forester/java/src/org/forester/rio/RIOUtil.java

   1
   2 package org.forester.rio;
   3
   4 import java.io.File;
   5 import java.io.FileNotFoundException;
   6 import java.io.IOException;
   7 import java.math.RoundingMode;
   8 import java.util.ArrayList;
   9 import java.util.List;
  10 import java.util.SortedMap;
  11 import java.util.SortedSet;
  12 import java.util.TreeSet;
  13
  14 import org.forester.datastructures.IntMatrix;
  15 import org.forester.io.parsers.IteratingPhylogenyParser;
  16 import org.forester.io.parsers.PhylogenyParser;
  17 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  18 import org.forester.io.parsers.nhx.NHXParser;
  19 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  20 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  21 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  22 import org.forester.io.parsers.util.ParserUtils;
  23 import org.forester.io.writers.PhylogenyWriter;
  24 import org.forester.phylogeny.Phylogeny;
  25 import org.forester.phylogeny.PhylogenyMethods;
  26 import org.forester.phylogeny.PhylogenyNode;
  27 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  28 import org.forester.phylogeny.data.Sequence;
  29 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  30 import org.forester.phylogeny.factories.PhylogenyFactory;
  31 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  32 import org.forester.rio.RIO.REROOTING;
  33 import org.forester.sdi.GSDIR;
  34 import org.forester.sdi.SDIException;
  35 import org.forester.sdi.SDIutil;
  36 import org.forester.sdi.SDIutil.ALGORITHM;
  37 import org.forester.util.BasicDescriptiveStatistics;
  38 import org.forester.util.BasicTable;
  39 import org.forester.util.BasicTableParser;
  40 import org.forester.util.EasyWriter;
  41 import org.forester.util.ForesterUtil;
  42
  43 public final class RIOUtil {
  44
  45     public final static String STRIPPED_SPECIES_TREE_SUFFIX   = "_RIO_stripped_species_tree.xml";
  46     public final static String ORTHO_OUTTABLE_SUFFIX          = "_RIO_orthologies.tsv";
  47     public final static String ORTHO_OUTTABLE_WITH_MAP_SUFFIX = "_RIO_orthologies_ext_map.tsv";
  48     public final static String OUT_MIN_DUP_GENE_TREE_SUFFIX   = "_RIO_gene_tree_min_dup_";
  49     public final static String OUT_MED_DUP_GENE_TREE_SUFFIX   = "_RIO_gene_tree_med_dup_";
  50     public final static String BEST_TREE_SUFFIX               = "_RIO_consensus_gene_tree_dup_";
  51     public final static String ORTHOLOG_GROUPS_SUFFIX         = "_RIO_ortholog_groups.tsv";
  52     public final static String LOGFILE_SUFFIX                 = "_RIO_log.tsv";
  53
  54     public static final void executeAnalysis( final File gene_trees_file,
  55                                               final File species_tree_file,
  56                                               final File orthology_outtable,
  57                                               final File orthology_outtable_with_mappings,
  58                                               final File orthology_groups_outfile,
  59                                               final File logfile,
  60                                               final String outgroup,
  61                                               final REROOTING rerooting,
  62                                               final int gt_first,
  63                                               final int gt_last,
  64                                               final File return_species_tree,
  65                                               final File return_min_dup_gene_tree,
  66                                               final File return_median_dup_gene_tree,
  67                                               final boolean transfer_taxonomy,
  68                                               final ALGORITHM algorithm,
  69                                               final boolean use_gene_trees_dir,
  70                                               final EasyWriter log,
  71                                               final double ortholog_group_cutoff,
  72                                               final boolean perform_id_mapping,
  73                                               final File id_mapping_dir,
  74                                               final String id_mapping_suffix,
  75                                               final boolean perform_gsdir_on_best_tree,
  76                                               final File outdir,
  77                                               final File best_trees_indir,
  78                                               final String best_trees_suffix ) {
  79         try {
  80             final SortedMap<String, String> id_map;
  81             if ( perform_id_mapping ) {
  82                 id_map = obtainMapping( id_mapping_dir, gene_trees_file.getName(), id_mapping_suffix );
  83             }
  84             else {
  85                 id_map = null;
  86             }
  87             final RIO rio;
  88             boolean iterating = false;
  89             final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true );
  90             if ( p instanceof PhyloXmlParser ) {
  91                 rio = RIO.executeAnalysis( gene_trees_file,
  92                                            species_tree_file,
  93                                            algorithm,
  94                                            rerooting,
  95                                            outgroup,
  96                                            gt_first,
  97                                            gt_last,
  98                                            logfile != null,
  99                                            true,
 100                                            transfer_taxonomy );
 101             }
 102             else {
 103                 iterating = true;
 104                 if ( p instanceof NHXParser ) {
 105                     final NHXParser nhx = ( NHXParser ) p;
 106                     nhx.setReplaceUnderscores( false );
 107                     nhx.setIgnoreQuotes( true );
 108                     nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
 109                 }
 110                 else if ( p instanceof NexusPhylogeniesParser ) {
 111                     final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
 112                     nex.setReplaceUnderscores( false );
 113                     nex.setIgnoreQuotes( true );
 114                     nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
 115                 }
 116                 else {
 117                     throw new RuntimeException( "unknown parser type: " + p );
 118                 }
 119                 final IteratingPhylogenyParser ip = ( IteratingPhylogenyParser ) p;
 120                 ip.setSource( gene_trees_file );
 121                 rio = RIO.executeAnalysis( ip,
 122                                            species_tree_file,
 123                                            algorithm,
 124                                            rerooting,
 125                                            outgroup,
 126                                            gt_first,
 127                                            gt_last,
 128                                            logfile != null,
 129                                            !use_gene_trees_dir,
 130                                            transfer_taxonomy );
 131             }
 132             if ( !use_gene_trees_dir ) {
 133                 if ( algorithm == ALGORITHM.GSDIR ) {
 134                     System.out.println( "Taxonomy linking based on           :\t" + rio.getGSDIRtaxCompBase() );
 135                 }
 136             }
 137             final IntMatrix m;
 138             if ( iterating ) {
 139                 m = rio.getOrthologTable();
 140             }
 141             else {
 142                 m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
 143             }
 144             final GSDIR gsdir_for_best_tree;
 145             if ( perform_gsdir_on_best_tree ) {
 146                 gsdir_for_best_tree = analyzeConsensusTree( gene_trees_file,
 147                                                             species_tree_file,
 148                                                             outdir,
 149                                                             best_trees_indir,
 150                                                             id_map,
 151                                                             best_trees_suffix );
 152             }
 153             else {
 154                 gsdir_for_best_tree = null;
 155             }
 156             final BasicDescriptiveStatistics stats = rio.getDuplicationsStatistics();
 157             if ( perform_id_mapping ) {
 158                 writeOrthologyTable( orthology_outtable, stats.getN(), m, !use_gene_trees_dir, id_map, true );
 159                 writeOrthologyTable( orthology_outtable_with_mappings,
 160                                      stats.getN(),
 161                                      m,
 162                                      !use_gene_trees_dir,
 163                                      id_map,
 164                                      false );
 165             }
 166             else {
 167                 writeOrthologyTable( orthology_outtable, stats.getN(), m, !use_gene_trees_dir, null, false );
 168             }
 169             final int ortholog_groups = writeOrtologGroups( orthology_groups_outfile,
 170                                                             ortholog_group_cutoff,
 171                                                             stats.getN(),
 172                                                             m,
 173                                                             !use_gene_trees_dir,
 174                                                             false,
 175                                                             id_map );
 176             final int ortholog_groups_005 = writeOrtologGroups( null, 0.05, stats.getN(), m, false, true, null );
 177             final int ortholog_groups_025 = writeOrtologGroups( null, 0.25, stats.getN(), m, false, true, null );
 178             final int ortholog_groups_05 = writeOrtologGroups( null, 0.5, stats.getN(), m, false, true, null );
 179             final int ortholog_groups_075 = writeOrtologGroups( null, 0.75, stats.getN(), m, false, true, null );
 180             final int ortholog_groups_095 = writeOrtologGroups( null, 0.95, stats.getN(), m, false, true, null );
 181             if ( ( algorithm != ALGORITHM.SDIR ) && ( logfile != null ) ) {
 182                 writeLogFile( logfile,
 183                               rio,
 184                               species_tree_file,
 185                               gene_trees_file,
 186                               orthology_outtable,
 187                               org.forester.application.rio.PRG_NAME,
 188                               org.forester.application.rio.PRG_VERSION,
 189                               org.forester.application.rio.PRG_DATE,
 190                               ForesterUtil.getForesterLibraryInformation(),
 191                               !use_gene_trees_dir );
 192             }
 193             if ( return_species_tree != null ) {
 194                 writeTree( rio.getSpeciesTree(),
 195                            return_species_tree,
 196                            use_gene_trees_dir ? null : "Wrote (stripped) species tree to    :\t",
 197                            null );
 198             }
 199             if ( return_min_dup_gene_tree != null && rio.getMinDuplicationsGeneTree() != null ) {
 200                 final int min = ( int ) rio.getDuplicationsStatistics().getMin();
 201                 writeTree( rio.getMinDuplicationsGeneTree(),
 202                            new File( return_min_dup_gene_tree.toString() + min + ".xml" ),
 203                            use_gene_trees_dir ? null : "Wrote one min duplication gene tree :\t",
 204                            id_map );
 205             }
 206             if ( return_median_dup_gene_tree != null && rio.getDuplicationsToTreeMap() != null ) {
 207                 final int med = ( int ) rio.getDuplicationsStatistics().median();
 208                 writeTree( rio.getDuplicationsToTreeMap().get( med ),
 209                            new File( return_median_dup_gene_tree.toString() + med + ".xml" ),
 210                            use_gene_trees_dir ? null : "Wrote one med duplication gene tree :\t",
 211                            id_map );
 212             }
 213             final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.##" );
 214             final int min = ( int ) stats.getMin();
 215             final int max = ( int ) stats.getMax();
 216             final int median = ( int ) stats.median();
 217             int min_count = 0;
 218             int max_count = 0;
 219             int median_count = 0;
 220             for( double d : stats.getData() ) {
 221                 if ( ( ( int ) d ) == min ) {
 222                     ++min_count;
 223                 }
 224                 if ( ( ( int ) d ) == max ) {
 225                     ++max_count;
 226                 }
 227                 if ( ( ( int ) d ) == median ) {
 228                     ++median_count;
 229                 }
 230             }
 231             final double min_count_percentage = ( 100.0 * min_count ) / stats.getN();
 232             final double max_count_percentage = ( 100.0 * max_count ) / stats.getN();
 233             final double median_count_percentage = ( 100.0 * median_count ) / stats.getN();
 234             if ( use_gene_trees_dir ) {
 235                 String name = gene_trees_file.getName();
 236                 if ( name.indexOf( "." ) > 0 ) {
 237                     name = name.substring( 0, name.lastIndexOf( "." ) );
 238                 }
 239                 log.print( name );
 240                 log.print( "\t" );
 241                 log.print( Integer.toString( rio.getExtNodesOfAnalyzedGeneTrees() ) );
 242                 log.print( "\t" );
 243                 log.print( Integer.toString( ortholog_groups ) );
 244                 //
 245                 log.print( "\t" );
 246                 log.print( Integer.toString( ortholog_groups_005 ) );
 247                 log.print( "\t" );
 248                 log.print( Integer.toString( ortholog_groups_025 ) );
 249                 log.print( "\t" );
 250                 log.print( Integer.toString( ortholog_groups_05 ) );
 251                 log.print( "\t" );
 252                 log.print( Integer.toString( ortholog_groups_075 ) );
 253                 log.print( "\t" );
 254                 log.print( Integer.toString( ortholog_groups_095 ) );
 255                 //
 256                 if ( true ) {
 257                     log.print( "\t" );
 258                     log.print( Integer.toString( gsdir_for_best_tree.getMinDuplicationsSum() ) );
 259                     log.print( "\t" );
 260                     log.print( df.format( median - gsdir_for_best_tree.getMinDuplicationsSum() ) );
 261                 }
 262                 //
 263                 log.print( "\t" );
 264                 if ( stats.getN() > 3 ) {
 265                     log.print( df.format( median ) );
 266                 }
 267                 else {
 268                     log.print( "" );
 269                 }
 270                 log.print( "\t" );
 271                 log.print( df.format( stats.arithmeticMean() ) );
 272                 log.print( "\t" );
 273                 if ( stats.getN() > 3 ) {
 274                     log.print( df.format( stats.sampleStandardDeviation() ) );
 275                 }
 276                 else {
 277                     log.print( "" );
 278                 }
 279                 log.print( "\t" );
 280                 log.print( Integer.toString( min ) );
 281                 log.print( "\t" );
 282                 log.print( Integer.toString( max ) );
 283                 log.print( "\t" );
 284                 log.print( Integer.toString( rio.getRemovedGeneTreeNodes().size() ) );
 285                 log.print( "\t" );
 286                 log.print( Integer.toString( stats.getN() ) );
 287                 log.println();
 288             }
 289             else {
 290                 System.out.println( "Gene tree internal nodes            :\t" + rio.getIntNodesOfAnalyzedGeneTrees() );
 291                 System.out.println( "Gene tree external nodes            :\t" + rio.getExtNodesOfAnalyzedGeneTrees() );
 292                 System.out.println( "Mean number of duplications         :\t" + df.format( stats.arithmeticMean() )
 293                         + "\t" + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() )
 294                         + "%\t(sd: " + df.format( stats.sampleStandardDeviation() ) + ")" );
 295                 if ( stats.getN() > 3 ) {
 296                     System.out.println( "Median number of duplications       :\t" + df.format( median ) + "\t"
 297                             + df.format( ( 100.0 * median ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
 298                 }
 299                 System.out.println( "Minimum duplications                :\t" + min + "\t"
 300                         + df.format( ( 100.0 * min ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
 301                 System.out.println( "Maximum duplications                :\t" + ( int ) max + "\t"
 302                         + df.format( ( 100.0 * max ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%" );
 303                 System.out.println( "Gene trees with median duplications :\t" + median_count + "\t"
 304                         + df.format( median_count_percentage ) + "%" );
 305                 System.out.println( "Gene trees with minimum duplications:\t" + min_count + "\t"
 306                         + df.format( min_count_percentage ) + "%" );
 307                 System.out.println( "Gene trees with maximum duplications:\t" + max_count + "\t"
 308                         + df.format( max_count_percentage ) + "%" );
 309                 if ( algorithm == ALGORITHM.GSDIR ) {
 310                     System.out.println( "Removed ext gene tree nodes         :\t"
 311                             + rio.getRemovedGeneTreeNodes().size() );
 312                 }
 313             }
 314         }
 315         catch ( final RIOException e ) {
 316             ForesterUtil.fatalError( e.getLocalizedMessage() );
 317         }
 318         catch ( final SDIException e ) {
 319             ForesterUtil.fatalError( e.getLocalizedMessage() );
 320         }
 321         catch ( final IOException e ) {
 322             ForesterUtil.fatalError( e.getLocalizedMessage() );
 323         }
 324         catch ( final OutOfMemoryError e ) {
 325             ForesterUtil.outOfMemoryError( e );
 326         }
 327         catch ( final Exception e ) {
 328             ForesterUtil.unexpectedFatalError( e );
 329         }
 330         catch ( final Error e ) {
 331             ForesterUtil.unexpectedFatalError( e );
 332         }
 333     }
 334
 335     private final static GSDIR analyzeConsensusTree( final File gene_trees_file,
 336                                                      final File species_tree_file,
 337                                                      final File outdir,
 338                                                      final File best_trees_indir,
 339                                                      final SortedMap<String, String> id_map,
 340                                                      final String best_trees_suffix )
 341             throws IOException, FileNotFoundException, PhyloXmlDataFormatException, SDIException {
 342         final File the_one = ForesterUtil.getMatchingFile( best_trees_indir,
 343                                                            gene_trees_file.getName(),
 344                                                            best_trees_suffix );
 345         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 346         final Phylogeny best_tree = factory.create( the_one, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
 347         final Phylogeny species_tree = SDIutil
 348                 .parseSpeciesTree( best_tree, species_tree_file, false, true, TAXONOMY_EXTRACTION.NO );
 349         PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree );
 350         best_tree.setRooted( true );
 351         species_tree.setRooted( true );
 352         if ( !best_tree.isCompletelyBinaryAllow3ChildrenAtRoot() ) {
 353             throw new IOException( "gene tree matching to ["
 354                     + ForesterUtil.removeFileExtension( gene_trees_file.getName() ) + "] is not completely binary" );
 355         }
 356         final PhylogenyNodeIterator it = best_tree.iteratorExternalForward();
 357         while ( it.hasNext() ) {
 358             final PhylogenyNode n = it.next();
 359             final String name = n.getName().trim();
 360             if ( !ForesterUtil.isEmpty( name ) ) {
 361                 try {
 362                     ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE );
 363                 }
 364                 catch ( final PhyloXmlDataFormatException e ) {
 365                     // Ignore.
 366                 }
 367             }
 368         }
 369         final GSDIR gsdir_for_best_tree = new GSDIR( best_tree, species_tree, true, true, true );
 370         final Phylogeny result_gene_tree = gsdir_for_best_tree.getMinDuplicationsSumGeneTree();
 371         result_gene_tree.setRerootable( false );
 372         PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 373         final String outname = ForesterUtil.removeFileExtension( the_one.getName() );
 374         final File outfile = new File( outdir.getCanonicalFile() + "/" + outname + RIOUtil.BEST_TREE_SUFFIX
 375                 + gsdir_for_best_tree.getMinDuplicationsSum() + ".xml" );
 376         writeTree( result_gene_tree, outfile, null, id_map );
 377         return gsdir_for_best_tree;
 378     }
 379
 380     private static final void writeOrthologyTable( final File table_outfile,
 381                                                    final int gene_trees_analyzed,
 382                                                    final IntMatrix m,
 383                                                    final boolean verbose,
 384                                                    final SortedMap<String, String> id_map,
 385                                                    final boolean replace_ids )
 386             throws IOException {
 387         final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile );
 388         final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
 389         df.setDecimalSeparatorAlwaysShown( false );
 390         df.setRoundingMode( RoundingMode.HALF_UP );
 391         for( int i = 0; i < m.size(); ++i ) {
 392             w.print( "\t" );
 393             if ( replace_ids ) {
 394                 if ( !id_map.containsKey( m.getLabel( i ) ) ) {
 395                     throw new IOException( "no id mapping for \"" + m.getLabel( i ) + "\" (attempting to write ["
 396                             + table_outfile + "])" );
 397                 }
 398                 w.print( id_map.get( m.getLabel( i ) ) );
 399             }
 400             else {
 401                 w.print( m.getLabel( i ) );
 402             }
 403         }
 404         w.println();
 405         for( int x = 0; x < m.size(); ++x ) {
 406             if ( replace_ids ) {
 407                 w.print( id_map.get( m.getLabel( x ) ) );
 408             }
 409             else {
 410                 w.print( m.getLabel( x ) );
 411             }
 412             for( int y = 0; y < m.size(); ++y ) {
 413                 w.print( "\t" );
 414                 if ( x == y ) {
 415                     if ( m.get( x, y ) != gene_trees_analyzed ) {
 416                         ForesterUtil.unexpectedFatalError( "diagonal value is off" );
 417                     }
 418                     w.print( "-" );
 419                 }
 420                 else {
 421                     w.print( df.format( ( ( double ) m.get( x, y ) ) / gene_trees_analyzed ) );
 422                 }
 423             }
 424             w.println();
 425         }
 426         if ( !replace_ids && id_map != null && id_map.size() > 0 ) {
 427             w.println();
 428             id_map.forEach( ( k, v ) -> {
 429                 try {
 430                     w.println( k + "\t" + v );
 431                 }
 432                 catch ( final IOException e ) {
 433                     //ignore
 434                 }
 435             } );
 436         }
 437         w.close();
 438         if ( verbose ) {
 439             System.out.println( "Wrote table to                      :\t" + table_outfile.getCanonicalPath() );
 440         }
 441     }
 442
 443     private static final int writeOrtologGroups( final File outfile,
 444                                                  final double cutoff,
 445                                                  final int gene_trees_analyzed,
 446                                                  final IntMatrix m,
 447                                                  final boolean verbose,
 448                                                  final boolean calc_conly,
 449                                                  final SortedMap<String, String> id_map )
 450             throws IOException {
 451         List<SortedSet<String>> groups = new ArrayList<SortedSet<String>>();
 452         BasicDescriptiveStatistics stats = new BasicDescriptiveStatistics();
 453         int below_075 = 0;
 454         int below_05 = 0;
 455         int below_025 = 0;
 456         for( int x = 1; x < m.size(); ++x ) {
 457             final String a = m.getLabel( x );
 458             for( int y = 0; y < x; ++y ) {
 459                 final String b = m.getLabel( y );
 460                 final double s = ( ( double ) m.get( x, y ) ) / gene_trees_analyzed;
 461                 stats.addValue( s );
 462                 if ( s < 0.75 ) {
 463                     below_075++;
 464                     if ( s < 0.5 ) {
 465                         below_05++;
 466                         if ( s < 0.25 ) {
 467                             below_025++;
 468                         }
 469                     }
 470                 }
 471                 if ( s >= cutoff ) {
 472                     boolean found = false;
 473                     for( final SortedSet<String> group : groups ) {
 474                         if ( group.contains( a ) ) {
 475                             group.add( b );
 476                             found = true;
 477                         }
 478                         if ( group.contains( b ) ) {
 479                             group.add( a );
 480                             found = true;
 481                         }
 482                     }
 483                     if ( !found ) {
 484                         final SortedSet<String> new_group = new TreeSet<String>();
 485                         new_group.add( a );
 486                         new_group.add( b );
 487                         groups.add( new_group );
 488                     }
 489                 }
 490             }
 491         }
 492         //Deal with singlets:
 493         for( int x = 0; x < m.size(); ++x ) {
 494             final String a = m.getLabel( x );
 495             boolean found = false;
 496             for( final SortedSet<String> group : groups ) {
 497                 if ( group.contains( a ) ) {
 498                     found = true;
 499                     break;
 500                 }
 501             }
 502             if ( !found ) {
 503                 final SortedSet<String> new_group = new TreeSet<String>();
 504                 new_group.add( a );
 505                 groups.add( new_group );
 506             }
 507         }
 508         if ( calc_conly ) {
 509             return groups.size();
 510         }
 511         final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
 512         df.setDecimalSeparatorAlwaysShown( false );
 513         df.setRoundingMode( RoundingMode.HALF_UP );
 514         final EasyWriter w = ForesterUtil.createEasyWriter( outfile );
 515         int counter = 1;
 516         for( final SortedSet<String> group : groups ) {
 517             w.print( Integer.toString( counter++ ) );
 518             for( final String s : group ) {
 519                 w.print( "\t" );
 520                 if ( id_map != null && id_map.size() > 0 ) {
 521                     if ( !id_map.containsKey( s ) ) {
 522                         throw new IOException( "no id mapping for \"" + s + "\" (attempting to write [" + outfile
 523                                 + "])" );
 524                     }
 525                     w.print( id_map.get( s ) );
 526                 }
 527                 else {
 528                     w.print( s );
 529                 }
 530             }
 531             w.println();
 532         }
 533         w.println();
 534         w.println( "# Cutoff\t" + df.format( cutoff ) );
 535         w.println();
 536         w.println( "# Orthology support statistics:" );
 537         if ( stats.getN() > 3 ) {
 538             w.println( "# Median\t" + df.format( stats.median() ) );
 539         }
 540         w.println( "# Mean\t" + df.format( stats.arithmeticMean() ) );
 541         if ( stats.getN() > 3 ) {
 542             w.println( "# SD\t" + df.format( stats.sampleStandardDeviation() ) );
 543         }
 544         w.println( "# Min\t" + df.format( stats.getMin() ) );
 545         w.println( "# Max\t" + df.format( stats.getMax() ) );
 546         w.println( "# Total\t" + df.format( stats.getN() ) );
 547         w.println( "# Below 0.75\t" + below_075 + "\t" + df.format( ( 100.0 * below_075 / stats.getN() ) ) + "%" );
 548         w.println( "# Below 0.5\t" + below_05 + "\t" + df.format( ( 100.0 * below_05 / stats.getN() ) ) + "%" );
 549         w.println( "# Below 0.25\t" + below_025 + "\t" + df.format( ( 100.0 * below_025 / stats.getN() ) ) + "%" );
 550         w.close();
 551         if ( verbose ) {
 552             System.out.println( "Number of ortholog groups           :\t" + groups.size() );
 553             System.out.println( "Wrote orthologs groups table to     :\t" + outfile.getCanonicalPath() );
 554         }
 555         return groups.size();
 556     }
 557
 558     private static void writeTree( final Phylogeny p,
 559                                    final File f,
 560                                    final String comment,
 561                                    final SortedMap<String, String> id_map )
 562             throws IOException {
 563         if ( id_map != null && id_map.size() > 0 ) {
 564             final PhylogenyNodeIterator it = p.iteratorExternalForward();
 565             while ( it.hasNext() ) {
 566                 final PhylogenyNode n = it.next();
 567                 if ( !id_map.containsKey( n.getName() ) ) {
 568                     throw new IOException( "no id mapping for \"" + n.getName() + "\" (attempting to write [" + f
 569                             + "])" );
 570                 }
 571                 final Sequence seq = new Sequence();
 572                 seq.setName( id_map.get( n.getName() ) );
 573                 n.getNodeData().addSequence( seq );
 574             }
 575         }
 576         final PhylogenyWriter writer = new PhylogenyWriter();
 577         writer.toPhyloXML( f, p, 0 );
 578         if ( comment != null ) {
 579             System.out.println( comment + f.getCanonicalPath() );
 580         }
 581     }
 582
 583     private static void writeLogFile( final File logfile,
 584                                       final RIO rio,
 585                                       final File species_tree_file,
 586                                       final File gene_trees_file,
 587                                       final File outtable,
 588                                       final String prg_name,
 589                                       final String prg_v,
 590                                       final String prg_date,
 591                                       final String f,
 592                                       final boolean verbose )
 593             throws IOException {
 594         final EasyWriter out = ForesterUtil.createEasyWriter( logfile );
 595         out.println( "# " + prg_name );
 596         out.println( "# version : " + prg_v );
 597         out.println( "# date    : " + prg_date );
 598         out.println( "# based on: " + f );
 599         out.println( "# ----------------------------------" );
 600         out.println( "Gene trees                          :\t" + gene_trees_file.getCanonicalPath() );
 601         out.println( "Species tree                        :\t" + species_tree_file.getCanonicalPath() );
 602         out.println( "All vs all orthology table          :\t" + outtable.getCanonicalPath() );
 603         out.flush();
 604         out.println( rio.getLog().toString() );
 605         out.close();
 606         if ( verbose ) {
 607             System.out.println( "Wrote log to                        :\t" + logfile.getCanonicalPath() );
 608         }
 609     }
 610
 611     private final static SortedMap<String, String> obtainMapping( final File dir,
 612                                                                   final String prefix,
 613                                                                   final String suffix )
 614             throws IOException {
 615         final File the_one = ForesterUtil.getMatchingFile( dir, prefix, suffix );
 616         final BasicTable<String> t = BasicTableParser.parse( the_one, '\t' );
 617         return t.getColumnsAsMap( 0, 1 );
 618     }
 619 }