JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that...

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 9fa11cc..fbc8a61 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -464,8 +464,7 @@ public class AlignedCodonFrame
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
-                  || ssm.mapping.to == sourceAligned)
+          if (ssm.covers(sourceAligned,true))
           {
             return sourceAligned;
           }
@@ -483,7 +482,7 @@ public class AlignedCodonFrame
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.fromSeq == sourceAligned.getDatasetSequence())
+          if (ssm.covers(sourceAligned,true))
           {
             return sourceAligned;
           }