQAN_PP_BOOL_233 1 +# define SEQAN_PP_BOOL_234 1 +# define SEQAN_PP_BOOL_235 1 +# define SEQAN_PP_BOOL_236 1 +# define SEQAN_PP_BOOL_237 1 +# define SEQAN_PP_BOOL_238 1 +# define SEQAN_PP_BOOL_239 1 +# define SEQAN_PP_BOOL_240 1 +# define SEQAN_PP_BOOL_241 1 +# define SEQAN_PP_BOOL_242 1 +# define SEQAN_PP_BOOL_243 1 +# define SEQAN_PP_BOOL_244 1 +# define SEQAN_PP_BOOL_245 1 +# define SEQAN_PP_BOOL_246 1 +# define SEQAN_PP_BOOL_247 1 +# define SEQAN_PP_BOOL_248 1 +# define SEQAN_PP_BOOL_249 1 +# define SEQAN_PP_BOOL_250 1 +# define SEQAN_PP_BOOL_251 1 +# define SEQAN_PP_BOOL_252 1 +# define SEQAN_PP_BOOL_253 1 +# define SEQAN_PP_BOOL_254 1 +# define SEQAN_PP_BOOL_255 1 +# define SEQAN_PP_BOOL_256 1 + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/control/expr_iif.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_CONTROL_EXPR_IIF_HPP +// # define SEQAN_PREPROCESSOR_CONTROL_EXPR_IIF_HPP +# +// # include +# +# /* SEQAN_PP_EXPR_IIF */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_EXPR_IIF(bit, expr) SEQAN_PP_EXPR_IIF_I(bit, expr) +// # else +// # define SEQAN_PP_EXPR_IIF(bit, expr) SEQAN_PP_EXPR_IIF_OO((bit, expr)) +// # define SEQAN_PP_EXPR_IIF_OO(par) SEQAN_PP_EXPR_IIF_I ## par +// # endif +# +# define SEQAN_PP_EXPR_IIF_I(bit, expr) SEQAN_PP_EXPR_IIF_ ## bit(expr) +# +# define SEQAN_PP_EXPR_IIF_0(expr) +# define SEQAN_PP_EXPR_IIF_1(expr) expr +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/control/iif.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_CONTROL_IIF_HPP +// # define SEQAN_PREPROCESSOR_CONTROL_IIF_HPP +# +// # include +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_IIF(bit, t, f) SEQAN_PP_IIF_I(bit, t, f) +// # else +// # define SEQAN_PP_IIF(bit, t, f) SEQAN_PP_IIF_OO((bit, t, f)) +// # define SEQAN_PP_IIF_OO(par) SEQAN_PP_IIF_I ## par +// # endif +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +#ifndef STDLIB_VS +# define SEQAN_PP_IIF_I(bit, t, f) SEQAN_PP_IIF_ ## bit(t, f) +# else // #ifndef STDLIB_VS +# define SEQAN_PP_IIF_I(bit, t, f) SEQAN_PP_IIF_II(SEQAN_PP_IIF_ ## bit(t, f)) +# define SEQAN_PP_IIF_II(id) id +# endif // #ifndef STDLIB_VS +# +# define SEQAN_PP_IIF_0(t, f) f +# define SEQAN_PP_IIF_1(t, f) t +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/control/if.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_CONTROL_IF_HPP +//# define SEQAN_PREPROCESSOR_CONTROL_IF_HPP +# +//# include +//# include +//# include +# +# /* SEQAN_PP_IF */ +# +//# if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_IF(cond, t, f) SEQAN_PP_IIF(SEQAN_PP_BOOL(cond), t, f) +//# else +//# define SEQAN_PP_IF(cond, t, f) SEQAN_PP_IF_I(cond, t, f) +//# define SEQAN_PP_IF_I(cond, t, f) SEQAN_PP_IIF(SEQAN_PP_BOOL(cond), t, f) +//# endif +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/facilities/empty.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_FACILITIES_EMPTY_HPP +//# define SEQAN_PREPROCESSOR_FACILITIES_EMPTY_HPP +# +# /* SEQAN_PP_EMPTY */ +# +# define SEQAN_PP_EMPTY() +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/punctuation/comma.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_PUNCTUATION_COMMA_HPP +//# define SEQAN_PREPROCESSOR_PUNCTUATION_COMMA_HPP +# +# /* SEQAN_PP_COMMA */ +# +# define SEQAN_PP_COMMA() , +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/punctuation/comma_if.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_PUNCTUATION_COMMA_IF_HPP +//# define SEQAN_PREPROCESSOR_PUNCTUATION_COMMA_IF_HPP +# +//# include +//# include +//# include +//# include +# +# /* SEQAN_PP_COMMA_IF */ +# +//# if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_COMMA_IF(cond) SEQAN_PP_IF(cond, SEQAN_PP_COMMA, SEQAN_PP_EMPTY)() +//# else +//# define SEQAN_PP_COMMA_IF(cond) SEQAN_PP_COMMA_IF_I(cond) +//# define SEQAN_PP_COMMA_IF_I(cond) SEQAN_PP_IF(cond, SEQAN_PP_COMMA, SEQAN_PP_EMPTY)() +//# endif +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/repetition/repeat.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_REPETITION_REPEAT_HPP +//# define SEQAN_PREPROCESSOR_REPETITION_REPEAT_HPP +# +//# include +//# include +//# include +//# include +//# include +# +# /* SEQAN_PP_REPEAT */ +# +# if 0 +# define SEQAN_PP_REPEAT(count, macro, data) +# endif +# +# define SEQAN_PP_REPEAT SEQAN_PP_CAT(SEQAN_PP_REPEAT_, SEQAN_PP_AUTO_REC(SEQAN_PP_REPEAT_P, 4)) +# +# define SEQAN_PP_REPEAT_P(n) SEQAN_PP_CAT(SEQAN_PP_REPEAT_CHECK_, SEQAN_PP_REPEAT_ ## n(1, SEQAN_PP_NIL SEQAN_PP_TUPLE_EAT_3, SEQAN_PP_NIL)) +# +# define SEQAN_PP_REPEAT_CHECK_SEQAN_PP_NIL 1 +# define SEQAN_PP_REPEAT_CHECK_SEQAN_PP_REPEAT_1(c, m, d) 0 +# define SEQAN_PP_REPEAT_CHECK_SEQAN_PP_REPEAT_2(c, m, d) 0 +# define SEQAN_PP_REPEAT_CHECK_SEQAN_PP_REPEAT_3(c, m, d) 0 +# +# define SEQAN_PP_REPEAT_1(c, m, d) SEQAN_PP_REPEAT_1_I(c, m, d) +# define SEQAN_PP_REPEAT_2(c, m, d) SEQAN_PP_REPEAT_2_I(c, m, d) +# define SEQAN_PP_REPEAT_3(c, m, d) SEQAN_PP_REPEAT_3_I(c, m, d) +# define SEQAN_PP_REPEAT_4(c, m, d) SEQAN_PP_ERROR(0x0003) +# +# define SEQAN_PP_REPEAT_1_I(c, m, d) SEQAN_PP_REPEAT_1_ ## c(m, d) +# define SEQAN_PP_REPEAT_2_I(c, m, d) SEQAN_PP_REPEAT_2_ ## c(m, d) +# define SEQAN_PP_REPEAT_3_I(c, m, d) SEQAN_PP_REPEAT_3_ ## c(m, d) +# +# define SEQAN_PP_REPEAT_1ST SEQAN_PP_REPEAT_1 +# define SEQAN_PP_REPEAT_2ND SEQAN_PP_REPEAT_2 +# define SEQAN_PP_REPEAT_3RD SEQAN_PP_REPEAT_3 +# +# define SEQAN_PP_REPEAT_1_0(m, d) +# define SEQAN_PP_REPEAT_1_1(m, d) m(2, 0, d) +# define SEQAN_PP_REPEAT_1_2(m, d) SEQAN_PP_REPEAT_1_1(m, d) m(2, 1, d) +# define SEQAN_PP_REPEAT_1_3(m, d) SEQAN_PP_REPEAT_1_2(m, d) m(2, 2, d) +# define SEQAN_PP_REPEAT_1_4(m, d) SEQAN_PP_REPEAT_1_3(m, d) m(2, 3, d) +# define SEQAN_PP_REPEAT_1_5(m, d) SEQAN_PP_REPEAT_1_4(m, d) m(2, 4, d) +# define SEQAN_PP_REPEAT_1_6(m, d) SEQAN_PP_REPEAT_1_5(m, d) m(2, 5, d) +# define SEQAN_PP_REPEAT_1_7(m, d) SEQAN_PP_REPEAT_1_6(m, d) m(2, 6, d) +# define SEQAN_PP_REPEAT_1_8(m, d) SEQAN_PP_REPEAT_1_7(m, d) m(2, 7, d) +# define SEQAN_PP_REPEAT_1_9(m, d) SEQAN_PP_REPEAT_1_8(m, d) m(2, 8, d) +# define SEQAN_PP_REPEAT_1_10(m, d) SEQAN_PP_REPEAT_1_9(m, d) m(2, 9, d) +# define SEQAN_PP_REPEAT_1_11(m, d) SEQAN_PP_REPEAT_1_10(m, d) m(2, 10, d) +# define SEQAN_PP_REPEAT_1_12(m, d) SEQAN_PP_REPEAT_1_11(m, d) m(2, 11, d) +# define SEQAN_PP_REPEAT_1_13(m, d) SEQAN_PP_REPEAT_1_12(m, d) m(2, 12, d) +# define SEQAN_PP_REPEAT_1_14(m, d) SEQAN_PP_REPEAT_1_13(m, d) m(2, 13, d) +# define SEQAN_PP_REPEAT_1_15(m, d) SEQAN_PP_REPEAT_1_14(m, d) m(2, 14, d) +# define SEQAN_PP_REPEAT_1_16(m, d) SEQAN_PP_REPEAT_1_15(m, d) m(2, 15, d) +# define SEQAN_PP_REPEAT_1_17(m, d) SEQAN_PP_REPEAT_1_16(m, d) m(2, 16, d) +# define SEQAN_PP_REPEAT_1_18(m, d) SEQAN_PP_REPEAT_1_17(m, d) m(2, 17, d) +# define SEQAN_PP_REPEAT_1_19(m, d) SEQAN_PP_REPEAT_1_18(m, d) m(2, 18, d) +# define SEQAN_PP_REPEAT_1_20(m, d) SEQAN_PP_REPEAT_1_19(m, d) m(2, 19, d) +# define SEQAN_PP_REPEAT_1_21(m, d) SEQAN_PP_REPEAT_1_20(m, d) m(2, 20, d) +# define SEQAN_PP_REPEAT_1_22(m, d) SEQAN_PP_REPEAT_1_21(m, d) m(2, 21, d) +# define SEQAN_PP_REPEAT_1_23(m, d) SEQAN_PP_REPEAT_1_22(m, d) m(2, 22, d) +# define SEQAN_PP_REPEAT_1_24(m, d) SEQAN_PP_REPEAT_1_23(m, d) m(2, 23, d) +# define SEQAN_PP_REPEAT_1_25(m, d) SEQAN_PP_REPEAT_1_24(m, d) m(2, 24, d) +# define SEQAN_PP_REPEAT_1_26(m, d) SEQAN_PP_REPEAT_1_25(m, d) m(2, 25, d) +# define SEQAN_PP_REPEAT_1_27(m, d) SEQAN_PP_REPEAT_1_26(m, d) m(2, 26, d) +# define SEQAN_PP_REPEAT_1_28(m, d) SEQAN_PP_REPEAT_1_27(m, d) m(2, 27, d) +# define SEQAN_PP_REPEAT_1_29(m, d) SEQAN_PP_REPEAT_1_28(m, d) m(2, 28, d) +# define SEQAN_PP_REPEAT_1_30(m, d) SEQAN_PP_REPEAT_1_29(m, d) m(2, 29, d) +# define SEQAN_PP_REPEAT_1_31(m, d) SEQAN_PP_REPEAT_1_30(m, d) m(2, 30, d) +# define SEQAN_PP_REPEAT_1_32(m, d) SEQAN_PP_REPEAT_1_31(m, d) m(2, 31, d) +# define SEQAN_PP_REPEAT_1_33(m, d) SEQAN_PP_REPEAT_1_32(m, d) m(2, 32, d) +# define SEQAN_PP_REPEAT_1_34(m, d) SEQAN_PP_REPEAT_1_33(m, d) m(2, 33, d) +# define SEQAN_PP_REPEAT_1_35(m, d) SEQAN_PP_REPEAT_1_34(m, d) m(2, 34, d) +# define SEQAN_PP_REPEAT_1_36(m, d) SEQAN_PP_REPEAT_1_35(m, d) m(2, 35, d) +# define SEQAN_PP_REPEAT_1_37(m, d) SEQAN_PP_REPEAT_1_36(m, d) m(2, 36, d) +# define SEQAN_PP_REPEAT_1_38(m, d) SEQAN_PP_REPEAT_1_37(m, d) m(2, 37, d) +# define SEQAN_PP_REPEAT_1_39(m, d) SEQAN_PP_REPEAT_1_38(m, d) m(2, 38, d) +# define SEQAN_PP_REPEAT_1_40(m, d) SEQAN_PP_REPEAT_1_39(m, d) m(2, 39, d) +# define SEQAN_PP_REPEAT_1_41(m, d) SEQAN_PP_REPEAT_1_40(m, d) m(2, 40, d) +# define SEQAN_PP_REPEAT_1_42(m, d) SEQAN_PP_REPEAT_1_41(m, d) m(2, 41, d) +# define SEQAN_PP_REPEAT_1_43(m, d) SEQAN_PP_REPEAT_1_42(m, d) m(2, 42, d) +# define SEQAN_PP_REPEAT_1_44(m, d) SEQAN_PP_REPEAT_1_43(m, d) m(2, 43, d) +# define SEQAN_PP_REPEAT_1_45(m, d) SEQAN_PP_REPEAT_1_44(m, d) m(2, 44, d) +# define SEQAN_PP_REPEAT_1_46(m, d) SEQAN_PP_REPEAT_1_45(m, d) m(2, 45, d) +# define SEQAN_PP_REPEAT_1_47(m, d) SEQAN_PP_REPEAT_1_46(m, d) m(2, 46, d) +# define SEQAN_PP_REPEAT_1_48(m, d) SEQAN_PP_REPEAT_1_47(m, d) m(2, 47, d) +# define SEQAN_PP_REPEAT_1_49(m, d) SEQAN_PP_REPEAT_1_48(m, d) m(2, 48, d) +# define SEQAN_PP_REPEAT_1_50(m, d) SEQAN_PP_REPEAT_1_49(m, d) m(2, 49, d) +# define SEQAN_PP_REPEAT_1_51(m, d) SEQAN_PP_REPEAT_1_50(m, d) m(2, 50, d) +# define SEQAN_PP_REPEAT_1_52(m, d) SEQAN_PP_REPEAT_1_51(m, d) m(2, 51, d) +# define SEQAN_PP_REPEAT_1_53(m, d) SEQAN_PP_REPEAT_1_52(m, d) m(2, 52, d) +# define SEQAN_PP_REPEAT_1_54(m, d) SEQAN_PP_REPEAT_1_53(m, d) m(2, 53, d) +# define SEQAN_PP_REPEAT_1_55(m, d) SEQAN_PP_REPEAT_1_54(m, d) m(2, 54, d) +# define SEQAN_PP_REPEAT_1_56(m, d) SEQAN_PP_REPEAT_1_55(m, d) m(2, 55, d) +# define SEQAN_PP_REPEAT_1_57(m, d) SEQAN_PP_REPEAT_1_56(m, d) m(2, 56, d) +# define SEQAN_PP_REPEAT_1_58(m, d) SEQAN_PP_REPEAT_1_57(m, d) m(2, 57, d) +# define SEQAN_PP_REPEAT_1_59(m, d) SEQAN_PP_REPEAT_1_58(m, d) m(2, 58, d) +# define SEQAN_PP_REPEAT_1_60(m, d) SEQAN_PP_REPEAT_1_59(m, d) m(2, 59, d) +# define SEQAN_PP_REPEAT_1_61(m, d) SEQAN_PP_REPEAT_1_60(m, d) m(2, 60, d) +# define SEQAN_PP_REPEAT_1_62(m, d) SEQAN_PP_REPEAT_1_61(m, d) m(2, 61, d) +# define SEQAN_PP_REPEAT_1_63(m, d) SEQAN_PP_REPEAT_1_62(m, d) m(2, 62, d) +# define SEQAN_PP_REPEAT_1_64(m, d) SEQAN_PP_REPEAT_1_63(m, d) m(2, 63, d) +# define SEQAN_PP_REPEAT_1_65(m, d) SEQAN_PP_REPEAT_1_64(m, d) m(2, 64, d) +# define SEQAN_PP_REPEAT_1_66(m, d) SEQAN_PP_REPEAT_1_65(m, d) m(2, 65, d) +# define SEQAN_PP_REPEAT_1_67(m, d) SEQAN_PP_REPEAT_1_66(m, d) m(2, 66, d) +# define SEQAN_PP_REPEAT_1_68(m, d) SEQAN_PP_REPEAT_1_67(m, d) m(2, 67, d) +# define SEQAN_PP_REPEAT_1_69(m, d) SEQAN_PP_REPEAT_1_68(m, d) m(2, 68, d) +# define SEQAN_PP_REPEAT_1_70(m, d) SEQAN_PP_REPEAT_1_69(m, d) m(2, 69, d) +# define SEQAN_PP_REPEAT_1_71(m, d) SEQAN_PP_REPEAT_1_70(m, d) m(2, 70, d) +# define SEQAN_PP_REPEAT_1_72(m, d) SEQAN_PP_REPEAT_1_71(m, d) m(2, 71, d) +# define SEQAN_PP_REPEAT_1_73(m, d) SEQAN_PP_REPEAT_1_72(m, d) m(2, 72, d) +# define SEQAN_PP_REPEAT_1_74(m, d) SEQAN_PP_REPEAT_1_73(m, d) m(2, 73, d) +# define SEQAN_PP_REPEAT_1_75(m, d) SEQAN_PP_REPEAT_1_74(m, d) m(2, 74, d) +# define SEQAN_PP_REPEAT_1_76(m, d) SEQAN_PP_REPEAT_1_75(m, d) m(2, 75, d) +# define SEQAN_PP_REPEAT_1_77(m, d) SEQAN_PP_REPEAT_1_76(m, d) m(2, 76, d) +# define SEQAN_PP_REPEAT_1_78(m, d) SEQAN_PP_REPEAT_1_77(m, d) m(2, 77, d) +# define SEQAN_PP_REPEAT_1_79(m, d) SEQAN_PP_REPEAT_1_78(m, d) m(2, 78, d) +# define SEQAN_PP_REPEAT_1_80(m, d) SEQAN_PP_REPEAT_1_79(m, d) m(2, 79, d) +# define SEQAN_PP_REPEAT_1_81(m, d) SEQAN_PP_REPEAT_1_80(m, d) m(2, 80, d) +# define SEQAN_PP_REPEAT_1_82(m, d) SEQAN_PP_REPEAT_1_81(m, d) m(2, 81, d) +# define SEQAN_PP_REPEAT_1_83(m, d) SEQAN_PP_REPEAT_1_82(m, d) m(2, 82, d) +# define SEQAN_PP_REPEAT_1_84(m, d) SEQAN_PP_REPEAT_1_83(m, d) m(2, 83, d) +# define SEQAN_PP_REPEAT_1_85(m, d) SEQAN_PP_REPEAT_1_84(m, d) m(2, 84, d) +# define SEQAN_PP_REPEAT_1_86(m, d) SEQAN_PP_REPEAT_1_85(m, d) m(2, 85, d) +# define SEQAN_PP_REPEAT_1_87(m, d) SEQAN_PP_REPEAT_1_86(m, d) m(2, 86, d) +# define SEQAN_PP_REPEAT_1_88(m, d) SEQAN_PP_REPEAT_1_87(m, d) m(2, 87, d) +# define SEQAN_PP_REPEAT_1_89(m, d) SEQAN_PP_REPEAT_1_88(m, d) m(2, 88, d) +# define SEQAN_PP_REPEAT_1_90(m, d) SEQAN_PP_REPEAT_1_89(m, d) m(2, 89, d) +# define SEQAN_PP_REPEAT_1_91(m, d) SEQAN_PP_REPEAT_1_90(m, d) m(2, 90, d) +# define SEQAN_PP_REPEAT_1_92(m, d) SEQAN_PP_REPEAT_1_91(m, d) m(2, 91, d) +# define SEQAN_PP_REPEAT_1_93(m, d) SEQAN_PP_REPEAT_1_92(m, d) m(2, 92, d) +# define SEQAN_PP_REPEAT_1_94(m, d) SEQAN_PP_REPEAT_1_93(m, d) m(2, 93, d) +# define SEQAN_PP_REPEAT_1_95(m, d) SEQAN_PP_REPEAT_1_94(m, d) m(2, 94, d) +# define SEQAN_PP_REPEAT_1_96(m, d) SEQAN_PP_REPEAT_1_95(m, d) m(2, 95, d) +# define SEQAN_PP_REPEAT_1_97(m, d) SEQAN_PP_REPEAT_1_96(m, d) m(2, 96, d) +# define SEQAN_PP_REPEAT_1_98(m, d) SEQAN_PP_REPEAT_1_97(m, d) m(2, 97, d) +# define SEQAN_PP_REPEAT_1_99(m, d) SEQAN_PP_REPEAT_1_98(m, d) m(2, 98, d) +# define SEQAN_PP_REPEAT_1_100(m, d) SEQAN_PP_REPEAT_1_99(m, d) m(2, 99, d) +# define SEQAN_PP_REPEAT_1_101(m, d) SEQAN_PP_REPEAT_1_100(m, d) m(2, 100, d) +# define SEQAN_PP_REPEAT_1_102(m, d) SEQAN_PP_REPEAT_1_101(m, d) m(2, 101, d) +# define SEQAN_PP_REPEAT_1_103(m, d) SEQAN_PP_REPEAT_1_102(m, d) m(2, 102, d) +# define SEQAN_PP_REPEAT_1_104(m, d) SEQAN_PP_REPEAT_1_103(m, d) m(2, 103, d) +# define SEQAN_PP_REPEAT_1_105(m, d) SEQAN_PP_REPEAT_1_104(m, d) m(2, 104, d) +# define SEQAN_PP_REPEAT_1_106(m, d) SEQAN_PP_REPEAT_1_105(m, d) m(2, 105, d) +# define SEQAN_PP_REPEAT_1_107(m, d) SEQAN_PP_REPEAT_1_106(m, d) m(2, 106, d) +# define SEQAN_PP_REPEAT_1_108(m, d) SEQAN_PP_REPEAT_1_107(m, d) m(2, 107, d) +# define SEQAN_PP_REPEAT_1_109(m, d) SEQAN_PP_REPEAT_1_108(m, d) m(2, 108, d) +# define SEQAN_PP_REPEAT_1_110(m, d) SEQAN_PP_REPEAT_1_109(m, d) m(2, 109, d) +# define SEQAN_PP_REPEAT_1_111(m, d) SEQAN_PP_REPEAT_1_110(m, d) m(2, 110, d) +# define SEQAN_PP_REPEAT_1_112(m, d) SEQAN_PP_REPEAT_1_111(m, d) m(2, 111, d) +# define SEQAN_PP_REPEAT_1_113(m, d) SEQAN_PP_REPEAT_1_112(m, d) m(2, 112, d) +# define SEQAN_PP_REPEAT_1_114(m, d) SEQAN_PP_REPEAT_1_113(m, d) m(2, 113, d) +# define SEQAN_PP_REPEAT_1_115(m, d) SEQAN_PP_REPEAT_1_114(m, d) m(2, 114, d) +# define SEQAN_PP_REPEAT_1_116(m, d) SEQAN_PP_REPEAT_1_115(m, d) m(2, 115, d) +# define SEQAN_PP_REPEAT_1_117(m, d) SEQAN_PP_REPEAT_1_116(m, d) m(2, 116, d) +# define SEQAN_PP_REPEAT_1_118(m, d) SEQAN_PP_REPEAT_1_117(m, d) m(2, 117, d) +# define SEQAN_PP_REPEAT_1_119(m, d) SEQAN_PP_REPEAT_1_118(m, d) m(2, 118, d) +# define SEQAN_PP_REPEAT_1_120(m, d) SEQAN_PP_REPEAT_1_119(m, d) m(2, 119, d) +# define SEQAN_PP_REPEAT_1_121(m, d) SEQAN_PP_REPEAT_1_120(m, d) m(2, 120, d) +# define SEQAN_PP_REPEAT_1_122(m, d) SEQAN_PP_REPEAT_1_121(m, d) m(2, 121, d) +# define SEQAN_PP_REPEAT_1_123(m, d) SEQAN_PP_REPEAT_1_122(m, d) m(2, 122, d) +# define SEQAN_PP_REPEAT_1_124(m, d) SEQAN_PP_REPEAT_1_123(m, d) m(2, 123, d) +# define SEQAN_PP_REPEAT_1_125(m, d) SEQAN_PP_REPEAT_1_124(m, d) m(2, 124, d) +# define SEQAN_PP_REPEAT_1_126(m, d) SEQAN_PP_REPEAT_1_125(m, d) m(2, 125, d) +# define SEQAN_PP_REPEAT_1_127(m, d) SEQAN_PP_REPEAT_1_126(m, d) m(2, 126, d) +# define SEQAN_PP_REPEAT_1_128(m, d) SEQAN_PP_REPEAT_1_127(m, d) m(2, 127, d) +# define SEQAN_PP_REPEAT_1_129(m, d) SEQAN_PP_REPEAT_1_128(m, d) m(2, 128, d) +# define SEQAN_PP_REPEAT_1_130(m, d) SEQAN_PP_REPEAT_1_129(m, d) m(2, 129, d) +# define SEQAN_PP_REPEAT_1_131(m, d) SEQAN_PP_REPEAT_1_130(m, d) m(2, 130, d) +# define SEQAN_PP_REPEAT_1_132(m, d) SEQAN_PP_REPEAT_1_131(m, d) m(2, 131, d) +# define SEQAN_PP_REPEAT_1_133(m, d) SEQAN_PP_REPEAT_1_132(m, d) m(2, 132, d) +# define SEQAN_PP_REPEAT_1_134(m, d) SEQAN_PP_REPEAT_1_133(m, d) m(2, 133, d) +# define SEQAN_PP_REPEAT_1_135(m, d) SEQAN_PP_REPEAT_1_134(m, d) m(2, 134, d) +# define SEQAN_PP_REPEAT_1_136(m, d) SEQAN_PP_REPEAT_1_135(m, d) m(2, 135, d) +# define SEQAN_PP_REPEAT_1_137(m, d) SEQAN_PP_REPEAT_1_136(m, d) m(2, 136, d) +# define SEQAN_PP_REPEAT_1_138(m, d) SEQAN_PP_REPEAT_1_137(m, d) m(2, 137, d) +# define SEQAN_PP_REPEAT_1_139(m, d) SEQAN_PP_REPEAT_1_138(m, d) m(2, 138, d) +# define SEQAN_PP_REPEAT_1_140(m, d) SEQAN_PP_REPEAT_1_139(m, d) m(2, 139, d) +# define SEQAN_PP_REPEAT_1_141(m, d) SEQAN_PP_REPEAT_1_140(m, d) m(2, 140, d) +# define SEQAN_PP_REPEAT_1_142(m, d) SEQAN_PP_REPEAT_1_141(m, d) m(2, 141, d) +# define SEQAN_PP_REPEAT_1_143(m, d) SEQAN_PP_REPEAT_1_142(m, d) m(2, 142, d) +# define SEQAN_PP_REPEAT_1_144(m, d) SEQAN_PP_REPEAT_1_143(m, d) m(2, 143, d) +# define SEQAN_PP_REPEAT_1_145(m, d) SEQAN_PP_REPEAT_1_144(m, d) m(2, 144, d) +# define SEQAN_PP_REPEAT_1_146(m, d) SEQAN_PP_REPEAT_1_145(m, d) m(2, 145, d) +# define SEQAN_PP_REPEAT_1_147(m, d) SEQAN_PP_REPEAT_1_146(m, d) m(2, 146, d) +# define SEQAN_PP_REPEAT_1_148(m, d) SEQAN_PP_REPEAT_1_147(m, d) m(2, 147, d) +# define SEQAN_PP_REPEAT_1_149(m, d) SEQAN_PP_REPEAT_1_148(m, d) m(2, 148, d) +# define SEQAN_PP_REPEAT_1_150(m, d) SEQAN_PP_REPEAT_1_149(m, d) m(2, 149, d) +# define SEQAN_PP_REPEAT_1_151(m, d) SEQAN_PP_REPEAT_1_150(m, d) m(2, 150, d) +# define SEQAN_PP_REPEAT_1_152(m, d) SEQAN_PP_REPEAT_1_151(m, d) m(2, 151, d) +# define SEQAN_PP_REPEAT_1_153(m, d) SEQAN_PP_REPEAT_1_152(m, d) m(2, 152, d) +# define SEQAN_PP_REPEAT_1_154(m, d) SEQAN_PP_REPEAT_1_153(m, d) m(2, 153, d) +# define SEQAN_PP_REPEAT_1_155(m, d) SEQAN_PP_REPEAT_1_154(m, d) m(2, 154, d) +# define SEQAN_PP_REPEAT_1_156(m, d) SEQAN_PP_REPEAT_1_155(m, d) m(2, 155, d) +# define SEQAN_PP_REPEAT_1_157(m, d) SEQAN_PP_REPEAT_1_156(m, d) m(2, 156, d) +# define SEQAN_PP_REPEAT_1_158(m, d) SEQAN_PP_REPEAT_1_157(m, d) m(2, 157, d) +# define SEQAN_PP_REPEAT_1_159(m, d) SEQAN_PP_REPEAT_1_158(m, d) m(2, 158, d) +# define SEQAN_PP_REPEAT_1_160(m, d) SEQAN_PP_REPEAT_1_159(m, d) m(2, 159, d) +# define SEQAN_PP_REPEAT_1_161(m, d) SEQAN_PP_REPEAT_1_160(m, d) m(2, 160, d) +# define SEQAN_PP_REPEAT_1_162(m, d) SEQAN_PP_REPEAT_1_161(m, d) m(2, 161, d) +# define SEQAN_PP_REPEAT_1_163(m, d) SEQAN_PP_REPEAT_1_162(m, d) m(2, 162, d) +# define SEQAN_PP_REPEAT_1_164(m, d) SEQAN_PP_REPEAT_1_163(m, d) m(2, 163, d) +# define SEQAN_PP_REPEAT_1_165(m, d) SEQAN_PP_REPEAT_1_164(m, d) m(2, 164, d) +# define SEQAN_PP_REPEAT_1_166(m, d) SEQAN_PP_REPEAT_1_165(m, d) m(2, 165, d) +# define SEQAN_PP_REPEAT_1_167(m, d) SEQAN_PP_REPEAT_1_166(m, d) m(2, 166, d) +# define SEQAN_PP_REPEAT_1_168(m, d) SEQAN_PP_REPEAT_1_167(m, d) m(2, 167, d) +# define SEQAN_PP_REPEAT_1_169(m, d) SEQAN_PP_REPEAT_1_168(m, d) m(2, 168, d) +# define SEQAN_PP_REPEAT_1_170(m, d) SEQAN_PP_REPEAT_1_169(m, d) m(2, 169, d) +# define SEQAN_PP_REPEAT_1_171(m, d) SEQAN_PP_REPEAT_1_170(m, d) m(2, 170, d) +# define SEQAN_PP_REPEAT_1_172(m, d) SEQAN_PP_REPEAT_1_171(m, d) m(2, 171, d) +# define SEQAN_PP_REPEAT_1_173(m, d) SEQAN_PP_REPEAT_1_172(m, d) m(2, 172, d) +# define SEQAN_PP_REPEAT_1_174(m, d) SEQAN_PP_REPEAT_1_173(m, d) m(2, 173, d) +# define SEQAN_PP_REPEAT_1_175(m, d) SEQAN_PP_REPEAT_1_174(m, d) m(2, 174, d) +# define SEQAN_PP_REPEAT_1_176(m, d) SEQAN_PP_REPEAT_1_175(m, d) m(2, 175, d) +# define SEQAN_PP_REPEAT_1_177(m, d) SEQAN_PP_REPEAT_1_176(m, d) m(2, 176, d) +# define SEQAN_PP_REPEAT_1_178(m, d) SEQAN_PP_REPEAT_1_177(m, d) m(2, 177, d) +# define SEQAN_PP_REPEAT_1_179(m, d) SEQAN_PP_REPEAT_1_178(m, d) m(2, 178, d) +# define SEQAN_PP_REPEAT_1_180(m, d) SEQAN_PP_REPEAT_1_179(m, d) m(2, 179, d) +# define SEQAN_PP_REPEAT_1_181(m, d) SEQAN_PP_REPEAT_1_180(m, d) m(2, 180, d) +# define SEQAN_PP_REPEAT_1_182(m, d) SEQAN_PP_REPEAT_1_181(m, d) m(2, 181, d) +# define SEQAN_PP_REPEAT_1_183(m, d) SEQAN_PP_REPEAT_1_182(m, d) m(2, 182, d) +# define SEQAN_PP_REPEAT_1_184(m, d) SEQAN_PP_REPEAT_1_183(m, d) m(2, 183, d) +# define SEQAN_PP_REPEAT_1_185(m, d) SEQAN_PP_REPEAT_1_184(m, d) m(2, 184, d) +# define SEQAN_PP_REPEAT_1_186(m, d) SEQAN_PP_REPEAT_1_185(m, d) m(2, 185, d) +# define SEQAN_PP_REPEAT_1_187(m, d) SEQAN_PP_REPEAT_1_186(m, d) m(2, 186, d) +# define SEQAN_PP_REPEAT_1_188(m, d) SEQAN_PP_REPEAT_1_187(m, d) m(2, 187, d) +# define SEQAN_PP_REPEAT_1_189(m, d) SEQAN_PP_REPEAT_1_188(m, d) m(2, 188, d) +# define SEQAN_PP_REPEAT_1_190(m, d) SEQAN_PP_REPEAT_1_189(m, d) m(2, 189, d) +# define SEQAN_PP_REPEAT_1_191(m, d) SEQAN_PP_REPEAT_1_190(m, d) m(2, 190, d) +# define SEQAN_PP_REPEAT_1_192(m, d) SEQAN_PP_REPEAT_1_191(m, d) m(2, 191, d) +# define SEQAN_PP_REPEAT_1_193(m, d) SEQAN_PP_REPEAT_1_192(m, d) m(2, 192, d) +# define SEQAN_PP_REPEAT_1_194(m, d) SEQAN_PP_REPEAT_1_193(m, d) m(2, 193, d) +# define SEQAN_PP_REPEAT_1_195(m, d) SEQAN_PP_REPEAT_1_194(m, d) m(2, 194, d) +# define SEQAN_PP_REPEAT_1_196(m, d) SEQAN_PP_REPEAT_1_195(m, d) m(2, 195, d) +# define SEQAN_PP_REPEAT_1_197(m, d) SEQAN_PP_REPEAT_1_196(m, d) m(2, 196, d) +# define SEQAN_PP_REPEAT_1_198(m, d) SEQAN_PP_REPEAT_1_197(m, d) m(2, 197, d) +# define SEQAN_PP_REPEAT_1_199(m, d) SEQAN_PP_REPEAT_1_198(m, d) m(2, 198, d) +# define SEQAN_PP_REPEAT_1_200(m, d) SEQAN_PP_REPEAT_1_199(m, d) m(2, 199, d) +# define SEQAN_PP_REPEAT_1_201(m, d) SEQAN_PP_REPEAT_1_200(m, d) m(2, 200, d) +# define SEQAN_PP_REPEAT_1_202(m, d) SEQAN_PP_REPEAT_1_201(m, d) m(2, 201, d) +# define SEQAN_PP_REPEAT_1_203(m, d) SEQAN_PP_REPEAT_1_202(m, d) m(2, 202, d) +# define SEQAN_PP_REPEAT_1_204(m, d) SEQAN_PP_REPEAT_1_203(m, d) m(2, 203, d) +# define SEQAN_PP_REPEAT_1_205(m, d) SEQAN_PP_REPEAT_1_204(m, d) m(2, 204, d) +# define SEQAN_PP_REPEAT_1_206(m, d) SEQAN_PP_REPEAT_1_205(m, d) m(2, 205, d) +# define SEQAN_PP_REPEAT_1_207(m, d) SEQAN_PP_REPEAT_1_206(m, d) m(2, 206, d) +# define SEQAN_PP_REPEAT_1_208(m, d) SEQAN_PP_REPEAT_1_207(m, d) m(2, 207, d) +# define SEQAN_PP_REPEAT_1_209(m, d) SEQAN_PP_REPEAT_1_208(m, d) m(2, 208, d) +# define SEQAN_PP_REPEAT_1_210(m, d) SEQAN_PP_REPEAT_1_209(m, d) m(2, 209, d) +# define SEQAN_PP_REPEAT_1_211(m, d) SEQAN_PP_REPEAT_1_210(m, d) m(2, 210, d) +# define SEQAN_PP_REPEAT_1_212(m, d) SEQAN_PP_REPEAT_1_211(m, d) m(2, 211, d) +# define SEQAN_PP_REPEAT_1_213(m, d) SEQAN_PP_REPEAT_1_212(m, d) m(2, 212, d) +# define SEQAN_PP_REPEAT_1_214(m, d) SEQAN_PP_REPEAT_1_213(m, d) m(2, 213, d) +# define SEQAN_PP_REPEAT_1_215(m, d) SEQAN_PP_REPEAT_1_214(m, d) m(2, 214, d) +# define SEQAN_PP_REPEAT_1_216(m, d) SEQAN_PP_REPEAT_1_215(m, d) m(2, 215, d) +# define SEQAN_PP_REPEAT_1_217(m, d) SEQAN_PP_REPEAT_1_216(m, d) m(2, 216, d) +# define SEQAN_PP_REPEAT_1_218(m, d) SEQAN_PP_REPEAT_1_217(m, d) m(2, 217, d) +# define SEQAN_PP_REPEAT_1_219(m, d) SEQAN_PP_REPEAT_1_218(m, d) m(2, 218, d) +# define SEQAN_PP_REPEAT_1_220(m, d) SEQAN_PP_REPEAT_1_219(m, d) m(2, 219, d) +# define SEQAN_PP_REPEAT_1_221(m, d) SEQAN_PP_REPEAT_1_220(m, d) m(2, 220, d) +# define SEQAN_PP_REPEAT_1_222(m, d) SEQAN_PP_REPEAT_1_221(m, d) m(2, 221, d) +# define SEQAN_PP_REPEAT_1_223(m, d) SEQAN_PP_REPEAT_1_222(m, d) m(2, 222, d) +# define SEQAN_PP_REPEAT_1_224(m, d) SEQAN_PP_REPEAT_1_223(m, d) m(2, 223, d) +# define SEQAN_PP_REPEAT_1_225(m, d) SEQAN_PP_REPEAT_1_224(m, d) m(2, 224, d) +# define SEQAN_PP_REPEAT_1_226(m, d) SEQAN_PP_REPEAT_1_225(m, d) m(2, 225, d) +# define SEQAN_PP_REPEAT_1_227(m, d) SEQAN_PP_REPEAT_1_226(m, d) m(2, 226, d) +# define SEQAN_PP_REPEAT_1_228(m, d) SEQAN_PP_REPEAT_1_227(m, d) m(2, 227, d) +# define SEQAN_PP_REPEAT_1_229(m, d) SEQAN_PP_REPEAT_1_228(m, d) m(2, 228, d) +# define SEQAN_PP_REPEAT_1_230(m, d) SEQAN_PP_REPEAT_1_229(m, d) m(2, 229, d) +# define SEQAN_PP_REPEAT_1_231(m, d) SEQAN_PP_REPEAT_1_230(m, d) m(2, 230, d) +# define SEQAN_PP_REPEAT_1_232(m, d) SEQAN_PP_REPEAT_1_231(m, d) m(2, 231, d) +# define SEQAN_PP_REPEAT_1_233(m, d) SEQAN_PP_REPEAT_1_232(m, d) m(2, 232, d) +# define SEQAN_PP_REPEAT_1_234(m, d) SEQAN_PP_REPEAT_1_233(m, d) m(2, 233, d) +# define SEQAN_PP_REPEAT_1_235(m, d) SEQAN_PP_REPEAT_1_234(m, d) m(2, 234, d) +# define SEQAN_PP_REPEAT_1_236(m, d) SEQAN_PP_REPEAT_1_235(m, d) m(2, 235, d) +# define SEQAN_PP_REPEAT_1_237(m, d) SEQAN_PP_REPEAT_1_236(m, d) m(2, 236, d) +# define SEQAN_PP_REPEAT_1_238(m, d) SEQAN_PP_REPEAT_1_237(m, d) m(2, 237, d) +# define SEQAN_PP_REPEAT_1_239(m, d) SEQAN_PP_REPEAT_1_238(m, d) m(2, 238, d) +# define SEQAN_PP_REPEAT_1_240(m, d) SEQAN_PP_REPEAT_1_239(m, d) m(2, 239, d) +# define SEQAN_PP_REPEAT_1_241(m, d) SEQAN_PP_REPEAT_1_240(m, d) m(2, 240, d) +# define SEQAN_PP_REPEAT_1_242(m, d) SEQAN_PP_REPEAT_1_241(m, d) m(2, 241, d) +# define SEQAN_PP_REPEAT_1_243(m, d) SEQAN_PP_REPEAT_1_242(m, d) m(2, 242, d) +# define SEQAN_PP_REPEAT_1_244(m, d) SEQAN_PP_REPEAT_1_243(m, d) m(2, 243, d) +# define SEQAN_PP_REPEAT_1_245(m, d) SEQAN_PP_REPEAT_1_244(m, d) m(2, 244, d) +# define SEQAN_PP_REPEAT_1_246(m, d) SEQAN_PP_REPEAT_1_245(m, d) m(2, 245, d) +# define SEQAN_PP_REPEAT_1_247(m, d) SEQAN_PP_REPEAT_1_246(m, d) m(2, 246, d) +# define SEQAN_PP_REPEAT_1_248(m, d) SEQAN_PP_REPEAT_1_247(m, d) m(2, 247, d) +# define SEQAN_PP_REPEAT_1_249(m, d) SEQAN_PP_REPEAT_1_248(m, d) m(2, 248, d) +# define SEQAN_PP_REPEAT_1_250(m, d) SEQAN_PP_REPEAT_1_249(m, d) m(2, 249, d) +# define SEQAN_PP_REPEAT_1_251(m, d) SEQAN_PP_REPEAT_1_250(m, d) m(2, 250, d) +# define SEQAN_PP_REPEAT_1_252(m, d) SEQAN_PP_REPEAT_1_251(m, d) m(2, 251, d) +# define SEQAN_PP_REPEAT_1_253(m, d) SEQAN_PP_REPEAT_1_252(m, d) m(2, 252, d) +# define SEQAN_PP_REPEAT_1_254(m, d) SEQAN_PP_REPEAT_1_253(m, d) m(2, 253, d) +# define SEQAN_PP_REPEAT_1_255(m, d) SEQAN_PP_REPEAT_1_254(m, d) m(2, 254, d) +# define SEQAN_PP_REPEAT_1_256(m, d) SEQAN_PP_REPEAT_1_255(m, d) m(2, 255, d) +# +# define SEQAN_PP_REPEAT_2_0(m, d) +# define SEQAN_PP_REPEAT_2_1(m, d) m(3, 0, d) +# define SEQAN_PP_REPEAT_2_2(m, d) SEQAN_PP_REPEAT_2_1(m, d) m(3, 1, d) +# define SEQAN_PP_REPEAT_2_3(m, d) SEQAN_PP_REPEAT_2_2(m, d) m(3, 2, d) +# define SEQAN_PP_REPEAT_2_4(m, d) SEQAN_PP_REPEAT_2_3(m, d) m(3, 3, d) +# define SEQAN_PP_REPEAT_2_5(m, d) SEQAN_PP_REPEAT_2_4(m, d) m(3, 4, d) +# define SEQAN_PP_REPEAT_2_6(m, d) SEQAN_PP_REPEAT_2_5(m, d) m(3, 5, d) +# define SEQAN_PP_REPEAT_2_7(m, d) SEQAN_PP_REPEAT_2_6(m, d) m(3, 6, d) +# define SEQAN_PP_REPEAT_2_8(m, d) SEQAN_PP_REPEAT_2_7(m, d) m(3, 7, d) +# define SEQAN_PP_REPEAT_2_9(m, d) SEQAN_PP_REPEAT_2_8(m, d) m(3, 8, d) +# define SEQAN_PP_REPEAT_2_10(m, d) SEQAN_PP_REPEAT_2_9(m, d) m(3, 9, d) +# define SEQAN_PP_REPEAT_2_11(m, d) SEQAN_PP_REPEAT_2_10(m, d) m(3, 10, d) +# define SEQAN_PP_REPEAT_2_12(m, d) SEQAN_PP_REPEAT_2_11(m, d) m(3, 11, d) +# define SEQAN_PP_REPEAT_2_13(m, d) SEQAN_PP_REPEAT_2_12(m, d) m(3, 12, d) +# define SEQAN_PP_REPEAT_2_14(m, d) SEQAN_PP_REPEAT_2_13(m, d) m(3, 13, d) +# define SEQAN_PP_REPEAT_2_15(m, d) SEQAN_PP_REPEAT_2_14(m, d) m(3, 14, d) +# define SEQAN_PP_REPEAT_2_16(m, d) SEQAN_PP_REPEAT_2_15(m, d) m(3, 15, d) +# define SEQAN_PP_REPEAT_2_17(m, d) SEQAN_PP_REPEAT_2_16(m, d) m(3, 16, d) +# define SEQAN_PP_REPEAT_2_18(m, d) SEQAN_PP_REPEAT_2_17(m, d) m(3, 17, d) +# define SEQAN_PP_REPEAT_2_19(m, d) SEQAN_PP_REPEAT_2_18(m, d) m(3, 18, d) +# define SEQAN_PP_REPEAT_2_20(m, d) SEQAN_PP_REPEAT_2_19(m, d) m(3, 19, d) +# define SEQAN_PP_REPEAT_2_21(m, d) SEQAN_PP_REPEAT_2_20(m, d) m(3, 20, d) +# define SEQAN_PP_REPEAT_2_22(m, d) SEQAN_PP_REPEAT_2_21(m, d) m(3, 21, d) +# define SEQAN_PP_REPEAT_2_23(m, d) SEQAN_PP_REPEAT_2_22(m, d) m(3, 22, d) +# define SEQAN_PP_REPEAT_2_24(m, d) SEQAN_PP_REPEAT_2_23(m, d) m(3, 23, d) +# define SEQAN_PP_REPEAT_2_25(m, d) SEQAN_PP_REPEAT_2_24(m, d) m(3, 24, d) +# define SEQAN_PP_REPEAT_2_26(m, d) SEQAN_PP_REPEAT_2_25(m, d) m(3, 25, d) +# define SEQAN_PP_REPEAT_2_27(m, d) SEQAN_PP_REPEAT_2_26(m, d) m(3, 26, d) +# define SEQAN_PP_REPEAT_2_28(m, d) SEQAN_PP_REPEAT_2_27(m, d) m(3, 27, d) +# define SEQAN_PP_REPEAT_2_29(m, d) SEQAN_PP_REPEAT_2_28(m, d) m(3, 28, d) +# define SEQAN_PP_REPEAT_2_30(m, d) SEQAN_PP_REPEAT_2_29(m, d) m(3, 29, d) +# define SEQAN_PP_REPEAT_2_31(m, d) SEQAN_PP_REPEAT_2_30(m, d) m(3, 30, d) +# define SEQAN_PP_REPEAT_2_32(m, d) SEQAN_PP_REPEAT_2_31(m, d) m(3, 31, d) +# define SEQAN_PP_REPEAT_2_33(m, d) SEQAN_PP_REPEAT_2_32(m, d) m(3, 32, d) +# define SEQAN_PP_REPEAT_2_34(m, d) SEQAN_PP_REPEAT_2_33(m, d) m(3, 33, d) +# define SEQAN_PP_REPEAT_2_35(m, d) SEQAN_PP_REPEAT_2_34(m, d) m(3, 34, d) +# define SEQAN_PP_REPEAT_2_36(m, d) SEQAN_PP_REPEAT_2_35(m, d) m(3, 35, d) +# define SEQAN_PP_REPEAT_2_37(m, d) SEQAN_PP_REPEAT_2_36(m, d) m(3, 36, d) +# define SEQAN_PP_REPEAT_2_38(m, d) SEQAN_PP_REPEAT_2_37(m, d) m(3, 37, d) +# define SEQAN_PP_REPEAT_2_39(m, d) SEQAN_PP_REPEAT_2_38(m, d) m(3, 38, d) +# define SEQAN_PP_REPEAT_2_40(m, d) SEQAN_PP_REPEAT_2_39(m, d) m(3, 39, d) +# define SEQAN_PP_REPEAT_2_41(m, d) SEQAN_PP_REPEAT_2_40(m, d) m(3, 40, d) +# define SEQAN_PP_REPEAT_2_42(m, d) SEQAN_PP_REPEAT_2_41(m, d) m(3, 41, d) +# define SEQAN_PP_REPEAT_2_43(m, d) SEQAN_PP_REPEAT_2_42(m, d) m(3, 42, d) +# define SEQAN_PP_REPEAT_2_44(m, d) SEQAN_PP_REPEAT_2_43(m, d) m(3, 43, d) +# define SEQAN_PP_REPEAT_2_45(m, d) SEQAN_PP_REPEAT_2_44(m, d) m(3, 44, d) +# define SEQAN_PP_REPEAT_2_46(m, d) SEQAN_PP_REPEAT_2_45(m, d) m(3, 45, d) +# define SEQAN_PP_REPEAT_2_47(m, d) SEQAN_PP_REPEAT_2_46(m, d) m(3, 46, d) +# define SEQAN_PP_REPEAT_2_48(m, d) SEQAN_PP_REPEAT_2_47(m, d) m(3, 47, d) +# define SEQAN_PP_REPEAT_2_49(m, d) SEQAN_PP_REPEAT_2_48(m, d) m(3, 48, d) +# define SEQAN_PP_REPEAT_2_50(m, d) SEQAN_PP_REPEAT_2_49(m, d) m(3, 49, d) +# define SEQAN_PP_REPEAT_2_51(m, d) SEQAN_PP_REPEAT_2_50(m, d) m(3, 50, d) +# define SEQAN_PP_REPEAT_2_52(m, d) SEQAN_PP_REPEAT_2_51(m, d) m(3, 51, d) +# define SEQAN_PP_REPEAT_2_53(m, d) SEQAN_PP_REPEAT_2_52(m, d) m(3, 52, d) +# define SEQAN_PP_REPEAT_2_54(m, d) SEQAN_PP_REPEAT_2_53(m, d) m(3, 53, d) +# define SEQAN_PP_REPEAT_2_55(m, d) SEQAN_PP_REPEAT_2_54(m, d) m(3, 54, d) +# define SEQAN_PP_REPEAT_2_56(m, d) SEQAN_PP_REPEAT_2_55(m, d) m(3, 55, d) +# define SEQAN_PP_REPEAT_2_57(m, d) SEQAN_PP_REPEAT_2_56(m, d) m(3, 56, d) +# define SEQAN_PP_REPEAT_2_58(m, d) SEQAN_PP_REPEAT_2_57(m, d) m(3, 57, d) +# define SEQAN_PP_REPEAT_2_59(m, d) SEQAN_PP_REPEAT_2_58(m, d) m(3, 58, d) +# define SEQAN_PP_REPEAT_2_60(m, d) SEQAN_PP_REPEAT_2_59(m, d) m(3, 59, d) +# define SEQAN_PP_REPEAT_2_61(m, d) SEQAN_PP_REPEAT_2_60(m, d) m(3, 60, d) +# define SEQAN_PP_REPEAT_2_62(m, d) SEQAN_PP_REPEAT_2_61(m, d) m(3, 61, d) +# define SEQAN_PP_REPEAT_2_63(m, d) SEQAN_PP_REPEAT_2_62(m, d) m(3, 62, d) +# define SEQAN_PP_REPEAT_2_64(m, d) SEQAN_PP_REPEAT_2_63(m, d) m(3, 63, d) +# define SEQAN_PP_REPEAT_2_65(m, d) SEQAN_PP_REPEAT_2_64(m, d) m(3, 64, d) +# define SEQAN_PP_REPEAT_2_66(m, d) SEQAN_PP_REPEAT_2_65(m, d) m(3, 65, d) +# define SEQAN_PP_REPEAT_2_67(m, d) SEQAN_PP_REPEAT_2_66(m, d) m(3, 66, d) +# define SEQAN_PP_REPEAT_2_68(m, d) SEQAN_PP_REPEAT_2_67(m, d) m(3, 67, d) +# define SEQAN_PP_REPEAT_2_69(m, d) SEQAN_PP_REPEAT_2_68(m, d) m(3, 68, d) +# define SEQAN_PP_REPEAT_2_70(m, d) SEQAN_PP_REPEAT_2_69(m, d) m(3, 69, d) +# define SEQAN_PP_REPEAT_2_71(m, d) SEQAN_PP_REPEAT_2_70(m, d) m(3, 70, d) +# define SEQAN_PP_REPEAT_2_72(m, d) SEQAN_PP_REPEAT_2_71(m, d) m(3, 71, d) +# define SEQAN_PP_REPEAT_2_73(m, d) SEQAN_PP_REPEAT_2_72(m, d) m(3, 72, d) +# define SEQAN_PP_REPEAT_2_74(m, d) SEQAN_PP_REPEAT_2_73(m, d) m(3, 73, d) +# define SEQAN_PP_REPEAT_2_75(m, d) SEQAN_PP_REPEAT_2_74(m, d) m(3, 74, d) +# define SEQAN_PP_REPEAT_2_76(m, d) SEQAN_PP_REPEAT_2_75(m, d) m(3, 75, d) +# define SEQAN_PP_REPEAT_2_77(m, d) SEQAN_PP_REPEAT_2_76(m, d) m(3, 76, d) +# define SEQAN_PP_REPEAT_2_78(m, d) SEQAN_PP_REPEAT_2_77(m, d) m(3, 77, d) +# define SEQAN_PP_REPEAT_2_79(m, d) SEQAN_PP_REPEAT_2_78(m, d) m(3, 78, d) +# define SEQAN_PP_REPEAT_2_80(m, d) SEQAN_PP_REPEAT_2_79(m, d) m(3, 79, d) +# define SEQAN_PP_REPEAT_2_81(m, d) SEQAN_PP_REPEAT_2_80(m, d) m(3, 80, d) +# define SEQAN_PP_REPEAT_2_82(m, d) SEQAN_PP_REPEAT_2_81(m, d) m(3, 81, d) +# define SEQAN_PP_REPEAT_2_83(m, d) SEQAN_PP_REPEAT_2_82(m, d) m(3, 82, d) +# define SEQAN_PP_REPEAT_2_84(m, d) SEQAN_PP_REPEAT_2_83(m, d) m(3, 83, d) +# define SEQAN_PP_REPEAT_2_85(m, d) SEQAN_PP_REPEAT_2_84(m, d) m(3, 84, d) +# define SEQAN_PP_REPEAT_2_86(m, d) SEQAN_PP_REPEAT_2_85(m, d) m(3, 85, d) +# define SEQAN_PP_REPEAT_2_87(m, d) SEQAN_PP_REPEAT_2_86(m, d) m(3, 86, d) +# define SEQAN_PP_REPEAT_2_88(m, d) SEQAN_PP_REPEAT_2_87(m, d) m(3, 87, d) +# define SEQAN_PP_REPEAT_2_89(m, d) SEQAN_PP_REPEAT_2_88(m, d) m(3, 88, d) +# define SEQAN_PP_REPEAT_2_90(m, d) SEQAN_PP_REPEAT_2_89(m, d) m(3, 89, d) +# define SEQAN_PP_REPEAT_2_91(m, d) SEQAN_PP_REPEAT_2_90(m, d) m(3, 90, d) +# define SEQAN_PP_REPEAT_2_92(m, d) SEQAN_PP_REPEAT_2_91(m, d) m(3, 91, d) +# define SEQAN_PP_REPEAT_2_93(m, d) SEQAN_PP_REPEAT_2_92(m, d) m(3, 92, d) +# define SEQAN_PP_REPEAT_2_94(m, d) SEQAN_PP_REPEAT_2_93(m, d) m(3, 93, d) +# define SEQAN_PP_REPEAT_2_95(m, d) SEQAN_PP_REPEAT_2_94(m, d) m(3, 94, d) +# define SEQAN_PP_REPEAT_2_96(m, d) SEQAN_PP_REPEAT_2_95(m, d) m(3, 95, d) +# define SEQAN_PP_REPEAT_2_97(m, d) SEQAN_PP_REPEAT_2_96(m, d) m(3, 96, d) +# define SEQAN_PP_REPEAT_2_98(m, d) SEQAN_PP_REPEAT_2_97(m, d) m(3, 97, d) +# define SEQAN_PP_REPEAT_2_99(m, d) SEQAN_PP_REPEAT_2_98(m, d) m(3, 98, d) +# define SEQAN_PP_REPEAT_2_100(m, d) SEQAN_PP_REPEAT_2_99(m, d) m(3, 99, d) +# define SEQAN_PP_REPEAT_2_101(m, d) SEQAN_PP_REPEAT_2_100(m, d) m(3, 100, d) +# define SEQAN_PP_REPEAT_2_102(m, d) SEQAN_PP_REPEAT_2_101(m, d) m(3, 101, d) +# define SEQAN_PP_REPEAT_2_103(m, d) SEQAN_PP_REPEAT_2_102(m, d) m(3, 102, d) +# define SEQAN_PP_REPEAT_2_104(m, d) SEQAN_PP_REPEAT_2_103(m, d) m(3, 103, d) +# define SEQAN_PP_REPEAT_2_105(m, d) SEQAN_PP_REPEAT_2_104(m, d) m(3, 104, d) +# define SEQAN_PP_REPEAT_2_106(m, d) SEQAN_PP_REPEAT_2_105(m, d) m(3, 105, d) +# define SEQAN_PP_REPEAT_2_107(m, d) SEQAN_PP_REPEAT_2_106(m, d) m(3, 106, d) +# define SEQAN_PP_REPEAT_2_108(m, d) SEQAN_PP_REPEAT_2_107(m, d) m(3, 107, d) +# define SEQAN_PP_REPEAT_2_109(m, d) SEQAN_PP_REPEAT_2_108(m, d) m(3, 108, d) +# define SEQAN_PP_REPEAT_2_110(m, d) SEQAN_PP_REPEAT_2_109(m, d) m(3, 109, d) +# define SEQAN_PP_REPEAT_2_111(m, d) SEQAN_PP_REPEAT_2_110(m, d) m(3, 110, d) +# define SEQAN_PP_REPEAT_2_112(m, d) SEQAN_PP_REPEAT_2_111(m, d) m(3, 111, d) +# define SEQAN_PP_REPEAT_2_113(m, d) SEQAN_PP_REPEAT_2_112(m, d) m(3, 112, d) +# define SEQAN_PP_REPEAT_2_114(m, d) SEQAN_PP_REPEAT_2_113(m, d) m(3, 113, d) +# define SEQAN_PP_REPEAT_2_115(m, d) SEQAN_PP_REPEAT_2_114(m, d) m(3, 114, d) +# define SEQAN_PP_REPEAT_2_116(m, d) SEQAN_PP_REPEAT_2_115(m, d) m(3, 115, d) +# define SEQAN_PP_REPEAT_2_117(m, d) SEQAN_PP_REPEAT_2_116(m, d) m(3, 116, d) +# define SEQAN_PP_REPEAT_2_118(m, d) SEQAN_PP_REPEAT_2_117(m, d) m(3, 117, d) +# define SEQAN_PP_REPEAT_2_119(m, d) SEQAN_PP_REPEAT_2_118(m, d) m(3, 118, d) +# define SEQAN_PP_REPEAT_2_120(m, d) SEQAN_PP_REPEAT_2_119(m, d) m(3, 119, d) +# define SEQAN_PP_REPEAT_2_121(m, d) SEQAN_PP_REPEAT_2_120(m, d) m(3, 120, d) +# define SEQAN_PP_REPEAT_2_122(m, d) SEQAN_PP_REPEAT_2_121(m, d) m(3, 121, d) +# define SEQAN_PP_REPEAT_2_123(m, d) SEQAN_PP_REPEAT_2_122(m, d) m(3, 122, d) +# define SEQAN_PP_REPEAT_2_124(m, d) SEQAN_PP_REPEAT_2_123(m, d) m(3, 123, d) +# define SEQAN_PP_REPEAT_2_125(m, d) SEQAN_PP_REPEAT_2_124(m, d) m(3, 124, d) +# define SEQAN_PP_REPEAT_2_126(m, d) SEQAN_PP_REPEAT_2_125(m, d) m(3, 125, d) +# define SEQAN_PP_REPEAT_2_127(m, d) SEQAN_PP_REPEAT_2_126(m, d) m(3, 126, d) +# define SEQAN_PP_REPEAT_2_128(m, d) SEQAN_PP_REPEAT_2_127(m, d) m(3, 127, d) +# define SEQAN_PP_REPEAT_2_129(m, d) SEQAN_PP_REPEAT_2_128(m, d) m(3, 128, d) +# define SEQAN_PP_REPEAT_2_130(m, d) SEQAN_PP_REPEAT_2_129(m, d) m(3, 129, d) +# define SEQAN_PP_REPEAT_2_131(m, d) SEQAN_PP_REPEAT_2_130(m, d) m(3, 130, d) +# define SEQAN_PP_REPEAT_2_132(m, d) SEQAN_PP_REPEAT_2_131(m, d) m(3, 131, d) +# define SEQAN_PP_REPEAT_2_133(m, d) SEQAN_PP_REPEAT_2_132(m, d) m(3, 132, d) +# define SEQAN_PP_REPEAT_2_134(m, d) SEQAN_PP_REPEAT_2_133(m, d) m(3, 133, d) +# define SEQAN_PP_REPEAT_2_135(m, d) SEQAN_PP_REPEAT_2_134(m, d) m(3, 134, d) +# define SEQAN_PP_REPEAT_2_136(m, d) SEQAN_PP_REPEAT_2_135(m, d) m(3, 135, d) +# define SEQAN_PP_REPEAT_2_137(m, d) SEQAN_PP_REPEAT_2_136(m, d) m(3, 136, d) +# define SEQAN_PP_REPEAT_2_138(m, d) SEQAN_PP_REPEAT_2_137(m, d) m(3, 137, d) +# define SEQAN_PP_REPEAT_2_139(m, d) SEQAN_PP_REPEAT_2_138(m, d) m(3, 138, d) +# define SEQAN_PP_REPEAT_2_140(m, d) SEQAN_PP_REPEAT_2_139(m, d) m(3, 139, d) +# define SEQAN_PP_REPEAT_2_141(m, d) SEQAN_PP_REPEAT_2_140(m, d) m(3, 140, d) +# define SEQAN_PP_REPEAT_2_142(m, d) SEQAN_PP_REPEAT_2_141(m, d) m(3, 141, d) +# define SEQAN_PP_REPEAT_2_143(m, d) SEQAN_PP_REPEAT_2_142(m, d) m(3, 142, d) +# define SEQAN_PP_REPEAT_2_144(m, d) SEQAN_PP_REPEAT_2_143(m, d) m(3, 143, d) +# define SEQAN_PP_REPEAT_2_145(m, d) SEQAN_PP_REPEAT_2_144(m, d) m(3, 144, d) +# define SEQAN_PP_REPEAT_2_146(m, d) SEQAN_PP_REPEAT_2_145(m, d) m(3, 145, d) +# define SEQAN_PP_REPEAT_2_147(m, d) SEQAN_PP_REPEAT_2_146(m, d) m(3, 146, d) +# define SEQAN_PP_REPEAT_2_148(m, d) SEQAN_PP_REPEAT_2_147(m, d) m(3, 147, d) +# define SEQAN_PP_REPEAT_2_149(m, d) SEQAN_PP_REPEAT_2_148(m, d) m(3, 148, d) +# define SEQAN_PP_REPEAT_2_150(m, d) SEQAN_PP_REPEAT_2_149(m, d) m(3, 149, d) +# define SEQAN_PP_REPEAT_2_151(m, d) SEQAN_PP_REPEAT_2_150(m, d) m(3, 150, d) +# define SEQAN_PP_REPEAT_2_152(m, d) SEQAN_PP_REPEAT_2_151(m, d) m(3, 151, d) +# define SEQAN_PP_REPEAT_2_153(m, d) SEQAN_PP_REPEAT_2_152(m, d) m(3, 152, d) +# define SEQAN_PP_REPEAT_2_154(m, d) SEQAN_PP_REPEAT_2_153(m, d) m(3, 153, d) +# define SEQAN_PP_REPEAT_2_155(m, d) SEQAN_PP_REPEAT_2_154(m, d) m(3, 154, d) +# define SEQAN_PP_REPEAT_2_156(m, d) SEQAN_PP_REPEAT_2_155(m, d) m(3, 155, d) +# define SEQAN_PP_REPEAT_2_157(m, d) SEQAN_PP_REPEAT_2_156(m, d) m(3, 156, d) +# define SEQAN_PP_REPEAT_2_158(m, d) SEQAN_PP_REPEAT_2_157(m, d) m(3, 157, d) +# define SEQAN_PP_REPEAT_2_159(m, d) SEQAN_PP_REPEAT_2_158(m, d) m(3, 158, d) +# define SEQAN_PP_REPEAT_2_160(m, d) SEQAN_PP_REPEAT_2_159(m, d) m(3, 159, d) +# define SEQAN_PP_REPEAT_2_161(m, d) SEQAN_PP_REPEAT_2_160(m, d) m(3, 160, d) +# define SEQAN_PP_REPEAT_2_162(m, d) SEQAN_PP_REPEAT_2_161(m, d) m(3, 161, d) +# define SEQAN_PP_REPEAT_2_163(m, d) SEQAN_PP_REPEAT_2_162(m, d) m(3, 162, d) +# define SEQAN_PP_REPEAT_2_164(m, d) SEQAN_PP_REPEAT_2_163(m, d) m(3, 163, d) +# define SEQAN_PP_REPEAT_2_165(m, d) SEQAN_PP_REPEAT_2_164(m, d) m(3, 164, d) +# define SEQAN_PP_REPEAT_2_166(m, d) SEQAN_PP_REPEAT_2_165(m, d) m(3, 165, d) +# define SEQAN_PP_REPEAT_2_167(m, d) SEQAN_PP_REPEAT_2_166(m, d) m(3, 166, d) +# define SEQAN_PP_REPEAT_2_168(m, d) SEQAN_PP_REPEAT_2_167(m, d) m(3, 167, d) +# define SEQAN_PP_REPEAT_2_169(m, d) SEQAN_PP_REPEAT_2_168(m, d) m(3, 168, d) +# define SEQAN_PP_REPEAT_2_170(m, d) SEQAN_PP_REPEAT_2_169(m, d) m(3, 169, d) +# define SEQAN_PP_REPEAT_2_171(m, d) SEQAN_PP_REPEAT_2_170(m, d) m(3, 170, d) +# define SEQAN_PP_REPEAT_2_172(m, d) SEQAN_PP_REPEAT_2_171(m, d) m(3, 171, d) +# define SEQAN_PP_REPEAT_2_173(m, d) SEQAN_PP_REPEAT_2_172(m, d) m(3, 172, d) +# define SEQAN_PP_REPEAT_2_174(m, d) SEQAN_PP_REPEAT_2_173(m, d) m(3, 173, d) +# define SEQAN_PP_REPEAT_2_175(m, d) SEQAN_PP_REPEAT_2_174(m, d) m(3, 174, d) +# define SEQAN_PP_REPEAT_2_176(m, d) SEQAN_PP_REPEAT_2_175(m, d) m(3, 175, d) +# define SEQAN_PP_REPEAT_2_177(m, d) SEQAN_PP_REPEAT_2_176(m, d) m(3, 176, d) +# define SEQAN_PP_REPEAT_2_178(m, d) SEQAN_PP_REPEAT_2_177(m, d) m(3, 177, d) +# define SEQAN_PP_REPEAT_2_179(m, d) SEQAN_PP_REPEAT_2_178(m, d) m(3, 178, d) +# define SEQAN_PP_REPEAT_2_180(m, d) SEQAN_PP_REPEAT_2_179(m, d) m(3, 179, d) +# define SEQAN_PP_REPEAT_2_181(m, d) SEQAN_PP_REPEAT_2_180(m, d) m(3, 180, d) +# define SEQAN_PP_REPEAT_2_182(m, d) SEQAN_PP_REPEAT_2_181(m, d) m(3, 181, d) +# define SEQAN_PP_REPEAT_2_183(m, d) SEQAN_PP_REPEAT_2_182(m, d) m(3, 182, d) +# define SEQAN_PP_REPEAT_2_184(m, d) SEQAN_PP_REPEAT_2_183(m, d) m(3, 183, d) +# define SEQAN_PP_REPEAT_2_185(m, d) SEQAN_PP_REPEAT_2_184(m, d) m(3, 184, d) +# define SEQAN_PP_REPEAT_2_186(m, d) SEQAN_PP_REPEAT_2_185(m, d) m(3, 185, d) +# define SEQAN_PP_REPEAT_2_187(m, d) SEQAN_PP_REPEAT_2_186(m, d) m(3, 186, d) +# define SEQAN_PP_REPEAT_2_188(m, d) SEQAN_PP_REPEAT_2_187(m, d) m(3, 187, d) +# define SEQAN_PP_REPEAT_2_189(m, d) SEQAN_PP_REPEAT_2_188(m, d) m(3, 188, d) +# define SEQAN_PP_REPEAT_2_190(m, d) SEQAN_PP_REPEAT_2_189(m, d) m(3, 189, d) +# define SEQAN_PP_REPEAT_2_191(m, d) SEQAN_PP_REPEAT_2_190(m, d) m(3, 190, d) +# define SEQAN_PP_REPEAT_2_192(m, d) SEQAN_PP_REPEAT_2_191(m, d) m(3, 191, d) +# define SEQAN_PP_REPEAT_2_193(m, d) SEQAN_PP_REPEAT_2_192(m, d) m(3, 192, d) +# define SEQAN_PP_REPEAT_2_194(m, d) SEQAN_PP_REPEAT_2_193(m, d) m(3, 193, d) +# define SEQAN_PP_REPEAT_2_195(m, d) SEQAN_PP_REPEAT_2_194(m, d) m(3, 194, d) +# define SEQAN_PP_REPEAT_2_196(m, d) SEQAN_PP_REPEAT_2_195(m, d) m(3, 195, d) +# define SEQAN_PP_REPEAT_2_197(m, d) SEQAN_PP_REPEAT_2_196(m, d) m(3, 196, d) +# define SEQAN_PP_REPEAT_2_198(m, d) SEQAN_PP_REPEAT_2_197(m, d) m(3, 197, d) +# define SEQAN_PP_REPEAT_2_199(m, d) SEQAN_PP_REPEAT_2_198(m, d) m(3, 198, d) +# define SEQAN_PP_REPEAT_2_200(m, d) SEQAN_PP_REPEAT_2_199(m, d) m(3, 199, d) +# define SEQAN_PP_REPEAT_2_201(m, d) SEQAN_PP_REPEAT_2_200(m, d) m(3, 200, d) +# define SEQAN_PP_REPEAT_2_202(m, d) SEQAN_PP_REPEAT_2_201(m, d) m(3, 201, d) +# define SEQAN_PP_REPEAT_2_203(m, d) SEQAN_PP_REPEAT_2_202(m, d) m(3, 202, d) +# define SEQAN_PP_REPEAT_2_204(m, d) SEQAN_PP_REPEAT_2_203(m, d) m(3, 203, d) +# define SEQAN_PP_REPEAT_2_205(m, d) SEQAN_PP_REPEAT_2_204(m, d) m(3, 204, d) +# define SEQAN_PP_REPEAT_2_206(m, d) SEQAN_PP_REPEAT_2_205(m, d) m(3, 205, d) +# define SEQAN_PP_REPEAT_2_207(m, d) SEQAN_PP_REPEAT_2_206(m, d) m(3, 206, d) +# define SEQAN_PP_REPEAT_2_208(m, d) SEQAN_PP_REPEAT_2_207(m, d) m(3, 207, d) +# define SEQAN_PP_REPEAT_2_209(m, d) SEQAN_PP_REPEAT_2_208(m, d) m(3, 208, d) +# define SEQAN_PP_REPEAT_2_210(m, d) SEQAN_PP_REPEAT_2_209(m, d) m(3, 209, d) +# define SEQAN_PP_REPEAT_2_211(m, d) SEQAN_PP_REPEAT_2_210(m, d) m(3, 210, d) +# define SEQAN_PP_REPEAT_2_212(m, d) SEQAN_PP_REPEAT_2_211(m, d) m(3, 211, d) +# define SEQAN_PP_REPEAT_2_213(m, d) SEQAN_PP_REPEAT_2_212(m, d) m(3, 212, d) +# define SEQAN_PP_REPEAT_2_214(m, d) SEQAN_PP_REPEAT_2_213(m, d) m(3, 213, d) +# define SEQAN_PP_REPEAT_2_215(m, d) SEQAN_PP_REPEAT_2_214(m, d) m(3, 214, d) +# define SEQAN_PP_REPEAT_2_216(m, d) SEQAN_PP_REPEAT_2_215(m, d) m(3, 215, d) +# define SEQAN_PP_REPEAT_2_217(m, d) SEQAN_PP_REPEAT_2_216(m, d) m(3, 216, d) +# define SEQAN_PP_REPEAT_2_218(m, d) SEQAN_PP_REPEAT_2_217(m, d) m(3, 217, d) +# define SEQAN_PP_REPEAT_2_219(m, d) SEQAN_PP_REPEAT_2_218(m, d) m(3, 218, d) +# define SEQAN_PP_REPEAT_2_220(m, d) SEQAN_PP_REPEAT_2_219(m, d) m(3, 219, d) +# define SEQAN_PP_REPEAT_2_221(m, d) SEQAN_PP_REPEAT_2_220(m, d) m(3, 220, d) +# define SEQAN_PP_REPEAT_2_222(m, d) SEQAN_PP_REPEAT_2_221(m, d) m(3, 221, d) +# define SEQAN_PP_REPEAT_2_223(m, d) SEQAN_PP_REPEAT_2_222(m, d) m(3, 222, d) +# define SEQAN_PP_REPEAT_2_224(m, d) SEQAN_PP_REPEAT_2_223(m, d) m(3, 223, d) +# define SEQAN_PP_REPEAT_2_225(m, d) SEQAN_PP_REPEAT_2_224(m, d) m(3, 224, d) +# define SEQAN_PP_REPEAT_2_226(m, d) SEQAN_PP_REPEAT_2_225(m, d) m(3, 225, d) +# define SEQAN_PP_REPEAT_2_227(m, d) SEQAN_PP_REPEAT_2_226(m, d) m(3, 226, d) +# define SEQAN_PP_REPEAT_2_228(m, d) SEQAN_PP_REPEAT_2_227(m, d) m(3, 227, d) +# define SEQAN_PP_REPEAT_2_229(m, d) SEQAN_PP_REPEAT_2_228(m, d) m(3, 228, d) +# define SEQAN_PP_REPEAT_2_230(m, d) SEQAN_PP_REPEAT_2_229(m, d) m(3, 229, d) +# define SEQAN_PP_REPEAT_2_231(m, d) SEQAN_PP_REPEAT_2_230(m, d) m(3, 230, d) +# define SEQAN_PP_REPEAT_2_232(m, d) SEQAN_PP_REPEAT_2_231(m, d) m(3, 231, d) +# define SEQAN_PP_REPEAT_2_233(m, d) SEQAN_PP_REPEAT_2_232(m, d) m(3, 232, d) +# define SEQAN_PP_REPEAT_2_234(m, d) SEQAN_PP_REPEAT_2_233(m, d) m(3, 233, d) +# define SEQAN_PP_REPEAT_2_235(m, d) SEQAN_PP_REPEAT_2_234(m, d) m(3, 234, d) +# define SEQAN_PP_REPEAT_2_236(m, d) SEQAN_PP_REPEAT_2_235(m, d) m(3, 235, d) +# define SEQAN_PP_REPEAT_2_237(m, d) SEQAN_PP_REPEAT_2_236(m, d) m(3, 236, d) +# define SEQAN_PP_REPEAT_2_238(m, d) SEQAN_PP_REPEAT_2_237(m, d) m(3, 237, d) +# define SEQAN_PP_REPEAT_2_239(m, d) SEQAN_PP_REPEAT_2_238(m, d) m(3, 238, d) +# define SEQAN_PP_REPEAT_2_240(m, d) SEQAN_PP_REPEAT_2_239(m, d) m(3, 239, d) +# define SEQAN_PP_REPEAT_2_241(m, d) SEQAN_PP_REPEAT_2_240(m, d) m(3, 240, d) +# define SEQAN_PP_REPEAT_2_242(m, d) SEQAN_PP_REPEAT_2_241(m, d) m(3, 241, d) +# define SEQAN_PP_REPEAT_2_243(m, d) SEQAN_PP_REPEAT_2_242(m, d) m(3, 242, d) +# define SEQAN_PP_REPEAT_2_244(m, d) SEQAN_PP_REPEAT_2_243(m, d) m(3, 243, d) +# define SEQAN_PP_REPEAT_2_245(m, d) SEQAN_PP_REPEAT_2_244(m, d) m(3, 244, d) +# define SEQAN_PP_REPEAT_2_246(m, d) SEQAN_PP_REPEAT_2_245(m, d) m(3, 245, d) +# define SEQAN_PP_REPEAT_2_247(m, d) SEQAN_PP_REPEAT_2_246(m, d) m(3, 246, d) +# define SEQAN_PP_REPEAT_2_248(m, d) SEQAN_PP_REPEAT_2_247(m, d) m(3, 247, d) +# define SEQAN_PP_REPEAT_2_249(m, d) SEQAN_PP_REPEAT_2_248(m, d) m(3, 248, d) +# define SEQAN_PP_REPEAT_2_250(m, d) SEQAN_PP_REPEAT_2_249(m, d) m(3, 249, d) +# define SEQAN_PP_REPEAT_2_251(m, d) SEQAN_PP_REPEAT_2_250(m, d) m(3, 250, d) +# define SEQAN_PP_REPEAT_2_252(m, d) SEQAN_PP_REPEAT_2_251(m, d) m(3, 251, d) +# define SEQAN_PP_REPEAT_2_253(m, d) SEQAN_PP_REPEAT_2_252(m, d) m(3, 252, d) +# define SEQAN_PP_REPEAT_2_254(m, d) SEQAN_PP_REPEAT_2_253(m, d) m(3, 253, d) +# define SEQAN_PP_REPEAT_2_255(m, d) SEQAN_PP_REPEAT_2_254(m, d) m(3, 254, d) +# define SEQAN_PP_REPEAT_2_256(m, d) SEQAN_PP_REPEAT_2_255(m, d) m(3, 255, d) +# +# define SEQAN_PP_REPEAT_3_0(m, d) +# define SEQAN_PP_REPEAT_3_1(m, d) m(4, 0, d) +# define SEQAN_PP_REPEAT_3_2(m, d) SEQAN_PP_REPEAT_3_1(m, d) m(4, 1, d) +# define SEQAN_PP_REPEAT_3_3(m, d) SEQAN_PP_REPEAT_3_2(m, d) m(4, 2, d) +# define SEQAN_PP_REPEAT_3_4(m, d) SEQAN_PP_REPEAT_3_3(m, d) m(4, 3, d) +# define SEQAN_PP_REPEAT_3_5(m, d) SEQAN_PP_REPEAT_3_4(m, d) m(4, 4, d) +# define SEQAN_PP_REPEAT_3_6(m, d) SEQAN_PP_REPEAT_3_5(m, d) m(4, 5, d) +# define SEQAN_PP_REPEAT_3_7(m, d) SEQAN_PP_REPEAT_3_6(m, d) m(4, 6, d) +# define SEQAN_PP_REPEAT_3_8(m, d) SEQAN_PP_REPEAT_3_7(m, d) m(4, 7, d) +# define SEQAN_PP_REPEAT_3_9(m, d) SEQAN_PP_REPEAT_3_8(m, d) m(4, 8, d) +# define SEQAN_PP_REPEAT_3_10(m, d) SEQAN_PP_REPEAT_3_9(m, d) m(4, 9, d) +# define SEQAN_PP_REPEAT_3_11(m, d) SEQAN_PP_REPEAT_3_10(m, d) m(4, 10, d) +# define SEQAN_PP_REPEAT_3_12(m, d) SEQAN_PP_REPEAT_3_11(m, d) m(4, 11, d) +# define SEQAN_PP_REPEAT_3_13(m, d) SEQAN_PP_REPEAT_3_12(m, d) m(4, 12, d) +# define SEQAN_PP_REPEAT_3_14(m, d) SEQAN_PP_REPEAT_3_13(m, d) m(4, 13, d) +# define SEQAN_PP_REPEAT_3_15(m, d) SEQAN_PP_REPEAT_3_14(m, d) m(4, 14, d) +# define SEQAN_PP_REPEAT_3_16(m, d) SEQAN_PP_REPEAT_3_15(m, d) m(4, 15, d) +# define SEQAN_PP_REPEAT_3_17(m, d) SEQAN_PP_REPEAT_3_16(m, d) m(4, 16, d) +# define SEQAN_PP_REPEAT_3_18(m, d) SEQAN_PP_REPEAT_3_17(m, d) m(4, 17, d) +# define SEQAN_PP_REPEAT_3_19(m, d) SEQAN_PP_REPEAT_3_18(m, d) m(4, 18, d) +# define SEQAN_PP_REPEAT_3_20(m, d) SEQAN_PP_REPEAT_3_19(m, d) m(4, 19, d) +# define SEQAN_PP_REPEAT_3_21(m, d) SEQAN_PP_REPEAT_3_20(m, d) m(4, 20, d) +# define SEQAN_PP_REPEAT_3_22(m, d) SEQAN_PP_REPEAT_3_21(m, d) m(4, 21, d) +# define SEQAN_PP_REPEAT_3_23(m, d) SEQAN_PP_REPEAT_3_22(m, d) m(4, 22, d) +# define SEQAN_PP_REPEAT_3_24(m, d) SEQAN_PP_REPEAT_3_23(m, d) m(4, 23, d) +# define SEQAN_PP_REPEAT_3_25(m, d) SEQAN_PP_REPEAT_3_24(m, d) m(4, 24, d) +# define SEQAN_PP_REPEAT_3_26(m, d) SEQAN_PP_REPEAT_3_25(m, d) m(4, 25, d) +# define SEQAN_PP_REPEAT_3_27(m, d) SEQAN_PP_REPEAT_3_26(m, d) m(4, 26, d) +# define SEQAN_PP_REPEAT_3_28(m, d) SEQAN_PP_REPEAT_3_27(m, d) m(4, 27, d) +# define SEQAN_PP_REPEAT_3_29(m, d) SEQAN_PP_REPEAT_3_28(m, d) m(4, 28, d) +# define SEQAN_PP_REPEAT_3_30(m, d) SEQAN_PP_REPEAT_3_29(m, d) m(4, 29, d) +# define SEQAN_PP_REPEAT_3_31(m, d) SEQAN_PP_REPEAT_3_30(m, d) m(4, 30, d) +# define SEQAN_PP_REPEAT_3_32(m, d) SEQAN_PP_REPEAT_3_31(m, d) m(4, 31, d) +# define SEQAN_PP_REPEAT_3_33(m, d) SEQAN_PP_REPEAT_3_32(m, d) m(4, 32, d) +# define SEQAN_PP_REPEAT_3_34(m, d) SEQAN_PP_REPEAT_3_33(m, d) m(4, 33, d) +# define SEQAN_PP_REPEAT_3_35(m, d) SEQAN_PP_REPEAT_3_34(m, d) m(4, 34, d) +# define SEQAN_PP_REPEAT_3_36(m, d) SEQAN_PP_REPEAT_3_35(m, d) m(4, 35, d) +# define SEQAN_PP_REPEAT_3_37(m, d) SEQAN_PP_REPEAT_3_36(m, d) m(4, 36, d) +# define SEQAN_PP_REPEAT_3_38(m, d) SEQAN_PP_REPEAT_3_37(m, d) m(4, 37, d) +# define SEQAN_PP_REPEAT_3_39(m, d) SEQAN_PP_REPEAT_3_38(m, d) m(4, 38, d) +# define SEQAN_PP_REPEAT_3_40(m, d) SEQAN_PP_REPEAT_3_39(m, d) m(4, 39, d) +# define SEQAN_PP_REPEAT_3_41(m, d) SEQAN_PP_REPEAT_3_40(m, d) m(4, 40, d) +# define SEQAN_PP_REPEAT_3_42(m, d) SEQAN_PP_REPEAT_3_41(m, d) m(4, 41, d) +# define SEQAN_PP_REPEAT_3_43(m, d) SEQAN_PP_REPEAT_3_42(m, d) m(4, 42, d) +# define SEQAN_PP_REPEAT_3_44(m, d) SEQAN_PP_REPEAT_3_43(m, d) m(4, 43, d) +# define SEQAN_PP_REPEAT_3_45(m, d) SEQAN_PP_REPEAT_3_44(m, d) m(4, 44, d) +# define SEQAN_PP_REPEAT_3_46(m, d) SEQAN_PP_REPEAT_3_45(m, d) m(4, 45, d) +# define SEQAN_PP_REPEAT_3_47(m, d) SEQAN_PP_REPEAT_3_46(m, d) m(4, 46, d) +# define SEQAN_PP_REPEAT_3_48(m, d) SEQAN_PP_REPEAT_3_47(m, d) m(4, 47, d) +# define SEQAN_PP_REPEAT_3_49(m, d) SEQAN_PP_REPEAT_3_48(m, d) m(4, 48, d) +# define SEQAN_PP_REPEAT_3_50(m, d) SEQAN_PP_REPEAT_3_49(m, d) m(4, 49, d) +# define SEQAN_PP_REPEAT_3_51(m, d) SEQAN_PP_REPEAT_3_50(m, d) m(4, 50, d) +# define SEQAN_PP_REPEAT_3_52(m, d) SEQAN_PP_REPEAT_3_51(m, d) m(4, 51, d) +# define SEQAN_PP_REPEAT_3_53(m, d) SEQAN_PP_REPEAT_3_52(m, d) m(4, 52, d) +# define SEQAN_PP_REPEAT_3_54(m, d) SEQAN_PP_REPEAT_3_53(m, d) m(4, 53, d) +# define SEQAN_PP_REPEAT_3_55(m, d) SEQAN_PP_REPEAT_3_54(m, d) m(4, 54, d) +# define SEQAN_PP_REPEAT_3_56(m, d) SEQAN_PP_REPEAT_3_55(m, d) m(4, 55, d) +# define SEQAN_PP_REPEAT_3_57(m, d) SEQAN_PP_REPEAT_3_56(m, d) m(4, 56, d) +# define SEQAN_PP_REPEAT_3_58(m, d) SEQAN_PP_REPEAT_3_57(m, d) m(4, 57, d) +# define SEQAN_PP_REPEAT_3_59(m, d) SEQAN_PP_REPEAT_3_58(m, d) m(4, 58, d) +# define SEQAN_PP_REPEAT_3_60(m, d) SEQAN_PP_REPEAT_3_59(m, d) m(4, 59, d) +# define SEQAN_PP_REPEAT_3_61(m, d) SEQAN_PP_REPEAT_3_60(m, d) m(4, 60, d) +# define SEQAN_PP_REPEAT_3_62(m, d) SEQAN_PP_REPEAT_3_61(m, d) m(4, 61, d) +# define SEQAN_PP_REPEAT_3_63(m, d) SEQAN_PP_REPEAT_3_62(m, d) m(4, 62, d) +# define SEQAN_PP_REPEAT_3_64(m, d) SEQAN_PP_REPEAT_3_63(m, d) m(4, 63, d) +# define SEQAN_PP_REPEAT_3_65(m, d) SEQAN_PP_REPEAT_3_64(m, d) m(4, 64, d) +# define SEQAN_PP_REPEAT_3_66(m, d) SEQAN_PP_REPEAT_3_65(m, d) m(4, 65, d) +# define SEQAN_PP_REPEAT_3_67(m, d) SEQAN_PP_REPEAT_3_66(m, d) m(4, 66, d) +# define SEQAN_PP_REPEAT_3_68(m, d) SEQAN_PP_REPEAT_3_67(m, d) m(4, 67, d) +# define SEQAN_PP_REPEAT_3_69(m, d) SEQAN_PP_REPEAT_3_68(m, d) m(4, 68, d) +# define SEQAN_PP_REPEAT_3_70(m, d) SEQAN_PP_REPEAT_3_69(m, d) m(4, 69, d) +# define SEQAN_PP_REPEAT_3_71(m, d) SEQAN_PP_REPEAT_3_70(m, d) m(4, 70, d) +# define SEQAN_PP_REPEAT_3_72(m, d) SEQAN_PP_REPEAT_3_71(m, d) m(4, 71, d) +# define SEQAN_PP_REPEAT_3_73(m, d) SEQAN_PP_REPEAT_3_72(m, d) m(4, 72, d) +# define SEQAN_PP_REPEAT_3_74(m, d) SEQAN_PP_REPEAT_3_73(m, d) m(4, 73, d) +# define SEQAN_PP_REPEAT_3_75(m, d) SEQAN_PP_REPEAT_3_74(m, d) m(4, 74, d) +# define SEQAN_PP_REPEAT_3_76(m, d) SEQAN_PP_REPEAT_3_75(m, d) m(4, 75, d) +# define SEQAN_PP_REPEAT_3_77(m, d) SEQAN_PP_REPEAT_3_76(m, d) m(4, 76, d) +# define SEQAN_PP_REPEAT_3_78(m, d) SEQAN_PP_REPEAT_3_77(m, d) m(4, 77, d) +# define SEQAN_PP_REPEAT_3_79(m, d) SEQAN_PP_REPEAT_3_78(m, d) m(4, 78, d) +# define SEQAN_PP_REPEAT_3_80(m, d) SEQAN_PP_REPEAT_3_79(m, d) m(4, 79, d) +# define SEQAN_PP_REPEAT_3_81(m, d) SEQAN_PP_REPEAT_3_80(m, d) m(4, 80, d) +# define SEQAN_PP_REPEAT_3_82(m, d) SEQAN_PP_REPEAT_3_81(m, d) m(4, 81, d) +# define SEQAN_PP_REPEAT_3_83(m, d) SEQAN_PP_REPEAT_3_82(m, d) m(4, 82, d) +# define SEQAN_PP_REPEAT_3_84(m, d) SEQAN_PP_REPEAT_3_83(m, d) m(4, 83, d) +# define SEQAN_PP_REPEAT_3_85(m, d) SEQAN_PP_REPEAT_3_84(m, d) m(4, 84, d) +# define SEQAN_PP_REPEAT_3_86(m, d) SEQAN_PP_REPEAT_3_85(m, d) m(4, 85, d) +# define SEQAN_PP_REPEAT_3_87(m, d) SEQAN_PP_REPEAT_3_86(m, d) m(4, 86, d) +# define SEQAN_PP_REPEAT_3_88(m, d) SEQAN_PP_REPEAT_3_87(m, d) m(4, 87, d) +# define SEQAN_PP_REPEAT_3_89(m, d) SEQAN_PP_REPEAT_3_88(m, d) m(4, 88, d) +# define SEQAN_PP_REPEAT_3_90(m, d) SEQAN_PP_REPEAT_3_89(m, d) m(4, 89, d) +# define SEQAN_PP_REPEAT_3_91(m, d) SEQAN_PP_REPEAT_3_90(m, d) m(4, 90, d) +# define SEQAN_PP_REPEAT_3_92(m, d) SEQAN_PP_REPEAT_3_91(m, d) m(4, 91, d) +# define SEQAN_PP_REPEAT_3_93(m, d) SEQAN_PP_REPEAT_3_92(m, d) m(4, 92, d) +# define SEQAN_PP_REPEAT_3_94(m, d) SEQAN_PP_REPEAT_3_93(m, d) m(4, 93, d) +# define SEQAN_PP_REPEAT_3_95(m, d) SEQAN_PP_REPEAT_3_94(m, d) m(4, 94, d) +# define SEQAN_PP_REPEAT_3_96(m, d) SEQAN_PP_REPEAT_3_95(m, d) m(4, 95, d) +# define SEQAN_PP_REPEAT_3_97(m, d) SEQAN_PP_REPEAT_3_96(m, d) m(4, 96, d) +# define SEQAN_PP_REPEAT_3_98(m, d) SEQAN_PP_REPEAT_3_97(m, d) m(4, 97, d) +# define SEQAN_PP_REPEAT_3_99(m, d) SEQAN_PP_REPEAT_3_98(m, d) m(4, 98, d) +# define SEQAN_PP_REPEAT_3_100(m, d) SEQAN_PP_REPEAT_3_99(m, d) m(4, 99, d) +# define SEQAN_PP_REPEAT_3_101(m, d) SEQAN_PP_REPEAT_3_100(m, d) m(4, 100, d) +# define SEQAN_PP_REPEAT_3_102(m, d) SEQAN_PP_REPEAT_3_101(m, d) m(4, 101, d) +# define SEQAN_PP_REPEAT_3_103(m, d) SEQAN_PP_REPEAT_3_102(m, d) m(4, 102, d) +# define SEQAN_PP_REPEAT_3_104(m, d) SEQAN_PP_REPEAT_3_103(m, d) m(4, 103, d) +# define SEQAN_PP_REPEAT_3_105(m, d) SEQAN_PP_REPEAT_3_104(m, d) m(4, 104, d) +# define SEQAN_PP_REPEAT_3_106(m, d) SEQAN_PP_REPEAT_3_105(m, d) m(4, 105, d) +# define SEQAN_PP_REPEAT_3_107(m, d) SEQAN_PP_REPEAT_3_106(m, d) m(4, 106, d) +# define SEQAN_PP_REPEAT_3_108(m, d) SEQAN_PP_REPEAT_3_107(m, d) m(4, 107, d) +# define SEQAN_PP_REPEAT_3_109(m, d) SEQAN_PP_REPEAT_3_108(m, d) m(4, 108, d) +# define SEQAN_PP_REPEAT_3_110(m, d) SEQAN_PP_REPEAT_3_109(m, d) m(4, 109, d) +# define SEQAN_PP_REPEAT_3_111(m, d) SEQAN_PP_REPEAT_3_110(m, d) m(4, 110, d) +# define SEQAN_PP_REPEAT_3_112(m, d) SEQAN_PP_REPEAT_3_111(m, d) m(4, 111, d) +# define SEQAN_PP_REPEAT_3_113(m, d) SEQAN_PP_REPEAT_3_112(m, d) m(4, 112, d) +# define SEQAN_PP_REPEAT_3_114(m, d) SEQAN_PP_REPEAT_3_113(m, d) m(4, 113, d) +# define SEQAN_PP_REPEAT_3_115(m, d) SEQAN_PP_REPEAT_3_114(m, d) m(4, 114, d) +# define SEQAN_PP_REPEAT_3_116(m, d) SEQAN_PP_REPEAT_3_115(m, d) m(4, 115, d) +# define SEQAN_PP_REPEAT_3_117(m, d) SEQAN_PP_REPEAT_3_116(m, d) m(4, 116, d) +# define SEQAN_PP_REPEAT_3_118(m, d) SEQAN_PP_REPEAT_3_117(m, d) m(4, 117, d) +# define SEQAN_PP_REPEAT_3_119(m, d) SEQAN_PP_REPEAT_3_118(m, d) m(4, 118, d) +# define SEQAN_PP_REPEAT_3_120(m, d) SEQAN_PP_REPEAT_3_119(m, d) m(4, 119, d) +# define SEQAN_PP_REPEAT_3_121(m, d) SEQAN_PP_REPEAT_3_120(m, d) m(4, 120, d) +# define SEQAN_PP_REPEAT_3_122(m, d) SEQAN_PP_REPEAT_3_121(m, d) m(4, 121, d) +# define SEQAN_PP_REPEAT_3_123(m, d) SEQAN_PP_REPEAT_3_122(m, d) m(4, 122, d) +# define SEQAN_PP_REPEAT_3_124(m, d) SEQAN_PP_REPEAT_3_123(m, d) m(4, 123, d) +# define SEQAN_PP_REPEAT_3_125(m, d) SEQAN_PP_REPEAT_3_124(m, d) m(4, 124, d) +# define SEQAN_PP_REPEAT_3_126(m, d) SEQAN_PP_REPEAT_3_125(m, d) m(4, 125, d) +# define SEQAN_PP_REPEAT_3_127(m, d) SEQAN_PP_REPEAT_3_126(m, d) m(4, 126, d) +# define SEQAN_PP_REPEAT_3_128(m, d) SEQAN_PP_REPEAT_3_127(m, d) m(4, 127, d) +# define SEQAN_PP_REPEAT_3_129(m, d) SEQAN_PP_REPEAT_3_128(m, d) m(4, 128, d) +# define SEQAN_PP_REPEAT_3_130(m, d) SEQAN_PP_REPEAT_3_129(m, d) m(4, 129, d) +# define SEQAN_PP_REPEAT_3_131(m, d) SEQAN_PP_REPEAT_3_130(m, d) m(4, 130, d) +# define SEQAN_PP_REPEAT_3_132(m, d) SEQAN_PP_REPEAT_3_131(m, d) m(4, 131, d) +# define SEQAN_PP_REPEAT_3_133(m, d) SEQAN_PP_REPEAT_3_132(m, d) m(4, 132, d) +# define SEQAN_PP_REPEAT_3_134(m, d) SEQAN_PP_REPEAT_3_133(m, d) m(4, 133, d) +# define SEQAN_PP_REPEAT_3_135(m, d) SEQAN_PP_REPEAT_3_134(m, d) m(4, 134, d) +# define SEQAN_PP_REPEAT_3_136(m, d) SEQAN_PP_REPEAT_3_135(m, d) m(4, 135, d) +# define SEQAN_PP_REPEAT_3_137(m, d) SEQAN_PP_REPEAT_3_136(m, d) m(4, 136, d) +# define SEQAN_PP_REPEAT_3_138(m, d) SEQAN_PP_REPEAT_3_137(m, d) m(4, 137, d) +# define SEQAN_PP_REPEAT_3_139(m, d) SEQAN_PP_REPEAT_3_138(m, d) m(4, 138, d) +# define SEQAN_PP_REPEAT_3_140(m, d) SEQAN_PP_REPEAT_3_139(m, d) m(4, 139, d) +# define SEQAN_PP_REPEAT_3_141(m, d) SEQAN_PP_REPEAT_3_140(m, d) m(4, 140, d) +# define SEQAN_PP_REPEAT_3_142(m, d) SEQAN_PP_REPEAT_3_141(m, d) m(4, 141, d) +# define SEQAN_PP_REPEAT_3_143(m, d) SEQAN_PP_REPEAT_3_142(m, d) m(4, 142, d) +# define SEQAN_PP_REPEAT_3_144(m, d) SEQAN_PP_REPEAT_3_143(m, d) m(4, 143, d) +# define SEQAN_PP_REPEAT_3_145(m, d) SEQAN_PP_REPEAT_3_144(m, d) m(4, 144, d) +# define SEQAN_PP_REPEAT_3_146(m, d) SEQAN_PP_REPEAT_3_145(m, d) m(4, 145, d) +# define SEQAN_PP_REPEAT_3_147(m, d) SEQAN_PP_REPEAT_3_146(m, d) m(4, 146, d) +# define SEQAN_PP_REPEAT_3_148(m, d) SEQAN_PP_REPEAT_3_147(m, d) m(4, 147, d) +# define SEQAN_PP_REPEAT_3_149(m, d) SEQAN_PP_REPEAT_3_148(m, d) m(4, 148, d) +# define SEQAN_PP_REPEAT_3_150(m, d) SEQAN_PP_REPEAT_3_149(m, d) m(4, 149, d) +# define SEQAN_PP_REPEAT_3_151(m, d) SEQAN_PP_REPEAT_3_150(m, d) m(4, 150, d) +# define SEQAN_PP_REPEAT_3_152(m, d) SEQAN_PP_REPEAT_3_151(m, d) m(4, 151, d) +# define SEQAN_PP_REPEAT_3_153(m, d) SEQAN_PP_REPEAT_3_152(m, d) m(4, 152, d) +# define SEQAN_PP_REPEAT_3_154(m, d) SEQAN_PP_REPEAT_3_153(m, d) m(4, 153, d) +# define SEQAN_PP_REPEAT_3_155(m, d) SEQAN_PP_REPEAT_3_154(m, d) m(4, 154, d) +# define SEQAN_PP_REPEAT_3_156(m, d) SEQAN_PP_REPEAT_3_155(m, d) m(4, 155, d) +# define SEQAN_PP_REPEAT_3_157(m, d) SEQAN_PP_REPEAT_3_156(m, d) m(4, 156, d) +# define SEQAN_PP_REPEAT_3_158(m, d) SEQAN_PP_REPEAT_3_157(m, d) m(4, 157, d) +# define SEQAN_PP_REPEAT_3_159(m, d) SEQAN_PP_REPEAT_3_158(m, d) m(4, 158, d) +# define SEQAN_PP_REPEAT_3_160(m, d) SEQAN_PP_REPEAT_3_159(m, d) m(4, 159, d) +# define SEQAN_PP_REPEAT_3_161(m, d) SEQAN_PP_REPEAT_3_160(m, d) m(4, 160, d) +# define SEQAN_PP_REPEAT_3_162(m, d) SEQAN_PP_REPEAT_3_161(m, d) m(4, 161, d) +# define SEQAN_PP_REPEAT_3_163(m, d) SEQAN_PP_REPEAT_3_162(m, d) m(4, 162, d) +# define SEQAN_PP_REPEAT_3_164(m, d) SEQAN_PP_REPEAT_3_163(m, d) m(4, 163, d) +# define SEQAN_PP_REPEAT_3_165(m, d) SEQAN_PP_REPEAT_3_164(m, d) m(4, 164, d) +# define SEQAN_PP_REPEAT_3_166(m, d) SEQAN_PP_REPEAT_3_165(m, d) m(4, 165, d) +# define SEQAN_PP_REPEAT_3_167(m, d) SEQAN_PP_REPEAT_3_166(m, d) m(4, 166, d) +# define SEQAN_PP_REPEAT_3_168(m, d) SEQAN_PP_REPEAT_3_167(m, d) m(4, 167, d) +# define SEQAN_PP_REPEAT_3_169(m, d) SEQAN_PP_REPEAT_3_168(m, d) m(4, 168, d) +# define SEQAN_PP_REPEAT_3_170(m, d) SEQAN_PP_REPEAT_3_169(m, d) m(4, 169, d) +# define SEQAN_PP_REPEAT_3_171(m, d) SEQAN_PP_REPEAT_3_170(m, d) m(4, 170, d) +# define SEQAN_PP_REPEAT_3_172(m, d) SEQAN_PP_REPEAT_3_171(m, d) m(4, 171, d) +# define SEQAN_PP_REPEAT_3_173(m, d) SEQAN_PP_REPEAT_3_172(m, d) m(4, 172, d) +# define SEQAN_PP_REPEAT_3_174(m, d) SEQAN_PP_REPEAT_3_173(m, d) m(4, 173, d) +# define SEQAN_PP_REPEAT_3_175(m, d) SEQAN_PP_REPEAT_3_174(m, d) m(4, 174, d) +# define SEQAN_PP_REPEAT_3_176(m, d) SEQAN_PP_REPEAT_3_175(m, d) m(4, 175, d) +# define SEQAN_PP_REPEAT_3_177(m, d) SEQAN_PP_REPEAT_3_176(m, d) m(4, 176, d) +# define SEQAN_PP_REPEAT_3_178(m, d) SEQAN_PP_REPEAT_3_177(m, d) m(4, 177, d) +# define SEQAN_PP_REPEAT_3_179(m, d) SEQAN_PP_REPEAT_3_178(m, d) m(4, 178, d) +# define SEQAN_PP_REPEAT_3_180(m, d) SEQAN_PP_REPEAT_3_179(m, d) m(4, 179, d) +# define SEQAN_PP_REPEAT_3_181(m, d) SEQAN_PP_REPEAT_3_180(m, d) m(4, 180, d) +# define SEQAN_PP_REPEAT_3_182(m, d) SEQAN_PP_REPEAT_3_181(m, d) m(4, 181, d) +# define SEQAN_PP_REPEAT_3_183(m, d) SEQAN_PP_REPEAT_3_182(m, d) m(4, 182, d) +# define SEQAN_PP_REPEAT_3_184(m, d) SEQAN_PP_REPEAT_3_183(m, d) m(4, 183, d) +# define SEQAN_PP_REPEAT_3_185(m, d) SEQAN_PP_REPEAT_3_184(m, d) m(4, 184, d) +# define SEQAN_PP_REPEAT_3_186(m, d) SEQAN_PP_REPEAT_3_185(m, d) m(4, 185, d) +# define SEQAN_PP_REPEAT_3_187(m, d) SEQAN_PP_REPEAT_3_186(m, d) m(4, 186, d) +# define SEQAN_PP_REPEAT_3_188(m, d) SEQAN_PP_REPEAT_3_187(m, d) m(4, 187, d) +# define SEQAN_PP_REPEAT_3_189(m, d) SEQAN_PP_REPEAT_3_188(m, d) m(4, 188, d) +# define SEQAN_PP_REPEAT_3_190(m, d) SEQAN_PP_REPEAT_3_189(m, d) m(4, 189, d) +# define SEQAN_PP_REPEAT_3_191(m, d) SEQAN_PP_REPEAT_3_190(m, d) m(4, 190, d) +# define SEQAN_PP_REPEAT_3_192(m, d) SEQAN_PP_REPEAT_3_191(m, d) m(4, 191, d) +# define SEQAN_PP_REPEAT_3_193(m, d) SEQAN_PP_REPEAT_3_192(m, d) m(4, 192, d) +# define SEQAN_PP_REPEAT_3_194(m, d) SEQAN_PP_REPEAT_3_193(m, d) m(4, 193, d) +# define SEQAN_PP_REPEAT_3_195(m, d) SEQAN_PP_REPEAT_3_194(m, d) m(4, 194, d) +# define SEQAN_PP_REPEAT_3_196(m, d) SEQAN_PP_REPEAT_3_195(m, d) m(4, 195, d) +# define SEQAN_PP_REPEAT_3_197(m, d) SEQAN_PP_REPEAT_3_196(m, d) m(4, 196, d) +# define SEQAN_PP_REPEAT_3_198(m, d) SEQAN_PP_REPEAT_3_197(m, d) m(4, 197, d) +# define SEQAN_PP_REPEAT_3_199(m, d) SEQAN_PP_REPEAT_3_198(m, d) m(4, 198, d) +# define SEQAN_PP_REPEAT_3_200(m, d) SEQAN_PP_REPEAT_3_199(m, d) m(4, 199, d) +# define SEQAN_PP_REPEAT_3_201(m, d) SEQAN_PP_REPEAT_3_200(m, d) m(4, 200, d) +# define SEQAN_PP_REPEAT_3_202(m, d) SEQAN_PP_REPEAT_3_201(m, d) m(4, 201, d) +# define SEQAN_PP_REPEAT_3_203(m, d) SEQAN_PP_REPEAT_3_202(m, d) m(4, 202, d) +# define SEQAN_PP_REPEAT_3_204(m, d) SEQAN_PP_REPEAT_3_203(m, d) m(4, 203, d) +# define SEQAN_PP_REPEAT_3_205(m, d) SEQAN_PP_REPEAT_3_204(m, d) m(4, 204, d) +# define SEQAN_PP_REPEAT_3_206(m, d) SEQAN_PP_REPEAT_3_205(m, d) m(4, 205, d) +# define SEQAN_PP_REPEAT_3_207(m, d) SEQAN_PP_REPEAT_3_206(m, d) m(4, 206, d) +# define SEQAN_PP_REPEAT_3_208(m, d) SEQAN_PP_REPEAT_3_207(m, d) m(4, 207, d) +# define SEQAN_PP_REPEAT_3_209(m, d) SEQAN_PP_REPEAT_3_208(m, d) m(4, 208, d) +# define SEQAN_PP_REPEAT_3_210(m, d) SEQAN_PP_REPEAT_3_209(m, d) m(4, 209, d) +# define SEQAN_PP_REPEAT_3_211(m, d) SEQAN_PP_REPEAT_3_210(m, d) m(4, 210, d) +# define SEQAN_PP_REPEAT_3_212(m, d) SEQAN_PP_REPEAT_3_211(m, d) m(4, 211, d) +# define SEQAN_PP_REPEAT_3_213(m, d) SEQAN_PP_REPEAT_3_212(m, d) m(4, 212, d) +# define SEQAN_PP_REPEAT_3_214(m, d) SEQAN_PP_REPEAT_3_213(m, d) m(4, 213, d) +# define SEQAN_PP_REPEAT_3_215(m, d) SEQAN_PP_REPEAT_3_214(m, d) m(4, 214, d) +# define SEQAN_PP_REPEAT_3_216(m, d) SEQAN_PP_REPEAT_3_215(m, d) m(4, 215, d) +# define SEQAN_PP_REPEAT_3_217(m, d) SEQAN_PP_REPEAT_3_216(m, d) m(4, 216, d) +# define SEQAN_PP_REPEAT_3_218(m, d) SEQAN_PP_REPEAT_3_217(m, d) m(4, 217, d) +# define SEQAN_PP_REPEAT_3_219(m, d) SEQAN_PP_REPEAT_3_218(m, d) m(4, 218, d) +# define SEQAN_PP_REPEAT_3_220(m, d) SEQAN_PP_REPEAT_3_219(m, d) m(4, 219, d) +# define SEQAN_PP_REPEAT_3_221(m, d) SEQAN_PP_REPEAT_3_220(m, d) m(4, 220, d) +# define SEQAN_PP_REPEAT_3_222(m, d) SEQAN_PP_REPEAT_3_221(m, d) m(4, 221, d) +# define SEQAN_PP_REPEAT_3_223(m, d) SEQAN_PP_REPEAT_3_222(m, d) m(4, 222, d) +# define SEQAN_PP_REPEAT_3_224(m, d) SEQAN_PP_REPEAT_3_223(m, d) m(4, 223, d) +# define SEQAN_PP_REPEAT_3_225(m, d) SEQAN_PP_REPEAT_3_224(m, d) m(4, 224, d) +# define SEQAN_PP_REPEAT_3_226(m, d) SEQAN_PP_REPEAT_3_225(m, d) m(4, 225, d) +# define SEQAN_PP_REPEAT_3_227(m, d) SEQAN_PP_REPEAT_3_226(m, d) m(4, 226, d) +# define SEQAN_PP_REPEAT_3_228(m, d) SEQAN_PP_REPEAT_3_227(m, d) m(4, 227, d) +# define SEQAN_PP_REPEAT_3_229(m, d) SEQAN_PP_REPEAT_3_228(m, d) m(4, 228, d) +# define SEQAN_PP_REPEAT_3_230(m, d) SEQAN_PP_REPEAT_3_229(m, d) m(4, 229, d) +# define SEQAN_PP_REPEAT_3_231(m, d) SEQAN_PP_REPEAT_3_230(m, d) m(4, 230, d) +# define SEQAN_PP_REPEAT_3_232(m, d) SEQAN_PP_REPEAT_3_231(m, d) m(4, 231, d) +# define SEQAN_PP_REPEAT_3_233(m, d) SEQAN_PP_REPEAT_3_232(m, d) m(4, 232, d) +# define SEQAN_PP_REPEAT_3_234(m, d) SEQAN_PP_REPEAT_3_233(m, d) m(4, 233, d) +# define SEQAN_PP_REPEAT_3_235(m, d) SEQAN_PP_REPEAT_3_234(m, d) m(4, 234, d) +# define SEQAN_PP_REPEAT_3_236(m, d) SEQAN_PP_REPEAT_3_235(m, d) m(4, 235, d) +# define SEQAN_PP_REPEAT_3_237(m, d) SEQAN_PP_REPEAT_3_236(m, d) m(4, 236, d) +# define SEQAN_PP_REPEAT_3_238(m, d) SEQAN_PP_REPEAT_3_237(m, d) m(4, 237, d) +# define SEQAN_PP_REPEAT_3_239(m, d) SEQAN_PP_REPEAT_3_238(m, d) m(4, 238, d) +# define SEQAN_PP_REPEAT_3_240(m, d) SEQAN_PP_REPEAT_3_239(m, d) m(4, 239, d) +# define SEQAN_PP_REPEAT_3_241(m, d) SEQAN_PP_REPEAT_3_240(m, d) m(4, 240, d) +# define SEQAN_PP_REPEAT_3_242(m, d) SEQAN_PP_REPEAT_3_241(m, d) m(4, 241, d) +# define SEQAN_PP_REPEAT_3_243(m, d) SEQAN_PP_REPEAT_3_242(m, d) m(4, 242, d) +# define SEQAN_PP_REPEAT_3_244(m, d) SEQAN_PP_REPEAT_3_243(m, d) m(4, 243, d) +# define SEQAN_PP_REPEAT_3_245(m, d) SEQAN_PP_REPEAT_3_244(m, d) m(4, 244, d) +# define SEQAN_PP_REPEAT_3_246(m, d) SEQAN_PP_REPEAT_3_245(m, d) m(4, 245, d) +# define SEQAN_PP_REPEAT_3_247(m, d) SEQAN_PP_REPEAT_3_246(m, d) m(4, 246, d) +# define SEQAN_PP_REPEAT_3_248(m, d) SEQAN_PP_REPEAT_3_247(m, d) m(4, 247, d) +# define SEQAN_PP_REPEAT_3_249(m, d) SEQAN_PP_REPEAT_3_248(m, d) m(4, 248, d) +# define SEQAN_PP_REPEAT_3_250(m, d) SEQAN_PP_REPEAT_3_249(m, d) m(4, 249, d) +# define SEQAN_PP_REPEAT_3_251(m, d) SEQAN_PP_REPEAT_3_250(m, d) m(4, 250, d) +# define SEQAN_PP_REPEAT_3_252(m, d) SEQAN_PP_REPEAT_3_251(m, d) m(4, 251, d) +# define SEQAN_PP_REPEAT_3_253(m, d) SEQAN_PP_REPEAT_3_252(m, d) m(4, 252, d) +# define SEQAN_PP_REPEAT_3_254(m, d) SEQAN_PP_REPEAT_3_253(m, d) m(4, 253, d) +# define SEQAN_PP_REPEAT_3_255(m, d) SEQAN_PP_REPEAT_3_254(m, d) m(4, 254, d) +# define SEQAN_PP_REPEAT_3_256(m, d) SEQAN_PP_REPEAT_3_255(m, d) m(4, 255, d) +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/repetition/for.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_REPETITION_FOR_HPP +// # define SEQAN_PREPROCESSOR_REPETITION_FOR_HPP +# +// # include +// # include +// # include +# +# /* SEQAN_PP_FOR */ +# +// # if 0 +// # define SEQAN_PP_FOR(state, pred, op, macro) +// # endif +# +# define SEQAN_PP_FOR SEQAN_PP_CAT(SEQAN_PP_FOR_, SEQAN_PP_AUTO_REC(SEQAN_PP_FOR_P, 256)) +# +# define SEQAN_PP_FOR_P(n) SEQAN_PP_CAT(SEQAN_PP_FOR_CHECK_, SEQAN_PP_FOR_ ## n(1, SEQAN_PP_FOR_SR_P, SEQAN_PP_FOR_SR_O, SEQAN_PP_FOR_SR_M)) +# +# define SEQAN_PP_FOR_SR_P(r, s) s +# define SEQAN_PP_FOR_SR_O(r, s) 0 +# define SEQAN_PP_FOR_SR_M(r, s) SEQAN_PP_NIL +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +// # include +// # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +// # include +// # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_DMC() +// # include +// # else +// # include +// # endif +# +# define SEQAN_PP_FOR_257(s, p, o, m) SEQAN_PP_ERROR(0x0002) +# +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_NIL 1 +# +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_1(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_2(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_3(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_4(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_5(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_6(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_7(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_8(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_9(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_10(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_11(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_12(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_13(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_14(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_15(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_16(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_17(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_18(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_19(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_20(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_21(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_22(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_23(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_24(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_25(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_26(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_27(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_28(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_29(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_30(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_31(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_32(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_33(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_34(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_35(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_36(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_37(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_38(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_39(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_40(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_41(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_42(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_43(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_44(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_45(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_46(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_47(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_48(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_49(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_50(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_51(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_52(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_53(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_54(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_55(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_56(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_57(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_58(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_59(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_60(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_61(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_62(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_63(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_64(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_65(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_66(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_67(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_68(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_69(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_70(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_71(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_72(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_73(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_74(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_75(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_76(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_77(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_78(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_79(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_80(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_81(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_82(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_83(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_84(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_85(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_86(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_87(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_88(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_89(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_90(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_91(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_92(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_93(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_94(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_95(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_96(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_97(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_98(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_99(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_100(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_101(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_102(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_103(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_104(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_105(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_106(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_107(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_108(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_109(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_110(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_111(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_112(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_113(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_114(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_115(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_116(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_117(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_118(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_119(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_120(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_121(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_122(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_123(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_124(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_125(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_126(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_127(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_128(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_129(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_130(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_131(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_132(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_133(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_134(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_135(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_136(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_137(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_138(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_139(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_140(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_141(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_142(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_143(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_144(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_145(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_146(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_147(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_148(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_149(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_150(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_151(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_152(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_153(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_154(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_155(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_156(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_157(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_158(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_159(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_160(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_161(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_162(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_163(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_164(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_165(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_166(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_167(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_168(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_169(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_170(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_171(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_172(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_173(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_174(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_175(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_176(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_177(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_178(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_179(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_180(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_181(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_182(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_183(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_184(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_185(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_186(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_187(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_188(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_189(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_190(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_191(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_192(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_193(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_194(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_195(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_196(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_197(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_198(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_199(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_200(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_201(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_202(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_203(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_204(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_205(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_206(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_207(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_208(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_209(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_210(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_211(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_212(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_213(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_214(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_215(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_216(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_217(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_218(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_219(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_220(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_221(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_222(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_223(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_224(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_225(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_226(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_227(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_228(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_229(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_230(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_231(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_232(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_233(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_234(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_235(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_236(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_237(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_238(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_239(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_240(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_241(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_242(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_243(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_244(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_245(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_246(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_247(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_248(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_249(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_250(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_251(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_252(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_253(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_254(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_255(s, p, o, m) 0 +# define SEQAN_PP_FOR_CHECK_SEQAN_PP_FOR_256(s, p, o, m) 0 + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/facilities/empty.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_FACILITIES_EMPTY_HPP +// # define SEQAN_PREPROCESSOR_FACILITIES_EMPTY_HPP +# +# /* SEQAN_PP_EMPTY */ +# +# define SEQAN_PP_EMPTY() +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/seq/elem.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_SEQ_ELEM_HPP +// # define SEQAN_PREPROCESSOR_SEQ_ELEM_HPP +# +// # include +// # include +// # include +# +# /* SEQAN_PP_SEQ_ELEM */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_SEQ_ELEM(i, seq) SEQAN_PP_SEQ_ELEM_I(i, seq) +// # else +// # define SEQAN_PP_SEQ_ELEM(i, seq) SEQAN_PP_SEQ_ELEM_I((i, seq)) +// # endif +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +#ifdef STDLIB_VS +# define SEQAN_PP_SEQ_ELEM_I(i, seq) SEQAN_PP_SEQ_ELEM_II((SEQAN_PP_SEQ_ELEM_ ## i seq)) +# define SEQAN_PP_SEQ_ELEM_II(res) SEQAN_PP_SEQ_ELEM_IV(SEQAN_PP_SEQ_ELEM_III res) +# define SEQAN_PP_SEQ_ELEM_III(x, _) x SEQAN_PP_EMPTY() +# define SEQAN_PP_SEQ_ELEM_IV(x) x +// # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +// # define SEQAN_PP_SEQ_ELEM_I(par) SEQAN_PP_SEQ_ELEM_II ## par +// # define SEQAN_PP_SEQ_ELEM_II(i, seq) SEQAN_PP_SEQ_ELEM_III(SEQAN_PP_SEQ_ELEM_ ## i ## seq) +// # define SEQAN_PP_SEQ_ELEM_III(im) SEQAN_PP_SEQ_ELEM_IV(im) +// # define SEQAN_PP_SEQ_ELEM_IV(x, _) x +# else // #ifdef STDLIB_VS +// # if defined(__IBMC__) || defined(__IBMCPP__) +// # define SEQAN_PP_SEQ_ELEM_I(i, seq) SEQAN_PP_SEQ_ELEM_II(SEQAN_PP_CAT(SEQAN_PP_SEQ_ELEM_ ## i, seq)) +// # else +# define SEQAN_PP_SEQ_ELEM_I(i, seq) SEQAN_PP_SEQ_ELEM_II(SEQAN_PP_SEQ_ELEM_ ## i seq) +// # endif +# define SEQAN_PP_SEQ_ELEM_II(im) SEQAN_PP_SEQ_ELEM_III(im) +# define SEQAN_PP_SEQ_ELEM_III(x, _) x +# endif // #ifdef STDLIB_VS +# +# define SEQAN_PP_SEQ_ELEM_0(x) x, SEQAN_PP_NIL +# define SEQAN_PP_SEQ_ELEM_1(_) SEQAN_PP_SEQ_ELEM_0 +# define SEQAN_PP_SEQ_ELEM_2(_) SEQAN_PP_SEQ_ELEM_1 +# define SEQAN_PP_SEQ_ELEM_3(_) SEQAN_PP_SEQ_ELEM_2 +# define SEQAN_PP_SEQ_ELEM_4(_) SEQAN_PP_SEQ_ELEM_3 +# define SEQAN_PP_SEQ_ELEM_5(_) SEQAN_PP_SEQ_ELEM_4 +# define SEQAN_PP_SEQ_ELEM_6(_) SEQAN_PP_SEQ_ELEM_5 +# define SEQAN_PP_SEQ_ELEM_7(_) SEQAN_PP_SEQ_ELEM_6 +# define SEQAN_PP_SEQ_ELEM_8(_) SEQAN_PP_SEQ_ELEM_7 +# define SEQAN_PP_SEQ_ELEM_9(_) SEQAN_PP_SEQ_ELEM_8 +# define SEQAN_PP_SEQ_ELEM_10(_) SEQAN_PP_SEQ_ELEM_9 +# define SEQAN_PP_SEQ_ELEM_11(_) SEQAN_PP_SEQ_ELEM_10 +# define SEQAN_PP_SEQ_ELEM_12(_) SEQAN_PP_SEQ_ELEM_11 +# define SEQAN_PP_SEQ_ELEM_13(_) SEQAN_PP_SEQ_ELEM_12 +# define SEQAN_PP_SEQ_ELEM_14(_) SEQAN_PP_SEQ_ELEM_13 +# define SEQAN_PP_SEQ_ELEM_15(_) SEQAN_PP_SEQ_ELEM_14 +# define SEQAN_PP_SEQ_ELEM_16(_) SEQAN_PP_SEQ_ELEM_15 +# define SEQAN_PP_SEQ_ELEM_17(_) SEQAN_PP_SEQ_ELEM_16 +# define SEQAN_PP_SEQ_ELEM_18(_) SEQAN_PP_SEQ_ELEM_17 +# define SEQAN_PP_SEQ_ELEM_19(_) SEQAN_PP_SEQ_ELEM_18 +# define SEQAN_PP_SEQ_ELEM_20(_) SEQAN_PP_SEQ_ELEM_19 +# define SEQAN_PP_SEQ_ELEM_21(_) SEQAN_PP_SEQ_ELEM_20 +# define SEQAN_PP_SEQ_ELEM_22(_) SEQAN_PP_SEQ_ELEM_21 +# define SEQAN_PP_SEQ_ELEM_23(_) SEQAN_PP_SEQ_ELEM_22 +# define SEQAN_PP_SEQ_ELEM_24(_) SEQAN_PP_SEQ_ELEM_23 +# define SEQAN_PP_SEQ_ELEM_25(_) SEQAN_PP_SEQ_ELEM_24 +# define SEQAN_PP_SEQ_ELEM_26(_) SEQAN_PP_SEQ_ELEM_25 +# define SEQAN_PP_SEQ_ELEM_27(_) SEQAN_PP_SEQ_ELEM_26 +# define SEQAN_PP_SEQ_ELEM_28(_) SEQAN_PP_SEQ_ELEM_27 +# define SEQAN_PP_SEQ_ELEM_29(_) SEQAN_PP_SEQ_ELEM_28 +# define SEQAN_PP_SEQ_ELEM_30(_) SEQAN_PP_SEQ_ELEM_29 +# define SEQAN_PP_SEQ_ELEM_31(_) SEQAN_PP_SEQ_ELEM_30 +# define SEQAN_PP_SEQ_ELEM_32(_) SEQAN_PP_SEQ_ELEM_31 +# define SEQAN_PP_SEQ_ELEM_33(_) SEQAN_PP_SEQ_ELEM_32 +# define SEQAN_PP_SEQ_ELEM_34(_) SEQAN_PP_SEQ_ELEM_33 +# define SEQAN_PP_SEQ_ELEM_35(_) SEQAN_PP_SEQ_ELEM_34 +# define SEQAN_PP_SEQ_ELEM_36(_) SEQAN_PP_SEQ_ELEM_35 +# define SEQAN_PP_SEQ_ELEM_37(_) SEQAN_PP_SEQ_ELEM_36 +# define SEQAN_PP_SEQ_ELEM_38(_) SEQAN_PP_SEQ_ELEM_37 +# define SEQAN_PP_SEQ_ELEM_39(_) SEQAN_PP_SEQ_ELEM_38 +# define SEQAN_PP_SEQ_ELEM_40(_) SEQAN_PP_SEQ_ELEM_39 +# define SEQAN_PP_SEQ_ELEM_41(_) SEQAN_PP_SEQ_ELEM_40 +# define SEQAN_PP_SEQ_ELEM_42(_) SEQAN_PP_SEQ_ELEM_41 +# define SEQAN_PP_SEQ_ELEM_43(_) SEQAN_PP_SEQ_ELEM_42 +# define SEQAN_PP_SEQ_ELEM_44(_) SEQAN_PP_SEQ_ELEM_43 +# define SEQAN_PP_SEQ_ELEM_45(_) SEQAN_PP_SEQ_ELEM_44 +# define SEQAN_PP_SEQ_ELEM_46(_) SEQAN_PP_SEQ_ELEM_45 +# define SEQAN_PP_SEQ_ELEM_47(_) SEQAN_PP_SEQ_ELEM_46 +# define SEQAN_PP_SEQ_ELEM_48(_) SEQAN_PP_SEQ_ELEM_47 +# define SEQAN_PP_SEQ_ELEM_49(_) SEQAN_PP_SEQ_ELEM_48 +# define SEQAN_PP_SEQ_ELEM_50(_) SEQAN_PP_SEQ_ELEM_49 +# define SEQAN_PP_SEQ_ELEM_51(_) SEQAN_PP_SEQ_ELEM_50 +# define SEQAN_PP_SEQ_ELEM_52(_) SEQAN_PP_SEQ_ELEM_51 +# define SEQAN_PP_SEQ_ELEM_53(_) SEQAN_PP_SEQ_ELEM_52 + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/seq/seq.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_SEQ_SEQ_HPP +// # define SEQAN_PREPROCESSOR_SEQ_SEQ_HPP +# +// # include +// # include +# +# /* SEQAN_PP_SEQ_HEAD */ +# +# define SEQAN_PP_SEQ_HEAD(seq) SEQAN_PP_SEQ_ELEM(0, seq) +# +# /* SEQAN_PP_SEQ_TAIL */ +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +// # define SEQAN_PP_SEQ_TAIL(seq) SEQAN_PP_SEQ_TAIL_1((seq)) +// # define SEQAN_PP_SEQ_TAIL_1(par) SEQAN_PP_SEQ_TAIL_2 ## par +// # define SEQAN_PP_SEQ_TAIL_2(seq) SEQAN_PP_SEQ_TAIL_I ## seq +// # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MSVC() +#ifdef STDLIB_VS +# define SEQAN_PP_SEQ_TAIL(seq) SEQAN_PP_SEQ_TAIL_ID(SEQAN_PP_SEQ_TAIL_I seq) +# define SEQAN_PP_SEQ_TAIL_ID(id) id +// # elif SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +// # define SEQAN_PP_SEQ_TAIL(seq) SEQAN_PP_SEQ_TAIL_D(seq) +// # define SEQAN_PP_SEQ_TAIL_D(seq) SEQAN_PP_SEQ_TAIL_I seq +# else // #ifdef STDLIB_VS +# define SEQAN_PP_SEQ_TAIL(seq) SEQAN_PP_SEQ_TAIL_I seq +# endif // #ifdef STDLIB_VS +# +# define SEQAN_PP_SEQ_TAIL_I(x) +# +# /* SEQAN_PP_SEQ_NIL */ +# +# define SEQAN_PP_SEQ_NIL(x) (x) +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/arithmetic/inc.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_ARITHMETIC_INC_HPP +//# define SEQAN_PREPROCESSOR_ARITHMETIC_INC_HPP +# +//# include +# +# /* SEQAN_PP_INC */ +# +//# if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_INC(x) SEQAN_PP_INC_I(x) +//# else +//# define SEQAN_PP_INC(x) SEQAN_PP_INC_OO((x)) +//# define SEQAN_PP_INC_OO(par) SEQAN_PP_INC_I ## par +//# endif +# +# define SEQAN_PP_INC_I(x) SEQAN_PP_INC_ ## x +# +# define SEQAN_PP_INC_0 1 +# define SEQAN_PP_INC_1 2 +# define SEQAN_PP_INC_2 3 +# define SEQAN_PP_INC_3 4 +# define SEQAN_PP_INC_4 5 +# define SEQAN_PP_INC_5 6 +# define SEQAN_PP_INC_6 7 +# define SEQAN_PP_INC_7 8 +# define SEQAN_PP_INC_8 9 +# define SEQAN_PP_INC_9 10 +# define SEQAN_PP_INC_10 11 +# define SEQAN_PP_INC_11 12 +# define SEQAN_PP_INC_12 13 +# define SEQAN_PP_INC_13 14 +# define SEQAN_PP_INC_14 15 +# define SEQAN_PP_INC_15 16 +# define SEQAN_PP_INC_16 17 +# define SEQAN_PP_INC_17 18 +# define SEQAN_PP_INC_18 19 +# define SEQAN_PP_INC_19 20 +# define SEQAN_PP_INC_20 21 +# define SEQAN_PP_INC_21 22 +# define SEQAN_PP_INC_22 23 +# define SEQAN_PP_INC_23 24 +# define SEQAN_PP_INC_24 25 +# define SEQAN_PP_INC_25 26 +# define SEQAN_PP_INC_26 27 +# define SEQAN_PP_INC_27 28 +# define SEQAN_PP_INC_28 29 +# define SEQAN_PP_INC_29 30 +# define SEQAN_PP_INC_30 31 +# define SEQAN_PP_INC_31 32 +# define SEQAN_PP_INC_32 33 +# define SEQAN_PP_INC_33 34 +# define SEQAN_PP_INC_34 35 +# define SEQAN_PP_INC_35 36 +# define SEQAN_PP_INC_36 37 +# define SEQAN_PP_INC_37 38 +# define SEQAN_PP_INC_38 39 +# define SEQAN_PP_INC_39 40 +# define SEQAN_PP_INC_40 41 +# define SEQAN_PP_INC_41 42 +# define SEQAN_PP_INC_42 43 +# define SEQAN_PP_INC_43 44 +# define SEQAN_PP_INC_44 45 +# define SEQAN_PP_INC_45 46 +# define SEQAN_PP_INC_46 47 +# define SEQAN_PP_INC_47 48 +# define SEQAN_PP_INC_48 49 +# define SEQAN_PP_INC_49 50 +# define SEQAN_PP_INC_50 51 +# define SEQAN_PP_INC_51 52 +# define SEQAN_PP_INC_52 53 +# define SEQAN_PP_INC_53 54 +# define SEQAN_PP_INC_54 55 +# define SEQAN_PP_INC_55 56 +# define SEQAN_PP_INC_56 57 +# define SEQAN_PP_INC_57 58 +# define SEQAN_PP_INC_58 59 +# define SEQAN_PP_INC_59 60 +# define SEQAN_PP_INC_60 61 +# define SEQAN_PP_INC_61 62 +# define SEQAN_PP_INC_62 63 +# define SEQAN_PP_INC_63 64 +# define SEQAN_PP_INC_64 65 +# define SEQAN_PP_INC_65 66 +# define SEQAN_PP_INC_66 67 +# define SEQAN_PP_INC_67 68 +# define SEQAN_PP_INC_68 69 +# define SEQAN_PP_INC_69 70 +# define SEQAN_PP_INC_70 71 +# define SEQAN_PP_INC_71 72 +# define SEQAN_PP_INC_72 73 +# define SEQAN_PP_INC_73 74 +# define SEQAN_PP_INC_74 75 +# define SEQAN_PP_INC_75 76 +# define SEQAN_PP_INC_76 77 +# define SEQAN_PP_INC_77 78 +# define SEQAN_PP_INC_78 79 +# define SEQAN_PP_INC_79 80 +# define SEQAN_PP_INC_80 81 +# define SEQAN_PP_INC_81 82 +# define SEQAN_PP_INC_82 83 +# define SEQAN_PP_INC_83 84 +# define SEQAN_PP_INC_84 85 +# define SEQAN_PP_INC_85 86 +# define SEQAN_PP_INC_86 87 +# define SEQAN_PP_INC_87 88 +# define SEQAN_PP_INC_88 89 +# define SEQAN_PP_INC_89 90 +# define SEQAN_PP_INC_90 91 +# define SEQAN_PP_INC_91 92 +# define SEQAN_PP_INC_92 93 +# define SEQAN_PP_INC_93 94 +# define SEQAN_PP_INC_94 95 +# define SEQAN_PP_INC_95 96 +# define SEQAN_PP_INC_96 97 +# define SEQAN_PP_INC_97 98 +# define SEQAN_PP_INC_98 99 +# define SEQAN_PP_INC_99 100 +# define SEQAN_PP_INC_100 101 +# define SEQAN_PP_INC_101 102 +# define SEQAN_PP_INC_102 103 +# define SEQAN_PP_INC_103 104 +# define SEQAN_PP_INC_104 105 +# define SEQAN_PP_INC_105 106 +# define SEQAN_PP_INC_106 107 +# define SEQAN_PP_INC_107 108 +# define SEQAN_PP_INC_108 109 +# define SEQAN_PP_INC_109 110 +# define SEQAN_PP_INC_110 111 +# define SEQAN_PP_INC_111 112 +# define SEQAN_PP_INC_112 113 +# define SEQAN_PP_INC_113 114 +# define SEQAN_PP_INC_114 115 +# define SEQAN_PP_INC_115 116 +# define SEQAN_PP_INC_116 117 +# define SEQAN_PP_INC_117 118 +# define SEQAN_PP_INC_118 119 +# define SEQAN_PP_INC_119 120 +# define SEQAN_PP_INC_120 121 +# define SEQAN_PP_INC_121 122 +# define SEQAN_PP_INC_122 123 +# define SEQAN_PP_INC_123 124 +# define SEQAN_PP_INC_124 125 +# define SEQAN_PP_INC_125 126 +# define SEQAN_PP_INC_126 127 +# define SEQAN_PP_INC_127 128 +# define SEQAN_PP_INC_128 129 +# define SEQAN_PP_INC_129 130 +# define SEQAN_PP_INC_130 131 +# define SEQAN_PP_INC_131 132 +# define SEQAN_PP_INC_132 133 +# define SEQAN_PP_INC_133 134 +# define SEQAN_PP_INC_134 135 +# define SEQAN_PP_INC_135 136 +# define SEQAN_PP_INC_136 137 +# define SEQAN_PP_INC_137 138 +# define SEQAN_PP_INC_138 139 +# define SEQAN_PP_INC_139 140 +# define SEQAN_PP_INC_140 141 +# define SEQAN_PP_INC_141 142 +# define SEQAN_PP_INC_142 143 +# define SEQAN_PP_INC_143 144 +# define SEQAN_PP_INC_144 145 +# define SEQAN_PP_INC_145 146 +# define SEQAN_PP_INC_146 147 +# define SEQAN_PP_INC_147 148 +# define SEQAN_PP_INC_148 149 +# define SEQAN_PP_INC_149 150 +# define SEQAN_PP_INC_150 151 +# define SEQAN_PP_INC_151 152 +# define SEQAN_PP_INC_152 153 +# define SEQAN_PP_INC_153 154 +# define SEQAN_PP_INC_154 155 +# define SEQAN_PP_INC_155 156 +# define SEQAN_PP_INC_156 157 +# define SEQAN_PP_INC_157 158 +# define SEQAN_PP_INC_158 159 +# define SEQAN_PP_INC_159 160 +# define SEQAN_PP_INC_160 161 +# define SEQAN_PP_INC_161 162 +# define SEQAN_PP_INC_162 163 +# define SEQAN_PP_INC_163 164 +# define SEQAN_PP_INC_164 165 +# define SEQAN_PP_INC_165 166 +# define SEQAN_PP_INC_166 167 +# define SEQAN_PP_INC_167 168 +# define SEQAN_PP_INC_168 169 +# define SEQAN_PP_INC_169 170 +# define SEQAN_PP_INC_170 171 +# define SEQAN_PP_INC_171 172 +# define SEQAN_PP_INC_172 173 +# define SEQAN_PP_INC_173 174 +# define SEQAN_PP_INC_174 175 +# define SEQAN_PP_INC_175 176 +# define SEQAN_PP_INC_176 177 +# define SEQAN_PP_INC_177 178 +# define SEQAN_PP_INC_178 179 +# define SEQAN_PP_INC_179 180 +# define SEQAN_PP_INC_180 181 +# define SEQAN_PP_INC_181 182 +# define SEQAN_PP_INC_182 183 +# define SEQAN_PP_INC_183 184 +# define SEQAN_PP_INC_184 185 +# define SEQAN_PP_INC_185 186 +# define SEQAN_PP_INC_186 187 +# define SEQAN_PP_INC_187 188 +# define SEQAN_PP_INC_188 189 +# define SEQAN_PP_INC_189 190 +# define SEQAN_PP_INC_190 191 +# define SEQAN_PP_INC_191 192 +# define SEQAN_PP_INC_192 193 +# define SEQAN_PP_INC_193 194 +# define SEQAN_PP_INC_194 195 +# define SEQAN_PP_INC_195 196 +# define SEQAN_PP_INC_196 197 +# define SEQAN_PP_INC_197 198 +# define SEQAN_PP_INC_198 199 +# define SEQAN_PP_INC_199 200 +# define SEQAN_PP_INC_200 201 +# define SEQAN_PP_INC_201 202 +# define SEQAN_PP_INC_202 203 +# define SEQAN_PP_INC_203 204 +# define SEQAN_PP_INC_204 205 +# define SEQAN_PP_INC_205 206 +# define SEQAN_PP_INC_206 207 +# define SEQAN_PP_INC_207 208 +# define SEQAN_PP_INC_208 209 +# define SEQAN_PP_INC_209 210 +# define SEQAN_PP_INC_210 211 +# define SEQAN_PP_INC_211 212 +# define SEQAN_PP_INC_212 213 +# define SEQAN_PP_INC_213 214 +# define SEQAN_PP_INC_214 215 +# define SEQAN_PP_INC_215 216 +# define SEQAN_PP_INC_216 217 +# define SEQAN_PP_INC_217 218 +# define SEQAN_PP_INC_218 219 +# define SEQAN_PP_INC_219 220 +# define SEQAN_PP_INC_220 221 +# define SEQAN_PP_INC_221 222 +# define SEQAN_PP_INC_222 223 +# define SEQAN_PP_INC_223 224 +# define SEQAN_PP_INC_224 225 +# define SEQAN_PP_INC_225 226 +# define SEQAN_PP_INC_226 227 +# define SEQAN_PP_INC_227 228 +# define SEQAN_PP_INC_228 229 +# define SEQAN_PP_INC_229 230 +# define SEQAN_PP_INC_230 231 +# define SEQAN_PP_INC_231 232 +# define SEQAN_PP_INC_232 233 +# define SEQAN_PP_INC_233 234 +# define SEQAN_PP_INC_234 235 +# define SEQAN_PP_INC_235 236 +# define SEQAN_PP_INC_236 237 +# define SEQAN_PP_INC_237 238 +# define SEQAN_PP_INC_238 239 +# define SEQAN_PP_INC_239 240 +# define SEQAN_PP_INC_240 241 +# define SEQAN_PP_INC_241 242 +# define SEQAN_PP_INC_242 243 +# define SEQAN_PP_INC_243 244 +# define SEQAN_PP_INC_244 245 +# define SEQAN_PP_INC_245 246 +# define SEQAN_PP_INC_246 247 +# define SEQAN_PP_INC_247 248 +# define SEQAN_PP_INC_248 249 +# define SEQAN_PP_INC_249 250 +# define SEQAN_PP_INC_250 251 +# define SEQAN_PP_INC_251 252 +# define SEQAN_PP_INC_252 253 +# define SEQAN_PP_INC_253 254 +# define SEQAN_PP_INC_254 255 +# define SEQAN_PP_INC_255 256 +# define SEQAN_PP_INC_256 256 +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/arithmetic/dec.hpp <== +// -------------------------------------------------------------------------- + +# /* Copyright (C) 2001 +# * Housemarque Oy +# * http://www.housemarque.com +# * +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# */ +# +# /* Revised by Paul Mensonides (2002) */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_ARITHMETIC_DEC_HPP +// # define SEQAN_PREPROCESSOR_ARITHMETIC_DEC_HPP +# +// # include +# +# /* SEQAN_PP_DEC */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_MWCC() +# define SEQAN_PP_DEC(x) SEQAN_PP_DEC_I(x) +// # else +// # define SEQAN_PP_DEC(x) SEQAN_PP_DEC_OO((x)) +// # define SEQAN_PP_DEC_OO(par) SEQAN_PP_DEC_I ## par +// # endif +# +# define SEQAN_PP_DEC_I(x) SEQAN_PP_DEC_ ## x +# +# define SEQAN_PP_DEC_0 0 +# define SEQAN_PP_DEC_1 0 +# define SEQAN_PP_DEC_2 1 +# define SEQAN_PP_DEC_3 2 +# define SEQAN_PP_DEC_4 3 +# define SEQAN_PP_DEC_5 4 +# define SEQAN_PP_DEC_6 5 +# define SEQAN_PP_DEC_7 6 +# define SEQAN_PP_DEC_8 7 +# define SEQAN_PP_DEC_9 8 +# define SEQAN_PP_DEC_10 9 +# define SEQAN_PP_DEC_11 10 +# define SEQAN_PP_DEC_12 11 +# define SEQAN_PP_DEC_13 12 +# define SEQAN_PP_DEC_14 13 +# define SEQAN_PP_DEC_15 14 +# define SEQAN_PP_DEC_16 15 +# define SEQAN_PP_DEC_17 16 +# define SEQAN_PP_DEC_18 17 +# define SEQAN_PP_DEC_19 18 +# define SEQAN_PP_DEC_20 19 +# define SEQAN_PP_DEC_21 20 +# define SEQAN_PP_DEC_22 21 +# define SEQAN_PP_DEC_23 22 +# define SEQAN_PP_DEC_24 23 +# define SEQAN_PP_DEC_25 24 +# define SEQAN_PP_DEC_26 25 +# define SEQAN_PP_DEC_27 26 +# define SEQAN_PP_DEC_28 27 +# define SEQAN_PP_DEC_29 28 +# define SEQAN_PP_DEC_30 29 +# define SEQAN_PP_DEC_31 30 +# define SEQAN_PP_DEC_32 31 +# define SEQAN_PP_DEC_33 32 +# define SEQAN_PP_DEC_34 33 +# define SEQAN_PP_DEC_35 34 +# define SEQAN_PP_DEC_36 35 +# define SEQAN_PP_DEC_37 36 +# define SEQAN_PP_DEC_38 37 +# define SEQAN_PP_DEC_39 38 +# define SEQAN_PP_DEC_40 39 +# define SEQAN_PP_DEC_41 40 +# define SEQAN_PP_DEC_42 41 +# define SEQAN_PP_DEC_43 42 +# define SEQAN_PP_DEC_44 43 +# define SEQAN_PP_DEC_45 44 +# define SEQAN_PP_DEC_46 45 +# define SEQAN_PP_DEC_47 46 +# define SEQAN_PP_DEC_48 47 +# define SEQAN_PP_DEC_49 48 +# define SEQAN_PP_DEC_50 49 +# define SEQAN_PP_DEC_51 50 +# define SEQAN_PP_DEC_52 51 +# define SEQAN_PP_DEC_53 52 +# define SEQAN_PP_DEC_54 53 +# define SEQAN_PP_DEC_55 54 +# define SEQAN_PP_DEC_56 55 +# define SEQAN_PP_DEC_57 56 +# define SEQAN_PP_DEC_58 57 +# define SEQAN_PP_DEC_59 58 +# define SEQAN_PP_DEC_60 59 +# define SEQAN_PP_DEC_61 60 +# define SEQAN_PP_DEC_62 61 +# define SEQAN_PP_DEC_63 62 +# define SEQAN_PP_DEC_64 63 +# define SEQAN_PP_DEC_65 64 +# define SEQAN_PP_DEC_66 65 +# define SEQAN_PP_DEC_67 66 +# define SEQAN_PP_DEC_68 67 +# define SEQAN_PP_DEC_69 68 +# define SEQAN_PP_DEC_70 69 +# define SEQAN_PP_DEC_71 70 +# define SEQAN_PP_DEC_72 71 +# define SEQAN_PP_DEC_73 72 +# define SEQAN_PP_DEC_74 73 +# define SEQAN_PP_DEC_75 74 +# define SEQAN_PP_DEC_76 75 +# define SEQAN_PP_DEC_77 76 +# define SEQAN_PP_DEC_78 77 +# define SEQAN_PP_DEC_79 78 +# define SEQAN_PP_DEC_80 79 +# define SEQAN_PP_DEC_81 80 +# define SEQAN_PP_DEC_82 81 +# define SEQAN_PP_DEC_83 82 +# define SEQAN_PP_DEC_84 83 +# define SEQAN_PP_DEC_85 84 +# define SEQAN_PP_DEC_86 85 +# define SEQAN_PP_DEC_87 86 +# define SEQAN_PP_DEC_88 87 +# define SEQAN_PP_DEC_89 88 +# define SEQAN_PP_DEC_90 89 +# define SEQAN_PP_DEC_91 90 +# define SEQAN_PP_DEC_92 91 +# define SEQAN_PP_DEC_93 92 +# define SEQAN_PP_DEC_94 93 +# define SEQAN_PP_DEC_95 94 +# define SEQAN_PP_DEC_96 95 +# define SEQAN_PP_DEC_97 96 +# define SEQAN_PP_DEC_98 97 +# define SEQAN_PP_DEC_99 98 +# define SEQAN_PP_DEC_100 99 +# define SEQAN_PP_DEC_101 100 +# define SEQAN_PP_DEC_102 101 +# define SEQAN_PP_DEC_103 102 +# define SEQAN_PP_DEC_104 103 +# define SEQAN_PP_DEC_105 104 +# define SEQAN_PP_DEC_106 105 +# define SEQAN_PP_DEC_107 106 +# define SEQAN_PP_DEC_108 107 +# define SEQAN_PP_DEC_109 108 +# define SEQAN_PP_DEC_110 109 +# define SEQAN_PP_DEC_111 110 +# define SEQAN_PP_DEC_112 111 +# define SEQAN_PP_DEC_113 112 +# define SEQAN_PP_DEC_114 113 +# define SEQAN_PP_DEC_115 114 +# define SEQAN_PP_DEC_116 115 +# define SEQAN_PP_DEC_117 116 +# define SEQAN_PP_DEC_118 117 +# define SEQAN_PP_DEC_119 118 +# define SEQAN_PP_DEC_120 119 +# define SEQAN_PP_DEC_121 120 +# define SEQAN_PP_DEC_122 121 +# define SEQAN_PP_DEC_123 122 +# define SEQAN_PP_DEC_124 123 +# define SEQAN_PP_DEC_125 124 +# define SEQAN_PP_DEC_126 125 +# define SEQAN_PP_DEC_127 126 +# define SEQAN_PP_DEC_128 127 +# define SEQAN_PP_DEC_129 128 +# define SEQAN_PP_DEC_130 129 +# define SEQAN_PP_DEC_131 130 +# define SEQAN_PP_DEC_132 131 +# define SEQAN_PP_DEC_133 132 +# define SEQAN_PP_DEC_134 133 +# define SEQAN_PP_DEC_135 134 +# define SEQAN_PP_DEC_136 135 +# define SEQAN_PP_DEC_137 136 +# define SEQAN_PP_DEC_138 137 +# define SEQAN_PP_DEC_139 138 +# define SEQAN_PP_DEC_140 139 +# define SEQAN_PP_DEC_141 140 +# define SEQAN_PP_DEC_142 141 +# define SEQAN_PP_DEC_143 142 +# define SEQAN_PP_DEC_144 143 +# define SEQAN_PP_DEC_145 144 +# define SEQAN_PP_DEC_146 145 +# define SEQAN_PP_DEC_147 146 +# define SEQAN_PP_DEC_148 147 +# define SEQAN_PP_DEC_149 148 +# define SEQAN_PP_DEC_150 149 +# define SEQAN_PP_DEC_151 150 +# define SEQAN_PP_DEC_152 151 +# define SEQAN_PP_DEC_153 152 +# define SEQAN_PP_DEC_154 153 +# define SEQAN_PP_DEC_155 154 +# define SEQAN_PP_DEC_156 155 +# define SEQAN_PP_DEC_157 156 +# define SEQAN_PP_DEC_158 157 +# define SEQAN_PP_DEC_159 158 +# define SEQAN_PP_DEC_160 159 +# define SEQAN_PP_DEC_161 160 +# define SEQAN_PP_DEC_162 161 +# define SEQAN_PP_DEC_163 162 +# define SEQAN_PP_DEC_164 163 +# define SEQAN_PP_DEC_165 164 +# define SEQAN_PP_DEC_166 165 +# define SEQAN_PP_DEC_167 166 +# define SEQAN_PP_DEC_168 167 +# define SEQAN_PP_DEC_169 168 +# define SEQAN_PP_DEC_170 169 +# define SEQAN_PP_DEC_171 170 +# define SEQAN_PP_DEC_172 171 +# define SEQAN_PP_DEC_173 172 +# define SEQAN_PP_DEC_174 173 +# define SEQAN_PP_DEC_175 174 +# define SEQAN_PP_DEC_176 175 +# define SEQAN_PP_DEC_177 176 +# define SEQAN_PP_DEC_178 177 +# define SEQAN_PP_DEC_179 178 +# define SEQAN_PP_DEC_180 179 +# define SEQAN_PP_DEC_181 180 +# define SEQAN_PP_DEC_182 181 +# define SEQAN_PP_DEC_183 182 +# define SEQAN_PP_DEC_184 183 +# define SEQAN_PP_DEC_185 184 +# define SEQAN_PP_DEC_186 185 +# define SEQAN_PP_DEC_187 186 +# define SEQAN_PP_DEC_188 187 +# define SEQAN_PP_DEC_189 188 +# define SEQAN_PP_DEC_190 189 +# define SEQAN_PP_DEC_191 190 +# define SEQAN_PP_DEC_192 191 +# define SEQAN_PP_DEC_193 192 +# define SEQAN_PP_DEC_194 193 +# define SEQAN_PP_DEC_195 194 +# define SEQAN_PP_DEC_196 195 +# define SEQAN_PP_DEC_197 196 +# define SEQAN_PP_DEC_198 197 +# define SEQAN_PP_DEC_199 198 +# define SEQAN_PP_DEC_200 199 +# define SEQAN_PP_DEC_201 200 +# define SEQAN_PP_DEC_202 201 +# define SEQAN_PP_DEC_203 202 +# define SEQAN_PP_DEC_204 203 +# define SEQAN_PP_DEC_205 204 +# define SEQAN_PP_DEC_206 205 +# define SEQAN_PP_DEC_207 206 +# define SEQAN_PP_DEC_208 207 +# define SEQAN_PP_DEC_209 208 +# define SEQAN_PP_DEC_210 209 +# define SEQAN_PP_DEC_211 210 +# define SEQAN_PP_DEC_212 211 +# define SEQAN_PP_DEC_213 212 +# define SEQAN_PP_DEC_214 213 +# define SEQAN_PP_DEC_215 214 +# define SEQAN_PP_DEC_216 215 +# define SEQAN_PP_DEC_217 216 +# define SEQAN_PP_DEC_218 217 +# define SEQAN_PP_DEC_219 218 +# define SEQAN_PP_DEC_220 219 +# define SEQAN_PP_DEC_221 220 +# define SEQAN_PP_DEC_222 221 +# define SEQAN_PP_DEC_223 222 +# define SEQAN_PP_DEC_224 223 +# define SEQAN_PP_DEC_225 224 +# define SEQAN_PP_DEC_226 225 +# define SEQAN_PP_DEC_227 226 +# define SEQAN_PP_DEC_228 227 +# define SEQAN_PP_DEC_229 228 +# define SEQAN_PP_DEC_230 229 +# define SEQAN_PP_DEC_231 230 +# define SEQAN_PP_DEC_232 231 +# define SEQAN_PP_DEC_233 232 +# define SEQAN_PP_DEC_234 233 +# define SEQAN_PP_DEC_235 234 +# define SEQAN_PP_DEC_236 235 +# define SEQAN_PP_DEC_237 236 +# define SEQAN_PP_DEC_238 237 +# define SEQAN_PP_DEC_239 238 +# define SEQAN_PP_DEC_240 239 +# define SEQAN_PP_DEC_241 240 +# define SEQAN_PP_DEC_242 241 +# define SEQAN_PP_DEC_243 242 +# define SEQAN_PP_DEC_244 243 +# define SEQAN_PP_DEC_245 244 +# define SEQAN_PP_DEC_246 245 +# define SEQAN_PP_DEC_247 246 +# define SEQAN_PP_DEC_248 247 +# define SEQAN_PP_DEC_249 248 +# define SEQAN_PP_DEC_250 249 +# define SEQAN_PP_DEC_251 250 +# define SEQAN_PP_DEC_252 251 +# define SEQAN_PP_DEC_253 252 +# define SEQAN_PP_DEC_254 253 +# define SEQAN_PP_DEC_255 254 +# define SEQAN_PP_DEC_256 255 + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/seq/for_each.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +// # ifndef SEQAN_PREPROCESSOR_SEQ_FOR_EACH_HPP +// # define SEQAN_PREPROCESSOR_SEQ_FOR_EACH_HPP +# +// # include +// # include +// # include +// # include +// # include +// # include +// # include +# +# /* SEQAN_PP_SEQ_FOR_EACH */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_SEQ_FOR_EACH(macro, data, seq) SEQAN_PP_FOR((macro, data, seq (nil)), SEQAN_PP_SEQ_FOR_EACH_P, SEQAN_PP_SEQ_FOR_EACH_O, SEQAN_PP_SEQ_FOR_EACH_M) +// # else +// # define SEQAN_PP_SEQ_FOR_EACH(macro, data, seq) SEQAN_PP_SEQ_FOR_EACH_D(macro, data, seq) +// # define SEQAN_PP_SEQ_FOR_EACH_D(macro, data, seq) SEQAN_PP_FOR((macro, data, seq (nil)), SEQAN_PP_SEQ_FOR_EACH_P, SEQAN_PP_SEQ_FOR_EACH_O, SEQAN_PP_SEQ_FOR_EACH_M) +// # endif +# +# define SEQAN_PP_SEQ_FOR_EACH_P(r, x) SEQAN_PP_DEC(SEQAN_PP_SEQ_SIZE(SEQAN_PP_TUPLE_ELEM(3, 2, x))) +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_STRICT() +#ifndef STDLIB_VS +# define SEQAN_PP_SEQ_FOR_EACH_O(r, x) SEQAN_PP_SEQ_FOR_EACH_O_I x +# else // #ifndef STDLIB_VS +# define SEQAN_PP_SEQ_FOR_EACH_O(r, x) SEQAN_PP_SEQ_FOR_EACH_O_I(SEQAN_PP_TUPLE_ELEM(3, 0, x), SEQAN_PP_TUPLE_ELEM(3, 1, x), SEQAN_PP_TUPLE_ELEM(3, 2, x)) +# endif // #ifndef STDLIB_VS +# +# define SEQAN_PP_SEQ_FOR_EACH_O_I(macro, data, seq) (macro, data, SEQAN_PP_SEQ_TAIL(seq)) +# +// # if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_STRICT() +#ifndef STDLIB_VS +# define SEQAN_PP_SEQ_FOR_EACH_M(r, x) SEQAN_PP_SEQ_FOR_EACH_M_IM(r, SEQAN_PP_TUPLE_REM_3 x) +# define SEQAN_PP_SEQ_FOR_EACH_M_IM(r, im) SEQAN_PP_SEQ_FOR_EACH_M_I(r, im) +# else // #ifndef STDLIB_VS +# define SEQAN_PP_SEQ_FOR_EACH_M(r, x) SEQAN_PP_SEQ_FOR_EACH_M_I(r, SEQAN_PP_TUPLE_ELEM(3, 0, x), SEQAN_PP_TUPLE_ELEM(3, 1, x), SEQAN_PP_TUPLE_ELEM(3, 2, x)) +# endif // #ifndef STDLIB_VS +# +# define SEQAN_PP_SEQ_FOR_EACH_M_I(r, macro, data, seq) macro(r, data, SEQAN_PP_SEQ_HEAD(seq)) +# +# /* SEQAN_PP_SEQ_FOR_EACH_R */ +# +// # if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_SEQ_FOR_EACH_R(r, macro, data, seq) SEQAN_PP_FOR_ ## r((macro, data, seq (nil)), SEQAN_PP_SEQ_FOR_EACH_P, SEQAN_PP_SEQ_FOR_EACH_O, SEQAN_PP_SEQ_FOR_EACH_M) +// # else +// # define SEQAN_PP_SEQ_FOR_EACH_R(r, macro, data, seq) SEQAN_PP_SEQ_FOR_EACH_R_I(r, macro, data, seq) +// # define SEQAN_PP_SEQ_FOR_EACH_R_I(r, macro, data, seq) SEQAN_PP_FOR_ ## r((macro, data, seq (nil)), SEQAN_PP_SEQ_FOR_EACH_P, SEQAN_PP_SEQ_FOR_EACH_O, SEQAN_PP_SEQ_FOR_EACH_M) +// # endif +# +// # endif + +// -------------------------------------------------------------------------- +// ==> boost/preprocessor/seq/for_each_i.hpp <== +// -------------------------------------------------------------------------- + +# /* ************************************************************************** +# * * +# * (C) Copyright Paul Mensonides 2002. +# * Distributed under the Boost Software License, Version 1.0. (See +# * accompanying file LICENSE_1_0.txt or copy at +# * http://www.boost.org/LICENSE_1_0.txt) +# * * +# ************************************************************************** */ +# +# /* See http://www.boost.org for most recent version. */ +# +//# ifndef SEQAN_PREPROCESSOR_SEQ_FOR_EACH_I_HPP +//# define SEQAN_PREPROCESSOR_SEQ_FOR_EACH_I_HPP +# +//# include +//# include +//# include +//# include +//# include +//# include +//# include +//# include +# +# /* SEQAN_PP_SEQ_FOR_EACH_I */ +# +//# if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_SEQ_FOR_EACH_I(macro, data, seq) SEQAN_PP_FOR((macro, data, seq (nil), 0), SEQAN_PP_SEQ_FOR_EACH_I_P, SEQAN_PP_SEQ_FOR_EACH_I_O, SEQAN_PP_SEQ_FOR_EACH_I_M) +//# else +//# define SEQAN_PP_SEQ_FOR_EACH_I(macro, data, seq) SEQAN_PP_SEQ_FOR_EACH_I_I(macro, data, seq) +//# define SEQAN_PP_SEQ_FOR_EACH_I_I(macro, data, seq) SEQAN_PP_FOR((macro, data, seq (nil), 0), SEQAN_PP_SEQ_FOR_EACH_I_P, SEQAN_PP_SEQ_FOR_EACH_I_O, SEQAN_PP_SEQ_FOR_EACH_I_M) +//# endif +# +# define SEQAN_PP_SEQ_FOR_EACH_I_P(r, x) SEQAN_PP_DEC(SEQAN_PP_SEQ_SIZE(SEQAN_PP_TUPLE_ELEM(4, 2, x))) +# +//# if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_STRICT() +# define SEQAN_PP_SEQ_FOR_EACH_I_O(r, x) SEQAN_PP_SEQ_FOR_EACH_I_O_I x +//# else +//# define SEQAN_PP_SEQ_FOR_EACH_I_O(r, x) SEQAN_PP_SEQ_FOR_EACH_I_O_I(SEQAN_PP_TUPLE_ELEM(4, 0, x), SEQAN_PP_TUPLE_ELEM(4, 1, x), SEQAN_PP_TUPLE_ELEM(4, 2, x), SEQAN_PP_TUPLE_ELEM(4, 3, x)) +//# endif +# +# define SEQAN_PP_SEQ_FOR_EACH_I_O_I(macro, data, seq, i) (macro, data, SEQAN_PP_SEQ_TAIL(seq), SEQAN_PP_INC(i)) +# +//# if SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_STRICT() +//# define SEQAN_PP_SEQ_FOR_EACH_I_M(r, x) SEQAN_PP_SEQ_FOR_EACH_I_M_IM(r, SEQAN_PP_TUPLE_REM_4 x) +//# define SEQAN_PP_SEQ_FOR_EACH_I_M_IM(r, im) SEQAN_PP_SEQ_FOR_EACH_I_M_I(r, im) +//# else +# define SEQAN_PP_SEQ_FOR_EACH_I_M(r, x) SEQAN_PP_SEQ_FOR_EACH_I_M_I(r, SEQAN_PP_TUPLE_ELEM(4, 0, x), SEQAN_PP_TUPLE_ELEM(4, 1, x), SEQAN_PP_TUPLE_ELEM(4, 2, x), SEQAN_PP_TUPLE_ELEM(4, 3, x)) +//# endif +# +# define SEQAN_PP_SEQ_FOR_EACH_I_M_I(r, macro, data, seq, i) macro(r, data, i, SEQAN_PP_SEQ_HEAD(seq)) +# +# /* SEQAN_PP_SEQ_FOR_EACH_I_R */ +# +//# if ~SEQAN_PP_CONFIG_FLAGS() & SEQAN_PP_CONFIG_EDG() +# define SEQAN_PP_SEQ_FOR_EACH_I_R(r, macro, data, seq) SEQAN_PP_FOR_ ## r((macro, data, seq (nil), 0), SEQAN_PP_SEQ_FOR_EACH_I_P, SEQAN_PP_SEQ_FOR_EACH_I_O, SEQAN_PP_SEQ_FOR_EACH_I_M) +//# else +//# define SEQAN_PP_SEQ_FOR_EACH_I_R(r, macro, data, seq) SEQAN_PP_SEQ_FOR_EACH_I_R_I(r, macro, data, seq) +//# define SEQAN_PP_SEQ_FOR_EACH_I_R_I(r, macro, data, seq) SEQAN_PP_FOR_ ## r((macro, data, seq (nil), 0), SEQAN_PP_SEQ_FOR_EACH_I_P, SEQAN_PP_SEQ_FOR_EACH_I_O, SEQAN_PP_SEQ_FOR_EACH_I_M) +//# endif +# +//# endif + +// -------------------------------------------------------------------------- +// ==> boost/config/suffix.hpp <== +// -------------------------------------------------------------------------- + +// Copyright (c) 2001-2003 John Maddock +// Copyright (c) 2001 Darin Adler +// Copyright (c) 2001 Peter Dimov +// Copyright (c) 2002 Bill Kempf +// Copyright (c) 2002 Jens Maurer +// Copyright (c) 2002-2003 David Abrahams +// Copyright (c) 2003 Gennaro Prota +// Copyright (c) 2003 Eric Friedman +// Copyright (c) 2010 Eric Jourdanneau, Joel Falcou +// Distributed under the Boost Software License, Version 1.0. (See +// accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt) + +// +// Helper macro SEQAN_JOIN: +// The following piece of macro magic joins the two +// arguments together, even when one of the arguments is +// itself a macro (see 16.3.1 in C++ standard). The key +// is that macro expansion of macro arguments does not +// occur in SEQAN_DO_JOIN2 but does in SEQAN_DO_JOIN. +// +#define SEQAN_JOIN( X, Y ) SEQAN_DO_JOIN( X, Y ) +#define SEQAN_DO_JOIN( X, Y ) SEQAN_DO_JOIN2(X,Y) +#define SEQAN_DO_JOIN2( X, Y ) X##Y + + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_SEQAN_PREPROCESSOR_SUBSET_H_ diff --git a/seqan/basic/builtin_functions.h b/seqan/basic/builtin_functions.h new file mode 100644 index 0000000..a16edfb --- /dev/null +++ b/seqan/basic/builtin_functions.h @@ -0,0 +1,63 @@ +// ========================================================================== +// builtin_functions.h +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: Manuel Holtgrewe +// ========================================================================== +// Documentation for built-in functions. +// +// This is used for documenting that certain global functions and operators +// are overridden for some classes. +// ========================================================================== + +#ifndef SEQAN_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_ +#define SEQAN_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_ + +namespace seqan { + +// ============================================================================ +// Forwards +// ============================================================================ + +// ============================================================================ +// Tags, Classes, Enums +// ============================================================================ + +// ============================================================================ +// Metafunctions +// ============================================================================ + +// ============================================================================ +// Functions +// ============================================================================ + +} // namespace seqan + +#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_BUILTIN_FUNCTIONS_H_ diff --git a/seqan/basic/concept_checking.h b/seqan/basic/concept_checking.h new file mode 100644 index 0000000..96dcc8a --- /dev/null +++ b/seqan/basic/concept_checking.h @@ -0,0 +1,731 @@ +// ========================================================================== +// SeqAn - The Library for Sequence Analysis +// ========================================================================== +// Copyright (c) 2006-2016, Knut Reinert, FU Berlin +// All rights reserved. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// * Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// * Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// * Neither the name of Knut Reinert or the FU Berlin nor the names of +// its contributors may be used to endorse or promote products derived +// from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE +// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +// DAMAGE. +// +// ========================================================================== +// Author: David Weese +// Author: Manuel Holtgrewe +// ========================================================================== +// A minimal subset of the Boost Concept Checking Library. A lot of the code +// in the BCCL deals with support of non-conforming compilers and we cut this +// away. The code here has been adjusted to work with the compilers supported +// by SeqAn and be as simple as possible while still creating useful compiler +// errors. +// ========================================================================== + +// SEQAN_NO_GENERATED_FORWARDS + +#ifndef INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_ +#define INCLUDE_SEQAN_BASIC_CONCEPT_CHECKING_H_ + +namespace seqan { + +// --------------------------------------------------------------------------- +// ==> boost/static_assert.hpp <== +// --------------------------------------------------------------------------- + +// (C) Copyright John Maddock 2000. +// Use, modification and distribution are subject to the +// Boost Software License, Version 1.0. (See accompanying file +// LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) + +// See http://www.boost.org/libs/static_assert for documentation. + +#define SEQAN_STATIC_ASSERT_MSG( B, Msg ) static_assert(B, Msg) + +// +// If the compiler issues warnings about old C style casts, +// then enable this: +// +#define SEQAN_STATIC_ASSERT_BOOL_CAST(x) (bool)(x) + +#define SEQAN_STATIC_ASSERT( B ) static_assert(B, #B) + +// --------------------------------------------------------------------------- +// ==> boost/parameter/aux_/paranthesized_type.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost Software +// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt). + +template +struct unaryfunptr_arg_type; + +template +struct unaryfunptr_arg_type +{ + typedef Arg type; +}; + +template <> +struct unaryfunptr_arg_type +{ + typedef void type; +}; + +// --------------------------------------------------------------------------- +// ==> boost/concept_check/general.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost Software +// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt). + +namespace concept_checking +{ +template struct instantiate {}; +} + +template struct concept_check_; + +template +void concept_check_failed() +{ + Model *p = static_cast(NULL); + p->~Model(); +} + +template +struct concept_check +{ + concept_checking::instantiate > x; + enum { instantiate = 1 }; +}; + +template +struct concept_check_ + : concept_check +{}; + +# define SEQAN_CONCEPT_ASSERT_FN( ModelFnPtr ) \ + typedef seqan::detail::instantiate< \ + &seqan::requirement_::failed> \ + SEQAN_PP_CAT(seqan_concept_check,__LINE__) SEQAN_UNUSED + +// --------------------------------------------------------------------------- +// ==> boost/concept/assert.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost Software +// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt). + +/*! + * @defgroup ConceptChecking Concept Checking + * @brief Macros for the concept checking system in SeqAn. + * + * SeqAn's concept checking system is copied from Boost. The license for the library is as follows: + * + * @code{.cpp} + * // Copyright David Abrahams 2006. Distributed under the Boost Software + * // License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at + * // http://www.boost.org/LICENSE_1_0.txt). + * @endcode + */ + +/*! + * @macro ConceptChecking#SEQAN_CONCEPT_ASSERT + * @brief Perform a concept check. + * @headerfile + * + * @signature SEQAN_CONCEPT_ASSERT((concept)) + * + * @param concept Concept specialized with a the type that should be checked. + * + * This macro is a compile-time assertion and requires the concept specialized + * with the tested types to compile. The check neither consumes memory nor + * running time. The macro can be used at the beginning of a function or within + * a struct/class definition. The checked concepts should be as restrictive and + * generic as possible to on the one hand cover all used functionality and on + * the other hand not limit the applicability of a function/class. + * + * @section Examples + * + * @code{.cpp} + * typedef typename Value::Type TValue; + * typedef typename Position::Type TPosition; + * typedef typename Difference::Type TDifference; + * + * SEQAN_CONCEPT_ASSERT((AlphabetConcept)); + * SEQAN_CONCEPT_ASSERT((SignedIntegerConcept)); + * SEQAN_CONCEPT_ASSERT((UnsignedIntegerConcept)); + * @endcode + * @see Is + */ + +// Usage, in class or function context: +// SEQAN_CONCEPT_ASSERT((UnaryFunctionConcept)); +# define SEQAN_CONCEPT_ASSERT(ModelInParens) \ + SEQAN_CONCEPT_ASSERT_FN(void(*)ModelInParens) + +// usage.hpp + +template +struct usage_requirements +{ + ~usage_requirements() + { + Model *p = static_cast(NULL); + p->~Model(); + } +}; + +/*! + * @macro ConceptChecking#SEQAN_CONCEPT_USAGE + * @headerfile + * @brief Defines valid expressions. + * + * @signature SEQAN_CONCEPT_USAGE(name) + * + * @param[in] name Identifier of the concept defined with @link ConceptChecking#SEQAN_CONCEPT @endlink or + * @link ConceptChecking#SEQAN_CONCEPT_REFINE @endlink. + * + * This macro should be used to introduce a block (enclosed with curly braces) of valid expressions within a newly + * defined concept. Valid expressions should test for available functions, operators and the correctness of return + * types. Use helper functions, e.g. @link ignoreUnusedVariableWarning @endlink, + * @link ConceptChecking#requireBooleanExpr @endlink and @link ConceptChecking#sameType @endlink. + * + * @section Examples + * + * @code{.cpp} + * SEQAN_CONCEPT(EqualityComparable,(T)) + * { + * SEQAN_CONCEPT_USAGE(EqualityComparable) + * { + * requireBooleanExpr(a == b); + * requireBooleanExpr(a != b); + * } + * private: + * T a, b; + * }; + * @endcode + * + * @see ConceptChecking#requireBooleanExpr + * @see ConceptChecking#SEQAN_CONCEPT + * @see ConceptChecking#SEQAN_CONCEPT_REFINE + */ + +#define SEQAN_CONCEPT_USAGE(model) \ + SEQAN_CONCEPT_ASSERT((seqan::usage_requirements)); \ + ~model() + +// --------------------------------------------------------------------------- +// ==> boost/concept/detail/has_constraints.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost Software +// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt). + +namespace detail { + typedef char yes; + typedef char (&no)[2]; + + template + struct wrap_constraints {}; + + template + inline yes has_constraints_(Model*, wrap_constraints* = 0); + inline no has_constraints_(...); +} + +// This would be called "detail::has_constraints," but it has a strong +// tendency to show up in error messages. +template +struct not_satisfied +{ + enum {value = sizeof( detail::has_constraints_((Model*)0) ) == sizeof(detail::yes) }; + typedef typename Eval::Type Type; +}; + +// --------------------------------------------------------------------------- +// ==> boost/concept_check/detail/general.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost Software +// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt). + +template +struct requirement_; + +namespace detail +{ + template struct instantiate {}; +} + +template +struct requirement +{ + static void failed() + { + Model *p = static_cast(NULL); + p->~Model(); + } +}; + +struct failed {}; + +template +struct requirement +{ + static void failed() + { + Model *p = static_cast(NULL); + p->~Model(); + } +}; + +template +struct constraint +{ + static void failed() + { + Model *p = static_cast(NULL); + p->constraints(); + } +}; + +template +struct requirement_ + : IfC::Type::VALUE, /* should be called "has_constraints", see above */ + constraint, + requirement + >::Type +{}; + +# define SEQAN_CONCEPT_ASSERT_FN( ModelFnPtr ) \ + typedef seqan::detail::instantiate< \ + &seqan::requirement_::failed> \ + SEQAN_PP_CAT(seqan_concept_check,__LINE__) SEQAN_UNUSED + +// --------------------------------------------------------------------------- +// ==> boost/concept_check/detail/requires.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost Software +// License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt). + +// Template for use in handwritten assertions +template +struct requires_ : More +{ + SEQAN_CONCEPT_ASSERT((Model)); +}; + +// Template for use by macros, where models must be wrapped in parens. +// This isn't in namespace detail to keep extra cruft out of resulting +// error messages. + +template +struct _requires_ +{ + enum { value = 0 }; + SEQAN_CONCEPT_ASSERT_FN(ModelFn); +}; + +template +struct Requires_ : unaryfunptr_arg_type +{}; + +# define SEQAN_CONCEPT_REQUIRES_(r,data,t) + (seqan::_requires_::value) + +#if defined(NDEBUG) + +# define SEQAN_CONCEPT_REQUIRES(models, result) \ + typename unaryfunptr_arg_type::type + +#else // #if defined(NDEBUG) + +# define SEQAN_CONCEPT_REQUIRES(models, result) \ + typename seqan::Requires_< \ + (0 SEQAN_PP_SEQ_FOR_EACH(SEQAN_CONCEPT_REQUIRES_, ~, models)), \ + void(*)result \ + >::type + +#endif // #if defined(NDEBUG) + +// --------------------------------------------------------------------------- +// ==> boost/concept_check.hpp <== +// --------------------------------------------------------------------------- + +// +// (C) Copyright Jeremy Siek 2000. +// Copyright 2002 The Trustees of Indiana University. +// +// Distributed under the Boost Software License, Version 1.0. (See +// accompanying file LICENSE_1_0.txt or copy at +// http://www.boost.org/LICENSE_1_0.txt) // +// Backward compatibility +// + +template +inline void functionRequires(Model* = 0) +{ + SEQAN_CONCEPT_ASSERT((Model)); +} + +/*! + * @fn ignoreUnusedVariableWarning + * @headerfile + * @brief Removes unused variable warning. + * + * @signature void ignoreUnusedVariableWarning(x); + * + * @param[in] x Variable that causes the unused variable warning. + * + * It sometimes is necessary to define variables which are not further used, e.g. to check available assignment + * operators. Use this functions to remove a compile warning that otherwise would be raised in this case. + */ + +template inline void ignoreUnusedVariableWarning(T const&) {} + +// --------------------------------------------------------------------------- +// ==> boost/concept/detail/concept_def.hpp <== +// --------------------------------------------------------------------------- + +// Copyright David Abrahams 2006. Distributed under the Boost +// Software License, Version 1.0. (See accompanying +// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) + +// SEQAN_CONCEPT_REFINE added by David Weese + +/*! + * @macro ConceptChecking#SEQAN_CONCEPT + * @brief Defines a new concept. + * @headerfile + * + * @signature SEQAN_CONCEPT(name, params) + * + * @param params Template paramter list in parantheses, e.g. (T) or (T1)(T2). + * Typically, template parameters are models, i.e. one or multiple + * classes that should be checked for fulfilling a concept.This is + * a sequence of the Boost Preprocessor Library, read more. + * @param name Concept identifier. Non-trivial concepts should have an + * identifier with a Concept-suffix. + * + * A concept is implemented as a template struct with name name and + * arguments params. The concept checking should be part of the struct + * definition. Associated types should be checked via @link ConceptChecking#SEQAN_CONCEPT_ASSERT + * @endlink and valid expressions in a function @link ConceptChecking#SEQAN_CONCEPT_USAGE + * @endlink, see below. Variables used in valid expressions should be (private) + * struct members instead of local variables in member functions (read more. + * + * @section Examples + * + * @code{.cpp} + * SEQAN_CONCEPT(Assignable,(T)) + * { + * SEQAN_CONCEPT_USAGE(Assignable) + * { + * a = b; // require assignment operator + * constConstraints(b); + * } + * private: + * void constConstraints(const T& x) + * { + * a = x; // const required for argument to assignment + * ignoreUnusedVariableWarning(x); + * } + * private: + * T a; + * T b; + * }; + * + * SEQAN_CONCEPT(EqualityComparable,(T)) + * { + * SEQAN_CONCEPT_USAGE(EqualityComparable) + * { + * requireBooleanExpr(a == b); + * requireBooleanExpr(a != b); + * } + * private: + * T a, b; + * }; + * @endcode + * + * @see ConceptChecking#SEQAN_CONCEPT_USAGE + */ + +# define SEQAN_CONCEPT(name, params) \ + template < SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_typename,~,params) > \ + struct name + +/*! + * @macro ConceptChecking#SEQAN_CONCEPT_REFINE + * @brief Defines a new concept as a refinement of existing concepts. + * @headerfile + * + * @signature SEQAN_CONCEPT_REFINE(name, params, refinedConcepts) + * + * @param params Template parameter list in parantheses, e.g. (T) or (T1)(T2). + * Typically, template parameters are models, i.e. one or multiple + * classes that should be checked for fulfilling a concept.This is + * a sequence of the Boost Preprocessor Library, read more. + * @param name Concept identifier. Non-trivial concepts should have an + * identifier with a Concept-suffix. + * @param refinedConcepts Identifiers of concepts that are refined by the new + * concept.Refined concepts are implicitly integrated + * into the requirements of the new concept.This is a + * sequence of the Boost Preprocessor Library, read + * more + * + * A concept is implemented as a template struct with name name and + * arguments params. The struct inherits all refined concept structs. + * The concept checking should be part of the struct definition. For more + * information, see @link ConceptChecking#SEQAN_CONCEPT @endlink. + * + * @section Examples + * + * @code{.cpp} + * SEQAN_CONCEPT_REFINE(AlphabetConcept, (TValue), (Assignable)(DefaultConstructible)(CopyConstructible)) + * { + * TValue val, val2; + * + * SEQAN_CONCEPT_USAGE(AlphabetConcept) + * { + * assign(val, val2); + * } + * }; + * @endcode + * @see ConceptChecking#SEQAN_CONCEPT_USAGE + */ + +# define SEQAN_CONCEPT_REFINE(name, params, refinedConcepts) \ + template < SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_typename,~,params) > \ + struct name; \ + \ + template < SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_typename,~,params) > \ + struct Refines< name > \ + { \ + typedef \ + SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_LIST_prefix,params,refinedConcepts) \ + SEQAN_PP_REPEAT(SEQAN_PP_SEQ_SIZE(refinedConcepts),SEQAN_CONCEPT_LIST_suffix,~) Type; \ + }; \ + \ + template < SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_typename,~,params) > \ + struct name: \ + SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_REFINE_superclass,params,refinedConcepts) + +/*! + * @macro ConceptChecking#SEQAN_CONCEPT_IMPL + * @brief Defines which concepts a model fulfills. + * @headerfile + * + * + * @signature template<> // required, even if name has no template arguments + * SEQAN_CONCEPT_IMPL((name), implementedConcepts) + * + * template + * SEQAN_CONCEPT_IMPL((name), implementedConcepts) + * + * @param implementedConcepts Identifiers of concepts that are fulfilled by the model. This is a sequence of the + * Boost Preprocessor Library, read more. + * @param name Model type, i.e. an identifier or an identifier with template + * arguments. + * + * The metafunction @link Is @endlink can be used to determine whether a class + * models (fulfills) a concepts. A model of a concept must pass the concept + * check via @link ConceptChecking#SEQAN_CONCEPT_ASSERT @endlink. + * + * @section Examples + * + * @code{.cpp} + * template + * SEQAN_CONCEPT_IMPL((String), (StringConcept)); + * @endcode + */ + + +// STRIP_PARENS macro by Steven Watanabe (http://lists.boost.org/boost-users/2010/08/61429.php) +#define SEQAN_APPLY(macro, args) SEQAN_APPLY_I(macro, args) +#define SEQAN_APPLY_I(macro, args) macro args +#define SEQAN_STRIP_PARENS(x) SEQAN_EVAL((SEQAN_STRIP_PARENS_I x), x) +#define SEQAN_STRIP_PARENS_I(...) 1,1 +#define SEQAN_EVAL(test, x) SEQAN_EVAL_I(test, x) +#define SEQAN_EVAL_I(test, x) SEQAN_MAYBE_STRIP_PARENS(SEQAN_TEST_ARITY test, x) +#define SEQAN_TEST_ARITY(...) SEQAN_APPLY(SEQAN_TEST_ARITY_I, (__VA_ARGS__, 2, 1)) +#define SEQAN_TEST_ARITY_I(a,b,c,...) c +#define SEQAN_MAYBE_STRIP_PARENS(cond, x) SEQAN_MAYBE_STRIP_PARENS_I(cond, x) +#define SEQAN_MAYBE_STRIP_PARENS_I(cond, x) SEQAN_PP_CAT(SEQAN_MAYBE_STRIP_PARENS_, cond)(x) +#define SEQAN_MAYBE_STRIP_PARENS_1(x) x +#define SEQAN_MAYBE_STRIP_PARENS_2(x) SEQAN_APPLY(SEQAN_MAYBE_STRIP_PARENS_2_I, x) +#define SEQAN_MAYBE_STRIP_PARENS_2_I(...) __VA_ARGS__ + +# define SEQAN_CONCEPT_IMPL(model, implementedConcepts) \ + struct Implements \ + { \ + typedef \ + SEQAN_PP_SEQ_FOR_EACH_I(SEQAN_CONCEPT_LIST_prefix,model,implementedConcepts) \ + SEQAN_PP_REPEAT(SEQAN_PP_SEQ_SIZE(implementedConcepts),SEQAN_CONCEPT_LIST_suffix,~) Type; \ + } + +// helper for the SEQAN_CONCEPT, above. +# define SEQAN_CONCEPT_typename(r, ignored, index, t) \ + SEQAN_PP_COMMA_IF(index) typename t + +// helper for the SEQAN_CONCEPT, above. +# define SEQAN_CONCEPT_REFINE_superclass(r, params, index, t) \ + SEQAN_PP_COMMA_IF(index) t +# define SEQAN_CONCEPT_LIST_prefix(r, params, index, t) \ + SEQAN_PP_COMMA_IF(index) TagList +# define SEQAN_CONCEPT_LIST_suffix(z, n, text) > + +// ============================================================================ +// Functions +// ============================================================================ + +/*! + * @fn ConceptChecking#sameType + * @brief Tests for equality of types. + * + * @signature void sameType(x, y); + * + * @param[in] x Object of a certain type. + * @param[in] y Object that must be of the same type. + * + * This function can be used to test for the correctness of function return types or the type of an expression in + * concept tests. + * + * @see ConceptChecking#SEQAN_CONCEPT_USAGE + */ + +template +void sameType(T, T) { } + + +// ============================================================================ +// Metafunctions +// ============================================================================ + +/*! + * @mfn Is + * @brief Returns whether a concept is fulfilled. + * @headerfile + * + * @signature Is::Type + * @signature Is::VALUE + * + * @tparam TConcept A concept that is specialized with type(s) that should be + * tested for fulfilling the concept. + * + * @return Type @link LogicalValuesTags#True @endlink/true if + * TConcept is a fulfilled concept, otherwise @link + * LogicalValuesTags#False @endlink/false. + * + * The @link Is @endlink-metafunction can be used to test types for fulfilling a concept without causing compilation + * errors. If True or true is returned, TConcept must pass the concept test via @link + * ConceptChecking#SEQAN_CONCEPT_ASSERT @endlink. It can be used to switch between different implementations + * depending on the concept of a type, or in combination with @link EnableIfFunctionality#SEQAN_FUNC_ENABLE_IF + * @endlink to make a function only visible to types of certain concepts. + * + * @section Examples + * + * @code{.cpp} + * Is >::Type + * IfC >::VALUE, T1, T2>::Type + * + * std::cout << Is >::VALUE << std::endl; // 1 + * std::cout << Is >::VALUE << std::endl; // 0 + * @endcode + * Define a hierarchy of concepts and two models Alice and Bob + * that implements some of them. @link Is @endlink determines which concepts are + * explicitly or implicitly fulfilled. + * + * @code{.cpp} + * struct Alice {}; + * struct Bob {}; + * + * SEQAN_CONCEPT(ConceptA, (T)) {}; + * SEQAN_CONCEPT(ConceptB, (T)) {}; + * SEQAN_CONCEPT_REFINE(ConceptC, (T), (ConceptA)(ConceptB)) {}; + * SEQAN_CONCEPT_REFINE(ConceptD, (T), (ConceptC)) {}; + * + * template<> // Alice has no template arguments + * SEQAN_CONCEPT_IMPL(Alice, (ConceptA)(ConceptB)); + * + * template<> // Bob has no template arguments + * SEQAN_CONCEPT_IMPL(Bob, (ConceptC)); + * + * std::cout << Is< ConceptA >::VALUE << std::endl; // 1 + * std::cout << Is< ConceptB >::VALUE << std::endl; // 1 + * std::cout << Is< ConceptC >::VALUE << std::endl; // 0 + * std::cout << Is< ConceptD >::VALUE << std::endl; // 0 + * + * std::cout << Is< ConceptA >::VALUE << std::endl; // 1 + * std::cout << Is< ConceptB >::VALUE << std::endl; // 1 + * std::cout << Is< ConceptC >::VALUE << std::endl; // 1 + * std::cout << Is< ConceptD >::VALUE << std::endl; // 0 + * @endcode + * + * @see EnableIfFunctionality#SEQAN_FUNC_ENABLE_IF + * @see ConceptChecking#SEQAN_CONCEPT_ASSERT + */ + +// test whether a concept is fulfilled (without concept checking) +template +struct Implements: False {}; + +template +struct Refines +{ + typedef void Type; +}; + + +template +struct IsRecurse_: False {}; + +template +struct IsRecurse_ >: True {}; + +template +struct IsRecurse_< TConceptModel, TagList >: + Or< + IsRecurse_::Type >, + IsRecurse_ + > {}; + +template +struct Is; + +template