// 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
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
+ 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( ( DistanceMatrix ) matrix ) );
}
final long end_time = new Date().getTime();
final PhylogenyWriter w = new PhylogenyWriter();
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" );