From e6b5a56d292caf8726569c63592f7d1a51cb70c7 Mon Sep 17 00:00:00 2001 From: Rajkumar-D Date: Mon, 11 Mar 2024 16:47:03 +0000 Subject: [PATCH 1/2] Updating setForceLineBreak for Note qualifier --- .../check/sourcefeature/SequenceCoverageCheck.java | 2 +- .../uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java | 1 + .../embl/flatfile/writer/embl/EmblQualifierWriterTest.java | 6 ++++-- .../flatfile/writer/genbank/GenbankQualifierWriterTest.java | 6 ++++-- 4 files changed, 10 insertions(+), 5 deletions(-) diff --git a/src/main/java/uk/ac/ebi/embl/api/validation/check/sourcefeature/SequenceCoverageCheck.java b/src/main/java/uk/ac/ebi/embl/api/validation/check/sourcefeature/SequenceCoverageCheck.java index 8021e0d1..6217eaf1 100644 --- a/src/main/java/uk/ac/ebi/embl/api/validation/check/sourcefeature/SequenceCoverageCheck.java +++ b/src/main/java/uk/ac/ebi/embl/api/validation/check/sourcefeature/SequenceCoverageCheck.java @@ -174,7 +174,7 @@ private boolean validateFullCoverageNoGapsOrOverlaps( } validateNoOverlapBetweenLocations(prevLocation, location, firstSourceOrigin); } - return validateEndPositionIsSequenceLength(location, sequenceLength, firstSourceOrigin); + return validateEndPositionIsSequenceLength(location, sequenceLength, firstSourceOrigin); } private boolean validateStartPositionIsOne(Location location, Origin firstSourceOrigin) { diff --git a/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java b/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java index 0df082af..686cb635 100644 --- a/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java +++ b/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java @@ -34,6 +34,7 @@ public QualifierWriter(Entry entry, Qualifier qualifier, WrapType wrapType, Stri setForceLineBreak(true); } else if (qualifier.getName().equals(Qualifier.NOTE_QUALIFIER_NAME)) { setMaximumLineLength(NOTE_MAX_LINE_LENGTH); + setForceLineBreak(true); } } } diff --git a/src/test/java/uk/ac/ebi/embl/flatfile/writer/embl/EmblQualifierWriterTest.java b/src/test/java/uk/ac/ebi/embl/flatfile/writer/embl/EmblQualifierWriterTest.java index a8d151b4..6bd8d57c 100644 --- a/src/test/java/uk/ac/ebi/embl/flatfile/writer/embl/EmblQualifierWriterTest.java +++ b/src/test/java/uk/ac/ebi/embl/flatfile/writer/embl/EmblQualifierWriterTest.java @@ -97,8 +97,10 @@ public void testWrite_Wrap() throws IOException { + "FT a note this is a note this is a note this is a note this is\n" + "FT a note this is a note this is a note this is a note this is\n" + "FT a note this is a note \"\n" - + "FT /note=\"thisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisa\n" - + "FT notethisisanotethisisanote\"\n", + + "FT /note=\"thisisanotethisisanotethisisanotethisisanotethisisan\n" + + "FT otethisisanotethisisanotethisisanotethisisanotethisisanotet\n" + + "FT hisisanotethisisanotethisisanotethisisanotethisisanotethisi\n" + + "FT sanotethisisanotethisisanote\"\n", writer.toString()); } diff --git a/src/test/java/uk/ac/ebi/embl/flatfile/writer/genbank/GenbankQualifierWriterTest.java b/src/test/java/uk/ac/ebi/embl/flatfile/writer/genbank/GenbankQualifierWriterTest.java index dac5e8da..936377ee 100644 --- a/src/test/java/uk/ac/ebi/embl/flatfile/writer/genbank/GenbankQualifierWriterTest.java +++ b/src/test/java/uk/ac/ebi/embl/flatfile/writer/genbank/GenbankQualifierWriterTest.java @@ -100,8 +100,10 @@ public void testWrite_Wrap() throws IOException { + " this is a note this is a note this is a note this is a\n" + " note this is a note this is a note this is a note this is\n" + " a note this is a note this is a note \"\n" - + " /note=\"thisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisanotethisisa\n" - + " notethisisanotethisisanote\"\n", + + " /note=\"thisisanotethisisanotethisisanotethisisanotethisisa\n" + + " notethisisanotethisisanotethisisanotethisisanotethisisanot\n" + + " ethisisanotethisisanotethisisanotethisisanotethisisanoteth\n" + + " isisanotethisisanotethisisanote\"\n", writer.toString()); } From 19ab4217a3850c124841db84b7a87e8dcf283d89 Mon Sep 17 00:00:00 2001 From: Rajkumar-D Date: Mon, 11 Mar 2024 16:57:00 +0000 Subject: [PATCH 2/2] Updating setForceLineBreak for Note qualifier --- .../java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java b/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java index 686cb635..4e5a43fd 100644 --- a/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java +++ b/src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java @@ -19,7 +19,7 @@ public class QualifierWriter extends FlatFileWriter { private final Qualifier qualifier; - private static final int NOTE_MAX_LINE_LENGTH = 200; + private static final int NOTE_MAX_LINE_LENGTH = 80; public QualifierWriter(Entry entry, Qualifier qualifier, WrapType wrapType, String header) { super(entry, wrapType);