forester/java/src/org/forester/application/rio.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2017 Christian M. Zmasek
   6 // All rights reserved
   7 //
   8 // This library is free software; you can redistribute it and/or
   9 // modify it under the terms of the GNU Lesser General Public
  10 // License as published by the Free Software Foundation; either
  11 // version 2.1 of the License, or (at your option) any later version.
  12 //
  13 // This library is distributed in the hope that it will be useful,
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  16 // Lesser General Public License for more details.
  17 //
  18 // You should have received a copy of the GNU Lesser General Public
  19 // License along with this library; if not, write to the Free Software
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  21 //
  22 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  23
  24 package org.forester.application;
  25
  26 import java.io.File;
  27 import java.io.FilenameFilter;
  28 import java.io.IOException;
  29 import java.util.ArrayList;
  30 import java.util.Arrays;
  31 import java.util.List;
  32
  33 import org.forester.rio.RIO;
  34 import org.forester.rio.RIO.REROOTING;
  35 import org.forester.rio.RIOUtil;
  36 import org.forester.sdi.SDIutil.ALGORITHM;
  37 import org.forester.util.CommandLineArguments;
  38 import org.forester.util.EasyWriter;
  39 import org.forester.util.ForesterUtil;
  40
  41 public class rio {
  42
  43     public final static String PRG_NAME                       = "rio";
  44     public final static String PRG_VERSION                    = "5.000";
  45     public final static String PRG_DATE                       = "170411";
  46     final static private String E_MAIL                         = "phyloxml@gmail.com";
  47     final static private String WWW                            = "https://sites.google.com/site/cmzmasek/home/software/forester";
  48     final static private String HELP_OPTION_1                  = "help";
  49     final static private String LOGFILE_SUFFIX                 = "_RIO_log.tsv";
  50     final static private String STRIPPED_SPECIES_TREE_SUFFIX   = "_RIO_sst.xml";
  51     final static private String ORTHO_OUTTABLE_SUFFIX          = "_RIO_orthologies.tsv";
  52     final static private String OUT_MIN_DUP_GENE_TREE_SUFFIX   = "_RIO_gene_tree_min_dup_";
  53     final static private String OUT_MED_DUP_GENE_TREE_SUFFIX   = "_RIO_gene_tree_med_dup_";
  54     final static private String ORTHOLOG_GROUPS_SUFFIX         = "_RIO_ortholog_groups.tsv";
  55     final static private String HELP_OPTION_2                  = "h";
  56     final static private String GT_FIRST                       = "f";
  57     final static private String GT_LAST                        = "l";
  58     final static private String REROOTING_OPT                  = "r";
  59     final static private String OUTGROUP                       = "o";
  60     final static private String USE_SDIR                       = "s";
  61     final static private String GENE_TREES_SUFFIX_OPTION       = "g";
  62     final static private String ORTHOLOG_GROUPS_CUTOFF_OPTION  = "c";
  63     final static private double ORTHOLOG_GROUPS_CUTOFF_DEFAULT = 0.5;
  64
  65     public static void main( final String[] args ) {
  66         ForesterUtil.printProgramInformation( PRG_NAME,
  67                                               "resampled inference of orthologs",
  68                                               PRG_VERSION,
  69                                               PRG_DATE,
  70                                               E_MAIL,
  71                                               WWW,
  72                                               ForesterUtil.getForesterLibraryInformation() );
  73         CommandLineArguments cla = null;
  74         try {
  75             cla = new CommandLineArguments( args );
  76         }
  77         catch ( final Exception e ) {
  78             ForesterUtil.fatalError( e.getMessage() );
  79         }
  80         if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
  81             printHelp();
  82         }
  83         if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) {
  84             System.out.println();
  85             System.out.println( "error: incorrect number of arguments" );
  86             System.out.println();
  87             printHelp();
  88         }
  89         final List<String> allowed_options = new ArrayList<String>();
  90         allowed_options.add( GT_FIRST );
  91         allowed_options.add( GT_LAST );
  92         allowed_options.add( REROOTING_OPT );
  93         allowed_options.add( OUTGROUP );
  94         allowed_options.add( USE_SDIR );
  95         allowed_options.add( GENE_TREES_SUFFIX_OPTION );
  96         allowed_options.add( ORTHOLOG_GROUPS_CUTOFF_OPTION );
  97         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  98         if ( dissallowed_options.length() > 0 ) {
  99             ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options );
 100         }
 101         final File gene_trees_file = cla.getFile( 0 );
 102         final boolean use_dir;
 103         File indir = null;
 104         File outdir = null;
 105         if ( gene_trees_file.isDirectory() ) {
 106             if ( !gene_trees_file.exists() ) {
 107                 ForesterUtil.fatalError( "gene trees directory \"" + gene_trees_file + "\" does not exist" );
 108             }
 109             use_dir = true;
 110             indir = gene_trees_file;
 111         }
 112         else {
 113             use_dir = false;
 114         }
 115         final File species_tree_file = cla.getFile( 1 );
 116         File orthology_outtable = null;
 117         if ( use_dir ) {
 118             outdir = cla.getFile( 2 );
 119         }
 120         else {
 121             orthology_outtable = cla.getFile( 2 );
 122         }
 123         File logfile;
 124         if ( use_dir ) {
 125             if ( ( cla.getNumberOfNames() < 4 ) ) {
 126                 System.out.println();
 127                 System.out.println( "error: incorrect number of arguments" );
 128                 System.out.println();
 129                 printHelp();
 130             }
 131             logfile = cla.getFile( 3 );
 132             if ( logfile.exists() ) {
 133                 ForesterUtil.fatalError( "\"" + logfile + "\" already exists" );
 134             }
 135         }
 136         else {
 137             if ( cla.getNumberOfNames() > 3 ) {
 138                 logfile = cla.getFile( 3 );
 139                 if ( logfile.exists() ) {
 140                     ForesterUtil.fatalError( "\"" + logfile + "\" already exists" );
 141                 }
 142             }
 143             else {
 144                 logfile = null;
 145             }
 146         }
 147         boolean sdir = false;
 148         if ( cla.isOptionSet( USE_SDIR ) ) {
 149             if ( cla.isOptionHasAValue( USE_SDIR ) ) {
 150                 ForesterUtil.fatalError( "no value allowed for -" + USE_SDIR );
 151             }
 152             sdir = true;
 153             if ( !use_dir && logfile != null ) {
 154                 ForesterUtil.fatalError( "no logfile output for SDIR algorithm" );
 155             }
 156         }
 157         String outgroup = null;
 158         if ( cla.isOptionSet( OUTGROUP ) ) {
 159             if ( sdir ) {
 160                 ForesterUtil.fatalError( "no outgroup option for SDIR algorithm" );
 161             }
 162             if ( use_dir ) {
 163                 ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" );
 164             }
 165             if ( !cla.isOptionHasAValue( OUTGROUP ) ) {
 166                 ForesterUtil.fatalError( "no value for -" + OUTGROUP );
 167             }
 168             outgroup = cla.getOptionValueAsCleanString( OUTGROUP );
 169         }
 170         REROOTING rerooting = REROOTING.BY_ALGORITHM;
 171         if ( cla.isOptionSet( REROOTING_OPT ) ) {
 172             if ( !cla.isOptionHasAValue( REROOTING_OPT ) ) {
 173                 ForesterUtil.fatalError( "no value for -" + REROOTING_OPT );
 174             }
 175             if ( sdir ) {
 176                 ForesterUtil.fatalError( "no re-rooting option for SDIR algorithm" );
 177             }
 178             final String rerooting_str = cla.getOptionValueAsCleanString( REROOTING_OPT ).toLowerCase();
 179             if ( rerooting_str.equals( "none" ) ) {
 180                 rerooting = REROOTING.NONE;
 181             }
 182             else if ( rerooting_str.equals( "midpoint" ) ) {
 183                 rerooting = REROOTING.MIDPOINT;
 184             }
 185             else if ( rerooting_str.equals( "outgroup" ) ) {
 186                 if ( use_dir ) {
 187                     ForesterUtil.fatalError( "no outgroup option for operating on gene trees directory" );
 188                 }
 189                 rerooting = REROOTING.OUTGROUP;
 190             }
 191             else {
 192                 ForesterUtil
 193                         .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" );
 194             }
 195         }
 196         if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) {
 197             ForesterUtil.fatalError( "selected re-rooting by outgroup, but outgroup not set" );
 198         }
 199         if ( !ForesterUtil.isEmpty( outgroup ) && ( rerooting != REROOTING.OUTGROUP ) ) {
 200             ForesterUtil.fatalError( "outgroup set, but selected re-rooting by other approach" );
 201         }
 202         int gt_first = RIO.DEFAULT_RANGE;
 203         int gt_last = RIO.DEFAULT_RANGE;
 204         if ( cla.isOptionSet( GT_FIRST ) ) {
 205             if ( sdir ) {
 206                 ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
 207             }
 208             if ( !cla.isOptionHasAValue( GT_FIRST ) ) {
 209                 ForesterUtil.fatalError( "no value for -" + GT_FIRST );
 210             }
 211             try {
 212                 gt_first = cla.getOptionValueAsInt( GT_FIRST );
 213             }
 214             catch ( final IOException e ) {
 215                 ForesterUtil.fatalError( "could not parse integer for -" + GT_FIRST + " option" );
 216             }
 217             if ( gt_first < 0 ) {
 218                 ForesterUtil.fatalError( "attempt to set index of first tree to analyze to: " + gt_first );
 219             }
 220         }
 221         if ( cla.isOptionSet( GT_LAST ) ) {
 222             if ( sdir ) {
 223                 ForesterUtil.fatalError( "no gene tree range option for SDIR algorithm" );
 224             }
 225             if ( !cla.isOptionHasAValue( GT_LAST ) ) {
 226                 ForesterUtil.fatalError( "no value for -" + GT_LAST );
 227             }
 228             try {
 229                 gt_last = cla.getOptionValueAsInt( GT_LAST );
 230             }
 231             catch ( final IOException e ) {
 232                 ForesterUtil.fatalError( "could not parse integer for -" + GT_LAST + " option" );
 233             }
 234             if ( gt_last < 0 ) {
 235                 ForesterUtil.fatalError( "attempt to set index of last tree to analyze to: " + gt_last );
 236             }
 237         }
 238         if ( ( ( gt_last != RIO.DEFAULT_RANGE ) && ( gt_first != RIO.DEFAULT_RANGE ) ) && ( ( gt_last < gt_first ) ) ) {
 239             ForesterUtil.fatalError( "attempt to set range (0-based) of gene to analyze to: from " + gt_first + " to "
 240                     + gt_last );
 241         }
 242         double ortholog_group_cutoff = ORTHOLOG_GROUPS_CUTOFF_DEFAULT;
 243         if ( cla.isOptionSet( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) {
 244             if ( sdir ) {
 245                 ForesterUtil.fatalError( "ortholog groups cutoff for SDIR algorithm" );
 246             }
 247             if ( !cla.isOptionHasAValue( ORTHOLOG_GROUPS_CUTOFF_OPTION ) ) {
 248                 ForesterUtil.fatalError( "no value for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION );
 249             }
 250             try {
 251                 ortholog_group_cutoff = cla.getOptionValueAsDouble( ORTHOLOG_GROUPS_CUTOFF_OPTION );
 252             }
 253             catch ( final IOException e ) {
 254                 ForesterUtil.fatalError( "could not parse double for -" + ORTHOLOG_GROUPS_CUTOFF_OPTION + " option" );
 255             }
 256             if ( ortholog_group_cutoff < 0 ) {
 257                 ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff );
 258             }
 259             if ( ortholog_group_cutoff > 1 ) {
 260                 ForesterUtil.fatalError( "attempt to set ortholog groups cutoff to: " + ortholog_group_cutoff );
 261             }
 262         }
 263         if ( !use_dir ) {
 264             ForesterUtil.fatalErrorIfFileNotReadable( gene_trees_file );
 265         }
 266         final String gene_trees_suffix;
 267         if ( cla.isOptionSet( GENE_TREES_SUFFIX_OPTION ) ) {
 268             if ( !use_dir ) {
 269                 ForesterUtil.fatalError( "no gene tree suffix option when operating on indivual gene trees" );
 270             }
 271             if ( !cla.isOptionHasAValue( GENE_TREES_SUFFIX_OPTION ) ) {
 272                 ForesterUtil.fatalError( "no value for -" + GENE_TREES_SUFFIX_OPTION );
 273             }
 274             gene_trees_suffix = cla.getOptionValueAsCleanString( GENE_TREES_SUFFIX_OPTION );
 275         }
 276         else {
 277             gene_trees_suffix = ".mlt";
 278         }
 279         ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file );
 280         if ( !use_dir && orthology_outtable.exists() ) {
 281             ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" );
 282         }
 283         long time = 0;
 284         try {
 285             if ( use_dir ) {
 286                 System.out.println( "Gene trees in-dir                   :\t" + indir.getCanonicalPath() );
 287                 System.out.println( "Gene trees suffix                   :\t" + gene_trees_suffix );
 288             }
 289             else {
 290                 System.out.println( "Gene trees                          :\t" + gene_trees_file.getCanonicalPath() );
 291             }
 292             System.out.println( "Species tree                        :\t" + species_tree_file.getCanonicalPath() );
 293         }
 294         catch ( final IOException e ) {
 295             ForesterUtil.fatalError( e.getLocalizedMessage() );
 296         }
 297         if ( use_dir ) {
 298             System.out.println( "Out-dir                             :\t" + outdir );
 299         }
 300         else {
 301             System.out.println( "All vs all orthology results table  :\t" + orthology_outtable );
 302         }
 303         if ( logfile != null ) {
 304             System.out.println( "Logfile                             :\t" + logfile );
 305         }
 306         System.out.println( "Ortholog groups cutoff              :\t" + ortholog_group_cutoff );
 307         if ( gt_first != RIO.DEFAULT_RANGE ) {
 308             System.out.println( "First gene tree to analyze          :\t" + gt_first );
 309         }
 310         if ( gt_last != RIO.DEFAULT_RANGE ) {
 311             System.out.println( "Last gene tree to analyze           :\t" + gt_last );
 312         }
 313         String rerooting_str = "";
 314         switch ( rerooting ) {
 315             case BY_ALGORITHM: {
 316                 rerooting_str = "by minimizing duplications";
 317                 break;
 318             }
 319             case MIDPOINT: {
 320                 rerooting_str = "by midpoint method";
 321                 break;
 322             }
 323             case OUTGROUP: {
 324                 rerooting_str = "by outgroup: " + outgroup;
 325                 break;
 326             }
 327             case NONE: {
 328                 rerooting_str = "none";
 329                 break;
 330             }
 331         }
 332         System.out.println( "Re-rooting                          : \t" + rerooting_str );
 333         if ( !sdir ) {
 334             System.out.println( "Non binary species tree             :\tallowed" );
 335         }
 336         else {
 337             System.out.println( "Non binary species tree             :\tdisallowed" );
 338         }
 339         time = System.currentTimeMillis();
 340         final ALGORITHM algorithm;
 341         if ( sdir ) {
 342             algorithm = ALGORITHM.SDIR;
 343         }
 344         else {
 345             algorithm = ALGORITHM.GSDIR;
 346         }
 347         EasyWriter log = null;
 348         if ( use_dir ) {
 349             if ( outdir.exists() ) {
 350                 if ( !outdir.isDirectory() ) {
 351                     ForesterUtil.fatalError( PRG_NAME,
 352                                              "out-directory [" + outdir + "] already exists but is not a directory" );
 353                 }
 354             }
 355             else {
 356                 final boolean success = outdir.mkdirs();
 357                 if ( !success ) {
 358                     ForesterUtil.fatalError( PRG_NAME, "could not create out-directory [" + outdir + "]" );
 359                 }
 360             }
 361             final String species_tree_file_name = species_tree_file.getName();
 362             final File gene_trees_files[] = indir.listFiles( new FilenameFilter() {
 363
 364                 @Override
 365                 public boolean accept( final File dir, final String name ) {
 366                     return ( ( name.endsWith( gene_trees_suffix ) ) && !( name.equals( species_tree_file_name ) ) );
 367                 }
 368             } );
 369             if ( gene_trees_files.length < 1 ) {
 370                 ForesterUtil.fatalError( PRG_NAME,
 371                                          "in-directory [" + indir
 372                                                  + "] does not contain any gene tree files with suffix "
 373                                                  + gene_trees_suffix );
 374             }
 375             try {
 376                 log = ForesterUtil.createEasyWriter( logfile );
 377             }
 378             catch ( final IOException e ) {
 379                 ForesterUtil.fatalError( PRG_NAME, "could not create [" + logfile + "]" );
 380             }
 381             Arrays.sort( gene_trees_files );
 382             try {
 383                 log.print( "# program" );
 384                 log.print( "\t" );
 385                 log.print( PRG_NAME );
 386                 log.println();
 387                 log.print( "# version" );
 388                 log.print( "\t" );
 389                 log.print( PRG_VERSION );
 390                 log.println();
 391                 log.print( "# date" );
 392                 log.print( "\t" );
 393                 log.print( PRG_DATE );
 394                 log.println();
 395                 log.print( "# Algorithm " );
 396                 log.print( "\t" );
 397                 log.print( algorithm.toString() );
 398                 log.println();
 399                 log.print( "# Gene trees in-dir" );
 400                 log.print( "\t" );
 401                 log.print( indir.getCanonicalPath() );
 402                 log.println();
 403                 log.print( "# Gene trees suffix" );
 404                 log.print( "\t" );
 405                 log.print( gene_trees_suffix );
 406                 log.println();
 407                 log.print( "# Species tree" );
 408                 log.print( "\t" );
 409                 log.print( species_tree_file.getCanonicalPath() );
 410                 log.println();
 411                 log.print( "# Out-dir" );
 412                 log.print( "\t" );
 413                 log.print( outdir.getCanonicalPath() );
 414                 log.println();
 415                 log.print( "# Logfile" );
 416                 log.print( "\t" );
 417                 log.print( logfile.getCanonicalPath() );
 418                 log.println();
 419                 log.print( "# Ortholog groups cutoff" );
 420                 log.print( "\t" );
 421                 log.print( Double.toString( ortholog_group_cutoff ) );
 422                 log.println();
 423                 if ( gt_first != RIO.DEFAULT_RANGE ) {
 424                     log.print( "# First gene tree to analyze" );
 425                     log.print( "\t" );
 426                     log.print( Integer.toString( gt_first ) );
 427                     log.println();
 428                 }
 429                 if ( gt_last != RIO.DEFAULT_RANGE ) {
 430                     log.print( "# Last gene tree to analyze" );
 431                     log.print( "\t" );
 432                     log.print( Integer.toString( gt_last ) );
 433                     log.println();
 434                 }
 435                 log.print( "# Re-rooting" );
 436                 log.print( "\t" );
 437                 log.print( rerooting_str );
 438                 log.println();
 439                 log.print( "# Non binary species tree" );
 440                 log.print( "\t" );
 441                 if ( !sdir ) {
 442                     log.print( "allowed" );
 443                 }
 444                 else {
 445                     log.print( "disallowed" );
 446                 }
 447                 log.println();
 448                 log.println();
 449                 log.print( "NAME" );
 450                 log.print( "\t" );
 451                 log.print( "EXT NODES" );
 452                 log.print( "\t" );
 453                 log.print(  ortholog_group_cutoff + " O GROUPS" );
 454                 log.print( "\t" );
 455                 log.print( "0.05 O GROUPS" );
 456                 log.print( "\t" );
 457                 log.print( "0.25 O GROUPS" );
 458                 log.print( "\t" );
 459                 log.print( "0.5 O GROUPS" );
 460                 log.print( "\t" );
 461                 log.print( "0.75 O GROUPS" );
 462                 log.print( "\t" );
 463                 log.print( "0.95 O GROUPS" );
 464                 log.print( "\t" );
 465                 log.print( "MEDIAN DUP" );
 466                 log.print( "\t" );
 467                 log.print( "MEAN DUP" );
 468                 log.print( "\t" );
 469                 log.print( "MEAN DUP SD" );
 470                 log.print( "\t" );
 471                 log.print( "MIN DUP" );
 472                 log.print( "\t" );
 473                 log.print( "MAX DUP" );
 474                 log.print( "\t" );
 475                 log.print( "REMOVED EXT NODES" );
 476                 log.print( "\t" );
 477                 log.print( "N" );
 478                 log.println();
 479             }
 480             catch ( IOException e ) {
 481                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 482             }
 483             int counter = 1;
 484             for( final File gf : gene_trees_files ) {
 485                 String outname = gf.getName();
 486                 System.out
 487                         .print( "\r                                                                                            " );
 488                 System.out.print( "\r" + counter + "/" + gene_trees_files.length + ": " + outname );
 489                 counter++;
 490                 if ( outname.indexOf( "." ) > 0 ) {
 491                     outname = outname.substring( 0, outname.lastIndexOf( "." ) );
 492                 }
 493                 try {
 494                     RIOUtil.executeAnalysis( gf,
 495                                      species_tree_file,
 496                                      new File( outdir.getCanonicalFile() + "/" + outname + ORTHO_OUTTABLE_SUFFIX ),
 497                                      new File( outdir.getCanonicalFile() + "/" + outname + ORTHOLOG_GROUPS_SUFFIX ),
 498                                      new File( outdir.getCanonicalFile() + "/" + outname + LOGFILE_SUFFIX ),
 499                                      outgroup,
 500                                      rerooting,
 501                                      gt_first,
 502                                      gt_last,
 503                                      new File( outdir.getCanonicalFile() + "/" + outname
 504                                              + STRIPPED_SPECIES_TREE_SUFFIX ),
 505                                      new File( outdir.getCanonicalFile() + "/" + outname
 506                                              + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
 507                                      new File( outdir.getCanonicalFile() + "/" + outname
 508                                              + OUT_MED_DUP_GENE_TREE_SUFFIX ),
 509                                      true,
 510                                      algorithm,
 511                                      true,
 512                                      log,
 513                                      ortholog_group_cutoff );
 514                 }
 515                 catch ( IOException e ) {
 516                     ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 517                 }
 518             }
 519             System.out
 520                     .print( "\r                                                                                        " );
 521             System.out.println();
 522         }
 523         else {
 524             String outname = orthology_outtable.toString();
 525             if ( outname.indexOf( "." ) > 0 ) {
 526                 outname = outname.substring( 0, outname.lastIndexOf( "." ) );
 527             }
 528             RIOUtil.executeAnalysis( gene_trees_file,
 529                              species_tree_file,
 530                              orthology_outtable,
 531                              new File( outname + ORTHOLOG_GROUPS_SUFFIX ),
 532                              logfile,
 533                              outgroup,
 534                              rerooting,
 535                              gt_first,
 536                              gt_last,
 537                              new File( outname + STRIPPED_SPECIES_TREE_SUFFIX ),
 538                              new File( outname + OUT_MIN_DUP_GENE_TREE_SUFFIX ),
 539                              new File( outname + OUT_MED_DUP_GENE_TREE_SUFFIX ),
 540                              algorithm == ALGORITHM.GSDIR,
 541                              algorithm,
 542                              false,
 543                              null,
 544                              ortholog_group_cutoff );
 545         }
 546         if ( !use_dir ) {
 547             time = System.currentTimeMillis() - time;
 548             System.out.println( "Time                                :\t" + time + "ms" );
 549         }
 550         else {
 551             try {
 552                 log.close();
 553             }
 554             catch ( IOException e ) {
 555                 ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 556             }
 557             time = System.currentTimeMillis() - time;
 558             System.out.println( "Time                                :\t" + time + "ms" );
 559         }
 560         System.exit( 0 );
 561     }
 562
 563     private final static void printHelp() {
 564         System.out.println( "Usage" );
 565         System.out.println();
 566         System.out.println( PRG_NAME
 567                 + " [options] <gene trees infile> <species tree infile> <all vs all orthology table outfile> [logfile]" );
 568         System.out.println();
 569         System.out.println( PRG_NAME + " [options] <gene trees indir> <species tree infile> <outdir> <logfile>" );
 570         System.out.println();
 571         System.out.println();
 572         System.out.println( " Options" );
 573         System.out.println( "  -" + GT_FIRST + "=<first>     : first gene tree to analyze (0-based index)" );
 574         System.out.println( "  -" + GT_LAST + "=<last>      : last gene tree to analyze (0-based index)" );
 575         System.out.println( "  -" + ORTHOLOG_GROUPS_CUTOFF_OPTION
 576                 + "=<cutoff>    : cutoff value for ortholog groups (default: " + ORTHOLOG_GROUPS_CUTOFF_DEFAULT + ")" );
 577         System.out.println( "  -" + REROOTING_OPT
 578                 + "=<re-rooting>: re-rooting method for gene trees, possible values or 'none', 'midpoint'," );
 579         System.out.println( "                   or 'outgroup' (default: by minizming duplications)" );
 580         System.out.println( "  -" + OUTGROUP
 581                 + "=<outgroup>  : for rooting by outgroup, name of outgroup (external gene tree node)" );
 582         System.out.println( "  -" + USE_SDIR
 583                 + "             : to use SDIR instead of GSDIR (faster, but non-binary species trees are" );
 584         System.out.println( "                   disallowed, as are most options)" );
 585         System.out.println( "  -" + GENE_TREES_SUFFIX_OPTION
 586                 + "=<suffix>    : suffix for gene trees when operating on gene tree directories (default: .mlt)" );
 587         System.out.println();
 588         System.out.println( " Formats" );
 589         System.out
 590                 .println( "  The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," );
 591         System.out
 592                 .println( "  but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" );
 593         System.out
 594                 .println( "  extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" );
 595         System.out.println( "  in the species tree." );
 596         System.out.println();
 597         System.out.println( " Examples" );
 598         System.out.println( "  rio -s gene_trees.nh species.xml outtable.tsv" );
 599         System.out.println( "  rio gene_trees.nh species.xml outtable.tsv log.txt" );
 600         System.out.println( "  rio -c=0.9 -f=10 -l=100 -r=none gene_trees.xml species.xml outtable.tsv log.txt" );
 601         System.out.println( "  rio -g=.xml gene_trees_dir species.xml out_dir log.tsv" );
 602         System.out.println();
 603         System.exit( -1 );
 604     }
 605 }