X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;fp=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=f28c6bc4acd381e4db3884d047f031efcf764944;hb=a547c517480867ed1bbb2334ee7c51e642588a41;hp=49c56c964f9e20d9b8e8a9e0e46691e2b446f13b;hpb=be27d7b3cadbfb5c488066034c48b1735799b429;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 49c56c9..f28c6bc 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -396,11 +396,6 @@ public abstract class TreeBuilder
   {
     double dist = distances.getValue(i, j);
   
-    /*
-     * add the members of cluster(j) to cluster(i)
-     */
-    clusters.get(i).or(clusters.get(j));
-  
     ri = findr(i, j);
     rj = findr(j, i);
   
@@ -422,10 +417,12 @@ public abstract class TreeBuilder
     node.setElementAt(sn, i);
   
     /*
-     * mark cluster j as disposed of
+     * move the members of cluster(j) to cluster(i)
+     * and mark cluster j as out of the game
      */
+    clusters.get(i).or(clusters.get(j));
+    clusters.get(j).clear();
     done.set(j);
-    clusters.setElementAt(null, j);
   }
 
   protected abstract void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,