X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAverageDistanceEngine.java;h=f4d69d5cb4b3e592df21768a2ada643d983ce886;hb=a6f0678764ea06034460236c7a811bbfcad682aa;hp=e6a763b62d2b97909c476ef6f6fb7218b911cf6d;hpb=43281ae2821768ea283161f12ab0eb91ea6bb3b5;p=jalview.git

diff --git a/src/jalview/analysis/AverageDistanceEngine.java b/src/jalview/analysis/AverageDistanceEngine.java
index e6a763b..f4d69d5 100644
--- 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++)
         {