forester/java/src/org/forester/surfacing/SurfacingUtil.java

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.surfacing;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.text.DecimalFormat;
  35 import java.text.NumberFormat;
  36 import java.util.ArrayList;
  37 import java.util.Arrays;
  38 import java.util.Collections;
  39 import java.util.Comparator;
  40 import java.util.HashMap;
  41 import java.util.HashSet;
  42 import java.util.Iterator;
  43 import java.util.List;
  44 import java.util.Map;
  45 import java.util.Map.Entry;
  46 import java.util.PriorityQueue;
  47 import java.util.Set;
  48 import java.util.SortedMap;
  49 import java.util.SortedSet;
  50 import java.util.TreeMap;
  51 import java.util.TreeSet;
  52 import java.util.regex.Matcher;
  53 import java.util.regex.Pattern;
  54
  55 import org.forester.application.surfacing;
  56 import org.forester.evoinference.distance.NeighborJoining;
  57 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  58 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  59 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  61 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  62 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  63 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  64 import org.forester.go.GoId;
  65 import org.forester.go.GoNameSpace;
  66 import org.forester.go.GoTerm;
  67 import org.forester.go.PfamToGoMapping;
  68 import org.forester.io.parsers.nexus.NexusConstants;
  69 import org.forester.io.writers.PhylogenyWriter;
  70 import org.forester.phylogeny.Phylogeny;
  71 import org.forester.phylogeny.PhylogenyMethods;
  72 import org.forester.phylogeny.PhylogenyNode;
  73 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  74 import org.forester.phylogeny.data.BinaryCharacters;
  75 import org.forester.phylogeny.data.Confidence;
  76 import org.forester.phylogeny.data.Taxonomy;
  77 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  78 import org.forester.protein.BasicDomain;
  79 import org.forester.protein.BasicProtein;
  80 import org.forester.protein.BinaryDomainCombination;
  81 import org.forester.protein.Domain;
  82 import org.forester.protein.Protein;
  83 import org.forester.species.Species;
  84 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  85 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  86 import org.forester.util.AsciiHistogram;
  87 import org.forester.util.BasicDescriptiveStatistics;
  88 import org.forester.util.BasicTable;
  89 import org.forester.util.BasicTableParser;
  90 import org.forester.util.DescriptiveStatistics;
  91 import org.forester.util.ForesterUtil;
  92
  93 public final class SurfacingUtil {
  94
  95     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  96     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  97
  98                                                                                  @Override
  99                                                                                  public int compare( final Domain d1,
 100                                                                                                      final Domain d2 ) {
 101                                                                                      if ( d1.getPerSequenceEvalue() < d2
 102                                                                                              .getPerSequenceEvalue() ) {
 103                                                                                          return -1;
 104                                                                                      }
 105                                                                                      else if ( d1
 106                                                                                              .getPerSequenceEvalue() > d2
 107                                                                                              .getPerSequenceEvalue() ) {
 108                                                                                          return 1;
 109                                                                                      }
 110                                                                                      else {
 111                                                                                          return d1.compareTo( d2 );
 112                                                                                      }
 113                                                                                  }
 114                                                                              };
 115     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 116
 117     private SurfacingUtil() {
 118         // Hidden constructor.
 119     }
 120
 121     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 122                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 123         final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 124         for( final String domain_id : all_cd.keySet() ) {
 125             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 126         }
 127     }
 128
 129     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 130                                              final SortedSet<String> domain_ids ) {
 131         final SortedSet<String> domains = genome.getAllDomainIds();
 132         for( final String domain : domains ) {
 133             domain_ids.add( domain );
 134         }
 135     }
 136
 137     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 138         w.write( SurfacingConstants.NL );
 139         w.write( "<head>" );
 140         w.write( "<title>" );
 141         w.write( title );
 142         w.write( "</title>" );
 143         w.write( SurfacingConstants.NL );
 144         w.write( "<style>" );
 145         w.write( SurfacingConstants.NL );
 146         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 147         w.write( SurfacingConstants.NL );
 148         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 149         w.write( SurfacingConstants.NL );
 150         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 151         w.write( SurfacingConstants.NL );
 152         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 153         w.write( SurfacingConstants.NL );
 154         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 155         w.write( SurfacingConstants.NL );
 156         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 157         w.write( SurfacingConstants.NL );
 158         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 159         w.write( SurfacingConstants.NL );
 160         w.write( "</style>" );
 161         w.write( SurfacingConstants.NL );
 162         w.write( "</head>" );
 163         w.write( SurfacingConstants.NL );
 164     }
 165
 166     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 167         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 168         for( final DomainSimilarity similarity : similarities ) {
 169             stats.addValue( similarity.getMeanSimilarityScore() );
 170         }
 171         return stats;
 172     }
 173
 174     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 175         int overlap_count = 0;
 176         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 177             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 178                 ++overlap_count;
 179             }
 180         }
 181         return overlap_count;
 182     }
 183
 184     public static void checkForOutputFileWriteability( final File outfile ) {
 185         final String error = ForesterUtil.isWritableFile( outfile );
 186         if ( !ForesterUtil.isEmpty( error ) ) {
 187             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 188         }
 189     }
 190
 191     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 192                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 193                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 194                                                                                            final boolean get_gains ) {
 195         final SortedSet<String> sorted_ids = new TreeSet<String>();
 196         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 197             sorted_ids.add( matrix.getIdentifier( i ) );
 198         }
 199         for( final String id : sorted_ids ) {
 200             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 201                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 202                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 203                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 204                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 205                                 .createInstance( matrix.getCharacter( c ) ) );
 206                     }
 207                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 208                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 209                                 .createInstance( matrix.getCharacter( c ) ) );
 210                     }
 211                     else {
 212                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 213                                 .getCharacter( c ) ) );
 214                     }
 215                 }
 216             }
 217         }
 218     }
 219
 220     public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 221         final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
 222         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 223             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 224                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 225             }
 226             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 227         }
 228         return domain_id_to_go_ids_map;
 229     }
 230
 231     public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 232             throws IOException {
 233         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
 234         final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
 235         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 236             final String domain_id = primary_table.getValue( 0, r );
 237             if ( !map.containsKey( domain_id ) ) {
 238                 map.put( domain_id, new HashSet<String>() );
 239             }
 240             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 241         }
 242         return map;
 243     }
 244
 245     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 246         checkForOutputFileWriteability( nj_tree_outfile );
 247         final NeighborJoining nj = NeighborJoining.createInstance();
 248         final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
 249         phylogeny.setName( nj_tree_outfile.getName() );
 250         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 251         return phylogeny;
 252     }
 253
 254     public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
 255         final Map<String, Integer> m = new HashMap<String, Integer>();
 256         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 257             final PhylogenyNode n = iter.next();
 258             if ( n.getNodeData().isHasTaxonomy() ) {
 259                 final Taxonomy t = n.getNodeData().getTaxonomy();
 260                 final String c = t.getTaxonomyCode();
 261                 if ( !ForesterUtil.isEmpty( c ) ) {
 262                     if ( n.getNodeData().getTaxonomy() == null ) {
 263                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 264                     }
 265                     final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
 266                     if ( ForesterUtil.isEmpty( id ) ) {
 267                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 268                     }
 269                     if ( m.containsKey( c ) ) {
 270                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
 271                     }
 272                     final int iid = Integer.valueOf( id );
 273                     if ( m.containsValue( iid ) ) {
 274                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
 275                     }
 276                     m.put( c, iid );
 277                 }
 278             }
 279             else {
 280                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
 281             }
 282         }
 283         return m;
 284     }
 285
 286     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 287                                                             final Detailedness detailedness ) {
 288         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 289             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 290                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 291                 printable_domain_similarity.setDetailedness( detailedness );
 292             }
 293         }
 294     }
 295
 296     public static void doit( final List<Protein> proteins,
 297                              final List<String> query_domain_ids_nc_order,
 298                              final Writer out,
 299                              final String separator,
 300                              final String limit_to_species,
 301                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
 302         for( final Protein protein : proteins ) {
 303             if ( ForesterUtil.isEmpty( limit_to_species )
 304                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 305                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 306                     out.write( protein.getSpecies().getSpeciesId() );
 307                     out.write( separator );
 308                     out.write( protein.getProteinId().getId() );
 309                     out.write( separator );
 310                     out.write( "[" );
 311                     final Set<String> visited_domain_ids = new HashSet<String>();
 312                     boolean first = true;
 313                     for( final Domain domain : protein.getProteinDomains() ) {
 314                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 315                             visited_domain_ids.add( domain.getDomainId() );
 316                             if ( first ) {
 317                                 first = false;
 318                             }
 319                             else {
 320                                 out.write( " " );
 321                             }
 322                             out.write( domain.getDomainId() );
 323                             out.write( " {" );
 324                             out.write( "" + domain.getTotalCount() );
 325                             out.write( "}" );
 326                         }
 327                     }
 328                     out.write( "]" );
 329                     out.write( separator );
 330                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 331                             .equals( SurfacingConstants.NONE ) ) ) {
 332                         out.write( protein.getDescription() );
 333                     }
 334                     out.write( separator );
 335                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 336                             .equals( SurfacingConstants.NONE ) ) ) {
 337                         out.write( protein.getAccession() );
 338                     }
 339                     out.write( SurfacingConstants.NL );
 340                 }
 341             }
 342         }
 343         out.flush();
 344     }
 345
 346     public static void domainsPerProteinsStatistics( final String genome,
 347                                                      final List<Protein> protein_list,
 348                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
 349                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
 350                                                      final SortedSet<String> domains_which_are_always_single,
 351                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
 352                                                      final SortedSet<String> domains_which_never_single,
 353                                                      final Writer writer ) {
 354         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 355         for( final Protein protein : protein_list ) {
 356             final int domains = protein.getNumberOfProteinDomains();
 357             //System.out.println( domains );
 358             stats.addValue( domains );
 359             all_genomes_domains_per_potein_stats.addValue( domains );
 360             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
 361                 all_genomes_domains_per_potein_histo.put( domains, 1 );
 362             }
 363             else {
 364                 all_genomes_domains_per_potein_histo.put( domains,
 365                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
 366             }
 367             if ( domains == 1 ) {
 368                 final String domain = protein.getProteinDomain( 0 ).getDomainId();
 369                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 370                     if ( domains_which_never_single.contains( domain ) ) {
 371                         domains_which_never_single.remove( domain );
 372                         domains_which_are_sometimes_single_sometimes_not.add( domain );
 373                     }
 374                     else {
 375                         domains_which_are_always_single.add( domain );
 376                     }
 377                 }
 378             }
 379             else if ( domains > 1 ) {
 380                 for( final Domain d : protein.getProteinDomains() ) {
 381                     final String domain = d.getDomainId();
 382                     // System.out.println( domain );
 383                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 384                         if ( domains_which_are_always_single.contains( domain ) ) {
 385                             domains_which_are_always_single.remove( domain );
 386                             domains_which_are_sometimes_single_sometimes_not.add( domain );
 387                         }
 388                         else {
 389                             domains_which_never_single.add( domain );
 390                         }
 391                     }
 392                 }
 393             }
 394         }
 395         try {
 396             writer.write( genome );
 397             writer.write( "\t" );
 398             if ( stats.getN() >= 1 ) {
 399                 writer.write( stats.arithmeticMean() + "" );
 400                 writer.write( "\t" );
 401                 if ( stats.getN() >= 2 ) {
 402                     writer.write( stats.sampleStandardDeviation() + "" );
 403                 }
 404                 else {
 405                     writer.write( "" );
 406                 }
 407                 writer.write( "\t" );
 408                 writer.write( stats.median() + "" );
 409                 writer.write( "\t" );
 410                 writer.write( stats.getN() + "" );
 411                 writer.write( "\t" );
 412                 writer.write( stats.getMin() + "" );
 413                 writer.write( "\t" );
 414                 writer.write( stats.getMax() + "" );
 415             }
 416             else {
 417                 writer.write( "\t" );
 418                 writer.write( "\t" );
 419                 writer.write( "\t" );
 420                 writer.write( "0" );
 421                 writer.write( "\t" );
 422                 writer.write( "\t" );
 423             }
 424             writer.write( "\n" );
 425         }
 426         catch ( final IOException e ) {
 427             e.printStackTrace();
 428         }
 429     }
 430
 431     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 432                                                     final int number_of_genomes,
 433                                                     final DomainLengthsTable domain_lengths_table,
 434                                                     final File outfile ) throws IOException {
 435         final DecimalFormat df = new DecimalFormat( "#.00" );
 436         checkForOutputFileWriteability( outfile );
 437         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 438         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 439         out.write( ForesterUtil.LINE_SEPARATOR );
 440         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 441         out.write( ForesterUtil.LINE_SEPARATOR );
 442         out.write( ForesterUtil.LINE_SEPARATOR );
 443         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 444         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 445         out.write( ForesterUtil.LINE_SEPARATOR );
 446         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 447             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 448             if ( species_list.size() > 0 ) {
 449                 out.write( domain_lengths.getDomainId() + "\t" );
 450                 for( final Species species : species_list ) {
 451                     out.write( species + "\t" );
 452                 }
 453                 out.write( ForesterUtil.LINE_SEPARATOR );
 454                 // DescriptiveStatistics stats_for_domain = domain_lengths
 455                 //         .calculateMeanBasedStatistics();
 456                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 457                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 458             }
 459         }
 460         out.write( ForesterUtil.LINE_SEPARATOR );
 461         out.write( ForesterUtil.LINE_SEPARATOR );
 462         out.write( "OUTLIER SPECIES (Z 1.0)" );
 463         out.write( ForesterUtil.LINE_SEPARATOR );
 464         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 465                 .calculateMeanBasedStatisticsForAllSpecies();
 466         out.write( stats_for_all_species.asSummary() );
 467         out.write( ForesterUtil.LINE_SEPARATOR );
 468         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 469         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 470         out.write( ForesterUtil.LINE_SEPARATOR );
 471         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 472         final double population_mean = stats_for_all_species.arithmeticMean();
 473         for( final Species species : domain_lengths_table.getSpecies() ) {
 474             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 475             final double z = ( x - population_mean ) / population_sd;
 476             out.write( species + "\t" + z );
 477             out.write( ForesterUtil.LINE_SEPARATOR );
 478         }
 479         out.write( ForesterUtil.LINE_SEPARATOR );
 480         for( final Species species : domain_lengths_table.getSpecies() ) {
 481             final DescriptiveStatistics stats_for_species = domain_lengths_table
 482                     .calculateMeanBasedStatisticsForSpecies( species );
 483             final double x = stats_for_species.arithmeticMean();
 484             final double z = ( x - population_mean ) / population_sd;
 485             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 486                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 487                 out.write( ForesterUtil.LINE_SEPARATOR );
 488             }
 489         }
 490         out.close();
 491         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 492         //        for( int i = 0; i < number_of_genomes; ++i ) {
 493         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 494         //            histogram_datas
 495         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 496         //                            .calculateMeanBasedStatisticsForSpecies( species )
 497         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 498         //        }
 499         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 500         //        hf.setVisible( true );
 501         System.gc();
 502     }
 503
 504     /**
 505      *
 506      * @param all_binary_domains_combination_lost_fitch
 507      * @param use_last_in_fitch_parsimony
 508      * @param consider_directedness_and_adjacency_for_bin_combinations
 509      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 510      * which were gained under unweighted (Fitch) parsimony.
 511      */
 512     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 513                                                  final boolean radomize_fitch_parsimony,
 514                                                  final String outfile_name,
 515                                                  final DomainParsimonyCalculator domain_parsimony,
 516                                                  final Phylogeny phylogeny,
 517                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
 518                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 519                                                  final GoNameSpace go_namespace_limit,
 520                                                  final String parameters_str,
 521                                                  final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
 522                                                  final SortedSet<String> positive_filter,
 523                                                  final boolean output_binary_domain_combinations_for_graphs,
 524                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 525                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 526                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 527                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 528                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 529                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
 530                                                  final Map<String, Integer> tax_code_to_id_map,
 531                                                  final boolean write_to_nexus,
 532                                                  final boolean use_last_in_fitch_parsimony ) {
 533         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 534         final String date_time = ForesterUtil.getCurrentDateTime();
 535         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 536         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 537         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 538         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 539         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 540         if ( write_to_nexus ) {
 541             writeToNexus( outfile_name, domain_parsimony, phylogeny );
 542         }
 543         // DOLLO DOMAINS
 544         // -------------
 545         Phylogeny local_phylogeny_l = phylogeny.copy();
 546         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 547             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 548         }
 549         else {
 550             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 551         }
 552         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 553                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 554         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 555                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 556         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 557                                                            CharacterStateMatrix.GainLossStates.GAIN,
 558                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 559                                                            sep,
 560                                                            ForesterUtil.LINE_SEPARATOR,
 561                                                            null );
 562         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 563                                                            CharacterStateMatrix.GainLossStates.LOSS,
 564                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 565                                                            sep,
 566                                                            ForesterUtil.LINE_SEPARATOR,
 567                                                            null );
 568         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 569                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 570         //HTML:
 571         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 572                                        go_id_to_term_map,
 573                                        go_namespace_limit,
 574                                        false,
 575                                        domain_parsimony.getGainLossMatrix(),
 576                                        CharacterStateMatrix.GainLossStates.GAIN,
 577                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 578                                        sep,
 579                                        ForesterUtil.LINE_SEPARATOR,
 580                                        "Dollo Parsimony | Gains | Domains",
 581                                        "+",
 582                                        domain_id_to_secondary_features_maps,
 583                                        all_pfams_encountered,
 584                                        all_pfams_gained_as_domains,
 585                                        "_dollo_gains_d",
 586                                        tax_code_to_id_map );
 587         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 588                                        go_id_to_term_map,
 589                                        go_namespace_limit,
 590                                        false,
 591                                        domain_parsimony.getGainLossMatrix(),
 592                                        CharacterStateMatrix.GainLossStates.LOSS,
 593                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 594                                        sep,
 595                                        ForesterUtil.LINE_SEPARATOR,
 596                                        "Dollo Parsimony | Losses | Domains",
 597                                        "-",
 598                                        domain_id_to_secondary_features_maps,
 599                                        all_pfams_encountered,
 600                                        all_pfams_lost_as_domains,
 601                                        "_dollo_losses_d",
 602                                        tax_code_to_id_map );
 603         //        writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 604         //                                       go_id_to_term_map,
 605         //                                       go_namespace_limit,
 606         //                                       false,
 607         //                                       domain_parsimony.getGainLossMatrix(),
 608         //                                       null,
 609         //                                       outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 610         //                                       sep,
 611         //                                       ForesterUtil.LINE_SEPARATOR,
 612         //                                       "Dollo Parsimony | Present | Domains",
 613         //                                       "",
 614         //                                       domain_id_to_secondary_features_maps,
 615         //                                       all_pfams_encountered,
 616         //                                       null,
 617         //                                       "_dollo_present_d",
 618         //                                       tax_code_to_id_map );
 619         preparePhylogeny( local_phylogeny_l,
 620                           domain_parsimony,
 621                           date_time,
 622                           "Dollo parsimony on domain presence/absence",
 623                           "dollo_on_domains_" + outfile_name,
 624                           parameters_str );
 625         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 626                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 627         try {
 628             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 629             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 630         }
 631         catch ( final IOException e ) {
 632             e.printStackTrace();
 633             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 634         }
 635         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 636             // FITCH DOMAIN COMBINATIONS
 637             // -------------------------
 638             local_phylogeny_l = phylogeny.copy();
 639             String randomization = "no";
 640             if ( radomize_fitch_parsimony ) {
 641                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 642                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 643             }
 644             else {
 645                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
 646             }
 647             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 648                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 649             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 650                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 651             SurfacingUtil
 652                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 653                                                           CharacterStateMatrix.GainLossStates.GAIN,
 654                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 655                                                           sep,
 656                                                           ForesterUtil.LINE_SEPARATOR,
 657                                                           null );
 658             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 659                                                                CharacterStateMatrix.GainLossStates.LOSS,
 660                                                                outfile_name
 661                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 662                                                                sep,
 663                                                                ForesterUtil.LINE_SEPARATOR,
 664                                                                null );
 665             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 666                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 667             if ( all_binary_domains_combination_gained_fitch != null ) {
 668                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 669                                                                                     dc_type,
 670                                                                                     all_binary_domains_combination_gained_fitch,
 671                                                                                     true );
 672             }
 673             if ( all_binary_domains_combination_lost_fitch != null ) {
 674                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 675                                                                                     dc_type,
 676                                                                                     all_binary_domains_combination_lost_fitch,
 677                                                                                     false );
 678             }
 679             if ( output_binary_domain_combinations_for_graphs ) {
 680                 SurfacingUtil
 681                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 682                                                                                                            .getGainLossMatrix(),
 683                                                                                                    null,
 684                                                                                                    outfile_name
 685                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 686                                                                                                    sep,
 687                                                                                                    ForesterUtil.LINE_SEPARATOR,
 688                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 689             }
 690             // HTML:
 691             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 692                                            go_id_to_term_map,
 693                                            go_namespace_limit,
 694                                            true,
 695                                            domain_parsimony.getGainLossMatrix(),
 696                                            CharacterStateMatrix.GainLossStates.GAIN,
 697                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 698                                            sep,
 699                                            ForesterUtil.LINE_SEPARATOR,
 700                                            "Fitch Parsimony | Gains | Domain Combinations",
 701                                            "+",
 702                                            null,
 703                                            all_pfams_encountered,
 704                                            all_pfams_gained_as_dom_combinations,
 705                                            "_fitch_gains_dc",
 706                                            tax_code_to_id_map );
 707             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 708                                            go_id_to_term_map,
 709                                            go_namespace_limit,
 710                                            true,
 711                                            domain_parsimony.getGainLossMatrix(),
 712                                            CharacterStateMatrix.GainLossStates.LOSS,
 713                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 714                                            sep,
 715                                            ForesterUtil.LINE_SEPARATOR,
 716                                            "Fitch Parsimony | Losses | Domain Combinations",
 717                                            "-",
 718                                            null,
 719                                            all_pfams_encountered,
 720                                            all_pfams_lost_as_dom_combinations,
 721                                            "_fitch_losses_dc",
 722                                            tax_code_to_id_map );
 723             //            writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 724             //                                           go_id_to_term_map,
 725             //                                           go_namespace_limit,
 726             //                                           true,
 727             //                                           domain_parsimony.getGainLossMatrix(),
 728             //                                           null,
 729             //                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 730             //                                           sep,
 731             //                                           ForesterUtil.LINE_SEPARATOR,
 732             //                                           "Fitch Parsimony | Present | Domain Combinations",
 733             //                                           "",
 734             //                                           null,
 735             //                                           all_pfams_encountered,
 736             //                                           null,
 737             //                                           "_fitch_present_dc",
 738             //                                           tax_code_to_id_map );
 739             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 740                                             go_id_to_term_map,
 741                                             outfile_name,
 742                                             all_pfams_encountered );
 743             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 744             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 745             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 746                               all_pfams_gained_as_dom_combinations );
 747             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 748             preparePhylogeny( local_phylogeny_l,
 749                               domain_parsimony,
 750                               date_time,
 751                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 752                                       + randomization,
 753                               "fitch_on_binary_domain_combinations_" + outfile_name,
 754                               parameters_str );
 755             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 756                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 757             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 758                                                         outfile_name
 759                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 760                                                         outfile_name
 761                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 762                                                         outfile_name
 763                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 764                                                         outfile_name
 765                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
 766                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
 767                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
 768                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
 769                                                         protein_length_stats_by_dc,
 770                                                         domain_number_stats_by_dc,
 771                                                         domain_length_stats_by_domain );
 772         }
 773     }
 774
 775     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 776                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 777                                                                      final Phylogeny phylogeny,
 778                                                                      final String parameters_str,
 779                                                                      final Map<Species, MappingResults> mapping_results_map,
 780                                                                      final boolean use_last_in_fitch_parsimony ) {
 781         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 782         final String date_time = ForesterUtil.getCurrentDateTime();
 783         System.out.println();
 784         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 785                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 786                       phylogeny );
 787         Phylogeny local_phylogeny_copy = phylogeny.copy();
 788         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 789         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 790                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 791         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 792                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 793         SurfacingUtil
 794                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 795                                                       CharacterStateMatrix.GainLossStates.GAIN,
 796                                                       outfile_name
 797                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 798                                                       sep,
 799                                                       ForesterUtil.LINE_SEPARATOR,
 800                                                       null );
 801         SurfacingUtil
 802                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 803                                                       CharacterStateMatrix.GainLossStates.LOSS,
 804                                                       outfile_name
 805                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 806                                                       sep,
 807                                                       ForesterUtil.LINE_SEPARATOR,
 808                                                       null );
 809         SurfacingUtil
 810                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 811                                                       null,
 812                                                       outfile_name
 813                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 814                                                       sep,
 815                                                       ForesterUtil.LINE_SEPARATOR,
 816                                                       null );
 817         preparePhylogeny( local_phylogeny_copy,
 818                           secondary_features_parsimony,
 819                           date_time,
 820                           "Dollo parsimony on secondary feature presence/absence",
 821                           "dollo_on_secondary_features_" + outfile_name,
 822                           parameters_str );
 823         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 824                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 825         // FITCH DOMAIN COMBINATIONS
 826         // -------------------------
 827         local_phylogeny_copy = phylogeny.copy();
 828         final String randomization = "no";
 829         secondary_features_parsimony
 830                 .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
 831         preparePhylogeny( local_phylogeny_copy,
 832                           secondary_features_parsimony,
 833                           date_time,
 834                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
 835                                   + randomization,
 836                           "fitch_on_binary_domain_combinations_" + outfile_name,
 837                           parameters_str );
 838         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 839                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
 840         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
 841                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
 842                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
 843                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
 844                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
 845                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
 846                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
 847     }
 848
 849     public static void extractProteinNames( final List<Protein> proteins,
 850                                             final List<String> query_domain_ids_nc_order,
 851                                             final Writer out,
 852                                             final String separator,
 853                                             final String limit_to_species ) throws IOException {
 854         for( final Protein protein : proteins ) {
 855             if ( ForesterUtil.isEmpty( limit_to_species )
 856                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 857                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 858                     out.write( protein.getSpecies().getSpeciesId() );
 859                     out.write( separator );
 860                     out.write( protein.getProteinId().getId() );
 861                     out.write( separator );
 862                     out.write( "[" );
 863                     final Set<String> visited_domain_ids = new HashSet<String>();
 864                     boolean first = true;
 865                     for( final Domain domain : protein.getProteinDomains() ) {
 866                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 867                             visited_domain_ids.add( domain.getDomainId() );
 868                             if ( first ) {
 869                                 first = false;
 870                             }
 871                             else {
 872                                 out.write( " " );
 873                             }
 874                             out.write( domain.getDomainId() );
 875                             out.write( " {" );
 876                             out.write( "" + domain.getTotalCount() );
 877                             out.write( "}" );
 878                         }
 879                     }
 880                     out.write( "]" );
 881                     out.write( separator );
 882                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 883                             .equals( SurfacingConstants.NONE ) ) ) {
 884                         out.write( protein.getDescription() );
 885                     }
 886                     out.write( separator );
 887                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 888                             .equals( SurfacingConstants.NONE ) ) ) {
 889                         out.write( protein.getAccession() );
 890                     }
 891                     out.write( SurfacingConstants.NL );
 892                 }
 893             }
 894         }
 895         out.flush();
 896     }
 897
 898     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
 899                                             final String domain_id,
 900                                             final Writer out,
 901                                             final String separator,
 902                                             final String limit_to_species,
 903                                             final double domain_e_cutoff ) throws IOException {
 904         System.out.println( "Per domain E-value: " + domain_e_cutoff );
 905         for( final Species species : protein_lists_per_species.keySet() ) {
 906             System.out.println( species + ":" );
 907             for( final Protein protein : protein_lists_per_species.get( species ) ) {
 908                 if ( ForesterUtil.isEmpty( limit_to_species )
 909                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 910                     final List<Domain> domains = protein.getProteinDomains( domain_id );
 911                     if ( domains.size() > 0 ) {
 912                         out.write( protein.getSpecies().getSpeciesId() );
 913                         out.write( separator );
 914                         out.write( protein.getProteinId().getId() );
 915                         out.write( separator );
 916                         out.write( domain_id.toString() );
 917                         out.write( separator );
 918                         int prev_to = -1;
 919                         for( final Domain domain : domains ) {
 920                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 921                                 out.write( "/" );
 922                                 out.write( domain.getFrom() + "-" + domain.getTo() );
 923                                 if ( prev_to >= 0 ) {
 924                                     final int l = domain.getFrom() - prev_to;
 925                                     System.out.println( l );
 926                                 }
 927                                 prev_to = domain.getTo();
 928                             }
 929                         }
 930                         out.write( "/" );
 931                         out.write( separator );
 932                         final List<Domain> domain_list = new ArrayList<Domain>();
 933                         for( final Domain domain : protein.getProteinDomains() ) {
 934                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 935                                 domain_list.add( domain );
 936                             }
 937                         }
 938                         final Domain domain_ary[] = new Domain[ domain_list.size() ];
 939                         for( int i = 0; i < domain_list.size(); ++i ) {
 940                             domain_ary[ i ] = domain_list.get( i );
 941                         }
 942                         Arrays.sort( domain_ary, new DomainComparator( true ) );
 943                         out.write( "{" );
 944                         boolean first = true;
 945                         for( final Domain domain : domain_ary ) {
 946                             if ( first ) {
 947                                 first = false;
 948                             }
 949                             else {
 950                                 out.write( "," );
 951                             }
 952                             out.write( domain.getDomainId().toString() );
 953                             out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
 954                             out.write( ":" + domain.getPerDomainEvalue() );
 955                         }
 956                         out.write( "}" );
 957                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 958                                 .equals( SurfacingConstants.NONE ) ) ) {
 959                             out.write( protein.getDescription() );
 960                         }
 961                         out.write( separator );
 962                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 963                                 .equals( SurfacingConstants.NONE ) ) ) {
 964                             out.write( protein.getAccession() );
 965                         }
 966                         out.write( SurfacingConstants.NL );
 967                     }
 968                 }
 969             }
 970         }
 971         out.flush();
 972     }
 973
 974     public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
 975         final SortedSet<String> all_domains_ids = new TreeSet<String>();
 976         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 977             final Set<String> all_domains = gwcd.getAllDomainIds();
 978             //    for( final Domain domain : all_domains ) {
 979             all_domains_ids.addAll( all_domains );
 980             //    }
 981         }
 982         return all_domains_ids;
 983     }
 984
 985     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
 986         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
 987         for( final Protein protein_domain_collection : protein_domain_collections ) {
 988             for( final Object name : protein_domain_collection.getProteinDomains() ) {
 989                 final BasicDomain protein_domain = ( BasicDomain ) name;
 990                 final String id = protein_domain.getDomainId();
 991                 if ( map.containsKey( id ) ) {
 992                     map.put( id, map.get( id ) + 1 );
 993                 }
 994                 else {
 995                     map.put( id, 1 );
 996                 }
 997             }
 998         }
 999         return map;
1000     }
1001
1002     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1003         final PhylogenyNodeIterator it = p.iteratorPostorder();
1004         int c = 0;
1005         while ( it.hasNext() ) {
1006             final PhylogenyNode n = it.next();
1007             if ( ForesterUtil.isEmpty( n.getName() )
1008                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1009                             .getScientificName() ) )
1010                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1011                             .getCommonName() ) ) ) {
1012                 if ( n.getParent() != null ) {
1013                     names.append( " " );
1014                     names.append( n.getParent().getName() );
1015                 }
1016                 final List l = n.getAllExternalDescendants();
1017                 for( final Object object : l ) {
1018                     System.out.println( l.toString() );
1019                 }
1020                 ++c;
1021             }
1022         }
1023         return c;
1024     }
1025
1026     /**
1027      * Returns true is Domain domain falls in an uninterrupted stretch of
1028      * covered positions.
1029      *
1030      * @param domain
1031      * @param covered_positions
1032      * @return
1033      */
1034     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1035         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1036             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1037                 return false;
1038             }
1039         }
1040         return true;
1041     }
1042
1043     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
1044                                                           final SortedMap<String, Integer> domain_architecuture_counts,
1045                                                           final int min_count,
1046                                                           final File da_counts_outfile,
1047                                                           final File unique_da_outfile ) {
1048         checkForOutputFileWriteability( da_counts_outfile );
1049         checkForOutputFileWriteability( unique_da_outfile );
1050         try {
1051             final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
1052             final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
1053             final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
1054             while ( it.hasNext() ) {
1055                 final Map.Entry<String, Integer> e = it.next();
1056                 final String da = e.getKey();
1057                 final int count = e.getValue();
1058                 if ( count >= min_count ) {
1059                     da_counts_out.write( da );
1060                     da_counts_out.write( "\t" );
1061                     da_counts_out.write( String.valueOf( count ) );
1062                     da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
1063                 }
1064                 if ( count == 1 ) {
1065                     final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
1066                     while ( it2.hasNext() ) {
1067                         final Map.Entry<String, Set<String>> e2 = it2.next();
1068                         final String genome = e2.getKey();
1069                         final Set<String> das = e2.getValue();
1070                         if ( das.contains( da ) ) {
1071                             unique_da_out.write( genome );
1072                             unique_da_out.write( "\t" );
1073                             unique_da_out.write( da );
1074                             unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
1075                         }
1076                     }
1077                 }
1078             }
1079             unique_da_out.close();
1080             da_counts_out.close();
1081         }
1082         catch ( final IOException e ) {
1083             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1084         }
1085         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
1086         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
1087         //
1088     }
1089
1090     public static void preparePhylogeny( final Phylogeny p,
1091                                          final DomainParsimonyCalculator domain_parsimony,
1092                                          final String date_time,
1093                                          final String method,
1094                                          final String name,
1095                                          final String parameters_str ) {
1096         domain_parsimony.decoratePhylogenyWithDomains( p );
1097         final StringBuilder desc = new StringBuilder();
1098         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1099         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1100         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1101         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1102         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1103         desc.append( "[Parameters: " + parameters_str + "]" );
1104         p.setName( name );
1105         p.setDescription( desc.toString() );
1106         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1107         p.setRerootable( false );
1108         p.setRooted( true );
1109     }
1110
1111     /*
1112      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1113      *
1114      *
1115      */
1116     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1117                                                             final String protein_id,
1118                                                             final String separator ) {
1119         final StringBuffer sb = new StringBuffer();
1120         if ( protein.getSpecies() == null ) {
1121             throw new IllegalArgumentException( "species must not be null" );
1122         }
1123         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1124             throw new IllegalArgumentException( "species id must not be empty" );
1125         }
1126         final List<Domain> domains = protein.getProteinDomains();
1127         if ( domains.size() > 1 ) {
1128             final Map<String, Integer> counts = new HashMap<String, Integer>();
1129             for( final Domain domain : domains ) {
1130                 final String id = domain.getDomainId();
1131                 if ( counts.containsKey( id ) ) {
1132                     counts.put( id, counts.get( id ) + 1 );
1133                 }
1134                 else {
1135                     counts.put( id, 1 );
1136                 }
1137             }
1138             final Set<String> dcs = new HashSet<String>();
1139             for( int i = 1; i < domains.size(); ++i ) {
1140                 for( int j = 0; j < i; ++j ) {
1141                     Domain domain_n = domains.get( i );
1142                     Domain domain_c = domains.get( j );
1143                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1144                         domain_n = domains.get( j );
1145                         domain_c = domains.get( i );
1146                     }
1147                     final String dc = domain_n.getDomainId() + domain_c.getDomainId();
1148                     if ( !dcs.contains( dc ) ) {
1149                         dcs.add( dc );
1150                         sb.append( protein.getSpecies() );
1151                         sb.append( separator );
1152                         sb.append( protein_id );
1153                         sb.append( separator );
1154                         sb.append( domain_n.getDomainId() );
1155                         sb.append( separator );
1156                         sb.append( domain_c.getDomainId() );
1157                         sb.append( separator );
1158                         sb.append( domain_n.getPerDomainEvalue() );
1159                         sb.append( separator );
1160                         sb.append( domain_c.getPerDomainEvalue() );
1161                         sb.append( separator );
1162                         sb.append( counts.get( domain_n.getDomainId() ) );
1163                         sb.append( separator );
1164                         sb.append( counts.get( domain_c.getDomainId() ) );
1165                         sb.append( ForesterUtil.LINE_SEPARATOR );
1166                     }
1167                 }
1168             }
1169         }
1170         else if ( domains.size() == 1 ) {
1171             sb.append( protein.getSpecies() );
1172             sb.append( separator );
1173             sb.append( protein_id );
1174             sb.append( separator );
1175             sb.append( domains.get( 0 ).getDomainId() );
1176             sb.append( separator );
1177             sb.append( separator );
1178             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1179             sb.append( separator );
1180             sb.append( separator );
1181             sb.append( 1 );
1182             sb.append( separator );
1183             sb.append( ForesterUtil.LINE_SEPARATOR );
1184         }
1185         else {
1186             sb.append( protein.getSpecies() );
1187             sb.append( separator );
1188             sb.append( protein_id );
1189             sb.append( separator );
1190             sb.append( separator );
1191             sb.append( separator );
1192             sb.append( separator );
1193             sb.append( separator );
1194             sb.append( separator );
1195             sb.append( ForesterUtil.LINE_SEPARATOR );
1196         }
1197         return sb;
1198     }
1199
1200     /**
1201      *
1202      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1203      * domain with 0.3 is ignored
1204      *
1205      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1206      *
1207      *
1208      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1209      * ignored
1210      *
1211      * @param max_allowed_overlap
1212      *            maximal allowed overlap (inclusive) to be still considered not
1213      *            overlapping (zero or negative value to allow any overlap)
1214      * @param remove_engulfed_domains
1215      *            to remove domains which are completely engulfed by coverage of
1216      *            domains with better support
1217      * @param protein
1218      * @return
1219      */
1220     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1221                                                     final boolean remove_engulfed_domains,
1222                                                     final Protein protein ) {
1223         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1224                 .getSpeciesId(), protein.getLength() );
1225         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1226         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1227         for( final Domain domain : sorted ) {
1228             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1229                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1230                 final int covered_positions_size = covered_positions.size();
1231                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1232                     covered_positions.add( false );
1233                 }
1234                 final int new_covered_positions_size = covered_positions.size();
1235                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1236                     if ( i < new_covered_positions_size ) {
1237                         covered_positions.set( i, true );
1238                     }
1239                     else {
1240                         covered_positions.add( true );
1241                     }
1242                 }
1243                 pruned_protein.addProteinDomain( domain );
1244             }
1245         }
1246         return pruned_protein;
1247     }
1248
1249     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1250         final List<Domain> domains = new ArrayList<Domain>();
1251         for( final Domain d : protein.getProteinDomains() ) {
1252             domains.add( d );
1253         }
1254         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1255         return domains;
1256     }
1257
1258     public static int storeDomainArchitectures( final String genome,
1259                                                 final SortedMap<String, Set<String>> domain_architecutures,
1260                                                 final List<Protein> protein_list,
1261                                                 final Map<String, Integer> distinct_domain_architecuture_counts ) {
1262         final Set<String> da = new HashSet<String>();
1263         domain_architecutures.put( genome, da );
1264         for( final Protein protein : protein_list ) {
1265             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
1266             if ( !da.contains( da_str ) ) {
1267                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
1268                     distinct_domain_architecuture_counts.put( da_str, 1 );
1269                 }
1270                 else {
1271                     distinct_domain_architecuture_counts.put( da_str,
1272                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
1273                 }
1274                 da.add( da_str );
1275             }
1276         }
1277         return da.size();
1278     }
1279
1280     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1281                                                             final boolean get_gains,
1282                                                             final String outdir,
1283                                                             final String suffix_for_filename ) throws IOException {
1284         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1285         if ( !get_gains ) {
1286             state = CharacterStateMatrix.GainLossStates.LOSS;
1287         }
1288         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1289                                                                   false,
1290                                                                   state,
1291                                                                   outdir );
1292         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1293             final PhylogenyNode node = it.next();
1294             if ( !node.isExternal() ) {
1295                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1296                 if ( domains.size() > 0 ) {
1297                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1298                             + node.getName() + suffix_for_filename );
1299                     for( final String domain : domains ) {
1300                         writer.write( domain );
1301                         writer.write( ForesterUtil.LINE_SEPARATOR );
1302                     }
1303                     writer.close();
1304                 }
1305             }
1306         }
1307     }
1308
1309     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1310                                                                           final File output_dir,
1311                                                                           final GenomeWideCombinableDomains gwcd,
1312                                                                           final int i,
1313                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1314         File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
1315                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1316         if ( output_dir != null ) {
1317             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1318         }
1319         checkForOutputFileWriteability( dc_outfile_dot );
1320         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1321         try {
1322             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1323             for( final BinaryDomainCombination bdc : binary_combinations ) {
1324                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1325                         .toString() );
1326                 out_dot.write( SurfacingConstants.NL );
1327             }
1328             out_dot.close();
1329         }
1330         catch ( final IOException e ) {
1331             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1332         }
1333         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1334                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1335                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1336     }
1337
1338     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1339                                                             final CharacterStateMatrix.GainLossStates state,
1340                                                             final String filename,
1341                                                             final String indentifier_characters_separator,
1342                                                             final String character_separator,
1343                                                             final Map<String, String> descriptions ) {
1344         final File outfile = new File( filename );
1345         checkForOutputFileWriteability( outfile );
1346         final SortedSet<String> sorted_ids = new TreeSet<String>();
1347         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1348             sorted_ids.add( matrix.getIdentifier( i ) );
1349         }
1350         try {
1351             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1352             for( final String id : sorted_ids ) {
1353                 out.write( indentifier_characters_separator );
1354                 out.write( "#" + id );
1355                 out.write( indentifier_characters_separator );
1356                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1357                     // Not nice:
1358                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1359                     if ( ( matrix.getState( id, c ) == state )
1360                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1361                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1362                         out.write( matrix.getCharacter( c ) );
1363                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1364                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1365                             out.write( "\t" );
1366                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1367                         }
1368                         out.write( character_separator );
1369                     }
1370                 }
1371             }
1372             out.flush();
1373             out.close();
1374         }
1375         catch ( final IOException e ) {
1376             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1377         }
1378         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1379     }
1380
1381     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1382                                                                                                  final CharacterStateMatrix.GainLossStates state,
1383                                                                                                  final String filename,
1384                                                                                                  final String indentifier_characters_separator,
1385                                                                                                  final String character_separator,
1386                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1387         final File outfile = new File( filename );
1388         checkForOutputFileWriteability( outfile );
1389         final SortedSet<String> sorted_ids = new TreeSet<String>();
1390         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1391             sorted_ids.add( matrix.getIdentifier( i ) );
1392         }
1393         try {
1394             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1395             for( final String id : sorted_ids ) {
1396                 out.write( indentifier_characters_separator );
1397                 out.write( "#" + id );
1398                 out.write( indentifier_characters_separator );
1399                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1400                     // Not nice:
1401                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1402                     if ( ( matrix.getState( id, c ) == state )
1403                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1404                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1405                         BinaryDomainCombination bdc = null;
1406                         try {
1407                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1408                         }
1409                         catch ( final Exception e ) {
1410                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1411                         }
1412                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1413                         out.write( character_separator );
1414                     }
1415                 }
1416             }
1417             out.flush();
1418             out.close();
1419         }
1420         catch ( final IOException e ) {
1421             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1422         }
1423         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1424     }
1425
1426     public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
1427                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1428                                                       final GoNameSpace go_namespace_limit,
1429                                                       final boolean domain_combinations,
1430                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1431                                                       final CharacterStateMatrix.GainLossStates state,
1432                                                       final String filename,
1433                                                       final String indentifier_characters_separator,
1434                                                       final String character_separator,
1435                                                       final String title_for_html,
1436                                                       final String prefix_for_html,
1437                                                       final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
1438                                                       final SortedSet<String> all_pfams_encountered,
1439                                                       final SortedSet<String> pfams_gained_or_lost,
1440                                                       final String suffix_for_per_node_events_file,
1441                                                       final Map<String, Integer> tax_code_to_id_map ) {
1442         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1443             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1444         }
1445         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1446             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1447         }
1448         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1449             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1450         }
1451         final File outfile = new File( filename );
1452         checkForOutputFileWriteability( outfile );
1453         final SortedSet<String> sorted_ids = new TreeSet<String>();
1454         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1455             sorted_ids.add( matrix.getIdentifier( i ) );
1456         }
1457         try {
1458             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1459             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1460                                                                                                                 domain_combinations,
1461                                                                                                                 state,
1462                                                                                                                 filename );
1463             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1464             File per_node_go_mapped_domain_gain_loss_outfile = null;
1465             int per_node_counter = 0;
1466             out.write( "<html>" );
1467             out.write( SurfacingConstants.NL );
1468             addHtmlHead( out, title_for_html );
1469             out.write( SurfacingConstants.NL );
1470             out.write( "<body>" );
1471             out.write( SurfacingConstants.NL );
1472             out.write( "<h1>" );
1473             out.write( SurfacingConstants.NL );
1474             out.write( title_for_html );
1475             out.write( SurfacingConstants.NL );
1476             out.write( "</h1>" );
1477             out.write( SurfacingConstants.NL );
1478             out.write( "<table>" );
1479             out.write( SurfacingConstants.NL );
1480             for( final String id : sorted_ids ) {
1481                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1482                 if ( matcher.matches() ) {
1483                     continue;
1484                 }
1485                 out.write( "<tr>" );
1486                 out.write( "<td>" );
1487                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1488                 out.write( "</td>" );
1489                 out.write( "</tr>" );
1490                 out.write( SurfacingConstants.NL );
1491             }
1492             out.write( "</table>" );
1493             out.write( SurfacingConstants.NL );
1494             for( final String id : sorted_ids ) {
1495                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1496                 if ( matcher.matches() ) {
1497                     continue;
1498                 }
1499                 out.write( SurfacingConstants.NL );
1500                 out.write( "<h2>" );
1501                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1502                 writeTaxonomyLinks( out, id, tax_code_to_id_map );
1503                 out.write( "</h2>" );
1504                 out.write( SurfacingConstants.NL );
1505                 out.write( "<table>" );
1506                 out.write( SurfacingConstants.NL );
1507                 out.write( "<tr>" );
1508                 out.write( "<td><b>" );
1509                 out.write( "Pfam domain(s)" );
1510                 out.write( "</b></td><td><b>" );
1511                 out.write( "GO term acc" );
1512                 out.write( "</b></td><td><b>" );
1513                 out.write( "GO term" );
1514                 out.write( "</b></td><td><b>" );
1515                 out.write( "GO namespace" );
1516                 out.write( "</b></td>" );
1517                 out.write( "</tr>" );
1518                 out.write( SurfacingConstants.NL );
1519                 out.write( "</tr>" );
1520                 out.write( SurfacingConstants.NL );
1521                 per_node_counter = 0;
1522                 if ( matrix.getNumberOfCharacters() > 0 ) {
1523                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1524                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1525                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1526                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1527                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1528                 }
1529                 else {
1530                     per_node_go_mapped_domain_gain_loss_outfile = null;
1531                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1532                 }
1533                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1534                     // Not nice:
1535                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1536                     if ( ( matrix.getState( id, c ) == state )
1537                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1538                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1539                         final String character = matrix.getCharacter( c );
1540                         String domain_0 = "";
1541                         String domain_1 = "";
1542                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1543                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1544                             if ( s.length != 2 ) {
1545                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1546                                         + character + "]" );
1547                             }
1548                             domain_0 = s[ 0 ];
1549                             domain_1 = s[ 1 ];
1550                         }
1551                         else {
1552                             domain_0 = character;
1553                         }
1554                         writeDomainData( domain_id_to_go_ids_map,
1555                                          go_id_to_term_map,
1556                                          go_namespace_limit,
1557                                          out,
1558                                          domain_0,
1559                                          domain_1,
1560                                          prefix_for_html,
1561                                          character_separator,
1562                                          domain_id_to_secondary_features_maps,
1563                                          null );
1564                         all_pfams_encountered.add( domain_0 );
1565                         if ( pfams_gained_or_lost != null ) {
1566                             pfams_gained_or_lost.add( domain_0 );
1567                         }
1568                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1569                             all_pfams_encountered.add( domain_1 );
1570                             if ( pfams_gained_or_lost != null ) {
1571                                 pfams_gained_or_lost.add( domain_1 );
1572                             }
1573                         }
1574                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1575                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1576                                                                      domain_0,
1577                                                                      domain_1 );
1578                             per_node_counter++;
1579                         }
1580                     }
1581                 }
1582                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1583                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1584                     if ( per_node_counter < 1 ) {
1585                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1586                     }
1587                     per_node_counter = 0;
1588                 }
1589                 out.write( "</table>" );
1590                 out.write( SurfacingConstants.NL );
1591                 out.write( "<hr>" );
1592                 out.write( SurfacingConstants.NL );
1593             } // for( final String id : sorted_ids ) {
1594             out.write( "</body>" );
1595             out.write( SurfacingConstants.NL );
1596             out.write( "</html>" );
1597             out.write( SurfacingConstants.NL );
1598             out.flush();
1599             out.close();
1600         }
1601         catch ( final IOException e ) {
1602             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1603         }
1604         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1605     }
1606
1607     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1608                                                           final File output_dir,
1609                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1610                                                           final GenomeWideCombinableDomains gwcd,
1611                                                           final int i,
1612                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1613         File dc_outfile = new File( input_file_properties[ i ][ 1 ]
1614                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1615         if ( output_dir != null ) {
1616             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1617         }
1618         checkForOutputFileWriteability( dc_outfile );
1619         try {
1620             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1621             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1622             out.close();
1623         }
1624         catch ( final IOException e ) {
1625             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1626         }
1627         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1628         try {
1629             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
1630             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1631             if ( stats.getN() < 2 ) {
1632                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1633             }
1634             else {
1635                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1636                         .sampleStandardDeviation() ) + "\t" );
1637             }
1638             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1639             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1640             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1641             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1642             final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
1643             for( final String mpd : mpds ) {
1644                 per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
1645             }
1646             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1647         }
1648         catch ( final IOException e ) {
1649             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1650         }
1651         if ( input_file_properties[ i ].length == 3 ) {
1652             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1653                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1654                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1655         }
1656         else {
1657             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1658                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1659                     + dc_outfile + "\"" );
1660         }
1661     }
1662
1663     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
1664                                                                        final StringBuilder html_title,
1665                                                                        final Writer single_writer,
1666                                                                        Map<Character, Writer> split_writers,
1667                                                                        final SortedSet<DomainSimilarity> similarities,
1668                                                                        final boolean treat_as_binary,
1669                                                                        final List<Species> species_order,
1670                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
1671                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
1672                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
1673                                                                        final boolean verbose,
1674                                                                        final Map<String, Integer> tax_code_to_id_map )
1675             throws IOException {
1676         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1677         String histogram_title = null;
1678         switch ( sort_field ) {
1679             case ABS_MAX_COUNTS_DIFFERENCE:
1680                 if ( treat_as_binary ) {
1681                     histogram_title = "absolute counts difference:";
1682                 }
1683                 else {
1684                     histogram_title = "absolute (maximal) counts difference:";
1685                 }
1686                 break;
1687             case MAX_COUNTS_DIFFERENCE:
1688                 if ( treat_as_binary ) {
1689                     histogram_title = "counts difference:";
1690                 }
1691                 else {
1692                     histogram_title = "(maximal) counts difference:";
1693                 }
1694                 break;
1695             case DOMAIN_ID:
1696                 histogram_title = "score mean:";
1697                 break;
1698             case MIN:
1699                 histogram_title = "score minimum:";
1700                 break;
1701             case MAX:
1702                 histogram_title = "score maximum:";
1703                 break;
1704             case MAX_DIFFERENCE:
1705                 if ( treat_as_binary ) {
1706                     histogram_title = "difference:";
1707                 }
1708                 else {
1709                     histogram_title = "(maximal) difference:";
1710                 }
1711                 break;
1712             case MEAN:
1713                 histogram_title = "score mean:";
1714                 break;
1715             case SD:
1716                 histogram_title = "score standard deviation:";
1717                 break;
1718             case SPECIES_COUNT:
1719                 histogram_title = "species number:";
1720                 break;
1721             default:
1722                 throw new AssertionError( "Unknown sort field: " + sort_field );
1723         }
1724         for( final DomainSimilarity similarity : similarities ) {
1725             switch ( sort_field ) {
1726                 case ABS_MAX_COUNTS_DIFFERENCE:
1727                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
1728                     break;
1729                 case MAX_COUNTS_DIFFERENCE:
1730                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
1731                     break;
1732                 case DOMAIN_ID:
1733                     stats.addValue( similarity.getMeanSimilarityScore() );
1734                     break;
1735                 case MIN:
1736                     stats.addValue( similarity.getMinimalSimilarityScore() );
1737                     break;
1738                 case MAX:
1739                     stats.addValue( similarity.getMaximalSimilarityScore() );
1740                     break;
1741                 case MAX_DIFFERENCE:
1742                     stats.addValue( similarity.getMaximalDifference() );
1743                     break;
1744                 case MEAN:
1745                     stats.addValue( similarity.getMeanSimilarityScore() );
1746                     break;
1747                 case SD:
1748                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
1749                     break;
1750                 case SPECIES_COUNT:
1751                     stats.addValue( similarity.getSpecies().size() );
1752                     break;
1753                 default:
1754                     throw new AssertionError( "Unknown sort field: " + sort_field );
1755             }
1756         }
1757         AsciiHistogram histo = null;
1758         try {
1759             if ( stats.getMin() < stats.getMax() ) {
1760                 histo = new AsciiHistogram( stats, histogram_title );
1761             }
1762         }
1763         catch ( Exception e ) {
1764             histo = null;
1765         }
1766         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
1767             split_writers = new HashMap<Character, Writer>();
1768             split_writers.put( '_', single_writer );
1769         }
1770         switch ( print_option ) {
1771             case SIMPLE_TAB_DELIMITED:
1772                 break;
1773             case HTML:
1774                 for( final Character key : split_writers.keySet() ) {
1775                     final Writer w = split_writers.get( key );
1776                     w.write( "<html>" );
1777                     w.write( SurfacingConstants.NL );
1778                     if ( key != '_' ) {
1779                         addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
1780                     }
1781                     else {
1782                         addHtmlHead( w, "DCs (" + html_title + ")" );
1783                     }
1784                     w.write( SurfacingConstants.NL );
1785                     w.write( "<body>" );
1786                     w.write( SurfacingConstants.NL );
1787                     w.write( html_desc.toString() );
1788                     w.write( SurfacingConstants.NL );
1789                     w.write( "<hr>" );
1790                     w.write( "<br>" );
1791                     w.write( SurfacingConstants.NL );
1792                     w.write( "<tt><pre>" );
1793                     w.write( SurfacingConstants.NL );
1794                     if ( histo != null ) {
1795                         w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
1796                         w.write( SurfacingConstants.NL );
1797                     }
1798                     w.write( "</pre></tt>" );
1799                     w.write( SurfacingConstants.NL );
1800                     w.write( "<table>" );
1801                     w.write( SurfacingConstants.NL );
1802                     w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
1803                     w.write( SurfacingConstants.NL );
1804                     w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
1805                     w.write( SurfacingConstants.NL );
1806                     w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
1807                     w.write( SurfacingConstants.NL );
1808                     w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
1809                     w.write( SurfacingConstants.NL );
1810                     if ( stats.getN() > 1 ) {
1811                         w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
1812                     }
1813                     else {
1814                         w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
1815                     }
1816                     w.write( SurfacingConstants.NL );
1817                     w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
1818                     w.write( SurfacingConstants.NL );
1819                     w.write( "</table>" );
1820                     w.write( SurfacingConstants.NL );
1821                     w.write( "<br>" );
1822                     w.write( SurfacingConstants.NL );
1823                     w.write( "<hr>" );
1824                     w.write( SurfacingConstants.NL );
1825                     w.write( "<br>" );
1826                     w.write( SurfacingConstants.NL );
1827                     w.write( "<table>" );
1828                     w.write( SurfacingConstants.NL );
1829                 }
1830                 break;
1831         }
1832         for( final Writer w : split_writers.values() ) {
1833             w.write( SurfacingConstants.NL );
1834         }
1835         //
1836         for( final DomainSimilarity similarity : similarities ) {
1837             if ( ( species_order != null ) && !species_order.isEmpty() ) {
1838                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
1839             }
1840             if ( single_writer != null ) {
1841                 single_writer.write( "<a href=\"#" + similarity.getDomainId() + "\">" + similarity.getDomainId()
1842                         + "</a><br>" );
1843                 single_writer.write( SurfacingConstants.NL );
1844             }
1845             else {
1846                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
1847                         .charAt( 0 ) );
1848                 if ( local_writer == null ) {
1849                     local_writer = split_writers.get( '0' );
1850                 }
1851                 local_writer.write( "<a href=\"#" + similarity.getDomainId() + "\">" + similarity.getDomainId()
1852                         + "</a><br>" );
1853                 local_writer.write( SurfacingConstants.NL );
1854             }
1855         }
1856         // w.write( "<hr>" );
1857         // w.write( SurfacingConstants.NL );
1858         //
1859         for( final DomainSimilarity similarity : similarities ) {
1860             if ( ( species_order != null ) && !species_order.isEmpty() ) {
1861                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
1862             }
1863             if ( single_writer != null ) {
1864                 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1865                 single_writer.write( SurfacingConstants.NL );
1866             }
1867             else {
1868                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
1869                         .charAt( 0 ) );
1870                 if ( local_writer == null ) {
1871                     local_writer = split_writers.get( '0' );
1872                 }
1873                 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1874                 local_writer.write( SurfacingConstants.NL );
1875             }
1876         }
1877         switch ( print_option ) {
1878             case HTML:
1879                 for( final Writer w : split_writers.values() ) {
1880                     w.write( SurfacingConstants.NL );
1881                     w.write( "</table>" );
1882                     w.write( SurfacingConstants.NL );
1883                     w.write( "</font>" );
1884                     w.write( SurfacingConstants.NL );
1885                     w.write( "</body>" );
1886                     w.write( SurfacingConstants.NL );
1887                     w.write( "</html>" );
1888                     w.write( SurfacingConstants.NL );
1889                 }
1890                 break;
1891         }
1892         for( final Writer w : split_writers.values() ) {
1893             w.close();
1894         }
1895         return stats;
1896     }
1897
1898     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
1899                                           final String filename,
1900                                           final Format format ) {
1901         final File outfile = new File( filename );
1902         checkForOutputFileWriteability( outfile );
1903         try {
1904             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1905             matrix.toWriter( out, format );
1906             out.flush();
1907             out.close();
1908         }
1909         catch ( final IOException e ) {
1910             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1911         }
1912         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
1913     }
1914
1915     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
1916         checkForOutputFileWriteability( matrix_outfile );
1917         try {
1918             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
1919             for( final DistanceMatrix distance_matrix : matrices ) {
1920                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
1921                 out.write( ForesterUtil.LINE_SEPARATOR );
1922                 out.flush();
1923             }
1924             out.close();
1925         }
1926         catch ( final IOException e ) {
1927             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1928         }
1929         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
1930     }
1931
1932     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
1933         final PhylogenyWriter writer = new PhylogenyWriter();
1934         try {
1935             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
1936         }
1937         catch ( final IOException e ) {
1938             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
1939                     + e );
1940         }
1941         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
1942     }
1943
1944     public static void writeTaxonomyLinks( final Writer writer,
1945                                            final String species,
1946                                            final Map<String, Integer> tax_code_to_id_map ) throws IOException {
1947         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
1948             writer.write( " [" );
1949             if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
1950                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
1951                         + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
1952             }
1953             else {
1954                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
1955                         + "\" target=\"taxonomy_window\">eol</a>" );
1956                 writer.write( "|" );
1957                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
1958                         + "\" target=\"taxonomy_window\">scholar</a>" );
1959                 writer.write( "|" );
1960                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
1961                         + "\" target=\"taxonomy_window\">google</a>" );
1962             }
1963             writer.write( "]" );
1964         }
1965     }
1966
1967     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
1968         if ( map.containsKey( s ) ) {
1969             map.put( s, map.get( s ) + 1 );
1970         }
1971         else {
1972             map.put( s, 1 );
1973         }
1974     }
1975
1976     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
1977                                                                     final String outfilename_for_counts,
1978                                                                     final String outfilename_for_dc,
1979                                                                     final String outfilename_for_dc_for_go_mapping,
1980                                                                     final String outfilename_for_dc_for_go_mapping_unique,
1981                                                                     final String outfilename_for_rank_counts,
1982                                                                     final String outfilename_for_ancestor_species_counts,
1983                                                                     final String outfilename_for_protein_stats,
1984                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
1985                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
1986                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
1987         try {
1988             //
1989             //            if ( protein_length_stats_by_dc != null ) {
1990             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
1991             //                    System.out.print( entry.getKey().toString() );
1992             //                    System.out.print( ": " );
1993             //                    double[] a = entry.getValue().getDataAsDoubleArray();
1994             //                    for( int i = 0; i < a.length; i++ ) {
1995             //                        System.out.print( a[ i ] + " " );
1996             //                    }
1997             //                    System.out.println();
1998             //                }
1999             //            }
2000             //            if ( domain_number_stats_by_dc != null ) {
2001             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
2002             //                    System.out.print( entry.getKey().toString() );
2003             //                    System.out.print( ": " );
2004             //                    double[] a = entry.getValue().getDataAsDoubleArray();
2005             //                    for( int i = 0; i < a.length; i++ ) {
2006             //                        System.out.print( a[ i ] + " " );
2007             //                    }
2008             //                    System.out.println();
2009             //                }
2010             //            }
2011             //
2012             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
2013             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
2014             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
2015             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
2016             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
2017             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
2018                 final PhylogenyNode n = it.next();
2019                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
2020                 for( final String dc : gained_dc ) {
2021                     if ( dc_gain_counts.containsKey( dc ) ) {
2022                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
2023                     }
2024                     else {
2025                         dc_gain_counts.put( dc, 1 );
2026                     }
2027                 }
2028             }
2029             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
2030             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
2031             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
2032             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
2033             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
2034             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
2035             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
2036             final Set<String> dcs = dc_gain_counts.keySet();
2037             final SortedSet<String> more_than_once = new TreeSet<String>();
2038             DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
2039             DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
2040             DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
2041             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
2042             long gained_multiple_times_domain_length_sum = 0;
2043             long gained_once_domain_length_sum = 0;
2044             long gained_multiple_times_domain_length_count = 0;
2045             long gained_once_domain_length_count = 0;
2046             for( final String dc : dcs ) {
2047                 final int count = dc_gain_counts.get( dc );
2048                 if ( histogram.containsKey( count ) ) {
2049                     histogram.put( count, histogram.get( count ) + 1 );
2050                     domain_lists.get( count ).append( ", " + dc );
2051                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
2052                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
2053                 }
2054                 else {
2055                     histogram.put( count, 1 );
2056                     domain_lists.put( count, new StringBuilder( dc ) );
2057                     final PriorityQueue<String> q = new PriorityQueue<String>();
2058                     q.addAll( splitDomainCombination( dc ) );
2059                     domain_lists_go.put( count, q );
2060                     final SortedSet<String> set = new TreeSet<String>();
2061                     set.addAll( splitDomainCombination( dc ) );
2062                     domain_lists_go_unique.put( count, set );
2063                 }
2064                 if ( protein_length_stats_by_dc != null ) {
2065                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
2066                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
2067                     }
2068                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
2069                             .arithmeticMean() );
2070                 }
2071                 if ( domain_number_stats_by_dc != null ) {
2072                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
2073                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
2074                     }
2075                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
2076                             .arithmeticMean() );
2077                 }
2078                 if ( domain_length_stats_by_domain != null ) {
2079                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
2080                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
2081                     }
2082                     final String[] ds = dc.split( "=" );
2083                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2084                             .get( ds[ 0 ] ).arithmeticMean() );
2085                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2086                             .get( ds[ 1 ] ).arithmeticMean() );
2087                 }
2088                 if ( count > 1 ) {
2089                     more_than_once.add( dc );
2090                     if ( protein_length_stats_by_dc != null ) {
2091                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2092                         for( final double element : s.getData() ) {
2093                             gained_multiple_times_lengths_stats.addValue( element );
2094                         }
2095                     }
2096                     if ( domain_number_stats_by_dc != null ) {
2097                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2098                         for( final double element : s.getData() ) {
2099                             gained_multiple_times_domain_count_stats.addValue( element );
2100                         }
2101                     }
2102                     if ( domain_length_stats_by_domain != null ) {
2103                         final String[] ds = dc.split( "=" );
2104                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2105                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2106                         for( final double element : s0.getData() ) {
2107                             gained_multiple_times_domain_length_sum += element;
2108                             ++gained_multiple_times_domain_length_count;
2109                         }
2110                         for( final double element : s1.getData() ) {
2111                             gained_multiple_times_domain_length_sum += element;
2112                             ++gained_multiple_times_domain_length_count;
2113                         }
2114                     }
2115                 }
2116                 else {
2117                     if ( protein_length_stats_by_dc != null ) {
2118                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2119                         for( final double element : s.getData() ) {
2120                             gained_once_lengths_stats.addValue( element );
2121                         }
2122                     }
2123                     if ( domain_number_stats_by_dc != null ) {
2124                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2125                         for( final double element : s.getData() ) {
2126                             gained_once_domain_count_stats.addValue( element );
2127                         }
2128                     }
2129                     if ( domain_length_stats_by_domain != null ) {
2130                         final String[] ds = dc.split( "=" );
2131                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2132                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2133                         for( final double element : s0.getData() ) {
2134                             gained_once_domain_length_sum += element;
2135                             ++gained_once_domain_length_count;
2136                         }
2137                         for( final double element : s1.getData() ) {
2138                             gained_once_domain_length_sum += element;
2139                             ++gained_once_domain_length_count;
2140                         }
2141                     }
2142                 }
2143             }
2144             final Set<Integer> histogram_keys = histogram.keySet();
2145             for( final Integer histogram_key : histogram_keys ) {
2146                 final int count = histogram.get( histogram_key );
2147                 final StringBuilder dc = domain_lists.get( histogram_key );
2148                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
2149                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
2150                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2151                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
2152                 Arrays.sort( sorted );
2153                 for( final Object domain : sorted ) {
2154                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
2155                 }
2156                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2157                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
2158                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
2159                 }
2160             }
2161             out_counts.close();
2162             out_dc.close();
2163             out_dc_for_go_mapping.close();
2164             out_dc_for_go_mapping_unique.close();
2165             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
2166             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
2167             for( final String dc : more_than_once ) {
2168                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
2169                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
2170                     final PhylogenyNode n = it.next();
2171                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
2172                         nodes.add( n );
2173                     }
2174                 }
2175                 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
2176                     for( int j = i + 1; j < nodes.size(); ++j ) {
2177                         final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
2178                         String rank = "unknown";
2179                         if ( lca.getNodeData().isHasTaxonomy()
2180                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
2181                             rank = lca.getNodeData().getTaxonomy().getRank();
2182                         }
2183                         addToCountMap( lca_rank_counts, rank );
2184                         String lca_species;
2185                         if ( lca.getNodeData().isHasTaxonomy()
2186                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
2187                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
2188                         }
2189                         else if ( lca.getNodeData().isHasTaxonomy()
2190                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
2191                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
2192                         }
2193                         else {
2194                             lca_species = lca.getName();
2195                         }
2196                         addToCountMap( lca_ancestor_species_counts, lca_species );
2197                     }
2198                 }
2199             }
2200             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
2201             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
2202             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
2203             ForesterUtil.map2writer( out_for_ancestor_species_counts,
2204                                      lca_ancestor_species_counts,
2205                                      "\t",
2206                                      ForesterUtil.LINE_SEPARATOR );
2207             out_for_rank_counts.close();
2208             out_for_ancestor_species_counts.close();
2209             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
2210                     && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
2211                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
2212                 w.write( "Domain Lengths: " );
2213                 w.write( "\n" );
2214                 if ( domain_length_stats_by_domain != null ) {
2215                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
2216                             .entrySet() ) {
2217                         w.write( entry.getKey().toString() );
2218                         w.write( "\t" + entry.getValue().arithmeticMean() );
2219                         w.write( "\t" + entry.getValue().median() );
2220                         w.write( "\n" );
2221                     }
2222                 }
2223                 w.flush();
2224                 w.write( "\n" );
2225                 w.write( "\n" );
2226                 w.write( "Protein Lengths: " );
2227                 w.write( "\n" );
2228                 if ( protein_length_stats_by_dc != null ) {
2229                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
2230                             .entrySet() ) {
2231                         w.write( entry.getKey().toString() );
2232                         w.write( "\t" + entry.getValue().arithmeticMean() );
2233                         w.write( "\t" + entry.getValue().median() );
2234                         w.write( "\n" );
2235                     }
2236                 }
2237                 w.flush();
2238                 w.write( "\n" );
2239                 w.write( "\n" );
2240                 w.write( "Number of domains: " );
2241                 w.write( "\n" );
2242                 if ( domain_number_stats_by_dc != null ) {
2243                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
2244                             .entrySet() ) {
2245                         w.write( entry.getKey().toString() );
2246                         w.write( "\t" + entry.getValue().arithmeticMean() );
2247                         w.write( "\t" + entry.getValue().median() );
2248                         w.write( "\n" );
2249                     }
2250                 }
2251                 w.flush();
2252                 w.write( "\n" );
2253                 w.write( "\n" );
2254                 w.write( "Gained once, domain lengths:" );
2255                 w.write( "\n" );
2256                 w.write( "N: " + gained_once_domain_length_count );
2257                 w.write( "\n" );
2258                 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
2259                 w.write( "\n" );
2260                 w.write( "\n" );
2261                 w.write( "Gained multiple times, domain lengths:" );
2262                 w.write( "\n" );
2263                 w.write( "N: " + gained_multiple_times_domain_length_count );
2264                 w.write( "\n" );
2265                 w.write( "Avg: "
2266                         + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
2267                 w.write( "\n" );
2268                 w.write( "\n" );
2269                 w.write( "\n" );
2270                 w.write( "\n" );
2271                 w.write( "Gained once, protein lengths:" );
2272                 w.write( "\n" );
2273                 w.write( gained_once_lengths_stats.toString() );
2274                 gained_once_lengths_stats = null;
2275                 w.write( "\n" );
2276                 w.write( "\n" );
2277                 w.write( "Gained once, domain counts:" );
2278                 w.write( "\n" );
2279                 w.write( gained_once_domain_count_stats.toString() );
2280                 gained_once_domain_count_stats = null;
2281                 w.write( "\n" );
2282                 w.write( "\n" );
2283                 w.write( "Gained multiple times, protein lengths:" );
2284                 w.write( "\n" );
2285                 w.write( gained_multiple_times_lengths_stats.toString() );
2286                 gained_multiple_times_lengths_stats = null;
2287                 w.write( "\n" );
2288                 w.write( "\n" );
2289                 w.write( "Gained multiple times, domain counts:" );
2290                 w.write( "\n" );
2291                 w.write( gained_multiple_times_domain_count_stats.toString() );
2292                 w.flush();
2293                 w.close();
2294             }
2295         }
2296         catch ( final IOException e ) {
2297             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2298         }
2299         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
2300                 + outfilename_for_counts + "]" );
2301         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
2302                 + outfilename_for_dc + "]" );
2303         ForesterUtil.programMessage( surfacing.PRG_NAME,
2304                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
2305                                              + outfilename_for_dc_for_go_mapping + "]" );
2306         ForesterUtil.programMessage( surfacing.PRG_NAME,
2307                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
2308                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
2309     }
2310
2311     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
2312                                                                         final boolean get_gains ) {
2313         final SortedSet<String> domains = new TreeSet<String>();
2314         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
2315             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
2316             if ( get_gains ) {
2317                 domains.addAll( chars.getGainedCharacters() );
2318             }
2319             else {
2320                 domains.addAll( chars.getLostCharacters() );
2321             }
2322         }
2323         return domains;
2324     }
2325
2326     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
2327                                                             final boolean domain_combinations,
2328                                                             final CharacterStateMatrix.GainLossStates state,
2329                                                             final String outfile ) {
2330         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
2331                 + ForesterUtil.FILE_SEPARATOR + base_dir );
2332         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2333             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2334         }
2335         if ( domain_combinations ) {
2336             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2337                     + ForesterUtil.FILE_SEPARATOR + "DC" );
2338         }
2339         else {
2340             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2341                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
2342         }
2343         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2344             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2345         }
2346         if ( state == GainLossStates.GAIN ) {
2347             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2348                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
2349         }
2350         else if ( state == GainLossStates.LOSS ) {
2351             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2352                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
2353         }
2354         else {
2355             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2356                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
2357         }
2358         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2359             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2360         }
2361         return per_node_go_mapped_domain_gain_loss_files_base_dir;
2362     }
2363
2364     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
2365         final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
2366         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
2367         for( final String domain_id : cds.keySet() ) {
2368             final CombinableDomains cd = cds.get( domain_id );
2369             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
2370         }
2371         return binary_combinations;
2372     }
2373
2374     private static List<String> splitDomainCombination( final String dc ) {
2375         final String[] s = dc.split( "=" );
2376         if ( s.length != 2 ) {
2377             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
2378                     + dc );
2379             System.exit( -1 );
2380         }
2381         final List<String> l = new ArrayList<String>( 2 );
2382         l.add( s[ 0 ] );
2383         l.add( s[ 1 ] );
2384         return l;
2385     }
2386
2387     private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2388                                                         final Map<GoId, GoTerm> go_id_to_term_map,
2389                                                         final String outfile_name,
2390                                                         final SortedSet<String> all_pfams_encountered ) {
2391         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
2392         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
2393                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
2394         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
2395         int biological_process_counter = 0;
2396         int cellular_component_counter = 0;
2397         int molecular_function_counter = 0;
2398         int pfams_with_mappings_counter = 0;
2399         int pfams_without_mappings_counter = 0;
2400         int pfams_without_mappings_to_bp_or_mf_counter = 0;
2401         int pfams_with_mappings_to_bp_or_mf_counter = 0;
2402         try {
2403             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
2404             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
2405             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
2406             summary_writer.write( "# Pfam to GO mapping summary" );
2407             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2408             summary_writer.write( "# Actual summary is at the end of this file." );
2409             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2410             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
2411             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2412             for( final String pfam : all_pfams_encountered ) {
2413                 all_pfams_encountered_writer.write( pfam );
2414                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
2415                 final String domain_id = new String( pfam );
2416                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2417                     ++pfams_with_mappings_counter;
2418                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
2419                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
2420                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
2421                     boolean maps_to_bp = false;
2422                     boolean maps_to_cc = false;
2423                     boolean maps_to_mf = false;
2424                     for( final GoId go_id : go_ids ) {
2425                         final GoTerm go_term = go_id_to_term_map.get( go_id );
2426                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
2427                             maps_to_bp = true;
2428                         }
2429                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
2430                             maps_to_cc = true;
2431                         }
2432                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
2433                             maps_to_mf = true;
2434                         }
2435                     }
2436                     if ( maps_to_bp ) {
2437                         ++biological_process_counter;
2438                     }
2439                     if ( maps_to_cc ) {
2440                         ++cellular_component_counter;
2441                     }
2442                     if ( maps_to_mf ) {
2443                         ++molecular_function_counter;
2444                     }
2445                     if ( maps_to_bp || maps_to_mf ) {
2446                         ++pfams_with_mappings_to_bp_or_mf_counter;
2447                     }
2448                     else {
2449                         ++pfams_without_mappings_to_bp_or_mf_counter;
2450                     }
2451                 }
2452                 else {
2453                     ++pfams_without_mappings_to_bp_or_mf_counter;
2454                     ++pfams_without_mappings_counter;
2455                     summary_writer.write( pfam );
2456                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2457                 }
2458             }
2459             all_pfams_encountered_writer.close();
2460             all_pfams_encountered_with_go_annotation_writer.close();
2461             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
2462                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
2463             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
2464                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
2465                     + "\"" );
2466             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
2467                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
2468                     + encountered_pfams_summary_file + "\"" );
2469             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
2470                     + all_pfams_encountered.size() );
2471             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
2472                     + pfams_without_mappings_counter + " ["
2473                     + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2474             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
2475                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2476                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2477             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
2478                     + pfams_with_mappings_counter + " ["
2479                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2480             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
2481                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2482                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2483             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
2484                     + biological_process_counter + " ["
2485                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2486             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
2487                     + molecular_function_counter + " ["
2488                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2489             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
2490                     + cellular_component_counter + " ["
2491                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2492             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2493             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
2494             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2495             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
2496                     + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2497             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2498             summary_writer.write( "# Pfams without mapping to proc. or func. : "
2499                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2500                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2501             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2502             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
2503                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2504             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2505             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
2506                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2507                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2508             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2509             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
2510                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2511             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2512             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
2513                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2514             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2515             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
2516                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2517             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2518             summary_writer.close();
2519         }
2520         catch ( final IOException e ) {
2521             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2522         }
2523     }
2524
2525     private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2526                                          final Map<GoId, GoTerm> go_id_to_term_map,
2527                                          final GoNameSpace go_namespace_limit,
2528                                          final Writer out,
2529                                          final String domain_0,
2530                                          final String domain_1,
2531                                          final String prefix_for_html,
2532                                          final String character_separator_for_non_html_output,
2533                                          final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
2534                                          final Set<GoId> all_go_ids ) throws IOException {
2535         boolean any_go_annotation_present = false;
2536         boolean first_has_no_go = false;
2537         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2538         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2539             domain_count = 1;
2540         }
2541         // The following has a difficult to understand logic.
2542         for( int d = 0; d < domain_count; ++d ) {
2543             List<GoId> go_ids = null;
2544             boolean go_annotation_present = false;
2545             if ( d == 0 ) {
2546                 if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
2547                     go_annotation_present = true;
2548                     any_go_annotation_present = true;
2549                     go_ids = domain_id_to_go_ids_map.get( domain_0 );
2550                 }
2551                 else {
2552                     first_has_no_go = true;
2553                 }
2554             }
2555             else {
2556                 if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
2557                     go_annotation_present = true;
2558                     any_go_annotation_present = true;
2559                     go_ids = domain_id_to_go_ids_map.get( domain_1 );
2560                 }
2561             }
2562             if ( go_annotation_present ) {
2563                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2564                 for( final GoId go_id : go_ids ) {
2565                     out.write( "<tr>" );
2566                     if ( first ) {
2567                         first = false;
2568                         writeDomainIdsToHtml( out,
2569                                               domain_0,
2570                                               domain_1,
2571                                               prefix_for_html,
2572                                               domain_id_to_secondary_features_maps );
2573                     }
2574                     else {
2575                         out.write( "<td></td>" );
2576                     }
2577                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2578                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2579                     }
2580                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2581                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2582                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2583                         final String go_id_str = go_id.getId();
2584                         out.write( "<td>" );
2585                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2586                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2587                         out.write( "</td><td>" );
2588                         out.write( go_term.getName() );
2589                         if ( domain_count == 2 ) {
2590                             out.write( " (" + d + ")" );
2591                         }
2592                         out.write( "</td><td>" );
2593                         // out.write( top );
2594                         // out.write( "</td><td>" );
2595                         out.write( "[" );
2596                         out.write( go_term.getGoNameSpace().toShortString() );
2597                         out.write( "]" );
2598                         out.write( "</td>" );
2599                         if ( all_go_ids != null ) {
2600                             all_go_ids.add( go_id );
2601                         }
2602                     }
2603                     else {
2604                         out.write( "<td>" );
2605                         out.write( "</td><td>" );
2606                         out.write( "</td><td>" );
2607                         out.write( "</td><td>" );
2608                         out.write( "</td>" );
2609                     }
2610                     out.write( "</tr>" );
2611                     out.write( SurfacingConstants.NL );
2612                 }
2613             }
2614         } //  for( int d = 0; d < domain_count; ++d )
2615         if ( !any_go_annotation_present ) {
2616             out.write( "<tr>" );
2617             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2618             out.write( "<td>" );
2619             out.write( "</td><td>" );
2620             out.write( "</td><td>" );
2621             out.write( "</td><td>" );
2622             out.write( "</td>" );
2623             out.write( "</tr>" );
2624             out.write( SurfacingConstants.NL );
2625         }
2626     }
2627
2628     private static void writeDomainIdsToHtml( final Writer out,
2629                                               final String domain_0,
2630                                               final String domain_1,
2631                                               final String prefix_for_detailed_html,
2632                                               final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
2633             throws IOException {
2634         out.write( "<td>" );
2635         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2636             out.write( prefix_for_detailed_html );
2637             out.write( " " );
2638         }
2639         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2640         out.write( "</td>" );
2641     }
2642
2643     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2644                                                                  final String domain_0,
2645                                                                  final String domain_1 ) throws IOException {
2646         individual_files_writer.write( domain_0 );
2647         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2648         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2649             individual_files_writer.write( domain_1 );
2650             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2651         }
2652     }
2653
2654     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2655         try {
2656             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2657             for( final String pfam : pfams ) {
2658                 writer.write( pfam );
2659                 writer.write( ForesterUtil.LINE_SEPARATOR );
2660             }
2661             writer.close();
2662             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2663                     + "]" );
2664         }
2665         catch ( final IOException e ) {
2666             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2667         }
2668     }
2669
2670     private static void writeToNexus( final String outfile_name,
2671                                       final CharacterStateMatrix<BinaryStates> matrix,
2672                                       final Phylogeny phylogeny ) {
2673         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2674             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2675                     + "] to nexus" );
2676         }
2677         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2678         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2679         phylogenies.add( phylogeny );
2680         try {
2681             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2682             w.write( NexusConstants.NEXUS );
2683             w.write( ForesterUtil.LINE_SEPARATOR );
2684             my_matrix.writeNexusTaxaBlock( w );
2685             my_matrix.writeNexusBinaryChractersBlock( w );
2686             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2687             w.flush();
2688             w.close();
2689             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2690         }
2691         catch ( final IOException e ) {
2692             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2693         }
2694     }
2695
2696     private static void writeToNexus( final String outfile_name,
2697                                       final DomainParsimonyCalculator domain_parsimony,
2698                                       final Phylogeny phylogeny ) {
2699         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2700                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2701                       phylogeny );
2702         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2703                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2704                       phylogeny );
2705     }
2706
2707     final static class DomainComparator implements Comparator<Domain> {
2708
2709         final private boolean _ascending;
2710
2711         public DomainComparator( final boolean ascending ) {
2712             _ascending = ascending;
2713         }
2714
2715         @Override
2716         public final int compare( final Domain d0, final Domain d1 ) {
2717             if ( d0.getFrom() < d1.getFrom() ) {
2718                 return _ascending ? -1 : 1;
2719             }
2720             else if ( d0.getFrom() > d1.getFrom() ) {
2721                 return _ascending ? 1 : -1;
2722             }
2723             return 0;
2724         }
2725     }
2726 }