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.GSDIR;
  52 import org.forester.sdi.SDI;
  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 SDISE_OPTION                           = "b";
  67     final static private String GSDIR_OPTION                           = "r";
  68     final static private String MOST_PARSIMONIOUS_OPTION               = "m";
  69     final static private String GUESS_FORMAT_OF_SPECIES_TREE           = "q";
  70     final static private String HELP_OPTION_1                          = "help";
  71     final static private String HELP_OPTION_2                          = "h";
  72     final static private String SUFFIX_FOR_SPECIES_TREE_USED           = "_species_tree_used.xml";
  73     final static private String LOGFILE_SUFFIX                         = "_gsdi_log.txt";
  74     final static private String REMAPPED_SUFFIX                        = "_gsdi_remapped.txt";
  75     final static private String PRG_NAME                               = "gsdi";
  76     final static private String PRG_VERSION                            = "1.000";
  77     final static private String PRG_DATE                               = "120629";
  78     final static private String PRG_DESC                               = "general speciation duplication inference";
  79     final static private String E_MAIL                                 = "phylosoft@gmail.com";
  80     final static private String WWW                                    = "www.phylosoft.org/forester";
  81
  82     public static void main( final String args[] ) {
  83         try {
  84             ForesterUtil.printProgramInformation( PRG_NAME,
  85                                                   PRG_DESC,
  86                                                   PRG_VERSION,
  87                                                   PRG_DATE,
  88                                                   E_MAIL,
  89                                                   WWW,
  90                                                   ForesterUtil.getForesterLibraryInformation() );
  91             CommandLineArguments cla = null;
  92             try {
  93                 cla = new CommandLineArguments( args );
  94             }
  95             catch ( final Exception e ) {
  96                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  97             }
  98             if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
  99                 System.out.println();
 100                 gsdi.print_help();
 101                 System.exit( 0 );
 102             }
 103             else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
 104                 System.out.println();
 105                 System.out.println( "Wrong number of arguments." );
 106                 System.out.println();
 107                 gsdi.print_help();
 108                 System.exit( -1 );
 109             }
 110             final List<String> allowed_options = new ArrayList<String>();
 111             allowed_options.add( gsdi.SDISE_OPTION );
 112             allowed_options.add( gsdi.GSDIR_OPTION );
 113             allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
 114             allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
 115             allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 116             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 117             if ( dissallowed_options.length() > 0 ) {
 118                 ForesterUtil.fatalError( gsdi.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( gsdi.GSDIR_OPTION ) ) {
 132             base_algorithm = ALGORITHM.GSDIR;
 133         }
 134         else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
 135             base_algorithm = ALGORITHM.SDI;
 136         }
 137         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
 138             if ( base_algorithm == ALGORITHM.SDI ) {
 139                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
 140             }
 141             most_parsimonous_duplication_model = true;
 142         }
 143         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 144             if ( base_algorithm == ALGORITHM.SDI ) {
 145                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
 146             }
 147             allow_stripping_of_gene_tree = true;
 148         }
 149         Phylogeny species_tree = null;
 150         Phylogeny gene_tree = null;
 151         File gene_tree_file = null;
 152         File species_tree_file = null;
 153         File out_file = null;
 154         File log_file = null;
 155         EasyWriter log_writer = null;
 156         try {
 157             gene_tree_file = cla.getFile( 0 );
 158             species_tree_file = cla.getFile( 1 );
 159             out_file = cla.getFile( 2 );
 160             log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 161         }
 162         catch ( final IllegalArgumentException e ) {
 163             ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
 164         }
 165         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 166             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 167         }
 168         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 169             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 170         }
 171         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 172             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 173         }
 174         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 175             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 176         }
 177         try {
 178             log_writer = ForesterUtil.createEasyWriter( log_file );
 179         }
 180         catch ( final IOException e ) {
 181             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 182         }
 183         try {
 184             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 185             gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 186         }
 187         catch ( final IOException e ) {
 188             fatalError( "ERROR",
 189                         "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 190                         log_writer );
 191         }
 192         try {
 193             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 194             final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
 195             if ( p instanceof PhyloXmlParser ) {
 196                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 197             }
 198             else {
 199                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
 200                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
 201                 }
 202                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 203                 final TaxonomyComparisonBase comp_base = SDIutil.determineTaxonomyComparisonBase( gene_tree );
 204                 switch ( comp_base ) {
 205                     case SCIENTIFIC_NAME:
 206                         try {
 207                             PhylogenyMethods
 208                                     .transferNodeNameToField( species_tree,
 209                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
 210                                                               true );
 211                         }
 212                         catch ( final PhyloXmlDataFormatException e ) {
 213                             fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
 214                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 215                         }
 216                         break;
 217                     case CODE:
 218                         try {
 219                             PhylogenyMethods
 220                                     .transferNodeNameToField( species_tree,
 221                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
 222                                                               true );
 223                         }
 224                         catch ( final PhyloXmlDataFormatException e ) {
 225                             fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
 226                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 227                         }
 228                         break;
 229                     case ID:
 230                         try {
 231                             PhylogenyMethods.transferNodeNameToField( species_tree,
 232                                                                       PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
 233                                                                       true );
 234                         }
 235                         catch ( final PhyloXmlDataFormatException e ) {
 236                             fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
 237                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 238                         }
 239                         break;
 240                     default:
 241                         fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
 242                 }
 243             }
 244         }
 245         catch ( final IOException e ) {
 246             fatalError( "ERROR",
 247                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 248                         log_writer );
 249         }
 250         gene_tree.setRooted( true );
 251         species_tree.setRooted( true );
 252         if ( !gene_tree.isCompletelyBinary() ) {
 253             fatalError( "user error", "gene tree is not completely binary", log_writer );
 254         }
 255         if ( base_algorithm == ALGORITHM.SDI ) {
 256             if ( !species_tree.isCompletelyBinary() ) {
 257                 fatalError( "user error",
 258                             "species tree is not completely binary, use GSDI or GSDIR instead",
 259                             log_writer );
 260             }
 261         }
 262         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 263         log_writer.println( "  version         : " + PRG_VERSION );
 264         log_writer.println( "  date            : " + PRG_DATE );
 265         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 266         log_writer.println();
 267         log_writer.println( "Start time                               : "
 268                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 269         System.out.println( "Start time                               : "
 270                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 271         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 272         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 273         log_writer.println( "Gene tree name                           : "
 274                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 275         System.out.println( "Gene tree name                           : "
 276                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 277         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 278         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 279         log_writer.println( "Species tree name                        : "
 280                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 281         System.out.println( "Species tree name                        : "
 282                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 283         Object sdi = null;
 284         final long start_time = new Date().getTime();
 285         try {
 286             if ( ( base_algorithm == ALGORITHM.GSDI ) || ( base_algorithm == ALGORITHM.GSDIR ) ) {
 287                 if ( base_algorithm == ALGORITHM.GSDI ) {
 288                     System.out.println( "Algorithm       : GSDI" );
 289                     log_writer.println( "Algorithm       : GSDI" );
 290                 }
 291                 else if ( base_algorithm == ALGORITHM.GSDIR ) {
 292                     System.out.println( "Algorithm       : GSDIR" );
 293                     log_writer.println( "Algorithm       : GSDIR" );
 294                 }
 295                 System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 296                 System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 297                 log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 298                 log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 299                 log_writer.flush();
 300                 if ( base_algorithm == ALGORITHM.GSDI ) {
 301                     sdi = new GSDI( gene_tree,
 302                                     species_tree,
 303                                     most_parsimonous_duplication_model,
 304                                     allow_stripping_of_gene_tree,
 305                                     true );
 306                 }
 307                 else if ( base_algorithm == ALGORITHM.GSDIR ) {
 308                     sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true );
 309                 }
 310             }
 311             else {
 312                 System.out.println();
 313                 System.out.println( "Algorithm       : SDI" );
 314                 log_writer.println( "Algorithm       : SDI" );
 315                 log_writer.flush();
 316                 sdi = new SDI( gene_tree, species_tree );
 317             }
 318         }
 319         catch ( final SDIException e ) {
 320             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 321         }
 322         catch ( final IOException e ) {
 323             fatalError( "error", e.toString(), log_writer );
 324         }
 325         catch ( final Exception e ) {
 326             e.printStackTrace();
 327             fatalError( "unexpected error", e.toString(), log_writer );
 328         }
 329         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 330                 + "ms" );
 331         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 332                 + "ms" );
 333         if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 334             final GSDI gsdi = ( GSDI ) sdi;
 335             System.out.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 336             log_writer.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 337         }
 338         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 339             final GSDIR gsdir = ( GSDIR ) sdi;
 340             System.out.println( "Mapping based on                         : " + gsdir.getTaxCompBase() );
 341             log_writer.println( "Mapping based on                         : " + gsdir.getTaxCompBase() );
 342             System.out.println( "Minimal duplications sum                 : " + gsdir.getMinDuplicationsSum() );
 343             log_writer.println( "Minimal duplications sum                 : " + gsdir.getMinDuplicationsSum() );
 344             System.out.println( "Duplications sum statistics              : " + gsdir.getMinDuplicationsSum() );
 345             log_writer.println( "Duplications sum statistics              : " + gsdir.getMinDuplicationsSum() );
 346         }
 347         try {
 348             final PhylogenyWriter writer = new PhylogenyWriter();
 349             if ( base_algorithm == ALGORITHM.GSDIR ) {
 350                 writer.toPhyloXML( out_file,
 351                                    ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(),
 352                                    0,
 353                                    ForesterUtil.LINE_SEPARATOR );
 354             }
 355             else {
 356                 writer.toPhyloXML( out_file, gene_tree, 0 );
 357             }
 358         }
 359         catch ( final IOException e ) {
 360             ForesterUtil.fatalError( PRG_NAME,
 361                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 362         }
 363         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 364         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 365         if ( base_algorithm == ALGORITHM.SDI ) {
 366             sdi = sdi;
 367             sdi.computeMappingCostL();
 368             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 369             log_writer.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 370         }
 371         else if ( ( base_algorithm == ALGORITHM.GSDI ) || ( base_algorithm == ALGORITHM.GSDIR ) ) {
 372             final GSDI gsdi = ( GSDI ) sdi;
 373             final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 374                     + SUFFIX_FOR_SPECIES_TREE_USED );
 375             try {
 376                 final PhylogenyWriter writer = new PhylogenyWriter();
 377                 writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
 378             }
 379             catch ( final IOException e ) {
 380                 ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
 381                         + "]: " + e.getMessage() );
 382             }
 383             System.out.println( "Wrote (stripped) species tree to         : "
 384                     + species_tree_used_file.getCanonicalPath() );
 385             log_writer.println( "Wrote (stripped) species tree to         : "
 386                     + species_tree_used_file.getCanonicalPath() );
 387             if ( ( gsdi.getReMappedScientificNamesFromGeneTree() != null )
 388                     && !gsdi.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
 389                 System.out.println( "Number of gene tree species remapped     : "
 390                         + gsdi.getReMappedScientificNamesFromGeneTree().size() );
 391                 log_writer.println( "Number of gene tree species remapped     : "
 392                         + gsdi.getReMappedScientificNamesFromGeneTree().size() );
 393                 writeToRemappedFile( out_file, gsdi.getReMappedScientificNamesFromGeneTree(), log_writer );
 394             }
 395         }
 396         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 397         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 398         System.out.println( "Number of external nodes in species tree : "
 399                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
 400         log_writer.println( "Number of external nodes in species tree : "
 401                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
 402         if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 403             final GSDI gsdi = ( GSDI ) sdi;
 404             final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
 405             System.out.println( "Number of polytomies in species tree     : " + poly );
 406             log_writer.println( "Number of polytomies in species tree     : " + poly );
 407             System.out.println( "External nodes stripped from gene tree   : "
 408                     + gsdi.getStrippedExternalGeneTreeNodes().size() );
 409             log_writer.println( "External nodes stripped from gene tree   : "
 410                     + gsdi.getStrippedExternalGeneTreeNodes().size() );
 411             System.out.println( "External nodes stripped from species tree: "
 412                     + gsdi.getStrippedSpeciesTreeNodes().size() );
 413             log_writer.println( "External nodes stripped from species tree: "
 414                     + gsdi.getStrippedSpeciesTreeNodes().size() );
 415         }
 416         System.out.println();
 417         System.out.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
 418         log_writer.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
 419         if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 420             final GSDI gsdi = ( GSDI ) sdi;
 421             if ( !most_parsimonous_duplication_model ) {
 422                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 423                 System.out.println( "Number of potential duplications         : " + u );
 424                 log_writer.println( "Number of potential duplications         : " + u );
 425             }
 426             System.out.println( "Number of speciations                    : " + gsdi.getSpeciationsSum() );
 427             log_writer.println( "Number of speciations                    : " + gsdi.getSpeciationsSum() );
 428             log_writer.println();
 429             printMappedNodesToLog( log_writer, gsdi );
 430             log_writer.println();
 431             printStrippedGeneTreeNodesToLog( log_writer, gsdi );
 432         }
 433         System.out.println();
 434         System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
 435         System.out.println();
 436         log_writer.close();
 437     }
 438
 439     private static void writeToRemappedFile( final File out_file,
 440                                              final SortedSet<String> remapped,
 441                                              final EasyWriter log_writer ) throws IOException {
 442         final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
 443         final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
 444         for( final String s : remapped ) {
 445             remapped_writer.println( s );
 446         }
 447         remapped_writer.close();
 448         System.out.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 449         log_writer.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 450     }
 451
 452     private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException {
 453         final SortedSet<String> ss = new TreeSet<String>();
 454         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 455             ss.add( n.toString() );
 456         }
 457         log_writer.println( "The following " + ss.size() + " species were used: " );
 458         for( final String s : ss ) {
 459             log_writer.println( "  " + s );
 460         }
 461     }
 462
 463     private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
 464         try {
 465             log_writer.flush();
 466             log_writer.println();
 467             log_writer.print( type.toUpperCase() + ": " );
 468             log_writer.println( msg );
 469             log_writer.close();
 470         }
 471         catch ( final IOException e ) {
 472             e.printStackTrace();
 473         }
 474         ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
 475     }
 476
 477     private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
 478             throws IOException {
 479         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 480         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 481             final String s = n.toString();
 482             if ( sm.containsKey( s ) ) {
 483                 sm.put( s, sm.get( s ) + 1 );
 484             }
 485             else {
 486                 sm.put( s, 1 );
 487             }
 488         }
 489         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 490         for( final String s : sm.keySet() ) {
 491             final int count = sm.get( s );
 492             if ( count == 1 ) {
 493                 log_writer.println( "  " + s );
 494             }
 495             else {
 496                 log_writer.println( "  " + s + " [" + count + "]" );
 497             }
 498         }
 499     }
 500
 501     private static void print_help() {
 502         System.out.println( "Usage: " + gsdi.PRG_NAME
 503                 + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
 504         System.out.println();
 505         System.out.println( "Options:" );
 506         System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 507                 + ": to allow stripping of gene tree nodes without a matching species" );
 508         System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
 509                 + ": use most parimonious duplication model for GSDI: " );
 510         System.out.println( "     assign nodes as speciations which would otherwise be assiged" );
 511         System.out.println( "     as potential duplications due to polytomies in the species tree" );
 512         System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
 513                 + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 514         System.out.println( " -" + gsdi.SDISE_OPTION
 515                 + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" );
 516         System.out.println( " -" + gsdi.GSDIR_OPTION
 517                 + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
 518         System.out.println();
 519         System.out.println( "Gene tree:" );
 520         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 521         System.out.println();
 522         System.out.println( "Species tree:" );
 523         System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 524         System.out.println();
 525         System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 526                 + " gene_tree.xml tree_of_life.xml out.xml" );
 527         System.out.println();
 528     }
 529 }