JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruc...

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 84a74b6..25f1c27 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -504,7 +504,9 @@ public class AlignedCodonFrame
     {
       int mStart=ssm.getMapping().getMap().getFromLowest(),mEnd=ssm.getMapping().map.getFromHighest();
       if ((ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
-              && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
+              // here AlignmentUtilsTest. testAlignProteinAsDna_incompleteStartCodon fails because mStart/mEnd is contained by seq
+              // without this filter, we don't get the correct mapping, however
+           )//   && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
       {
         for (SequenceI sourceAligned : al.getSequences())
         {