JAL-2349 fix off by one when resolving columns for sequence associated contact matrix

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 321eee3..517a6dd 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2080,10 +2080,10 @@ public class Alignment implements AlignmentI, AutoCloseable
       if (spos >= _aa.sequenceRef.getStart()
               && spos <= 1 + _aa.sequenceRef.getEnd())
       {
-        cl = _aa.sequenceRef.getContactListFor(_aa, spos);
+        cl = _aa.sequenceRef.getContactListFor(_aa, spos-_aa.sequenceRef.getStart());
         if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
         {
-          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos);
+          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos-_aa.sequenceRef.getStart());
         }
       }
     }