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)
     {
-      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();
-        Mapping map = mapping.getMappingBetween(cdsSeq, peptide);
+        Mapping map = foundMap.get(0).getMapping();
         if (map != null)
         {
           MapList mapList = map.getMap();