From a0750c32b58b2861716f812331b4aea4ba7710b4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 4 Oct 2024 16:06:49 +0100
Subject: [PATCH] fix for JAL-4471 - secondary structure similarity tree can
 only be computed for sequence-associated annotation(s)

---
 .../analysis/scoremodels/SecondaryStructureDistanceModel.java      |    4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index 473abcf..164bd9e 100644
--- 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
-- 
1.7.10.2