Merge branch 'develop' into improvement/JAL-4193_cl_arg_prevent_startup_file

[jalview.git] / src / jalview / analysis / AverageDistanceEngine.java

diff --git a/src/jalview/analysis/AverageDistanceEngine.java b/src/jalview/analysis/AverageDistanceEngine.java
index e6a763b..f4d69d5 100644 (file)
--- a/src/jalview/analysis/AverageDistanceEngine.java
+++ b/src/jalview/analysis/AverageDistanceEngine.java
@@ -100,11 +100,18 @@ public class AverageDistanceEngine extends TreeEngine
 
       // compute distance matrix element
       ContactListI ith = cm.getContactList(i);
-
+      distances.setValue(i, i, 0);
+      if (ith==null)
+      {
+        continue;
+      }
       for (int j = 0; j < i; j++)
       {
-        distances.setValue(i, i, 0);
         ContactListI jth = cm.getContactList(j);
+        if (jth == null)
+        {
+          break;
+        }
         double prd = 0;
         for (int indx = 0; indx < cm.getHeight(); indx++)
         {