forester/java/src/org/forester/application/gsdi.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.text.SimpleDateFormat;
  31 import java.util.ArrayList;
  32 import java.util.Date;
  33 import java.util.List;
  34 import java.util.SortedMap;
  35 import java.util.SortedSet;
  36 import java.util.TreeMap;
  37 import java.util.TreeSet;
  38
  39 import org.forester.io.parsers.PhylogenyParser;
  40 import org.forester.io.parsers.nhx.NHXParser;
  41 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  42 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  43 import org.forester.io.parsers.util.ParserUtils;
  44 import org.forester.io.writers.PhylogenyWriter;
  45 import org.forester.phylogeny.Phylogeny;
  46 import org.forester.phylogeny.PhylogenyMethods;
  47 import org.forester.phylogeny.PhylogenyNode;
  48 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  49 import org.forester.phylogeny.factories.PhylogenyFactory;
  50 import org.forester.sdi.GSDI;
  51 import org.forester.sdi.GSDII;
  52 import org.forester.sdi.GSDIR;
  53 import org.forester.sdi.SDIException;
  54 import org.forester.sdi.SDIutil;
  55 import org.forester.sdi.SDIutil.ALGORITHM;
  56 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
  57 import org.forester.util.CommandLineArguments;
  58 import org.forester.util.EasyWriter;
  59 import org.forester.util.ForesterConstants;
  60 import org.forester.util.ForesterUtil;
  61
  62 public final class gsdi {
  63
  64     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
  65     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION    = "g";
  66     final static private String GSDIR_OPTION                           = "r";
  67     final static private String MOST_PARSIMONIOUS_OPTION               = "m";
  68     final static private String GUESS_FORMAT_OF_SPECIES_TREE           = "q";
  69     final static private String HELP_OPTION_1                          = "help";
  70     final static private String HELP_OPTION_2                          = "h";
  71     final static private String SUFFIX_FOR_SPECIES_TREE_USED           = "_species_tree_used.xml";
  72     final static private String LOGFILE_SUFFIX                         = "_gsdi_log.txt";
  73     final static private String REMAPPED_SUFFIX                        = "_gsdi_remapped.txt";
  74     final static private String PRG_NAME                               = "gsdi";
  75     final static private String PRG_VERSION                            = "1.000";
  76     final static private String PRG_DATE                               = "120629";
  77     final static private String PRG_DESC                               = "general speciation duplication inference";
  78     final static private String E_MAIL                                 = "phylosoft@gmail.com";
  79     final static private String WWW                                    = "www.phylosoft.org/forester";
  80
  81     public static void main( final String args[] ) {
  82         try {
  83             ForesterUtil.printProgramInformation( PRG_NAME,
  84                                                   PRG_DESC,
  85                                                   PRG_VERSION,
  86                                                   PRG_DATE,
  87                                                   E_MAIL,
  88                                                   WWW,
  89                                                   ForesterUtil.getForesterLibraryInformation() );
  90             CommandLineArguments cla = null;
  91             try {
  92                 cla = new CommandLineArguments( args );
  93             }
  94             catch ( final Exception e ) {
  95                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  96             }
  97             if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
  98                 System.out.println();
  99                 gsdi.print_help();
 100                 System.exit( 0 );
 101             }
 102             else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
 103                 System.out.println();
 104                 System.out.println( "Wrong number of arguments." );
 105                 System.out.println();
 106                 gsdi.print_help();
 107                 System.exit( -1 );
 108             }
 109             final List<String> allowed_options = new ArrayList<String>();
 110
 111             allowed_options.add( gsdi.GSDIR_OPTION );
 112             allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
 113             allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
 114             allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 115             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 116             if ( dissallowed_options.length() > 0 ) {
 117                 ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
 118             }
 119             execute( cla );
 120         }
 121         catch ( final IOException e ) {
 122             ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
 123         }
 124     }
 125
 126     private static void execute( final CommandLineArguments cla ) throws IOException {
 127         ALGORITHM base_algorithm = ALGORITHM.GSDI;
 128         boolean most_parsimonous_duplication_model = false;
 129         boolean allow_stripping_of_gene_tree = false;
 130         if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) {
 131             base_algorithm = ALGORITHM.GSDIR;
 132         }
 133
 134         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
 135             if ( base_algorithm == ALGORITHM.SDI ) {
 136                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
 137             }
 138             most_parsimonous_duplication_model = true;
 139         }
 140         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 141             if ( base_algorithm == ALGORITHM.SDI ) {
 142                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
 143             }
 144             allow_stripping_of_gene_tree = true;
 145         }
 146         Phylogeny species_tree = null;
 147         Phylogeny gene_tree = null;
 148         File gene_tree_file = null;
 149         File species_tree_file = null;
 150         File out_file = null;
 151         File log_file = null;
 152         EasyWriter log_writer = null;
 153         try {
 154             gene_tree_file = cla.getFile( 0 );
 155             species_tree_file = cla.getFile( 1 );
 156             out_file = cla.getFile( 2 );
 157             log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 158         }
 159         catch ( final IllegalArgumentException e ) {
 160             ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
 161         }
 162         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 163             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 164         }
 165         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 166             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 167         }
 168         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 169             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 170         }
 171         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 172             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 173         }
 174         try {
 175             log_writer = ForesterUtil.createEasyWriter( log_file );
 176         }
 177         catch ( final IOException e ) {
 178             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 179         }
 180         try {
 181             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 182             gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 183         }
 184         catch ( final IOException e ) {
 185             fatalError( "ERROR",
 186                         "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 187                         log_writer );
 188         }
 189         try {
 190             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 191             final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
 192             if ( p instanceof PhyloXmlParser ) {
 193                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 194             }
 195             else {
 196                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
 197                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
 198                 }
 199                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 200                 final TaxonomyComparisonBase comp_base = SDIutil.determineTaxonomyComparisonBase( gene_tree );
 201                 switch ( comp_base ) {
 202                     case SCIENTIFIC_NAME:
 203                         try {
 204                             PhylogenyMethods
 205                                     .transferNodeNameToField( species_tree,
 206                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
 207                                                               true );
 208                         }
 209                         catch ( final PhyloXmlDataFormatException e ) {
 210                             fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
 211                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 212                         }
 213                         break;
 214                     case CODE:
 215                         try {
 216                             PhylogenyMethods
 217                                     .transferNodeNameToField( species_tree,
 218                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
 219                                                               true );
 220                         }
 221                         catch ( final PhyloXmlDataFormatException e ) {
 222                             fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
 223                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 224                         }
 225                         break;
 226                     case ID:
 227                         try {
 228                             PhylogenyMethods.transferNodeNameToField( species_tree,
 229                                                                       PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
 230                                                                       true );
 231                         }
 232                         catch ( final PhyloXmlDataFormatException e ) {
 233                             fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
 234                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 235                         }
 236                         break;
 237                     default:
 238                         fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
 239                 }
 240             }
 241         }
 242         catch ( final IOException e ) {
 243             fatalError( "ERROR",
 244                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 245                         log_writer );
 246         }
 247         gene_tree.setRooted( true );
 248         species_tree.setRooted( true );
 249         if ( !gene_tree.isCompletelyBinary() ) {
 250             fatalError( "user error", "gene tree is not completely binary", log_writer );
 251         }
 252         if ( base_algorithm == ALGORITHM.SDI ) {
 253             if ( !species_tree.isCompletelyBinary() ) {
 254                 fatalError( "user error",
 255                             "species tree is not completely binary, use GSDI or GSDIR instead",
 256                             log_writer );
 257             }
 258         }
 259         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 260         log_writer.println( "  version         : " + PRG_VERSION );
 261         log_writer.println( "  date            : " + PRG_DATE );
 262         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 263         log_writer.println();
 264         log_writer.println( "Start time                               : "
 265                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 266         System.out.println( "Start time                               : "
 267                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 268         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 269         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 270         log_writer.println( "Gene tree name                           : "
 271                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 272         System.out.println( "Gene tree name                           : "
 273                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 274         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 275         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 276         log_writer.println( "Species tree name                        : "
 277                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 278         System.out.println( "Species tree name                        : "
 279                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 280         GSDII gsdii = null;
 281         final long start_time = new Date().getTime();
 282         try {
 283             if ( base_algorithm == ALGORITHM.GSDI ) {
 284                 System.out.println( "Algorithm       : GSDI" );
 285                 log_writer.println( "Algorithm       : GSDI" );
 286             }
 287             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 288                 System.out.println( "Algorithm       : GSDIR" );
 289                 log_writer.println( "Algorithm       : GSDIR" );
 290             }
 291             System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 292             System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 293             log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 294             log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 295             log_writer.flush();
 296             if ( base_algorithm == ALGORITHM.GSDI ) {
 297                 gsdii = new GSDI( gene_tree,
 298                                 species_tree,
 299                                 most_parsimonous_duplication_model,
 300                                 allow_stripping_of_gene_tree,
 301                                 true );
 302             }
 303             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 304                 gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true );
 305             }
 306         }
 307         catch ( final SDIException e ) {
 308             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 309         }
 310         catch ( final IOException e ) {
 311             fatalError( "error", e.toString(), log_writer );
 312         }
 313         catch ( final Exception e ) {
 314             e.printStackTrace();
 315             fatalError( "unexpected error", e.toString(), log_writer );
 316         }
 317         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 318                 + "ms" );
 319         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 320                 + "ms" );
 321         System.out.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 322         log_writer.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 323         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 324             final GSDIR gsdir = ( GSDIR ) gsdii;
 325            System.out.println( "Duplications sum statistics              : " + gsdir.getMinDuplicationsSum() );
 326             log_writer.println( "Duplications sum statistics              : " + gsdir.getMinDuplicationsSum() );
 327         }
 328         try {
 329             final PhylogenyWriter writer = new PhylogenyWriter();
 330             if ( base_algorithm == ALGORITHM.GSDIR ) {
 331                 writer.toPhyloXML( out_file,
 332                                    ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTrees(),
 333                                    0,
 334                                    ForesterUtil.LINE_SEPARATOR );
 335             }
 336             else {
 337                 writer.toPhyloXML( out_file, gene_tree, 0 );
 338             }
 339         }
 340         catch ( final IOException e ) {
 341             ForesterUtil.fatalError( PRG_NAME,
 342                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 343         }
 344         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 345         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 346         final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 347                 + SUFFIX_FOR_SPECIES_TREE_USED );
 348         try {
 349             final PhylogenyWriter writer = new PhylogenyWriter();
 350             writer.toPhyloXML( species_tree_used_file, species_tree, 0 );
 351         }
 352         catch ( final IOException e ) {
 353             ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
 354                     + "]: " + e.getMessage() );
 355         }
 356         System.out.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 357         log_writer.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 358         if ( ( gsdii.getReMappedScientificNamesFromGeneTree() != null )
 359                 && !gsdii.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
 360             System.out.println( "Number of gene tree species remapped     : "
 361                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 362             log_writer.println( "Number of gene tree species remapped     : "
 363                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 364             writeToRemappedFile( out_file, gsdii.getReMappedScientificNamesFromGeneTree(), log_writer );
 365         }
 366         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 367         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 368         System.out.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 369         log_writer.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 370         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 371         System.out.println( "Number of polytomies in species tree     : " + poly );
 372         log_writer.println( "Number of polytomies in species tree     : " + poly );
 373         System.out.println( "External nodes stripped from gene tree   : "
 374                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 375         log_writer.println( "External nodes stripped from gene tree   : "
 376                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 377         System.out.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 378         log_writer.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 379         System.out.println();
 380         System.out.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 381         log_writer.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 382         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 383             final GSDIR gsdir = ( GSDIR ) gsdii;
 384             System.out.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 385             log_writer.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 386         }
 387         else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 388             final GSDI gsdi = ( GSDI ) gsdii;
 389             System.out.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 390             log_writer.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 391             if ( !most_parsimonous_duplication_model ) {
 392                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 393                 System.out.println( "Number of potential duplications         : " + u );
 394                 log_writer.println( "Number of potential duplications         : " + u );
 395             }
 396
 397         }
 398         log_writer.println();
 399         printMappedNodesToLog( log_writer, gsdii );
 400         log_writer.println();
 401         printStrippedGeneTreeNodesToLog( log_writer, gsdii );
 402         System.out.println();
 403         System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
 404         System.out.println();
 405         log_writer.close();
 406     }
 407
 408     private static void writeToRemappedFile( final File out_file,
 409                                              final SortedSet<String> remapped,
 410                                              final EasyWriter log_writer ) throws IOException {
 411         final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
 412         final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
 413         for( final String s : remapped ) {
 414             remapped_writer.println( s );
 415         }
 416         remapped_writer.close();
 417         System.out.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 418         log_writer.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 419     }
 420
 421     private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException {
 422         final SortedSet<String> ss = new TreeSet<String>();
 423         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 424             ss.add( n.toString() );
 425         }
 426         log_writer.println( "The following " + ss.size() + " species were used: " );
 427         for( final String s : ss ) {
 428             log_writer.println( "  " + s );
 429         }
 430     }
 431
 432     private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
 433         try {
 434             log_writer.flush();
 435             log_writer.println();
 436             log_writer.print( type.toUpperCase() + ": " );
 437             log_writer.println( msg );
 438             log_writer.close();
 439         }
 440         catch ( final IOException e ) {
 441             e.printStackTrace();
 442         }
 443         ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
 444     }
 445
 446     private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
 447             throws IOException {
 448         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 449         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 450             final String s = n.toString();
 451             if ( sm.containsKey( s ) ) {
 452                 sm.put( s, sm.get( s ) + 1 );
 453             }
 454             else {
 455                 sm.put( s, 1 );
 456             }
 457         }
 458         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 459         for( final String s : sm.keySet() ) {
 460             final int count = sm.get( s );
 461             if ( count == 1 ) {
 462                 log_writer.println( "  " + s );
 463             }
 464             else {
 465                 log_writer.println( "  " + s + " [" + count + "]" );
 466             }
 467         }
 468     }
 469
 470     private static void print_help() {
 471         System.out.println( "Usage: " + gsdi.PRG_NAME
 472                 + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
 473         System.out.println();
 474         System.out.println( "Options:" );
 475         System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 476                 + ": to allow stripping of gene tree nodes without a matching species" );
 477         System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
 478                 + ": use most parimonious duplication model for GSDI: " );
 479         System.out.println( "     assign nodes as speciations which would otherwise be assiged" );
 480         System.out.println( "     as potential duplications due to polytomies in the species tree" );
 481         System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
 482                 + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 483         System.out.println( " -" + gsdi.GSDIR_OPTION
 484                 + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
 485         System.out.println();
 486         System.out.println( "Gene tree:" );
 487         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 488         System.out.println();
 489         System.out.println( "Species tree:" );
 490         System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 491         System.out.println();
 492         System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 493                 + " gene_tree.xml tree_of_life.xml out.xml" );
 494         System.out.println();
 495     }
 496 }