X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2Fdistance%2FNeighborJoining.java;h=c624bfff21f3dabe41e904e4a7d5028e2faa9b9e;hb=391381d661a230af98751dd6eba77bb2353c4d3e;hp=164599de97d981fd1b7427941ece0ef52f98b46c;hpb=5a79605dde82b956c0cf429dd016c3b478012f9c;p=jalview.git

diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index 164599d..c624bff 100644
--- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
+++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.evoinference.distance;
 
@@ -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;
@@ -60,7 +60,7 @@ public final class NeighborJoining {
             }
             //  _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
             i_m = _mappings[ i ];
-            _d_values[ otu1_m ][ i_m ] = ( _d_values[ otu1_m ][ i_m ] + _d_values[ i_m ][ otu2_m ] - 2 ) / 2;
+            _d_values[ otu1_m ][ i_m ] = ( ( _d_values[ otu1_m ][ i_m ] + _d_values[ i_m ][ otu2_m ] ) - 2 ) / 2;
         }
     }
 
@@ -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();
     }
 
@@ -196,14 +195,14 @@ public final class NeighborJoining {
             j_m = _mappings[ j ];
             for( int i = 0; i < j; ++i ) {
                 //  _m_values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + r_j ) / ( _n - 2 );
-                _m_values[ i ][ j ] = _d_values[ _mappings[ i ] ][ j_m ] - ( _r[ i ] + r_j ) / ( _n_2 );
+                _m_values[ i ][ j ] = _d_values[ _mappings[ i ] ][ j_m ] - ( ( _r[ i ] + r_j ) / ( _n_2 ) );
             }
         }
     }
 
     // otu2 will, in effect, be "deleted" from the matrix.
     private final void updateMappings( final int otu2 ) {
-        for( int i = otu2; i < _mappings.length - 1; ++i ) {
+        for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
             _mappings[ i ] = _mappings[ i + 1 ];
         }
     }