X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=cd142ca7a3434cbc19810d704cba8e11fde391b2;hb=ce93212014c116c4c516c6dc85c5032449d311eb;hp=2b88cb064e77660f39437d8829cc9e6520d007f4;hpb=bde972cad13060894eadcb189afc9fa3d8ec265a;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 2b88cb0..cd142ca 100644
--- 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();