X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=cfd6aee05b6f61624b167b24dfa6c553f5368537;hb=c1d8867e99833bcb9019aaebddfabb99dd852f66;hp=514a32662fdf2318a146249c0c9346daf7e01c0f;hpb=1730be35c0c3fda8f9c63f1fb6dcea7b5fb2ba35;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 514a326..cfd6aee 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2057,7 +2057,7 @@ public class Alignment implements AlignmentI, AutoCloseable
     if (cm == null && _aa.sequenceRef != null)
     {
       cm = _aa.sequenceRef.getContactMatrixFor(_aa);
-      if (cm == null)
+      if (cm == null && _aa.sequenceRef.getDatasetSequence()!=null)
       {
         // TODO fix up this logic and unify with getContactListFor
         cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);