JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid...

[jalview.git] / src / jalview / datamodel / AlignedCodonFrame.java

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 3c33063..eda1a13 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -445,7 +445,9 @@ public class AlignedCodonFrame
     SequenceI ds = seq.getDatasetSequence();
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq || ssm.fromSeq == ds)
+      if (ssm.covers(seq,true,true))
+      {
+      if ((ssm.fromSeq == seq || ssm.fromSeq == ds))
       {
         codon = ssm.mapping.map.locateInTo(index, index);
         if (codon != null)
@@ -456,7 +458,7 @@ public class AlignedCodonFrame
           }
         }
       }
-      else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
+      else if ((ssm.mapping.to == seq || ssm.mapping.to == ds))
       {
         {
           codon = ssm.mapping.map.locateInFrom(index, index);
@@ -468,7 +470,7 @@ public class AlignedCodonFrame
             }
           }
         }
-      }
+      }}
     }
   }