// $Id: support_transfer.java,v 1.15 2010/06/23 22:20:31 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// 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
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// 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: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.application;
import java.io.File;
import java.io.IOException;
import java.util.List;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nhx.NHXParser;
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.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
public final class support_transfer {
/**
* Transfers branch length values from one Phylogeny to another. It is
* mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )"
* of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.
*
* @param args[0]
* Filename (String) for Phylogeny which has correct branch
* length values
* @param args[1]
* String Filename (String) for Phylogeny to which the branch
* lengths of the first Phylogeny are to be copied, both Trees
* must only differ in their branch length values, i.e. topology
* and sequence names, etc. must be the same
* @param args[2]
* String Filename (String) for outputfile
* @param args[3]
* String [number of tree with correct bl to use in case treefile contains more than one, default 0]
*/
public static void main( final String args[] ) {
Phylogeny phylogeny_w_bl = null; // Has correct branch lengths
Phylogeny phylogeny_w_support_vals = null; // Has bootsrap in the b.l.
// field (will be
// transferred
// to the bootstrap field by the Phylogeny constructor) or
// has regular boostraps (NHX, :B=...).
File infile_bl = null;
File infile_support_vals = null;
File outfile = null;
int index_of_tree_w_bl = 0;
if ( ( args.length != 3 ) && ( args.length != 4 ) ) {
System.err.println( "SupportTransfer: Wrong number" + " of arguments. Usage: \"java transfersBranchLenghts"
+ " <treefile with correct b.l.> <treefile with bootstraps>" + "<outputfile> "
+ "[number of tree with correct bl to use in case treefile contains more than one, default 0]\"" );
System.exit( -1 );
}
if ( args.length == 4 ) {
index_of_tree_w_bl = ( new Integer( args[ 3 ] ) ).intValue();
}
try {
infile_bl = new File( args[ 0 ] );
infile_support_vals = new File( args[ 1 ] );
outfile = new File( args[ 2 ] );
if ( outfile.exists() ) {
System.out.println( "transfersBranchLenghts: " + outfile.getAbsolutePath() + " does already exist." );
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 );
if ( pp_bl instanceof NHXParser ) {
( ( NHXParser ) pp_bl ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.YES );
}
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 ];
}
catch ( final IOException e ) {
System.out.println( "SupportTransfer: Could not read tree(s): " + e );
System.exit( -1 );
}
try {
final double max_bs = PhylogenyMethods.getMaximumConfidenceValue( phylogeny_w_support_vals );
PhylogenyMethods.normalizeBootstrapValues( phylogeny_w_support_vals, max_bs, 100 );
support_transfer.transferSupportValues( phylogeny_w_support_vals, phylogeny_w_bl );
}
catch ( final IllegalArgumentException e ) {
System.out.println( e.getMessage() );
System.exit( -1 );
}
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( outfile, phylogeny_w_bl, 0 );
}
catch ( final IOException e ) {
System.out.println( "Failure to write phylogeny \'" + outfile + "\" [" + e.getMessage() + "]" );
System.exit( -1 );
}
}
/**
* Moves the values in the branch length field to the bootstrap field, for
* each PhylogenyNode of this Phylogeny. Converts a Phylogeny originating
* from a phylip treefile after bootstrapping and which therefore has its
* bootstrap values where the branch lenghts would be.
*/
public final static void moveBranchLengthsToBootstrap( final Phylogeny p ) {
for( final PhylogenyNodeIterator iter = p.iteratorPreorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( node.isInternal() && ( node.getDistanceToParent() > 0 ) ) {
PhylogenyMethods.setBootstrapConfidence( node, node.getDistanceToParent() );
}
else {
PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
}
node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
}
} // moveBranchLengthsToBootstrap()
/**
* Modifies Phylogeny to with the support values from Phylogeny from.
* Important (but obvious): The topology of both trees needs to be the same.
* The method is not robust, and might produce wrong results if the internal
* topology differs or if the external node names are not unique.
*
* @param from
* the Phylogeny to copy the support values from
* @param to
* the Phylogeny to copy the support values to
*/
public final static void transferSupportValues( final Phylogeny from, final Phylogeny to ) {
to: for( final PhylogenyNodeIterator it_to = to.iteratorPostorder(); it_to.hasNext(); ) {
final PhylogenyNode node_to = it_to.next();
if ( !node_to.isExternal() ) {
final List<String> ext_children_to = node_to.getAllExternalDescendantsNames();
for( final PhylogenyNodeIterator it_from = from.iteratorPostorder(); it_from.hasNext(); ) {
final PhylogenyNode node_from = it_from.next();
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 ) );
continue to;
}
}
final String message = "Attempt to transfer support values from nonidentical topologies";
throw new IllegalArgumentException( message );
}
}
}
}