JAL-3855 JAL-2349 AlignmentI.getContactList takes care of mapping columns to sequence...

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3ae6831..fe65829 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2062,10 +2062,15 @@ public class Alignment implements AlignmentI, AutoCloseable
     }
     if (cl == null && _aa.sequenceRef != null)
     {
-      cl = _aa.sequenceRef.getContactListFor(_aa, column);
-      if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+      int spos = _aa.sequenceRef.findPosition(column) - 1;
+      if (spos >= _aa.sequenceRef.getStart()
+              && spos <= 1 + _aa.sequenceRef.getEnd())
       {
-        _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, column);
+        cl = _aa.sequenceRef.getContactListFor(_aa, spos);
+        if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+        {
+          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos);
+        }
       }
     }
     return cl;