X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=517a6dd02ec7e63f564a2a436c00b2c6b699350b;hb=a3125b0190d8f97ea9543006686d5fe4b8247ff2;hp=321eee3c5ab502839122a17286318fec97d94c6d;hpb=31c6e45ee34d7a9b531fc01a0da478b911f35570;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 321eee3..517a6dd 100755
--- 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());
         }
       }
     }