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: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.FilenameFilter;
  30 import java.io.IOException;
  31 import java.text.SimpleDateFormat;
  32 import java.util.ArrayList;
  33 import java.util.Date;
  34 import java.util.List;
  35 import java.util.SortedMap;
  36 import java.util.SortedSet;
  37 import java.util.TreeMap;
  38 import java.util.TreeSet;
  39
  40 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  41 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  42 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  43 import org.forester.io.writers.PhylogenyWriter;
  44 import org.forester.phylogeny.Phylogeny;
  45 import org.forester.phylogeny.PhylogenyMethods;
  46 import org.forester.phylogeny.PhylogenyNode;
  47 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  48 import org.forester.phylogeny.factories.PhylogenyFactory;
  49 import org.forester.sdi.GSDI;
  50 import org.forester.sdi.GSDII;
  51 import org.forester.sdi.GSDIR;
  52 import org.forester.sdi.SDIException;
  53 import org.forester.sdi.SDIutil;
  54 import org.forester.sdi.SDIutil.ALGORITHM;
  55 import org.forester.util.CommandLineArguments;
  56 import org.forester.util.EasyWriter;
  57 import org.forester.util.ForesterConstants;
  58 import org.forester.util.ForesterUtil;
  59
  60 public final class gsdi {
  61
  62     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
  63     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION    = "g";
  64     final static private String GSDIR_OPTION                           = "r";
  65     final static private String MOST_PARSIMONIOUS_OPTION               = "m";
  66     final static private String SUFFIX_FOR_DIR_OPTION                  = "s";
  67     final static private String GUESS_FORMAT_OF_SPECIES_TREE           = "q";
  68     final static private String TRANSFER_TAXONOMY_OPTION               = "t";
  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                            = "1.001";
  76     final static private String PRG_DATE                               = "170327";
  77     final static private String PRG_DESC                               = "general speciation duplication inference";
  78     final static private String E_MAIL                                 = "phyloxml@gmail.com";
  79     final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/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( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
  98                 System.out.println();
  99                 gsdi.print_help();
 100                 System.exit( 0 );
 101             }
 102             else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 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             allowed_options.add( GSDIR_OPTION );
 111             allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE );
 112             allowed_options.add( MOST_PARSIMONIOUS_OPTION );
 113             allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 114             allowed_options.add( TRANSFER_TAXONOMY_OPTION );
 115             allowed_options.add( SUFFIX_FOR_DIR_OPTION );
 116             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 117             if ( dissallowed_options.length() > 0 ) {
 118                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
 119             }
 120             execute( cla );
 121         }
 122         catch ( final IOException e ) {
 123             ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
 124         }
 125     }
 126
 127     private static void execute( final CommandLineArguments cla ) throws IOException {
 128         ALGORITHM base_algorithm = ALGORITHM.GSDI;
 129         boolean most_parsimonous_duplication_model = false;
 130         boolean allow_stripping_of_gene_tree = false;
 131         if ( cla.isOptionSet( GSDIR_OPTION ) ) {
 132             base_algorithm = ALGORITHM.GSDIR;
 133         }
 134         if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
 135             if ( base_algorithm == ALGORITHM.SDI ) {
 136                 ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
 137             }
 138             most_parsimonous_duplication_model = true;
 139         }
 140         if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 141             if ( base_algorithm == ALGORITHM.SDI ) {
 142                 ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
 143             }
 144             allow_stripping_of_gene_tree = true;
 145         }
 146         boolean transfer_taxonomy = false;
 147         if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
 148             transfer_taxonomy = true;
 149         }
 150         boolean use_gene_tree_dir = false;
 151         final String gene_tree_suffix;
 152         if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) {
 153             gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION );
 154             use_gene_tree_dir = true;
 155         }
 156         else {
 157             gene_tree_suffix = null;
 158         }
 159         File gene_tree_file = null;
 160         File species_tree_file = null;
 161         File out_file = null;
 162         File log_file = null;
 163         try {
 164             gene_tree_file = cla.getFile( 0 );
 165             species_tree_file = cla.getFile( 1 );
 166             if ( cla.getNumberOfNames() == 3 ) {
 167                 out_file = cla.getFile( 2 );
 168                 log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 169             }
 170         }
 171         catch ( final IllegalArgumentException e ) {
 172             ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
 173         }
 174         if ( use_gene_tree_dir ) {
 175             final File dir = new File( gene_tree_file.toString() );
 176             final File gene_tree_files[] = dir.listFiles( new FilenameFilter() {
 177
 178                 @Override
 179                 public boolean accept( final File dir, final String name ) {
 180                     return name.endsWith( gene_tree_suffix );
 181                 }
 182             } );
 183             for( final File file : gene_tree_files ) {
 184                 System.out.println( file );
 185             }
 186             execute( base_algorithm,
 187                      most_parsimonous_duplication_model,
 188                      allow_stripping_of_gene_tree,
 189                      transfer_taxonomy,
 190                      gene_tree_files,
 191                      species_tree_file );
 192         }
 193         else {
 194             execute( base_algorithm,
 195                      most_parsimonous_duplication_model,
 196                      allow_stripping_of_gene_tree,
 197                      transfer_taxonomy,
 198                      gene_tree_file,
 199                      species_tree_file,
 200                      out_file,
 201                      log_file );
 202         }
 203     }
 204
 205     private static void execute( final ALGORITHM base_algorithm,
 206                                  final boolean most_parsimonous_duplication_model,
 207                                  final boolean allow_stripping_of_gene_tree,
 208                                  final boolean transfer_taxonomy,
 209                                  final File gene_tree_files[],
 210                                  final File species_tree_file )
 211             throws IOException {
 212         for( final File gene_tree_file : gene_tree_files ) {
 213             if (gene_tree_file.getName().equals( species_tree_file.getName() )) {
 214                 continue;
 215             }
 216             execute( base_algorithm,
 217                      most_parsimonous_duplication_model,
 218                      allow_stripping_of_gene_tree,
 219                      transfer_taxonomy,
 220                      gene_tree_file,
 221                      species_tree_file,
 222                      new File( gene_tree_file + "gsdi" ),
 223                      new File( gene_tree_file + "gsdi_log" ) );
 224         }
 225     }
 226
 227     private static void execute( final ALGORITHM base_algorithm,
 228                                  final boolean most_parsimonous_duplication_model,
 229                                  final boolean allow_stripping_of_gene_tree,
 230                                  final boolean transfer_taxonomy,
 231                                  final File gene_tree_file,
 232                                  final File species_tree_file,
 233                                  final File out_file,
 234                                  final File log_file )
 235             throws IOException {
 236         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 237             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 238         }
 239         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 240             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 241         }
 242         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 243             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 244         }
 245         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 246             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 247         }
 248         EasyWriter log_writer = null;
 249         try {
 250             log_writer = ForesterUtil.createEasyWriter( log_file );
 251         }
 252         catch ( final IOException e ) {
 253             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 254         }
 255         Phylogeny species_tree = null;
 256         Phylogeny gene_tree = null;
 257         try {
 258             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 259             gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
 260         }
 261         catch ( final IOException e ) {
 262             fatalError( "error",
 263                         "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 264                         log_writer );
 265         }
 266         try {
 267             species_tree = SDIutil.parseSpeciesTree( gene_tree,
 268                                                      species_tree_file,
 269                                                      REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
 270                                                      true,
 271                                                      TAXONOMY_EXTRACTION.NO );
 272         }
 273         catch ( final PhyloXmlDataFormatException e ) {
 274             fatalError( "user error",
 275                         "failed to transfer general node name, in [" + species_tree_file + "]: " + e.getMessage(),
 276                         log_writer );
 277         }
 278         catch ( final SDIException e ) {
 279             fatalError( "user error", e.getMessage(), log_writer );
 280         }
 281         catch ( final IOException e ) {
 282             fatalError( "error",
 283                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 284                         log_writer );
 285         }
 286         gene_tree.setRooted( true );
 287         species_tree.setRooted( true );
 288         if ( !gene_tree.isCompletelyBinary() ) {
 289             fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer );
 290         }
 291         if ( base_algorithm == ALGORITHM.SDI ) {
 292             if ( !species_tree.isCompletelyBinary() ) {
 293                 fatalError( "user error",
 294                             "species tree is not completely binary, use GSDI or GSDIR instead",
 295                             log_writer );
 296             }
 297         }
 298         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 299         log_writer.println( "  version         : " + PRG_VERSION );
 300         log_writer.println( "  date            : " + PRG_DATE );
 301         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 302         log_writer.println();
 303         log_writer.println( "Start time                               : "
 304                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 305         System.out.println( "Start time                               : "
 306                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 307         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 308         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 309         log_writer.println( "Gene tree name                           : "
 310                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 311         System.out.println( "Gene tree name                           : "
 312                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 313         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 314         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 315         log_writer.println( "Species tree name                        : "
 316                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 317         System.out.println( "Species tree name                        : "
 318                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 319         System.out.println( "Transfer taxonomy                        : " + transfer_taxonomy );
 320         GSDII gsdii = null;
 321         final long start_time = new Date().getTime();
 322         try {
 323             if ( base_algorithm == ALGORITHM.GSDI ) {
 324                 System.out.println( "Algorithm                                : GSDI" );
 325                 log_writer.println( "Algorithm                                : GSDI" );
 326             }
 327             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 328                 System.out.println( "Algorithm                                : GSDIR" );
 329                 log_writer.println( "Algorithm                                : GSDIR" );
 330             }
 331             System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 332             System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 333             log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 334             log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 335             log_writer.flush();
 336             if ( base_algorithm == ALGORITHM.GSDI ) {
 337                 gsdii = new GSDI( gene_tree,
 338                                   species_tree,
 339                                   most_parsimonous_duplication_model,
 340                                   allow_stripping_of_gene_tree,
 341                                   true,
 342                                   transfer_taxonomy );
 343             }
 344             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 345                 gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy );
 346             }
 347         }
 348         catch ( final SDIException e ) {
 349             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 350         }
 351         catch ( final IOException e ) {
 352             fatalError( "error", e.toString(), log_writer );
 353         }
 354         catch ( final OutOfMemoryError e ) {
 355             ForesterUtil.outOfMemoryError( e );
 356         }
 357         catch ( final Exception e ) {
 358             e.printStackTrace();
 359             fatalError( "unexpected error", e.toString(), log_writer );
 360         }
 361         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 362                 + "ms" );
 363         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 364                 + "ms" );
 365         System.out.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 366         log_writer.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 367         try {
 368             final PhylogenyWriter writer = new PhylogenyWriter();
 369             if ( base_algorithm == ALGORITHM.GSDIR ) {
 370                 writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
 371             }
 372             else {
 373                 writer.toPhyloXML( out_file, gene_tree, 0 );
 374             }
 375         }
 376         catch ( final IOException e ) {
 377             ForesterUtil.fatalError( PRG_NAME,
 378                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 379         }
 380         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 381         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 382         final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 383                 + SUFFIX_FOR_SPECIES_TREE_USED );
 384         try {
 385             final PhylogenyWriter writer = new PhylogenyWriter();
 386             writer.toPhyloXML( species_tree_used_file, species_tree, 0 );
 387         }
 388         catch ( final IOException e ) {
 389             ForesterUtil.fatalError( PRG_NAME,
 390                                      "Failed to write to [" + species_tree_used_file.getCanonicalPath() + "]: "
 391                                              + e.getMessage() );
 392         }
 393         System.out.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 394         log_writer.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 395         if ( ( gsdii.getReMappedScientificNamesFromGeneTree() != null )
 396                 && !gsdii.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
 397             System.out.println( "Number of gene tree species remapped     : "
 398                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 399             log_writer.println( "Number of gene tree species remapped     : "
 400                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 401             writeToRemappedFile( out_file, gsdii.getReMappedScientificNamesFromGeneTree(), log_writer );
 402         }
 403         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 404         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 405         System.out.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 406         log_writer.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 407         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 408         System.out.println( "Number of polytomies in species tree     : " + poly );
 409         log_writer.println( "Number of polytomies in species tree     : " + poly );
 410         System.out.println( "External nodes stripped from gene tree   : "
 411                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 412         log_writer.println( "External nodes stripped from gene tree   : "
 413                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 414         System.out
 415                 .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 416         log_writer
 417                 .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 418         System.out.println();
 419         System.out.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 420         log_writer.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 421         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 422             final GSDIR gsdir = ( GSDIR ) gsdii;
 423             System.out.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 424             log_writer.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 425         }
 426         else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 427             final GSDI gsdi = ( GSDI ) gsdii;
 428             System.out.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 429             log_writer.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 430             if ( !most_parsimonous_duplication_model ) {
 431                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 432                 System.out.println( "Number of potential duplications         : " + u );
 433                 log_writer.println( "Number of potential duplications         : " + u );
 434             }
 435         }
 436         log_writer.println();
 437         printMappedNodesToLog( log_writer, gsdii );
 438         log_writer.println();
 439         printStrippedGeneTreeNodesToLog( log_writer, gsdii );
 440         System.out.println();
 441         System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
 442         System.out.println();
 443         log_writer.close();
 444     }
 445
 446     private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
 447         try {
 448             log_writer.flush();
 449             log_writer.println();
 450             log_writer.print( type.toUpperCase() + ": " );
 451             log_writer.println( msg );
 452             log_writer.close();
 453         }
 454         catch ( final IOException e ) {
 455             e.printStackTrace();
 456         }
 457         ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
 458     }
 459
 460     private static void print_help() {
 461         System.out.println( "Usage: " + PRG_NAME
 462                 + " [-options] <gene tree in phyloXML format, or directory with gene trees> <species tree> [outfile]" );
 463         System.out.println();
 464         System.out.println( "Options:" );
 465         System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 466                 + "         : to allow stripping of gene tree nodes without a matching species" );
 467         System.out.println( " -" + MOST_PARSIMONIOUS_OPTION
 468                 + "         : use most parimonious duplication model for GSDI: " );
 469         System.out.println( "              assign nodes as speciations which would otherwise be assiged" );
 470         System.out.println( "              as potential duplications due to polytomies in the species tree" );
 471         System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE
 472                 + "         : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 473         System.out.println( " -" + GSDIR_OPTION
 474                 + "         : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
 475         System.out.println( " -" + TRANSFER_TAXONOMY_OPTION
 476                 + "         : to transfer taxonomic data from species tree to gene tree" );
 477         System.out.println( " -" + SUFFIX_FOR_DIR_OPTION
 478                 + "=<suffix>: suffix for gene trees for analyzing entire directory of trees" );
 479         System.out.println();
 480         System.out.println();
 481         System.out.println( "Gene tree(s):" );
 482         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 483         System.out.println();
 484         System.out.println( "Species tree:" );
 485         System.out.println( " in phyloXML format (unless option -" + GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 486         System.out.println();
 487         System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 488                 + " gene_tree.xml tree_of_life.xml out.xml" );
 489         System.out.println( "          gsdi -" + SUFFIX_FOR_DIR_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml"
 490                 + " gene_tree_dir tree_of_life.xml" );
 491         System.out.println();
 492     }
 493
 494     private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException {
 495         final SortedSet<String> ss = new TreeSet<String>();
 496         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 497             ss.add( n.toString() );
 498         }
 499         log_writer.println( "The following " + ss.size() + " species were used: " );
 500         for( final String s : ss ) {
 501             log_writer.println( "  " + s );
 502         }
 503     }
 504
 505     private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
 506             throws IOException {
 507         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 508         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 509             final String s = n.toString();
 510             if ( sm.containsKey( s ) ) {
 511                 sm.put( s, sm.get( s ) + 1 );
 512             }
 513             else {
 514                 sm.put( s, 1 );
 515             }
 516         }
 517         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 518         for( final String s : sm.keySet() ) {
 519             final int count = sm.get( s );
 520             if ( count == 1 ) {
 521                 log_writer.println( "  " + s );
 522             }
 523             else {
 524                 log_writer.println( "  " + s + " [" + count + "]" );
 525             }
 526         }
 527     }
 528
 529     private static void writeToRemappedFile( final File out_file,
 530                                              final SortedSet<String> remapped,
 531                                              final EasyWriter log_writer )
 532             throws IOException {
 533         final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
 534         final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
 535         for( final String s : remapped ) {
 536             remapped_writer.println( s );
 537         }
 538         remapped_writer.close();
 539         System.out.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 540         log_writer.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 541     }
 542 }