"rio" work

[jalview.git] / forester / java / src / org / forester / evoinference / TestPhylogenyReconstruction.java

diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index 5849ac1..9ff8457 100644 (file)
--- 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
@@ -17,7 +17,7 @@
 // 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
@@ -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." );