X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2FTestPhylogenyReconstruction.java;h=3529d1e352b63081dd57d2fa958fe4bfa1a4c8eb;hb=612e51e63eb66025a04439fc380384a945a4a30f;hp=5849ac1c7d68a4dbfccaa2f3b343fa914cab9cab;hpb=eccc2fdb674f76be1815fd7984295661bff8a2be;p=jalview.git

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 5849ac1..3529d1e 100644
--- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@ -7,7 +7,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -17,13 +17,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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;
 
@@ -1925,7 +1925,6 @@ public class TestPhylogenyReconstruction {
             m.setIdentifier( 4, "E" );
             m.setIdentifier( 5, "F" );
             final NeighborJoining nj = NeighborJoining.createInstance();
-            nj.setVerbose( false );
             nj.execute( m );
             m = new BasicSymmetricalDistanceMatrix( 7 );
             m.setIdentifier( 0, "Bovine" );
@@ -2347,10 +2346,14 @@ public class TestPhylogenyReconstruction {
 
     private static void timeNeighborJoining() {
         final NeighborJoining nj = NeighborJoining.createInstance();
-        for( int n = 3; n <= 12; ++n ) {
+        for( int n = 3; n <= 13; ++n ) {
             final int x = ( int ) Math.pow( 2, n );
             final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
             mt.randomize( new Date().getTime() );
+            //  for( int i = 0; i < mt.getSize(); i++ ) {
+            //      mt.setIdentifier( i, i + "i" );
+            //  }
+            //  System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
             final long start_time = new Date().getTime();
             nj.execute( mt );
             System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms." );