X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fnj.java;h=dca5d08dcd43d20b8fc44916eb3a4b5f44b83fb3;hb=1d0bff367b887d510b89b73364d656247125771f;hp=7ef1d56f15a7b31f256bc7610c226c2b236ddc6e;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/application/nj.java b/forester/java/src/org/forester/application/nj.java
index 7ef1d56..dca5d08 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;
 
@@ -33,6 +33,7 @@ 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;
@@ -118,11 +119,10 @@ public class nj {
                     + matrices[ 0 ].getSize() );
         }
         final List<Phylogeny> ps = new ArrayList<Phylogeny>();
-        final NeighborJoining nj = NeighborJoining.createInstance();
-        nj.setVerbose( verbose );
+        final NeighborJoining nj = NeighborJoining.createInstance( verbose, 6 );
         final long start_time = new Date().getTime();
         for( final DistanceMatrix matrix : matrices ) {
-            ps.add( nj.execute( matrix ) );
+            ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
         }
         final long end_time = new Date().getTime();
         final PhylogenyWriter w = new PhylogenyWriter();
@@ -142,7 +142,7 @@ 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" );