From 2493af6c253a5a33cf783b9beb76caaaf1c777ec Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 3 Oct 2005 08:33:08 +0000
Subject: [PATCH] Remove redundancy from eclipse

---
 src/jalview/analysis/NJTree.java |   24 ++++--------------------
 1 file changed, 4 insertions(+), 20 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 6c239be..46a2ced 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);
@@ -375,12 +375,7 @@ 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];
@@ -1121,15 +1114,6 @@ public class NJTree
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void setMaxDist(SequenceNode node)
-    {
-        this.maxdist = maxdist;
-    }
 
     /**
      * DOCUMENT ME!
-- 
1.7.10.2