Ena 6648 fasta reader

src/main/java/uk/ac/ebi/embl/gff3tools/exception/FastaFileException.java

@@ -0,0 +1,28 @@
+/*
+ * Copyright 2025 EMBL - European Bioinformatics Institute
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+ * CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ */
+package uk.ac.ebi.embl.gff3tools.exception;
+
+public class FastaFileException extends Exception {
+
+    public FastaFileException() {}
+
+    public FastaFileException(String message) {
+        super(message);
+    }
+
+    public FastaFileException(Throwable cause) {
+        super(cause);
+    }
+
+    public FastaFileException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}

src/main/java/uk/ac/ebi/embl/gff3tools/fasta/FastaEntry.java

@@ -0,0 +1,27 @@
+/*
+ * Copyright 2025 EMBL - European Bioinformatics Institute
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+ * CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ */
+package uk.ac.ebi.embl.gff3tools.fasta;
+
+import lombok.Getter;
+import lombok.Setter;
+import uk.ac.ebi.embl.gff3tools.fasta.headerutils.FastaHeader;
+
+@Getter
+@Setter
+public class FastaEntry {
+    public String submissionId;
+    public String accessionId;
+    public FastaHeader header; // json info
+    public long totalBases;
+    public long totalBasesWithoutNBases;
+    public long leadingNsCount;
+    public long trailingNsCount;
+}

src/main/java/uk/ac/ebi/embl/gff3tools/fasta/FastaEntryInternal.java

@@ -0,0 +1,27 @@
+/*
+ * Copyright 2025 EMBL - European Bioinformatics Institute
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+ * CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ */
+package uk.ac.ebi.embl.gff3tools.fasta;
+
+import lombok.Getter;
+import lombok.Setter;
+import uk.ac.ebi.embl.gff3tools.fasta.headerutils.FastaHeader;
+import uk.ac.ebi.embl.gff3tools.fasta.sequenceutils.SequenceIndex;
+
+@Getter
+@Setter
+class FastaEntryInternal {
+    String submissionId;
+    String accessionId;
+    FastaHeader header;
+    // information needed for accessing the file
+    long fastaStartByte; // position of '>' in the file
+    SequenceIndex sequenceIndex; // a smart index for querying ranges in the file
+}

src/main/java/uk/ac/ebi/embl/gff3tools/fasta/FastaFileService.java

@@ -0,0 +1,154 @@
+/*
+ * Copyright 2025 EMBL - European Bioinformatics Institute
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+ * CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ */
+package uk.ac.ebi.embl.gff3tools.fasta;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.*;
+import lombok.Getter;
+import lombok.Setter;
+import uk.ac.ebi.embl.gff3tools.exception.FastaFileException;
+import uk.ac.ebi.embl.gff3tools.fasta.sequenceutils.ByteSpan;
+import uk.ac.ebi.embl.gff3tools.fasta.sequenceutils.SequenceIndex;
+
+/**
+ * Owns a SequentialFastaEntryReader, keeps all entries + indexes in memory, supports ID renames,
+ * and serves base-range slices by mapping (N..M bases) -> byte span via the cached SequenceIndex,
+ * then asking the reader to stream bytes while skipping newlines.
+ */
+@Getter
+@Setter
+public final class FastaFileService {
+
+    public List<FastaEntry> fastaEntries = new ArrayList<>();
+
+    private HashMap<String, SequenceIndex> sequenceIndexes = new HashMap<>();
+    private File file;
+    private SequentialFastaFileReader reader;
+
+    public FastaFileService() {
+        this.file = null;
+    }
+
+    // ---------------------------- queries ----------------------------
+
+    public Optional<FastaEntry> setAccessionId(String submissionId, String accessionId) throws FastaFileException {
+        Optional<FastaEntry> target = fastaEntries.stream()
+                .filter(entry -> entry.getSubmissionId().equals(submissionId))
+                .findFirst();
+        target.ifPresent(entry -> entry.setAccessionId(accessionId));
+        return target;
+    }
+
+    public Optional<FastaEntry> getFastaWithSubmissionId(String submissionId) throws FastaFileException {
+        return fastaEntries.stream()
+                .filter(entry -> entry.getSubmissionId().equals(submissionId))
+                .findFirst();
+    }
+
+    /** Return a sequence slice as a String (no EOLs) for [fromBase..toBase] inclusive. */
+    public String getSequenceSliceString(SequenceRangeOption option, String submissionId, long fromBase, long toBase)
+            throws FastaFileException {
+        ensureFileReaderOpen();
+        SequenceIndex index = sequenceIndexes.get(submissionId);
+        if (index == null) {
+            throw new FastaFileException("No sequence index found for submissionId " + submissionId);
+        }
+
+        final ByteSpan span;
+        switch (option) {
+            case WHOLE_SEQUENCE:
+                span = index.byteSpanForBaseRangeIncludingEdgeNBases(fromBase, toBase);
+                break;
+            case WITHOUT_N_BASES:
+                span = index.byteSpanForBaseRange(fromBase, toBase);
+                break;
+            default:
+                throw new IllegalStateException("Unknown option " + option);
+        }
+
+        try {
+            return reader.getSequenceSliceString(span);
+        } catch (IOException ioe) {
+            throw new FastaFileException(
+                    "I/O while reading slice for " + submissionId + " bytes " + span.start + ".." + (span.endEx - 1),
+                    ioe);
+        }
+    }
+
+    /**
+     * Return a sequence slice for reader [fromBase..toBase] (1-based, inclusive) for the given ID.
+     * Uses the cached index to translate bases -> bytes, then asks the reader to stream
+     * ASCII bytes while skipping '\n' and '\r' on the fly.
+     */
+    public Reader getSequenceSliceReader(SequenceRangeOption option, String submissionId, long fromBase, long toBase)
+            throws FastaFileException {
+        ensureFileReaderOpen();
+        var index = sequenceIndexes.get(submissionId);
+        if (index == null) {
+            throw new FastaFileException("No sequence index found for submissionId " + submissionId);
+        }
+
+        ByteSpan span;
+        switch (option) {
+            case WHOLE_SEQUENCE:
+                span = index.byteSpanForBaseRangeIncludingEdgeNBases(fromBase, toBase);
+                break;
+            case WITHOUT_N_BASES:
+                span = index.byteSpanForBaseRange(fromBase, toBase);
+                break;
+            default:
+                throw new IllegalStateException("Unknown option " + option);
+        }
+
+        return reader.getSequenceSliceReader(span);
+    }
+
+    // ---------------------------- interactions with the reader ----------------------------
+
+    public void openNewFile(File fastaFile) throws FastaFileException, IOException {
+        close(); // if already open, close first
+        this.file = Objects.requireNonNull(fastaFile, "file");
+        this.fastaEntries.clear();
+        this.sequenceIndexes.clear();
+        reader = new SequentialFastaFileReader(fastaFile);
+        var readEntries = reader.readAll();
+        for (var entry : readEntries) {
+            FastaEntry fastaEntry = new FastaEntry();
+            fastaEntry.setSubmissionId(entry.getSubmissionId());
+            fastaEntry.setHeader(entry.getHeader());
+            fastaEntry.setTotalBases(entry.sequenceIndex.totalBases());
+            fastaEntry.setLeadingNsCount(entry.sequenceIndex.startNBasesCount);
+            fastaEntry.setTrailingNsCount(entry.sequenceIndex.endNBasesCount);
+            long adjustedBases = entry.sequenceIndex.totalBases()
+                    - entry.sequenceIndex.startNBasesCount
+                    - entry.sequenceIndex.endNBasesCount;
+            fastaEntry.setTotalBasesWithoutNBases(adjustedBases);
+            fastaEntries.add(fastaEntry);
+
+            sequenceIndexes.put(entry.getSubmissionId(), entry.sequenceIndex);
+        }
+    }
+
+    /** Close the reader. Safe to call multiple times. */
+    public void close() throws IOException {
+        if (reader != null) {
+            reader.close();
+            reader = null;
+        }
+    }
+
+    private void ensureFileReaderOpen() {
+        if (reader == null || !reader.readingFile())
+            throw new IllegalStateException("Service is not open. Call open() first.");
+    }
+}

src/main/java/uk/ac/ebi/embl/gff3tools/fasta/SequenceRangeOption.java

@@ -0,0 +1,16 @@
+/*
+ * Copyright 2025 EMBL - European Bioinformatics Institute
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this
+ * file except in compliance with the License. You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the
+ * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+ * CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ */
+package uk.ac.ebi.embl.gff3tools.fasta;
+
+public enum SequenceRangeOption {
+    WHOLE_SEQUENCE,
+    WITHOUT_N_BASES
+}