// 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 org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
public final class support_transfer {
System.exit( -1 );
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp_bl = ForesterUtil.createParserDependingOnFileType( infile_bl, true );
- final PhylogenyParser pp_s = ForesterUtil.createParserDependingOnFileType( infile_support_vals, true );
+ final PhylogenyParser pp_bl = ParserUtils.createParserDependingOnFileType( infile_bl, true );
+ final PhylogenyParser pp_s = ParserUtils.createParserDependingOnFileType( infile_support_vals, true );
if ( pp_bl instanceof NHXParser ) {
- ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.YES );
+ ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
}
phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];
else {
PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
}
- node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+ node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
}
} // moveBranchLengthsToBootstrap()
final List<String> ext_children_from = node_from.getAllExternalDescendantsNames();
if ( ( ext_children_from.size() == ext_children_to.size() )
&& ext_children_from.containsAll( ext_children_to ) ) {
- PhylogenyMethods.setBootstrapConfidence( node_to, PhylogenyMethods
- .getConfidenceValue( node_from ) );
+ PhylogenyMethods.setBootstrapConfidence( node_to,
+ PhylogenyMethods.getConfidenceValue( node_from ) );
continue to;
}
}