// 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
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.phylogeny.Phylogeny;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( species_tree_file, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
species_tree = factory.create( species_tree_file, pp )[ 0 ];
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "Failed to read species tree from \"" + gene_tree_file + "\" ["
- + e.getMessage() + "]" );
+ ForesterUtil.fatalError( PRG_NAME,
+ "Failed to read species tree from \"" + gene_tree_file + "\" [" + e.getMessage()
+ + "]" );
}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( gene_tree_file, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( gene_tree_file, true );
gene_tree = factory.create( gene_tree_file, pp )[ 0 ];
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( PRG_NAME, "Failed to read gene tree from \"" + gene_tree_file + "\" ["
- + e.getMessage() + "]" );
+ ForesterUtil.fatalError( PRG_NAME,
+ "Failed to read gene tree from \"" + gene_tree_file + "\" [" + e.getMessage()
+ + "]" );
}
gene_tree.setRooted( true );
species_tree.setRooted( true );