fix for JAL-4471 - secondary structure similarity tree can only be computed for seque...

diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index 473abcf..164bd9e 100644 (file)
--- a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
@@ -147,6 +147,10 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel
     {
       for (AlignmentAnnotation aa : alignAnnotList)
       {
+        if (aa.sequenceRef==null)
+        {
+          continue;
+        }
         if (selectedSSSource.equals(aa.label))
         {
           ssAlignmentAnnotationForSequences