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.ArrayList;
31 import java.util.Arrays;
32 import java.util.List;
34 import org.forester.io.parsers.PhylogenyParser;
35 import org.forester.io.parsers.util.ParserUtils;
36 import org.forester.io.writers.PhylogenyWriter;
37 import org.forester.phylogeny.Phylogeny;
38 import org.forester.phylogeny.PhylogenyMethods;
39 import org.forester.phylogeny.PhylogenyNode;
40 import org.forester.phylogeny.data.Confidence;
41 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
42 import org.forester.phylogeny.factories.PhylogenyFactory;
43 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
44 import org.forester.tools.SupportCount;
45 import org.forester.util.CommandLineArguments;
46 import org.forester.util.ForesterUtil;
48 public class count_support {
50 final static private String PRG_NAME = "count_support";
51 final static private String PRG_VERSION = "1.0";
52 final static private String PRG_DATE = "2008.03.04";
53 private final static boolean WRITE_EVALUATORS_AS_NHX = false;
55 public static void main( final String args[] ) {
57 .printProgramInformation( count_support.PRG_NAME, count_support.PRG_VERSION, count_support.PRG_DATE );
58 if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
60 System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
63 .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
64 + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
66 .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
67 System.out.println( " : -t=<d> threshold for similarity (0.0 to 1.0)" );
68 System.out.println( " : -n no branch lengths in outfile for evaluator phylogenies" );
72 CommandLineArguments cla = null;
74 cla = new CommandLineArguments( args );
76 catch ( final Exception e ) {
77 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
79 final List<String> allowed_options = new ArrayList<String>();
80 allowed_options.add( "s" );
81 allowed_options.add( "t" );
82 allowed_options.add( "n" );
83 final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
84 if ( dissallowed_options.length() > 0 ) {
85 ForesterUtil.fatalError( count_support.PRG_NAME, "Unknown option(s): " + dissallowed_options );
87 final File phylogeny_infile = cla.getFile( 0 );
88 final File evaluators_infile = cla.getFile( 1 );
89 final File phylogeny_outfile = cla.getFile( 2 );
90 File evaluators_outfile = null;
91 boolean branch_lengths_in_ev_out = true;
92 if ( cla.isOptionSet( "n" ) ) {
93 branch_lengths_in_ev_out = false;
95 if ( cla.getNumberOfNames() == 4 ) {
96 evaluators_outfile = cla.getFile( 3 );
99 if ( !branch_lengths_in_ev_out ) {
100 ForesterUtil.fatalError( count_support.PRG_NAME,
101 "Cannot use -n option if no outfile for evaluators specified" );
105 Phylogeny[] ev = null;
107 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
108 final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogeny_infile, true );
109 p = factory.create( phylogeny_infile, pp )[ 0 ];
111 catch ( final Exception e ) {
112 ForesterUtil.fatalError( count_support.PRG_NAME,
113 "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]" );
116 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
117 final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( evaluators_infile, true );
118 ev = factory.create( evaluators_infile, pp );
120 catch ( final Exception e ) {
121 ForesterUtil.fatalError( count_support.PRG_NAME,
122 "Could not read \"" + evaluators_infile + "\" [" + e.getMessage() + "]" );
124 boolean strip = false;
125 if ( cla.isOptionSet( "s" ) ) {
128 double threshhold = -1.0;
129 if ( cla.isOptionSet( "t" ) ) {
131 threshhold = cla.getOptionValueAsDouble( "t" );
133 catch ( final Exception e ) {
134 ForesterUtil.fatalError( count_support.PRG_NAME, "error in command line arguments: " + e.getMessage() );
136 if ( ( threshhold < 0 ) || ( threshhold > 1.0 ) ) {
137 ForesterUtil.fatalError( count_support.PRG_NAME,
138 "support threshold has to be between 0.0 and 1.0 (inclusive)" );
141 List<Phylogeny> evaluator_phylogenies_above_threshold = null;
143 if ( threshhold >= 0 ) {
144 evaluator_phylogenies_above_threshold = SupportCount.count( p, ev, strip, threshhold, true );
145 if ( evaluator_phylogenies_above_threshold.size() < 1 ) {
146 ForesterUtil.fatalError( "count_support", "appears like threshold for similarity is set too high" );
150 SupportCount.count( p, ev, strip, true );
153 catch ( final Exception e ) {
154 ForesterUtil.fatalError( count_support.PRG_NAME, "Failure during support counting: " + e.getMessage() );
156 if ( threshhold >= 0 ) {
157 count_support.normalizeSupport( p, 100, evaluator_phylogenies_above_threshold.size() );
158 System.out.println( evaluator_phylogenies_above_threshold.size() + " out of " + ev.length
159 + " evaluator phylogenies are above threshold of " + threshhold );
162 final PhylogenyWriter w = new PhylogenyWriter();
163 w.toPhyloXML( phylogeny_outfile, p, 1 );
165 catch ( final IOException e ) {
166 ForesterUtil.fatalError( count_support.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
168 System.out.println();
169 System.out.println( "Wrote phylogeny with support values to: " + phylogeny_outfile );
170 if ( evaluators_outfile != null ) {
172 final PhylogenyWriter w = new PhylogenyWriter();
173 if ( evaluator_phylogenies_above_threshold != null ) {
174 System.out.println( "Writing " + evaluator_phylogenies_above_threshold.size()
175 + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
176 if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
177 w.toNewHampshireX( evaluator_phylogenies_above_threshold, evaluators_outfile, ";"
178 + ForesterUtil.getLineSeparator() );
181 w.toNewHampshire( evaluator_phylogenies_above_threshold,
183 branch_lengths_in_ev_out,
185 ";" + ForesterUtil.getLineSeparator() );
189 System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
190 if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
191 w.toNewHampshireX( Arrays.asList( ev ),
193 ";" + ForesterUtil.getLineSeparator() );
196 w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"
197 + ForesterUtil.getLineSeparator() );
201 catch ( final IOException e ) {
202 ForesterUtil.fatalError( count_support.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
205 System.out.println();
206 System.out.println( "Done." );
207 System.out.println();
210 private static void normalizeSupport( final Phylogeny p, final double normalized_max, final int number_phylos ) {
211 double min = Double.MAX_VALUE;
212 double max = -Double.MAX_VALUE;
215 for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
216 final PhylogenyNode node = iter.next();
217 if ( !node.isRoot() && !node.isExternal() ) {
218 final double b = PhylogenyMethods.getConfidenceValue( node );
222 if ( ( b >= 0 ) && ( b < min ) ) {
230 System.out.println( "Max support before normalization is : " + max );
231 System.out.println( "Min support before normalization is : " + min );
232 System.out.println( "Average support before normalization is: " + av + " (=" + sum + "/" + n + ")" );
233 System.out.println( "Normalizing so that theoretical maximum support value is: " + normalized_max );
234 System.out.println( "Number of phylogenies used in support analysis: " + number_phylos );
235 final double f = normalized_max / number_phylos;
236 min = Double.MAX_VALUE;
237 max = -Double.MAX_VALUE;
240 for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
241 final PhylogenyNode node = iter.next();
242 if ( node.isRoot() || node.isExternal() ) {
243 PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
246 double b = PhylogenyMethods.getConfidenceValue( node );
248 PhylogenyMethods.setBootstrapConfidence( node, b );
252 if ( ( b >= 0 ) && ( b < min ) ) {
260 System.out.println( "Max support after normalization is : " + max );
261 System.out.println( "Min support after normalization is : " + min );
262 System.out.println( "Average support after normalization is: " + av + " (=" + sum + "/" + n + ")" );