// 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 org.forester.io.parsers.util.ParserUtils;
import org.forester.io.parsers.util.PhylogenyParserException;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
final boolean is_rooted ) throws IOException {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final NHXParser pars = new NHXParser();
- pars.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+ pars.setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
pars.setReplaceUnderscores( isReplaceUnderscores() );
pars.setIgnoreQuotes( isIgnoreQuotes() );
if ( rooted_info_present ) {
return _replace_underscores;
}
+ @Override
public Phylogeny[] parse() throws IOException, NHXFormatException {
reset();
final BufferedReader reader = ParserUtils.createReader( getNexusSource() );
_replace_underscores = replace_underscores;
}
+ @Override
public void setSource( final Object nexus_source ) throws PhylogenyParserException, IOException {
if ( nexus_source == null ) {
throw new PhylogenyParserException( getClass() + ": attempt to parse null object." );