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JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSo...
[jalview.git]
/
src
/
jalview
/
io
/
EMBLLikeFlatFile.java
diff --git
a/src/jalview/io/EMBLLikeFlatFile.java
b/src/jalview/io/EMBLLikeFlatFile.java
index
64943b2
..
100fb8d
100644
(file)
--- a/
src/jalview/io/EMBLLikeFlatFile.java
+++ b/
src/jalview/io/EMBLLikeFlatFile.java
@@
-83,8
+83,7
@@
public abstract class EMBLLikeFlatFile extends AlignFile
/**
* Truncates (if necessary) the exon intervals to match 3 times the length of
/**
* Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
+ * the protein(including truncation for stop codon included in exon)
*
* @param proteinLength
* @param exon
*
* @param proteinLength
* @param exon
@@
-102,11
+101,9
@@
public abstract class EMBLLikeFlatFile extends AlignFile
int exonLength = MappingUtils.getLength(Arrays.asList(exon));
/*
int exonLength = MappingUtils.getLength(Arrays.asList(exon));
/*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
+ * if exon length matches protein, or is shorter, then leave it unchanged
*/
*/
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
+ if (expectedCdsLength >= exonLength)
{
return exon;
}
{
return exon;
}