X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=0683265921bb81b97c2573d5d0606d6ca307ae9c;hb=748cffd412de4d6951d8f746428ff601861fe144;hp=6c239be1de8a3c2311e99ca0c59a2c0dc95a8ee2;hpb=83193bc5c3e150dc7331b5b27a67cb5f9efb477c;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 6c239be..0683265 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -253,11 +253,11 @@ public class NJTree
         {
             if (type.equals("NJ"))
             {
-                float mind = findMinNJDistance();
+                findMinNJDistance();
             }
             else
             {
-                float mind = findMinDistance();
+                findMinDistance();
             }
 
             Cluster c = joinClusters(mini, minj);
@@ -291,7 +291,7 @@ public class NJTree
             }
         }
 
-        Cluster c = joinClusters(one, two);
+        joinClusters(one, two);
         top = (SequenceNode) (node.elementAt(one));
 
         reCount(top);
@@ -375,11 +375,6 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
         float dist)
     {
-        float ih = 0;
-        float jh = 0;
-
-        SequenceNode sni = tmpi;
-        SequenceNode snj = tmpj;
 
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
@@ -469,8 +464,6 @@ public class NJTree
      */
     public void findClusterNJDistance(int i, int j)
     {
-        int noi = ((Cluster) cluster.elementAt(i)).value.length;
-        int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
         // New distances from cluster to others
         float[] newdist = new float[noseqs];
@@ -665,7 +658,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
                     as.calcScoreMatrix();
                     as.traceAlignment();
-                    as.printAlignment();
+                    as.printAlignment(System.out);
                     distance[i][j] = (float) as.maxscore;
 
                     if (max < distance[i][j])
@@ -1121,15 +1114,6 @@ public class NJTree
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void setMaxDist(SequenceNode node)
-    {
-        this.maxdist = maxdist;
-    }
 
     /**
      * DOCUMENT ME!