// 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
// 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
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" );
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." );