X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fnj.java;h=f21005894253ab7e10a0ccd9fbdef2dbaacb1973;hb=b5fe992f707cdad84255eb85040effbee97d61b3;hp=6bce55340938c128e1dfe92f7203421b6a752cc5;hpb=e2785e20355846acd9e81d50cf9a8a56b04ec095;p=jalview.git

diff --git a/forester/java/src/org/forester/application/nj.java b/forester/java/src/org/forester/application/nj.java
index 6bce553..f210058 100644
--- a/forester/java/src/org/forester/application/nj.java
+++ b/forester/java/src/org/forester/application/nj.java
@@ -22,7 +22,7 @@
 // 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.application;
 
@@ -33,7 +33,6 @@ import java.util.Date;
 import java.util.List;
 
 import org.forester.evoinference.distance.NeighborJoining;
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
 import org.forester.io.writers.PhylogenyWriter;
@@ -119,10 +118,10 @@ public class nj {
                     + matrices[ 0 ].getSize() );
         }
         final List<Phylogeny> ps = new ArrayList<Phylogeny>();
-        final NeighborJoining nj = NeighborJoining.createInstance( verbose );
+        final NeighborJoining nj = NeighborJoining.createInstance( verbose, 6 );
         final long start_time = new Date().getTime();
         for( final DistanceMatrix matrix : matrices ) {
-            ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
+            ps.add( nj.execute( ( DistanceMatrix ) matrix ) );
         }
         final long end_time = new Date().getTime();
         final PhylogenyWriter w = new PhylogenyWriter();
@@ -142,7 +141,7 @@ public class nj {
         System.out.println( "Usage:" );
         System.out.println();
         System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME
-                + " [options] <pairwise distances infile> <out file>" );
+                            + " [options] <pairwise distances infile> <out file>" );
         System.out.println();
         System.out.println( " Options: " );
         System.out.println( VERBOSE_OPTION + ": verbose on" );