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Updating setForceLineBreak for Note qualifier #156

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Updating setForceLineBreak for Note qualifier #156

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e6b5a56
Updating setForceLineBreak for Note qualifier
Rajkumar-D Mar 11, 2024
19ab421
Updating setForceLineBreak for Note qualifier
Rajkumar-D Mar 11, 2024
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2 changes: 1 addition & 1 deletion src/main/java/uk/ac/ebi/embl/api/validation/check/sourcefeature/SequenceCoverageCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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) {
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3 changes: 2 additions & 1 deletion src/main/java/uk/ac/ebi/embl/flatfile/writer/QualifierWriter.java
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Expand Up @@ -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);
Expand All @@ -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);
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@raskoleinonen raskoleinonen Mar 12, 2024

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Let's only make the change where we add the following to note qualifier:

setForceLineBreak(true);

}
}
}
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6 changes: 4 additions & 2 deletions src/test/java/uk/ac/ebi/embl/flatfile/writer/embl/EmblQualifierWriterTest.java
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Expand Up @@ -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());
}

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6 changes: 4 additions & 2 deletions src/test/java/uk/ac/ebi/embl/flatfile/writer/genbank/GenbankQualifierWriterTest.java
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Expand Up @@ -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());
}

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