forester/java/src/org/forester/application/count_support.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   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.
  13 //
  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.
  18 //
  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
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.util.ArrayList;
  31 import java.util.Arrays;
  32 import java.util.List;
  33
  34 import org.forester.io.parsers.PhylogenyParser;
  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.factories.ParserBasedPhylogenyFactory;
  41 import org.forester.phylogeny.factories.PhylogenyFactory;
  42 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  43 import org.forester.tools.SupportCount;
  44 import org.forester.util.CommandLineArguments;
  45 import org.forester.util.ForesterUtil;
  46
  47 public class count_support {
  48
  49     final static private String  PRG_NAME                = "count_support";
  50     final static private String  PRG_VERSION             = "1.0";
  51     final static private String  PRG_DATE                = "2008.03.04";
  52     private final static boolean WRITE_EVALUATORS_AS_NHX = false;
  53
  54     public static void main( final String args[] ) {
  55         ForesterUtil
  56                 .printProgramInformation( count_support.PRG_NAME, count_support.PRG_VERSION, count_support.PRG_DATE );
  57         if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
  58             System.out.println();
  59             System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
  60             System.out.println();
  61             System.out
  62                     .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
  63                             + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
  64             System.out
  65                     .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
  66             System.out.println( "        : -t=<d> threshold for similarity (0.0 to 1.0)" );
  67             System.out.println( "        : -n no branch lengths in outfile for evaluator phylogenies" );
  68             System.out.println();
  69             System.exit( -1 );
  70         }
  71         CommandLineArguments cla = null;
  72         try {
  73             cla = new CommandLineArguments( args );
  74         }
  75         catch ( final Exception e ) {
  76             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  77         }
  78         final List<String> allowed_options = new ArrayList<String>();
  79         allowed_options.add( "s" );
  80         allowed_options.add( "t" );
  81         allowed_options.add( "n" );
  82         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  83         if ( dissallowed_options.length() > 0 ) {
  84             ForesterUtil.fatalError( count_support.PRG_NAME, "Unknown option(s): " + dissallowed_options );
  85         }
  86         final File phylogeny_infile = cla.getFile( 0 );
  87         final File evaluators_infile = cla.getFile( 1 );
  88         final File phylogeny_outfile = cla.getFile( 2 );
  89         File evaluators_outfile = null;
  90         boolean branch_lengths_in_ev_out = true;
  91         if ( cla.isOptionSet( "n" ) ) {
  92             branch_lengths_in_ev_out = false;
  93         }
  94         if ( cla.getNumberOfNames() == 4 ) {
  95             evaluators_outfile = cla.getFile( 3 );
  96         }
  97         else {
  98             if ( !branch_lengths_in_ev_out ) {
  99                 ForesterUtil.fatalError( count_support.PRG_NAME,
 100                                          "Cannot use -n option if no outfile for evaluators specified" );
 101             }
 102         }
 103         Phylogeny p = null;
 104         Phylogeny[] ev = null;
 105         try {
 106             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 107             final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
 108             p = factory.create( phylogeny_infile, pp )[ 0 ];
 109         }
 110         catch ( final Exception e ) {
 111             ForesterUtil.fatalError( count_support.PRG_NAME,
 112                                      "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]" );
 113         }
 114         try {
 115             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 116             final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( evaluators_infile, true );
 117             ev = factory.create( evaluators_infile, pp );
 118         }
 119         catch ( final Exception e ) {
 120             ForesterUtil.fatalError( count_support.PRG_NAME,
 121                                      "Could not read \"" + evaluators_infile + "\" [" + e.getMessage() + "]" );
 122         }
 123         boolean strip = false;
 124         if ( cla.isOptionSet( "s" ) ) {
 125             strip = true;
 126         }
 127         double threshhold = -1.0;
 128         if ( cla.isOptionSet( "t" ) ) {
 129             try {
 130                 threshhold = cla.getOptionValueAsDouble( "t" );
 131             }
 132             catch ( final Exception e ) {
 133                 ForesterUtil.fatalError( count_support.PRG_NAME, "error in command line arguments: " + e.getMessage() );
 134             }
 135             if ( ( threshhold < 0 ) || ( threshhold > 1.0 ) ) {
 136                 ForesterUtil.fatalError( count_support.PRG_NAME,
 137                                          "support threshold has to be between 0.0 and 1.0 (inclusive)" );
 138             }
 139         }
 140         List<Phylogeny> evaluator_phylogenies_above_threshold = null;
 141         try {
 142             if ( threshhold >= 0 ) {
 143                 evaluator_phylogenies_above_threshold = SupportCount.count( p, ev, strip, threshhold, true );
 144                 if ( evaluator_phylogenies_above_threshold.size() < 1 ) {
 145                     ForesterUtil.fatalError( "count_support", "appears like threshold for similarity is set too high" );
 146                 }
 147             }
 148             else {
 149                 SupportCount.count( p, ev, strip, true );
 150             }
 151         }
 152         catch ( final Exception e ) {
 153             ForesterUtil.fatalError( count_support.PRG_NAME, "Failure during support counting: " + e.getMessage() );
 154         }
 155         if ( threshhold >= 0 ) {
 156             count_support.normalizeSupport( p, 100, evaluator_phylogenies_above_threshold.size() );
 157             System.out.println( evaluator_phylogenies_above_threshold.size() + " out of " + ev.length
 158                     + " evaluator phylogenies are above threshold of " + threshhold );
 159         }
 160         try {
 161             final PhylogenyWriter w = new PhylogenyWriter();
 162             w.toPhyloXML( phylogeny_outfile, p, 1 );
 163         }
 164         catch ( final IOException e ) {
 165             ForesterUtil.fatalError( count_support.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
 166         }
 167         System.out.println();
 168         System.out.println( "Wrote phylogeny with support values to: " + phylogeny_outfile );
 169         if ( evaluators_outfile != null ) {
 170             try {
 171                 final PhylogenyWriter w = new PhylogenyWriter();
 172                 if ( evaluator_phylogenies_above_threshold != null ) {
 173                     System.out.println( "Writing " + evaluator_phylogenies_above_threshold.size()
 174                             + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
 175                     if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
 176                         w.toNewHampshireX( evaluator_phylogenies_above_threshold, evaluators_outfile, ";"
 177                                 + ForesterUtil.getLineSeparator() );
 178                     }
 179                     else {
 180                         w.toNewHampshire( evaluator_phylogenies_above_threshold,
 181                                           true,
 182                                           branch_lengths_in_ev_out,
 183                                           evaluators_outfile,
 184                                           ";" + ForesterUtil.getLineSeparator() );
 185                     }
 186                 }
 187                 else {
 188                     System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
 189                     if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
 190                         w.toNewHampshireX( Arrays.asList( ev ),
 191                                            evaluators_outfile,
 192                                            ";" + ForesterUtil.getLineSeparator() );
 193                     }
 194                     else {
 195                         w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"
 196                                 + ForesterUtil.getLineSeparator() );
 197                     }
 198                 }
 199             }
 200             catch ( final IOException e ) {
 201                 ForesterUtil.fatalError( count_support.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
 202             }
 203         }
 204         System.out.println();
 205         System.out.println( "Done." );
 206         System.out.println();
 207     }
 208
 209     private static void normalizeSupport( final Phylogeny p, final double normalized_max, final int number_phylos ) {
 210         double min = Double.MAX_VALUE;
 211         double max = -Double.MAX_VALUE;
 212         double sum = 0.0;
 213         int n = 0;
 214         for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
 215             final PhylogenyNode node = iter.next();
 216             if ( !node.isRoot() && !node.isExternal() ) {
 217                 final double b = PhylogenyMethods.getConfidenceValue( node );
 218                 if ( b > max ) {
 219                     max = b;
 220                 }
 221                 if ( ( b >= 0 ) && ( b < min ) ) {
 222                     min = b;
 223                 }
 224                 sum += b;
 225                 ++n;
 226             }
 227         }
 228         double av = sum / n;
 229         System.out.println( "Max support before normalization is    : " + max );
 230         System.out.println( "Min support before normalization is    : " + min );
 231         System.out.println( "Average support before normalization is: " + av + " (=" + sum + "/" + n + ")" );
 232         System.out.println( "Normalizing so that theoretical maximum support value is: " + normalized_max );
 233         System.out.println( "Number of phylogenies used in support analysis: " + number_phylos );
 234         final double f = normalized_max / number_phylos;
 235         min = Double.MAX_VALUE;
 236         max = -Double.MAX_VALUE;
 237         sum = 0.0;
 238         n = 0;
 239         for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
 240             final PhylogenyNode node = iter.next();
 241             if ( node.isRoot() || node.isExternal() ) {
 242                 PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
 243             }
 244             else {
 245                 double b = PhylogenyMethods.getConfidenceValue( node );
 246                 b = f * b;
 247                 PhylogenyMethods.setBootstrapConfidence( node, b );
 248                 if ( b > max ) {
 249                     max = b;
 250                 }
 251                 if ( ( b >= 0 ) && ( b < min ) ) {
 252                     min = b;
 253                 }
 254                 sum += b;
 255                 ++n;
 256             }
 257         }
 258         av = sum / n;
 259         System.out.println( "Max support after normalization is    : " + max );
 260         System.out.println( "Min support after normalization is    : " + min );
 261         System.out.println( "Average support after normalization is: " + av + " (=" + sum + "/" + n + ")" );
 262     }
 263 }