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 OUTTREE_SUFFIX                         = "_gsdir.xml";
  73     final static private String LOGFILE_NAME                           = "00_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                            = "1.100";
  77     final static private String PRG_DATE                               = "170331";
  78     final static private String PRG_DESC                               = "general speciation duplication inference";
  79     final static private String E_MAIL                                 = "phyloxml@gmail.com";
  80     final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/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( HELP_OPTION_1 ) || cla.isOptionSet( 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( GSDIR_OPTION );
 112             allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE );
 113             allowed_options.add( MOST_PARSIMONIOUS_OPTION );
 114             allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 115             allowed_options.add( TRANSFER_TAXONOMY_OPTION );
 116             allowed_options.add( SUFFIX_FOR_DIR_OPTION );
 117             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 118             if ( dissallowed_options.length() > 0 ) {
 119                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
 120             }
 121             execute( cla );
 122         }
 123         catch ( final IOException e ) {
 124             ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
 125         }
 126     }
 127
 128     private static void execute( final CommandLineArguments cla ) throws IOException {
 129         ALGORITHM base_algorithm = ALGORITHM.GSDI;
 130         boolean most_parsimonous_duplication_model = false;
 131         boolean allow_stripping_of_gene_tree = false;
 132         if ( cla.isOptionSet( GSDIR_OPTION ) ) {
 133             base_algorithm = ALGORITHM.GSDIR;
 134         }
 135         if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
 136             if ( base_algorithm == ALGORITHM.SDI ) {
 137                 ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
 138             }
 139             most_parsimonous_duplication_model = true;
 140         }
 141         if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 142             if ( base_algorithm == ALGORITHM.SDI ) {
 143                 ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
 144             }
 145             allow_stripping_of_gene_tree = true;
 146         }
 147         boolean transfer_taxonomy = false;
 148         if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
 149             transfer_taxonomy = true;
 150         }
 151         boolean use_gene_tree_dir = false;
 152         final String gene_tree_suffix;
 153         if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) {
 154             gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION );
 155             use_gene_tree_dir = true;
 156         }
 157         else {
 158             gene_tree_suffix = null;
 159         }
 160         File gene_tree_file = null;
 161         File species_tree_file = null;
 162         File out_file = null;
 163         File log_file = null;
 164         File out_dir = null;
 165         try {
 166             gene_tree_file = cla.getFile( 0 );
 167             species_tree_file = cla.getFile( 1 );
 168             if ( use_gene_tree_dir ) {
 169                 out_dir = cla.getFile( 2 );
 170                 if ( out_dir.exists() ) {
 171                     if ( !out_dir.isDirectory() ) {
 172                         ForesterUtil
 173                                 .fatalError( gsdi.PRG_NAME,
 174                                              "out-directory [" + out_dir + "] already exists but is not a directory" );
 175                     }
 176                 }
 177                 else {
 178                     final boolean success = out_dir.mkdirs();
 179                     if ( !success ) {
 180                         ForesterUtil.fatalError( gsdi.PRG_NAME, "could not create out-directory [" + out_dir + "]" );
 181                     }
 182                 }
 183             }
 184             else {
 185                 out_file = cla.getFile( 2 );
 186             }
 187         }
 188         catch ( final IllegalArgumentException e ) {
 189             ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
 190         }
 191         if ( use_gene_tree_dir ) {
 192             final File indir = new File( gene_tree_file.toString() );
 193             if ( !indir.exists() ) {
 194                 ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] does not exist" );
 195             }
 196             if ( !indir.isDirectory() ) {
 197                 ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] is not a directory" );
 198             }
 199             final String species_tree_file_name = species_tree_file.getName();
 200             final File gene_tree_files[] = indir.listFiles( new FilenameFilter() {
 201
 202                 @Override
 203                 public boolean accept( final File dir, final String name ) {
 204                     return (( name.endsWith( gene_tree_suffix) ) && !(name.equals( species_tree_file_name)));
 205                 }
 206             } );
 207
 208             if ( gene_tree_files.length < 1 ) {
 209                 ForesterUtil.fatalError( gsdi.PRG_NAME,
 210                                          "in-directory [" + indir + "] does not contain any gene tree files with suffix "
 211                                                  + gene_tree_suffix );
 212             }
 213
 214             execute( base_algorithm,
 215                      most_parsimonous_duplication_model,
 216                      allow_stripping_of_gene_tree,
 217                      transfer_taxonomy,
 218                      gene_tree_files,
 219                      species_tree_file,
 220                      out_dir );
 221         }
 222         else {
 223             execute( base_algorithm,
 224                      most_parsimonous_duplication_model,
 225                      allow_stripping_of_gene_tree,
 226                      transfer_taxonomy,
 227                      gene_tree_file,
 228                      species_tree_file,
 229                      out_file,
 230                      log_file );
 231         }
 232     }
 233
 234     private static void execute( final ALGORITHM base_algorithm,
 235                                  final boolean most_parsimonous_duplication_model,
 236                                  final boolean allow_stripping_of_gene_tree,
 237                                  final boolean transfer_taxonomy,
 238                                  final File gene_tree_files[],
 239                                  final File species_tree_file,
 240                                  final File outdir )
 241             throws IOException {
 242         final File log_file = new File( outdir, LOGFILE_NAME );
 243         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 244             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 245         }
 246         EasyWriter log_writer = null;
 247         try {
 248             log_writer = ForesterUtil.createEasyWriter( log_file );
 249         }
 250         catch ( final IOException e ) {
 251             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 252         }
 253         log_writer.println( "# " + PRG_NAME );
 254         log_writer.println( "# Version\t" + PRG_VERSION );
 255         log_writer.println( "# Date\t" + PRG_DATE );
 256         log_writer.println( "# Forester version\t" + ForesterConstants.FORESTER_VERSION );
 257         log_writer.println( "# Species tree\t" + species_tree_file.getCanonicalPath() );
 258         if ( base_algorithm == ALGORITHM.GSDI ) {
 259             log_writer.println( "# Algorithm\tGSDI" );
 260         }
 261         else if ( base_algorithm == ALGORITHM.GSDIR ) {
 262             log_writer.println( "# Algorithm\tGSDIR" );
 263         }
 264         log_writer.println( "# Use most parsimonous duplication model\t" + most_parsimonous_duplication_model );
 265         log_writer.println( "# Allow stripping of gene tree nodes\t" + allow_stripping_of_gene_tree );
 266         log_writer.println( "# Start time\t" + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 267         int counter = 0;
 268         for( final File gene_tree_file : gene_tree_files ) {
 269
 270             String outname = gene_tree_file.getName();
 271             if ( outname.indexOf( "." ) > 0 ) {
 272                 outname = outname.substring( 0, outname.lastIndexOf( "." ) );
 273             }
 274             outname = outname + OUTTREE_SUFFIX;
 275             execute( base_algorithm,
 276                      most_parsimonous_duplication_model,
 277                      allow_stripping_of_gene_tree,
 278                      transfer_taxonomy,
 279                      gene_tree_file,
 280                      species_tree_file,
 281                      new File( outdir, outname ),
 282                      log_writer );
 283             System.out.print( "\r" + counter++ );
 284
 285         }
 286         System.out.print( "\r" );
 287         log_writer.close();
 288         System.out.println("Analyzed " + counter + " gene trees");
 289         System.out.println();
 290         System.out.println( "Wrote log to: " + log_file.getCanonicalPath() );
 291         System.out.println();
 292     }
 293
 294     private static void execute( final ALGORITHM base_algorithm,
 295                                  final boolean most_parsimonous_duplication_model,
 296                                  final boolean allow_stripping_of_gene_tree,
 297                                  final boolean transfer_taxonomy,
 298                                  final File gene_tree_file,
 299                                  final File species_tree_file,
 300                                  final File out_file,
 301                                  final EasyWriter log_writer )
 302             throws IOException {
 303         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 304             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 305         }
 306         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 307             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 308         }
 309         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 310             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 311         }
 312         Phylogeny species_tree = null;
 313         Phylogeny gene_tree = null;
 314         try {
 315             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 316             gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
 317         }
 318         catch ( final IOException e ) {
 319             fatalError( "error",
 320                         "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 321                         log_writer );
 322         }
 323         try {
 324             species_tree = SDIutil.parseSpeciesTree( gene_tree,
 325                                                      species_tree_file,
 326                                                      REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
 327                                                      true,
 328                                                      TAXONOMY_EXTRACTION.NO );
 329         }
 330         catch ( final PhyloXmlDataFormatException e ) {
 331             fatalError( "user error",
 332                         "failed to transfer general node name, in [" + species_tree_file + "]: " + e.getMessage(),
 333                         log_writer );
 334         }
 335         catch ( final SDIException e ) {
 336             fatalError( "user error", e.getMessage(), log_writer );
 337         }
 338         catch ( final IOException e ) {
 339             fatalError( "error",
 340                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 341                         log_writer );
 342         }
 343         gene_tree.setRooted( true );
 344         species_tree.setRooted( true );
 345         if ( !gene_tree.isCompletelyBinary() ) {
 346             fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer );
 347         }
 348         if ( base_algorithm == ALGORITHM.SDI ) {
 349             if ( !species_tree.isCompletelyBinary() ) {
 350                 fatalError( "user error",
 351                             "species tree is not completely binary, use GSDI or GSDIR instead",
 352                             log_writer );
 353             }
 354         }
 355         log_writer.print( gene_tree_file.getName() );
 356         log_writer.print( "\t" );
 357         log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 358         log_writer.print( "\t" );
 359         GSDII gsdii = null;
 360         try {
 361             log_writer.flush();
 362             if ( base_algorithm == ALGORITHM.GSDI ) {
 363                 gsdii = new GSDI( gene_tree,
 364                                   species_tree,
 365                                   most_parsimonous_duplication_model,
 366                                   allow_stripping_of_gene_tree,
 367                                   true,
 368                                   transfer_taxonomy );
 369             }
 370             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 371                 gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy );
 372             }
 373         }
 374         catch ( final SDIException e ) {
 375             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 376         }
 377         catch ( final IOException e ) {
 378             fatalError( "error", e.toString(), log_writer );
 379         }
 380         catch ( final OutOfMemoryError e ) {
 381             ForesterUtil.outOfMemoryError( e );
 382         }
 383         catch ( final Exception e ) {
 384             e.printStackTrace();
 385             fatalError( "unexpected error", e.toString(), log_writer );
 386         }
 387         try {
 388             final PhylogenyWriter writer = new PhylogenyWriter();
 389             if ( base_algorithm == ALGORITHM.GSDIR ) {
 390                 writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
 391             }
 392             else {
 393                 writer.toPhyloXML( out_file, gene_tree, 0 );
 394             }
 395         }
 396         catch ( final IOException e ) {
 397             ForesterUtil.fatalError( PRG_NAME,
 398                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 399         }
 400         log_writer.print( gene_tree.getNumberOfExternalNodes() + "\t" );
 401         log_writer.print( gsdii.getSpeciationsSum() + "\t" );
 402         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 403             final GSDIR gsdir = ( GSDIR ) gsdii;
 404             log_writer.print( gsdir.getMinDuplicationsSum() + "\t" );
 405         }
 406         else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 407             final GSDI gsdi = ( GSDI ) gsdii;
 408             log_writer.print( gsdi.getDuplicationsSum() + "\t" );
 409             if ( !most_parsimonous_duplication_model ) {
 410                 log_writer.print( gsdi.getSpeciationOrDuplicationEventsSum() + "\t" );
 411             }
 412         }
 413         log_writer.print( gsdii.getTaxCompBase() + "\t" );
 414         log_writer.println();
 415     }
 416
 417     private static void execute( final ALGORITHM base_algorithm,
 418                                  final boolean most_parsimonous_duplication_model,
 419                                  final boolean allow_stripping_of_gene_tree,
 420                                  final boolean transfer_taxonomy,
 421                                  final File gene_tree_file,
 422                                  final File species_tree_file,
 423                                  final File out_file,
 424                                  final File log_file )
 425             throws IOException {
 426         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 427             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 428         }
 429         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 430             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 431         }
 432         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 433             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 434         }
 435         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 436             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 437         }
 438         EasyWriter log_writer = null;
 439         try {
 440             log_writer = ForesterUtil.createEasyWriter( log_file );
 441         }
 442         catch ( final IOException e ) {
 443             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 444         }
 445         Phylogeny species_tree = null;
 446         Phylogeny gene_tree = null;
 447         try {
 448             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 449             gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
 450         }
 451         catch ( final IOException e ) {
 452             fatalError( "error",
 453                         "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 454                         log_writer );
 455         }
 456         try {
 457             species_tree = SDIutil.parseSpeciesTree( gene_tree,
 458                                                      species_tree_file,
 459                                                      REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
 460                                                      true,
 461                                                      TAXONOMY_EXTRACTION.NO );
 462         }
 463         catch ( final PhyloXmlDataFormatException e ) {
 464             fatalError( "user error",
 465                         "failed to transfer general node name, in [" + species_tree_file + "]: " + e.getMessage(),
 466                         log_writer );
 467         }
 468         catch ( final SDIException e ) {
 469             fatalError( "user error", e.getMessage(), log_writer );
 470         }
 471         catch ( final IOException e ) {
 472             fatalError( "error",
 473                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 474                         log_writer );
 475         }
 476         gene_tree.setRooted( true );
 477         species_tree.setRooted( true );
 478         if ( !gene_tree.isCompletelyBinary() ) {
 479             fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer );
 480         }
 481         if ( base_algorithm == ALGORITHM.SDI ) {
 482             if ( !species_tree.isCompletelyBinary() ) {
 483                 fatalError( "user error",
 484                             "species tree is not completely binary, use GSDI or GSDIR instead",
 485                             log_writer );
 486             }
 487         }
 488         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 489         log_writer.println( "  version         : " + PRG_VERSION );
 490         log_writer.println( "  date            : " + PRG_DATE );
 491         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 492         log_writer.println();
 493         log_writer.println( "Start time                               : "
 494                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 495         System.out.println( "Start time                               : "
 496                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 497         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 498         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 499         log_writer.println( "Gene tree name                           : "
 500                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 501         System.out.println( "Gene tree name                           : "
 502                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 503         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 504         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 505         log_writer.println( "Species tree name                        : "
 506                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 507         System.out.println( "Species tree name                        : "
 508                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 509         System.out.println( "Transfer taxonomy                        : " + transfer_taxonomy );
 510         GSDII gsdii = null;
 511         final long start_time = new Date().getTime();
 512         try {
 513             if ( base_algorithm == ALGORITHM.GSDI ) {
 514                 System.out.println( "Algorithm                                : GSDI" );
 515                 log_writer.println( "Algorithm                                : GSDI" );
 516             }
 517             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 518                 System.out.println( "Algorithm                                : GSDIR" );
 519                 log_writer.println( "Algorithm                                : GSDIR" );
 520             }
 521             System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 522             System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 523             log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 524             log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 525             log_writer.flush();
 526             if ( base_algorithm == ALGORITHM.GSDI ) {
 527                 gsdii = new GSDI( gene_tree,
 528                                   species_tree,
 529                                   most_parsimonous_duplication_model,
 530                                   allow_stripping_of_gene_tree,
 531                                   true,
 532                                   transfer_taxonomy );
 533             }
 534             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 535                 gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy );
 536             }
 537         }
 538         catch ( final SDIException e ) {
 539             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 540         }
 541         catch ( final IOException e ) {
 542             fatalError( "error", e.toString(), log_writer );
 543         }
 544         catch ( final OutOfMemoryError e ) {
 545             ForesterUtil.outOfMemoryError( e );
 546         }
 547         catch ( final Exception e ) {
 548             e.printStackTrace();
 549             fatalError( "unexpected error", e.toString(), log_writer );
 550         }
 551         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 552                 + "ms" );
 553         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 554                 + "ms" );
 555         System.out.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 556         log_writer.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 557         try {
 558             final PhylogenyWriter writer = new PhylogenyWriter();
 559             if ( base_algorithm == ALGORITHM.GSDIR ) {
 560                 writer.toPhyloXML( out_file, ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree(), 0 );
 561             }
 562             else {
 563                 writer.toPhyloXML( out_file, gene_tree, 0 );
 564             }
 565         }
 566         catch ( final IOException e ) {
 567             ForesterUtil.fatalError( PRG_NAME,
 568                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 569         }
 570         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 571         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 572         final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 573                 + SUFFIX_FOR_SPECIES_TREE_USED );
 574         try {
 575             final PhylogenyWriter writer = new PhylogenyWriter();
 576             writer.toPhyloXML( species_tree_used_file, species_tree, 0 );
 577         }
 578         catch ( final IOException e ) {
 579             ForesterUtil.fatalError( PRG_NAME,
 580                                      "Failed to write to [" + species_tree_used_file.getCanonicalPath() + "]: "
 581                                              + e.getMessage() );
 582         }
 583         System.out.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 584         log_writer.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 585         if ( ( gsdii.getReMappedScientificNamesFromGeneTree() != null )
 586                 && !gsdii.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
 587             System.out.println( "Number of gene tree species remapped     : "
 588                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 589             log_writer.println( "Number of gene tree species remapped     : "
 590                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 591             writeToRemappedFile( out_file, gsdii.getReMappedScientificNamesFromGeneTree(), log_writer );
 592         }
 593         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 594         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 595         System.out.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 596         log_writer.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 597         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 598         System.out.println( "Number of polytomies in species tree     : " + poly );
 599         log_writer.println( "Number of polytomies in species tree     : " + poly );
 600         System.out.println( "External nodes stripped from gene tree   : "
 601                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 602         log_writer.println( "External nodes stripped from gene tree   : "
 603                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 604         System.out
 605                 .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 606         log_writer
 607                 .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 608         System.out.println();
 609         System.out.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 610         log_writer.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 611         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 612             final GSDIR gsdir = ( GSDIR ) gsdii;
 613             System.out.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 614             log_writer.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 615         }
 616         else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 617             final GSDI gsdi = ( GSDI ) gsdii;
 618             System.out.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 619             log_writer.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 620             if ( !most_parsimonous_duplication_model ) {
 621                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 622                 System.out.println( "Number of potential duplications         : " + u );
 623                 log_writer.println( "Number of potential duplications         : " + u );
 624             }
 625         }
 626         log_writer.println();
 627         printMappedNodesToLog( log_writer, gsdii );
 628         log_writer.println();
 629         printStrippedGeneTreeNodesToLog( log_writer, gsdii );
 630         System.out.println();
 631         System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
 632         System.out.println();
 633         log_writer.close();
 634     }
 635
 636     private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
 637         try {
 638             log_writer.flush();
 639             log_writer.println();
 640             log_writer.print( type.toUpperCase() + ": " );
 641             log_writer.println( msg );
 642             log_writer.close();
 643         }
 644         catch ( final IOException e ) {
 645             e.printStackTrace();
 646         }
 647         ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
 648     }
 649
 650     private static void print_help() {
 651         System.out.println( "Usage: " + PRG_NAME
 652                 + " [-options] <gene tree file, or gene trees in-directory> <species tree> <outfile, or out-directory>" );
 653         System.out.println();
 654         System.out.println( "Options:" );
 655         System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 656                 + "         : to allow stripping of gene tree nodes without a matching species" );
 657         System.out.println( " -" + MOST_PARSIMONIOUS_OPTION
 658                 + "         : use most parimonious duplication model for GSDI: " );
 659         System.out.println( "              assign nodes as speciations which would otherwise be assiged" );
 660         System.out.println( "              as potential duplications due to polytomies in the species tree" );
 661         System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE
 662                 + "         : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 663         System.out.println( " -" + GSDIR_OPTION
 664                 + "         : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
 665         System.out.println( " -" + TRANSFER_TAXONOMY_OPTION
 666                 + "         : to transfer taxonomic data from species tree to gene tree" );
 667         System.out.println( " -" + SUFFIX_FOR_DIR_OPTION
 668                 + "=<suffix>: suffix for gene trees for analyzing entire directory of trees" );
 669         System.out.println();
 670         System.out.println();
 671         System.out.println( "Gene tree(s):" );
 672         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 673         System.out.println();
 674         System.out.println( "Species tree:" );
 675         System.out.println( " in phyloXML format (unless option -" + GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 676         System.out.println();
 677         System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 678                 + " gene_tree.xml tree_of_life.xml out.xml" );
 679         System.out.println( "          gsdi -" + SUFFIX_FOR_DIR_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml"
 680                 + " gene_tree_dir tree_of_life.xml out_dir" );
 681         System.out.println();
 682     }
 683
 684     private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi ) throws IOException {
 685         final SortedSet<String> ss = new TreeSet<String>();
 686         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 687             ss.add( n.toString() );
 688         }
 689         log_writer.println( "The following " + ss.size() + " species were used: " );
 690         for( final String s : ss ) {
 691             log_writer.println( "  " + s );
 692         }
 693     }
 694
 695     private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
 696             throws IOException {
 697         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 698         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 699             final String s = n.toString();
 700             if ( sm.containsKey( s ) ) {
 701                 sm.put( s, sm.get( s ) + 1 );
 702             }
 703             else {
 704                 sm.put( s, 1 );
 705             }
 706         }
 707         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 708         for( final String s : sm.keySet() ) {
 709             final int count = sm.get( s );
 710             if ( count == 1 ) {
 711                 log_writer.println( "  " + s );
 712             }
 713             else {
 714                 log_writer.println( "  " + s + " [" + count + "]" );
 715             }
 716         }
 717     }
 718
 719     private static void writeToRemappedFile( final File out_file,
 720                                              final SortedSet<String> remapped,
 721                                              final EasyWriter log_writer )
 722             throws IOException {
 723         final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
 724         final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
 725         for( final String s : remapped ) {
 726             remapped_writer.println( s );
 727         }
 728         remapped_writer.close();
 729         System.out.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 730         log_writer.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 731     }
 732 }