JAL-2428 correct order of processing in joinClusters()

diff --git a/src/jalview/analysis/AverageDistanceTree.java b/src/jalview/analysis/AverageDistanceTree.java
index 7e3cfe1..5b0e20a 100644 (file)
--- a/src/jalview/analysis/AverageDistanceTree.java
+++ b/src/jalview/analysis/AverageDistanceTree.java
@@ -55,9 +55,6 @@ public class AverageDistanceTree extends TreeBuilder
     {
       distances.setValue(i, ii, newdist[ii]);
       distances.setValue(ii, i, newdist[ii]);
-      System.out.println(String.format(
-              "findClusterDistance(%d, %d) newdist to %d is %f", i, j, ii,
-              newdist[ii]));
     }
   }
 
@@ -88,8 +85,6 @@ public class AverageDistanceTree extends TreeBuilder
         }
       }
     }
-    System.out.println("findMinDistance found " + min + " at " + mini + ","
-            + minj);
     return min;
   }
 
@@ -127,8 +122,6 @@ public class AverageDistanceTree extends TreeBuilder
 
     tmpi.dist = ((dist / 2) - ih);
     tmpj.dist = ((dist / 2) - jh);
-    System.out.println("findNewDistances set tmpi to " + tmpi.dist
-            + ", tmpj to " + tmpj.dist);
   }
 
 }

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 49c56c9..f28c6bc 100644 (file)
--- 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,