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JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via alignAs if guide peptide doesn...
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
d8c1cdf
..
d04d810
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-979,10
+979,10
@@
public class AlignmentUtils
.getFromRanges());
int mappedToLength = MappingUtils
.getLength(mapList.getToRanges());
.getFromRanges());
int mappedToLength = MappingUtils
.getLength(mapList.getToRanges());
- boolean addStopCodon = (cdsLength == mappedFromLength
+ boolean addStopCodon = peptide.getDatasetSequence().getEnd()==peptide.getEnd() && ((cdsLength == mappedFromLength
* CODON_LENGTH + CODON_LENGTH)
|| (peptide.getDatasetSequence()
* CODON_LENGTH + CODON_LENGTH)
|| (peptide.getDatasetSequence()
- .getLength() == mappedFromLength - 1);
+ .getLength() == mappedFromLength - 1));
if (cdsLength != mappedToLength && !addStopCodon)
{
System.err.println(String.format(
if (cdsLength != mappedToLength && !addStopCodon)
{
System.err.println(String.format(