2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.application;
29 import java.io.IOException;
30 import java.util.List;
32 import org.forester.io.parsers.PhylogenyParser;
33 import org.forester.io.parsers.nhx.NHXParser;
34 import org.forester.io.parsers.util.ParserUtils;
35 import org.forester.io.writers.PhylogenyWriter;
36 import org.forester.phylogeny.Phylogeny;
37 import org.forester.phylogeny.PhylogenyMethods;
38 import org.forester.phylogeny.PhylogenyNode;
39 import org.forester.phylogeny.data.Confidence;
40 import org.forester.phylogeny.data.PhylogenyDataUtil;
41 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
42 import org.forester.phylogeny.factories.PhylogenyFactory;
43 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
45 public final class support_transfer {
48 * Transfers branch length values from one Phylogeny to another. It is
49 * mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )"
50 * of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.
53 * Filename (String) for Phylogeny which has correct branch
56 * String Filename (String) for Phylogeny to which the branch
57 * lengths of the first Phylogeny are to be copied, both Trees
58 * must only differ in their branch length values, i.e. topology
59 * and sequence names, etc. must be the same
61 * String Filename (String) for outputfile
63 * String [number of tree with correct bl to use in case treefile contains more than one, default 0]
66 public static void main( final String args[] ) {
67 Phylogeny phylogeny_w_bl = null; // Has correct branch lengths
68 Phylogeny phylogeny_w_support_vals = null; // Has bootsrap in the b.l.
71 // to the bootstrap field by the Phylogeny constructor) or
72 // has regular boostraps (NHX, :B=...).
73 File infile_bl = null;
74 File infile_support_vals = null;
76 int index_of_tree_w_bl = 0;
77 if ( ( args.length != 3 ) && ( args.length != 4 ) ) {
78 System.err.println( "SupportTransfer: Wrong number" + " of arguments. Usage: \"java transfersBranchLenghts"
79 + " <treefile with correct b.l.> <treefile with bootstraps>" + "<outputfile> "
80 + "[number of tree with correct bl to use in case treefile contains more than one, default 0]\"" );
83 if ( args.length == 4 ) {
84 index_of_tree_w_bl = ( new Integer( args[ 3 ] ) ).intValue();
87 infile_bl = new File( args[ 0 ] );
88 infile_support_vals = new File( args[ 1 ] );
89 outfile = new File( args[ 2 ] );
90 if ( outfile.exists() ) {
91 System.out.println( "transfersBranchLenghts: " + outfile.getAbsolutePath() + " does already exist." );
94 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
95 final PhylogenyParser pp_bl = ParserUtils.createParserDependingOnFileType( infile_bl, true );
96 final PhylogenyParser pp_s = ParserUtils.createParserDependingOnFileType( infile_support_vals, true );
97 if ( pp_bl instanceof NHXParser ) {
98 ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
100 phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
101 phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];
103 catch ( final IOException e ) {
104 System.out.println( "SupportTransfer: Could not read tree(s): " + e );
108 final double max_bs = PhylogenyMethods.getMaximumConfidenceValue( phylogeny_w_support_vals );
109 PhylogenyMethods.normalizeBootstrapValues( phylogeny_w_support_vals, max_bs, 100 );
110 support_transfer.transferSupportValues( phylogeny_w_support_vals, phylogeny_w_bl );
112 catch ( final IllegalArgumentException e ) {
113 System.out.println( e.getMessage() );
117 final PhylogenyWriter writer = new PhylogenyWriter();
118 writer.toPhyloXML( outfile, phylogeny_w_bl, 0 );
120 catch ( final IOException e ) {
121 System.out.println( "Failure to write phylogeny \'" + outfile + "\" [" + e.getMessage() + "]" );
127 * Moves the values in the branch length field to the bootstrap field, for
128 * each PhylogenyNode of this Phylogeny. Converts a Phylogeny originating
129 * from a phylip treefile after bootstrapping and which therefore has its
130 * bootstrap values where the branch lenghts would be.
132 public final static void moveBranchLengthsToBootstrap( final Phylogeny p ) {
133 for( final PhylogenyNodeIterator iter = p.iteratorPreorder(); iter.hasNext(); ) {
134 final PhylogenyNode node = iter.next();
135 if ( node.isInternal() && ( node.getDistanceToParent() > 0 ) ) {
136 PhylogenyMethods.setBootstrapConfidence( node, node.getDistanceToParent() );
139 PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
141 node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
143 } // moveBranchLengthsToBootstrap()
146 * Modifies Phylogeny to with the support values from Phylogeny from.
147 * Important (but obvious): The topology of both trees needs to be the same.
148 * The method is not robust, and might produce wrong results if the internal
149 * topology differs or if the external node names are not unique.
152 * the Phylogeny to copy the support values from
154 * the Phylogeny to copy the support values to
156 public final static void transferSupportValues( final Phylogeny from, final Phylogeny to ) {
157 to: for( final PhylogenyNodeIterator it_to = to.iteratorPostorder(); it_to.hasNext(); ) {
158 final PhylogenyNode node_to = it_to.next();
159 if ( !node_to.isExternal() ) {
160 final List<String> ext_children_to = node_to.getAllExternalDescendantsNames();
161 for( final PhylogenyNodeIterator it_from = from.iteratorPostorder(); it_from.hasNext(); ) {
162 final PhylogenyNode node_from = it_from.next();
163 final List<String> ext_children_from = node_from.getAllExternalDescendantsNames();
164 if ( ( ext_children_from.size() == ext_children_to.size() )
165 && ext_children_from.containsAll( ext_children_to ) ) {
166 PhylogenyMethods.setBootstrapConfidence( node_to,
167 PhylogenyMethods.getConfidenceValue( node_from ) );
171 final String message = "Attempt to transfer support values from nonidentical topologies";
172 throw new IllegalArgumentException( message );