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JAL-3748 pass a list to findAlignedSequence to return mapping that relates CDS and...
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
2b88cb0
..
cd142ca
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-960,11
+960,12
@@
public class AlignmentUtils
.findMappingsForSequence(cdsSeq, mappings);
for (AlignedCodonFrame mapping : dnaMappings)
{
.findMappingsForSequence(cdsSeq, mappings);
for (AlignedCodonFrame mapping : dnaMappings)
{
- SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein);
+ List<SequenceToSequenceMapping> foundMap=new ArrayList<>();
+ SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein,foundMap);
if (peptide != null)
{
final int peptideLength = peptide.getLength();
if (peptide != null)
{
final int peptideLength = peptide.getLength();
- Mapping map = mapping.getMappingBetween(cdsSeq, peptide);
+ Mapping map = foundMap.get(0).getMapping();
if (map != null)
{
MapList mapList = map.getMap();
if (map != null)
{
MapList mapList = map.getMap();