JAL-2349 allow contact map to be associated with a reference sequence

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 7f73110..9e55911 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2062,6 +2062,11 @@ public class Alignment implements AlignmentI, AutoCloseable
     aa.editable = false;
     // aa.autoCalculated = true;
     contactmaps.put(aa.annotationId, cm);
+    // TODO: contact matrices could be intra or inter - more than one refseq possible! 
+    if (cm.hasReferenceSeq())
+    {
+      aa.setSequenceRef(cm.getReferenceSeq());
+    }
     addAnnotation(aa);
     return aa;
   }