// 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.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;
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( PhylogenyMethods.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()