// 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;
import java.util.List;
import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.pccx.BasicExternalNodeBasedCoverageExtender;
import org.forester.pccx.Coverage;
Phylogeny[] phylogenies = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogenies_infile, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infile, true );
phylogenies = factory.create( phylogenies_infile, pp );
}
catch ( final IOException e ) {
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( pccx.PRG_NAME, error );
}
- intable = BasicTableParser.parse( infile, " ", false );
+ intable = BasicTableParser.parse( infile, ' ', false, false );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( pccx.PRG_NAME, "failed to read \"" + infile + "\" [" + e.getMessage() + "]" );