From 83193bc5c3e150dc7331b5b27a67cb5f9efb477c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 30 Sep 2005 17:18:22 +0000
Subject: [PATCH] Restore file before eclipse changes

---
 src/jalview/analysis/NJTree.java |   32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 97b8519..6c239be 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -251,14 +251,14 @@ public class NJTree
     {
         while (noClus > 2)
         {
-           /* if (type.equals("NJ"))
+            if (type.equals("NJ"))
             {
                 float mind = findMinNJDistance();
             }
             else
             {
                 float mind = findMinDistance();
-            }*/
+            }
 
             Cluster c = joinClusters(mini, minj);
 
@@ -273,7 +273,7 @@ public class NJTree
         boolean onefound = false;
 
         int one = -1;
-        //int two = -1;
+        int two = -1;
 
         for (int i = 0; i < noseqs; i++)
         {
@@ -281,7 +281,7 @@ public class NJTree
             {
                 if (onefound == false)
                 {
-                    //two = i;
+                    two = i;
                     onefound = true;
                 }
                 else
@@ -291,7 +291,7 @@ public class NJTree
             }
         }
 
-       // Cluster c = joinClusters(one, two);
+        Cluster c = joinClusters(one, two);
         top = (SequenceNode) (node.elementAt(one));
 
         reCount(top);
@@ -375,11 +375,11 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
         float dist)
     {
-        //float ih = 0;
-       // float jh = 0;
+        float ih = 0;
+        float jh = 0;
 
-        //SequenceNode sni = tmpi;
-        //SequenceNode snj = tmpj;
+        SequenceNode sni = tmpi;
+        SequenceNode snj = tmpj;
 
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
@@ -469,8 +469,8 @@ 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;
+        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];
@@ -1121,6 +1121,15 @@ public class NJTree
         }
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param node DOCUMENT ME!
+     */
+    public void setMaxDist(SequenceNode node)
+    {
+        this.maxdist = maxdist;
+    }
 
     /**
      * DOCUMENT ME!
@@ -1164,3 +1173,4 @@ class Cluster
         this.value = value;
     }
 }
+
-- 
1.7.10.2