From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 26 May 2012 04:21:07 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7e1f3a610d68fed02e1accd576714f3871c776fa;hp=d4d7988fb570204203333a5097f074e0c0937c1a;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index 164599d..33f3f6e 100644
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
@@ -36,7 +36,7 @@ import org.forester.util.ForesterUtil;
 public final class NeighborJoining {
 
     private BasicSymmetricalDistanceMatrix _d;
-    private BasicSymmetricalDistanceMatrix _m;
+    // private BasicSymmetricalDistanceMatrix _m;
     private double[][]                     _d_values;
     private double[][]                     _m_values;
     private double[]                       _r;
@@ -178,11 +178,10 @@ public final class NeighborJoining {
     private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
         _n = distances.getSize();
         _d = distances;
-        _m = new BasicSymmetricalDistanceMatrix( _n );
         _r = new double[ _n ];
         _mappings = new int[ _n ];
         _d_values = _d.getValues();
-        _m_values = _m.getValues();
+        _m_values = new double[ _n ][ _n ];
         initExternalNodes();
     }