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             }
 455         }
 456         out.write( ForesterUtil.LINE_SEPARATOR );
 457         out.write( ForesterUtil.LINE_SEPARATOR );
 458         out.write( "OUTLIER SPECIES (Z 1.0)" );
 459         out.write( ForesterUtil.LINE_SEPARATOR );
 460         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 461                 .calculateMeanBasedStatisticsForAllSpecies();
 462         out.write( stats_for_all_species.asSummary() );
 463         out.write( ForesterUtil.LINE_SEPARATOR );
 464         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 465         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 466         out.write( ForesterUtil.LINE_SEPARATOR );
 467         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 468         final double population_mean = stats_for_all_species.arithmeticMean();
 469         for( final Species species : domain_lengths_table.getSpecies() ) {
 470             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 471             final double z = ( x - population_mean ) / population_sd;
 472             out.write( species + "\t" + z );
 473             out.write( ForesterUtil.LINE_SEPARATOR );
 474         }
 475         out.write( ForesterUtil.LINE_SEPARATOR );
 476         for( final Species species : domain_lengths_table.getSpecies() ) {
 477             final DescriptiveStatistics stats_for_species = domain_lengths_table
 478                     .calculateMeanBasedStatisticsForSpecies( species );
 479             final double x = stats_for_species.arithmeticMean();
 480             final double z = ( x - population_mean ) / population_sd;
 481             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 482                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 483                 out.write( ForesterUtil.LINE_SEPARATOR );
 484             }
 485         }
 486         out.close();
 487         System.gc();
 488     }
 489
 490     /**
 491      *
 492      * @param all_binary_domains_combination_lost_fitch
 493      * @param use_last_in_fitch_parsimony
 494      * @param consider_directedness_and_adjacency_for_bin_combinations
 495      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 496      * which were gained under unweighted (Fitch) parsimony.
 497      */
 498     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 499                                                  final boolean radomize_fitch_parsimony,
 500                                                  final String outfile_name,
 501                                                  final DomainParsimonyCalculator domain_parsimony,
 502                                                  final Phylogeny phylogeny,
 503                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
 504                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 505                                                  final GoNameSpace go_namespace_limit,
 506                                                  final String parameters_str,
 507                                                  final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
 508                                                  final SortedSet<String> positive_filter,
 509                                                  final boolean output_binary_domain_combinations_for_graphs,
 510                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 511                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 512                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 513                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 514                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 515                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
 516                                                  final Map<String, Integer> tax_code_to_id_map,
 517                                                  final boolean write_to_nexus,
 518                                                  final boolean use_last_in_fitch_parsimony ) {
 519         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 520         final String date_time = ForesterUtil.getCurrentDateTime();
 521         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 522         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 523         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 524         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 525         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 526         if ( write_to_nexus ) {
 527             writeToNexus( outfile_name, domain_parsimony, phylogeny );
 528         }
 529         // DOLLO DOMAINS
 530         // -------------
 531         Phylogeny local_phylogeny_l = phylogeny.copy();
 532         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 533             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 534         }
 535         else {
 536             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 537         }
 538         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 539                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 540         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 541                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 542         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 543                                                            CharacterStateMatrix.GainLossStates.GAIN,
 544                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 545                                                            sep,
 546                                                            ForesterUtil.LINE_SEPARATOR,
 547                                                            null );
 548         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 549                                                            CharacterStateMatrix.GainLossStates.LOSS,
 550                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 551                                                            sep,
 552                                                            ForesterUtil.LINE_SEPARATOR,
 553                                                            null );
 554         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 555                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 556         //HTML:
 557         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 558                                        go_id_to_term_map,
 559                                        go_namespace_limit,
 560                                        false,
 561                                        domain_parsimony.getGainLossMatrix(),
 562                                        CharacterStateMatrix.GainLossStates.GAIN,
 563                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 564                                        sep,
 565                                        ForesterUtil.LINE_SEPARATOR,
 566                                        "Dollo Parsimony | Gains | Domains",
 567                                        "+",
 568                                        domain_id_to_secondary_features_maps,
 569                                        all_pfams_encountered,
 570                                        all_pfams_gained_as_domains,
 571                                        "_dollo_gains_d",
 572                                        tax_code_to_id_map );
 573         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 574                                        go_id_to_term_map,
 575                                        go_namespace_limit,
 576                                        false,
 577                                        domain_parsimony.getGainLossMatrix(),
 578                                        CharacterStateMatrix.GainLossStates.LOSS,
 579                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 580                                        sep,
 581                                        ForesterUtil.LINE_SEPARATOR,
 582                                        "Dollo Parsimony | Losses | Domains",
 583                                        "-",
 584                                        domain_id_to_secondary_features_maps,
 585                                        all_pfams_encountered,
 586                                        all_pfams_lost_as_domains,
 587                                        "_dollo_losses_d",
 588                                        tax_code_to_id_map );
 589         //        writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 590         //                                       go_id_to_term_map,
 591         //                                       go_namespace_limit,
 592         //                                       false,
 593         //                                       domain_parsimony.getGainLossMatrix(),
 594         //                                       null,
 595         //                                       outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 596         //                                       sep,
 597         //                                       ForesterUtil.LINE_SEPARATOR,
 598         //                                       "Dollo Parsimony | Present | Domains",
 599         //                                       "",
 600         //                                       domain_id_to_secondary_features_maps,
 601         //                                       all_pfams_encountered,
 602         //                                       null,
 603         //                                       "_dollo_present_d",
 604         //                                       tax_code_to_id_map );
 605         preparePhylogeny( local_phylogeny_l,
 606                           domain_parsimony,
 607                           date_time,
 608                           "Dollo parsimony on domain presence/absence",
 609                           "dollo_on_domains_" + outfile_name,
 610                           parameters_str );
 611         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 612                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 613         try {
 614             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 615             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 616         }
 617         catch ( final IOException e ) {
 618             e.printStackTrace();
 619             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 620         }
 621         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 622             // FITCH DOMAIN COMBINATIONS
 623             // -------------------------
 624             local_phylogeny_l = phylogeny.copy();
 625             String randomization = "no";
 626             if ( radomize_fitch_parsimony ) {
 627                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 628                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 629             }
 630             else {
 631                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
 632             }
 633             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 634                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 635             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 636                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 637             SurfacingUtil
 638                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 639                                                           CharacterStateMatrix.GainLossStates.GAIN,
 640                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 641                                                           sep,
 642                                                           ForesterUtil.LINE_SEPARATOR,
 643                                                           null );
 644             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 645                                                                CharacterStateMatrix.GainLossStates.LOSS,
 646                                                                outfile_name
 647                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 648                                                                sep,
 649                                                                ForesterUtil.LINE_SEPARATOR,
 650                                                                null );
 651             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 652                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 653             if ( all_binary_domains_combination_gained_fitch != null ) {
 654                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 655                                                                                     dc_type,
 656                                                                                     all_binary_domains_combination_gained_fitch,
 657                                                                                     true );
 658             }
 659             if ( all_binary_domains_combination_lost_fitch != null ) {
 660                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 661                                                                                     dc_type,
 662                                                                                     all_binary_domains_combination_lost_fitch,
 663                                                                                     false );
 664             }
 665             if ( output_binary_domain_combinations_for_graphs ) {
 666                 SurfacingUtil
 667                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 668                                                                                                            .getGainLossMatrix(),
 669                                                                                                    null,
 670                                                                                                    outfile_name
 671                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 672                                                                                                    sep,
 673                                                                                                    ForesterUtil.LINE_SEPARATOR,
 674                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 675             }
 676             // HTML:
 677             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 678                                            go_id_to_term_map,
 679                                            go_namespace_limit,
 680                                            true,
 681                                            domain_parsimony.getGainLossMatrix(),
 682                                            CharacterStateMatrix.GainLossStates.GAIN,
 683                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 684                                            sep,
 685                                            ForesterUtil.LINE_SEPARATOR,
 686                                            "Fitch Parsimony | Gains | Domain Combinations",
 687                                            "+",
 688                                            null,
 689                                            all_pfams_encountered,
 690                                            all_pfams_gained_as_dom_combinations,
 691                                            "_fitch_gains_dc",
 692                                            tax_code_to_id_map );
 693             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 694                                            go_id_to_term_map,
 695                                            go_namespace_limit,
 696                                            true,
 697                                            domain_parsimony.getGainLossMatrix(),
 698                                            CharacterStateMatrix.GainLossStates.LOSS,
 699                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 700                                            sep,
 701                                            ForesterUtil.LINE_SEPARATOR,
 702                                            "Fitch Parsimony | Losses | Domain Combinations",
 703                                            "-",
 704                                            null,
 705                                            all_pfams_encountered,
 706                                            all_pfams_lost_as_dom_combinations,
 707                                            "_fitch_losses_dc",
 708                                            tax_code_to_id_map );
 709             //            writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 710             //                                           go_id_to_term_map,
 711             //                                           go_namespace_limit,
 712             //                                           true,
 713             //                                           domain_parsimony.getGainLossMatrix(),
 714             //                                           null,
 715             //                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 716             //                                           sep,
 717             //                                           ForesterUtil.LINE_SEPARATOR,
 718             //                                           "Fitch Parsimony | Present | Domain Combinations",
 719             //                                           "",
 720             //                                           null,
 721             //                                           all_pfams_encountered,
 722             //                                           null,
 723             //                                           "_fitch_present_dc",
 724             //                                           tax_code_to_id_map );
 725             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 726                                             go_id_to_term_map,
 727                                             outfile_name,
 728                                             all_pfams_encountered );
 729             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 730             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 731             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 732                               all_pfams_gained_as_dom_combinations );
 733             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 734             preparePhylogeny( local_phylogeny_l,
 735                               domain_parsimony,
 736                               date_time,
 737                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 738                                       + randomization,
 739                               "fitch_on_binary_domain_combinations_" + outfile_name,
 740                               parameters_str );
 741             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 742                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 743             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 744                                                         outfile_name
 745                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 746                                                         outfile_name
 747                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 748                                                         outfile_name
 749                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 750                                                         outfile_name
 751                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
 752                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
 753                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
 754                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
 755                                                         protein_length_stats_by_dc,
 756                                                         domain_number_stats_by_dc,
 757                                                         domain_length_stats_by_domain );
 758         }
 759     }
 760
 761     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 762                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 763                                                                      final Phylogeny phylogeny,
 764                                                                      final String parameters_str,
 765                                                                      final Map<Species, MappingResults> mapping_results_map,
 766                                                                      final boolean use_last_in_fitch_parsimony ) {
 767         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 768         final String date_time = ForesterUtil.getCurrentDateTime();
 769         System.out.println();
 770         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 771                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 772                       phylogeny );
 773         Phylogeny local_phylogeny_copy = phylogeny.copy();
 774         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 775         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 776                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 777         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 778                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 779         SurfacingUtil
 780                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 781                                                       CharacterStateMatrix.GainLossStates.GAIN,
 782                                                       outfile_name
 783                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 784                                                       sep,
 785                                                       ForesterUtil.LINE_SEPARATOR,
 786                                                       null );
 787         SurfacingUtil
 788                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 789                                                       CharacterStateMatrix.GainLossStates.LOSS,
 790                                                       outfile_name
 791                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 792                                                       sep,
 793                                                       ForesterUtil.LINE_SEPARATOR,
 794                                                       null );
 795         SurfacingUtil
 796                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 797                                                       null,
 798                                                       outfile_name
 799                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 800                                                       sep,
 801                                                       ForesterUtil.LINE_SEPARATOR,
 802                                                       null );
 803         preparePhylogeny( local_phylogeny_copy,
 804                           secondary_features_parsimony,
 805                           date_time,
 806                           "Dollo parsimony on secondary feature presence/absence",
 807                           "dollo_on_secondary_features_" + outfile_name,
 808                           parameters_str );
 809         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 810                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 811         // FITCH DOMAIN COMBINATIONS
 812         // -------------------------
 813         local_phylogeny_copy = phylogeny.copy();
 814         final String randomization = "no";
 815         secondary_features_parsimony
 816                 .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
 817         preparePhylogeny( local_phylogeny_copy,
 818                           secondary_features_parsimony,
 819                           date_time,
 820                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
 821                                   + randomization,
 822                           "fitch_on_binary_domain_combinations_" + outfile_name,
 823                           parameters_str );
 824         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 825                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
 826         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
 827                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
 828                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
 829                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
 830                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
 831                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
 832                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
 833     }
 834
 835     public static void extractProteinNames( final List<Protein> proteins,
 836                                             final List<String> query_domain_ids_nc_order,
 837                                             final Writer out,
 838                                             final String separator,
 839                                             final String limit_to_species ) throws IOException {
 840         for( final Protein protein : proteins ) {
 841             if ( ForesterUtil.isEmpty( limit_to_species )
 842                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 843                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 844                     out.write( protein.getSpecies().getSpeciesId() );
 845                     out.write( separator );
 846                     out.write( protein.getProteinId().getId() );
 847                     out.write( separator );
 848                     out.write( "[" );
 849                     final Set<String> visited_domain_ids = new HashSet<String>();
 850                     boolean first = true;
 851                     for( final Domain domain : protein.getProteinDomains() ) {
 852                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 853                             visited_domain_ids.add( domain.getDomainId() );
 854                             if ( first ) {
 855                                 first = false;
 856                             }
 857                             else {
 858                                 out.write( " " );
 859                             }
 860                             out.write( domain.getDomainId() );
 861                             out.write( " {" );
 862                             out.write( "" + domain.getTotalCount() );
 863                             out.write( "}" );
 864                         }
 865                     }
 866                     out.write( "]" );
 867                     out.write( separator );
 868                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 869                             .equals( SurfacingConstants.NONE ) ) ) {
 870                         out.write( protein.getDescription() );
 871                     }
 872                     out.write( separator );
 873                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 874                             .equals( SurfacingConstants.NONE ) ) ) {
 875                         out.write( protein.getAccession() );
 876                     }
 877                     out.write( SurfacingConstants.NL );
 878                 }
 879             }
 880         }
 881         out.flush();
 882     }
 883
 884     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
 885                                             final String domain_id,
 886                                             final Writer out,
 887                                             final String separator,
 888                                             final String limit_to_species,
 889                                             final double domain_e_cutoff ) throws IOException {
 890         System.out.println( "Per domain E-value: " + domain_e_cutoff );
 891         for( final Species species : protein_lists_per_species.keySet() ) {
 892             System.out.println( species + ":" );
 893             for( final Protein protein : protein_lists_per_species.get( species ) ) {
 894                 if ( ForesterUtil.isEmpty( limit_to_species )
 895                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 896                     final List<Domain> domains = protein.getProteinDomains( domain_id );
 897                     if ( domains.size() > 0 ) {
 898                         out.write( protein.getSpecies().getSpeciesId() );
 899                         out.write( separator );
 900                         out.write( protein.getProteinId().getId() );
 901                         out.write( separator );
 902                         out.write( domain_id.toString() );
 903                         out.write( separator );
 904                         int prev_to = -1;
 905                         for( final Domain domain : domains ) {
 906                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 907                                 out.write( "/" );
 908                                 out.write( domain.getFrom() + "-" + domain.getTo() );
 909                                 if ( prev_to >= 0 ) {
 910                                     final int l = domain.getFrom() - prev_to;
 911                                     System.out.println( l );
 912                                 }
 913                                 prev_to = domain.getTo();
 914                             }
 915                         }
 916                         out.write( "/" );
 917                         out.write( separator );
 918                         final List<Domain> domain_list = new ArrayList<Domain>();
 919                         for( final Domain domain : protein.getProteinDomains() ) {
 920                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 921                                 domain_list.add( domain );
 922                             }
 923                         }
 924                         final Domain domain_ary[] = new Domain[ domain_list.size() ];
 925                         for( int i = 0; i < domain_list.size(); ++i ) {
 926                             domain_ary[ i ] = domain_list.get( i );
 927                         }
 928                         Arrays.sort( domain_ary, new DomainComparator( true ) );
 929                         out.write( "{" );
 930                         boolean first = true;
 931                         for( final Domain domain : domain_ary ) {
 932                             if ( first ) {
 933                                 first = false;
 934                             }
 935                             else {
 936                                 out.write( "," );
 937                             }
 938                             out.write( domain.getDomainId().toString() );
 939                             out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
 940                             out.write( ":" + domain.getPerDomainEvalue() );
 941                         }
 942                         out.write( "}" );
 943                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 944                                 .equals( SurfacingConstants.NONE ) ) ) {
 945                             out.write( protein.getDescription() );
 946                         }
 947                         out.write( separator );
 948                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 949                                 .equals( SurfacingConstants.NONE ) ) ) {
 950                             out.write( protein.getAccession() );
 951                         }
 952                         out.write( SurfacingConstants.NL );
 953                     }
 954                 }
 955             }
 956         }
 957         out.flush();
 958     }
 959
 960     public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
 961         final SortedSet<String> all_domains_ids = new TreeSet<String>();
 962         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 963             final Set<String> all_domains = gwcd.getAllDomainIds();
 964             //    for( final Domain domain : all_domains ) {
 965             all_domains_ids.addAll( all_domains );
 966             //    }
 967         }
 968         return all_domains_ids;
 969     }
 970
 971     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
 972         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
 973         for( final Protein protein_domain_collection : protein_domain_collections ) {
 974             for( final Object name : protein_domain_collection.getProteinDomains() ) {
 975                 final BasicDomain protein_domain = ( BasicDomain ) name;
 976                 final String id = protein_domain.getDomainId();
 977                 if ( map.containsKey( id ) ) {
 978                     map.put( id, map.get( id ) + 1 );
 979                 }
 980                 else {
 981                     map.put( id, 1 );
 982                 }
 983             }
 984         }
 985         return map;
 986     }
 987
 988     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
 989         final PhylogenyNodeIterator it = p.iteratorPostorder();
 990         int c = 0;
 991         while ( it.hasNext() ) {
 992             final PhylogenyNode n = it.next();
 993             if ( ForesterUtil.isEmpty( n.getName() )
 994                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
 995                             .getScientificName() ) )
 996                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
 997                             .getCommonName() ) ) ) {
 998                 if ( n.getParent() != null ) {
 999                     names.append( " " );
1000                     names.append( n.getParent().getName() );
1001                 }
1002                 final List l = n.getAllExternalDescendants();
1003                 for( final Object object : l ) {
1004                     System.out.println( l.toString() );
1005                 }
1006                 ++c;
1007             }
1008         }
1009         return c;
1010     }
1011
1012     /**
1013      * Returns true is Domain domain falls in an uninterrupted stretch of
1014      * covered positions.
1015      *
1016      * @param domain
1017      * @param covered_positions
1018      * @return
1019      */
1020     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1021         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1022             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1023                 return false;
1024             }
1025         }
1026         return true;
1027     }
1028
1029     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
1030                                                           final SortedMap<String, Integer> domain_architecuture_counts,
1031                                                           final int min_count,
1032                                                           final File da_counts_outfile,
1033                                                           final File unique_da_outfile ) {
1034         checkForOutputFileWriteability( da_counts_outfile );
1035         checkForOutputFileWriteability( unique_da_outfile );
1036         try {
1037             final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
1038             final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
1039             final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
1040             while ( it.hasNext() ) {
1041                 final Map.Entry<String, Integer> e = it.next();
1042                 final String da = e.getKey();
1043                 final int count = e.getValue();
1044                 if ( count >= min_count ) {
1045                     da_counts_out.write( da );
1046                     da_counts_out.write( "\t" );
1047                     da_counts_out.write( String.valueOf( count ) );
1048                     da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
1049                 }
1050                 if ( count == 1 ) {
1051                     final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
1052                     while ( it2.hasNext() ) {
1053                         final Map.Entry<String, Set<String>> e2 = it2.next();
1054                         final String genome = e2.getKey();
1055                         final Set<String> das = e2.getValue();
1056                         if ( das.contains( da ) ) {
1057                             unique_da_out.write( genome );
1058                             unique_da_out.write( "\t" );
1059                             unique_da_out.write( da );
1060                             unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
1061                         }
1062                     }
1063                 }
1064             }
1065             unique_da_out.close();
1066             da_counts_out.close();
1067         }
1068         catch ( final IOException e ) {
1069             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1070         }
1071         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
1072         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
1073         //
1074     }
1075
1076     public static void preparePhylogeny( final Phylogeny p,
1077                                          final DomainParsimonyCalculator domain_parsimony,
1078                                          final String date_time,
1079                                          final String method,
1080                                          final String name,
1081                                          final String parameters_str ) {
1082         domain_parsimony.decoratePhylogenyWithDomains( p );
1083         final StringBuilder desc = new StringBuilder();
1084         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1085         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1086         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1087         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1088         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1089         desc.append( "[Parameters: " + parameters_str + "]" );
1090         p.setName( name );
1091         p.setDescription( desc.toString() );
1092         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1093         p.setRerootable( false );
1094         p.setRooted( true );
1095     }
1096
1097     /*
1098      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1099      *
1100      *
1101      */
1102     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1103                                                             final String protein_id,
1104                                                             final String separator ) {
1105         final StringBuffer sb = new StringBuffer();
1106         if ( protein.getSpecies() == null ) {
1107             throw new IllegalArgumentException( "species must not be null" );
1108         }
1109         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1110             throw new IllegalArgumentException( "species id must not be empty" );
1111         }
1112         final List<Domain> domains = protein.getProteinDomains();
1113         if ( domains.size() > 1 ) {
1114             final Map<String, Integer> counts = new HashMap<String, Integer>();
1115             for( final Domain domain : domains ) {
1116                 final String id = domain.getDomainId();
1117                 if ( counts.containsKey( id ) ) {
1118                     counts.put( id, counts.get( id ) + 1 );
1119                 }
1120                 else {
1121                     counts.put( id, 1 );
1122                 }
1123             }
1124             final Set<String> dcs = new HashSet<String>();
1125             for( int i = 1; i < domains.size(); ++i ) {
1126                 for( int j = 0; j < i; ++j ) {
1127                     Domain domain_n = domains.get( i );
1128                     Domain domain_c = domains.get( j );
1129                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1130                         domain_n = domains.get( j );
1131                         domain_c = domains.get( i );
1132                     }
1133                     final String dc = domain_n.getDomainId() + domain_c.getDomainId();
1134                     if ( !dcs.contains( dc ) ) {
1135                         dcs.add( dc );
1136                         sb.append( protein.getSpecies() );
1137                         sb.append( separator );
1138                         sb.append( protein_id );
1139                         sb.append( separator );
1140                         sb.append( domain_n.getDomainId() );
1141                         sb.append( separator );
1142                         sb.append( domain_c.getDomainId() );
1143                         sb.append( separator );
1144                         sb.append( domain_n.getPerDomainEvalue() );
1145                         sb.append( separator );
1146                         sb.append( domain_c.getPerDomainEvalue() );
1147                         sb.append( separator );
1148                         sb.append( counts.get( domain_n.getDomainId() ) );
1149                         sb.append( separator );
1150                         sb.append( counts.get( domain_c.getDomainId() ) );
1151                         sb.append( ForesterUtil.LINE_SEPARATOR );
1152                     }
1153                 }
1154             }
1155         }
1156         else if ( domains.size() == 1 ) {
1157             sb.append( protein.getSpecies() );
1158             sb.append( separator );
1159             sb.append( protein_id );
1160             sb.append( separator );
1161             sb.append( domains.get( 0 ).getDomainId() );
1162             sb.append( separator );
1163             sb.append( separator );
1164             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1165             sb.append( separator );
1166             sb.append( separator );
1167             sb.append( 1 );
1168             sb.append( separator );
1169             sb.append( ForesterUtil.LINE_SEPARATOR );
1170         }
1171         else {
1172             sb.append( protein.getSpecies() );
1173             sb.append( separator );
1174             sb.append( protein_id );
1175             sb.append( separator );
1176             sb.append( separator );
1177             sb.append( separator );
1178             sb.append( separator );
1179             sb.append( separator );
1180             sb.append( separator );
1181             sb.append( ForesterUtil.LINE_SEPARATOR );
1182         }
1183         return sb;
1184     }
1185
1186     /**
1187      *
1188      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1189      * domain with 0.3 is ignored
1190      *
1191      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1192      *
1193      *
1194      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1195      * ignored
1196      *
1197      * @param max_allowed_overlap
1198      *            maximal allowed overlap (inclusive) to be still considered not
1199      *            overlapping (zero or negative value to allow any overlap)
1200      * @param remove_engulfed_domains
1201      *            to remove domains which are completely engulfed by coverage of
1202      *            domains with better support
1203      * @param protein
1204      * @return
1205      */
1206     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1207                                                     final boolean remove_engulfed_domains,
1208                                                     final Protein protein ) {
1209         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1210                 .getSpeciesId(), protein.getLength() );
1211         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1212         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1213         for( final Domain domain : sorted ) {
1214             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1215                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1216                 final int covered_positions_size = covered_positions.size();
1217                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1218                     covered_positions.add( false );
1219                 }
1220                 final int new_covered_positions_size = covered_positions.size();
1221                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1222                     if ( i < new_covered_positions_size ) {
1223                         covered_positions.set( i, true );
1224                     }
1225                     else {
1226                         covered_positions.add( true );
1227                     }
1228                 }
1229                 pruned_protein.addProteinDomain( domain );
1230             }
1231         }
1232         return pruned_protein;
1233     }
1234
1235     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1236         final List<Domain> domains = new ArrayList<Domain>();
1237         for( final Domain d : protein.getProteinDomains() ) {
1238             domains.add( d );
1239         }
1240         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1241         return domains;
1242     }
1243
1244     public static int storeDomainArchitectures( final String genome,
1245                                                 final SortedMap<String, Set<String>> domain_architecutures,
1246                                                 final List<Protein> protein_list,
1247                                                 final Map<String, Integer> distinct_domain_architecuture_counts ) {
1248         final Set<String> da = new HashSet<String>();
1249         domain_architecutures.put( genome, da );
1250         for( final Protein protein : protein_list ) {
1251             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
1252             if ( !da.contains( da_str ) ) {
1253                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
1254                     distinct_domain_architecuture_counts.put( da_str, 1 );
1255                 }
1256                 else {
1257                     distinct_domain_architecuture_counts.put( da_str,
1258                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
1259                 }
1260                 da.add( da_str );
1261             }
1262         }
1263         return da.size();
1264     }
1265
1266     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1267                                                             final boolean get_gains,
1268                                                             final String outdir,
1269                                                             final String suffix_for_filename ) throws IOException {
1270         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1271         if ( !get_gains ) {
1272             state = CharacterStateMatrix.GainLossStates.LOSS;
1273         }
1274         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1275                                                                   false,
1276                                                                   state,
1277                                                                   outdir );
1278         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1279             final PhylogenyNode node = it.next();
1280             if ( !node.isExternal() ) {
1281                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1282                 if ( domains.size() > 0 ) {
1283                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1284                             + node.getName() + suffix_for_filename );
1285                     for( final String domain : domains ) {
1286                         writer.write( domain );
1287                         writer.write( ForesterUtil.LINE_SEPARATOR );
1288                     }
1289                     writer.close();
1290                 }
1291             }
1292         }
1293     }
1294
1295     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1296                                                                           final File output_dir,
1297                                                                           final GenomeWideCombinableDomains gwcd,
1298                                                                           final int i,
1299                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1300         File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
1301                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1302         if ( output_dir != null ) {
1303             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1304         }
1305         checkForOutputFileWriteability( dc_outfile_dot );
1306         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1307         try {
1308             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1309             for( final BinaryDomainCombination bdc : binary_combinations ) {
1310                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1311                         .toString() );
1312                 out_dot.write( SurfacingConstants.NL );
1313             }
1314             out_dot.close();
1315         }
1316         catch ( final IOException e ) {
1317             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1318         }
1319         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1320                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1321                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1322     }
1323
1324     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1325                                                             final CharacterStateMatrix.GainLossStates state,
1326                                                             final String filename,
1327                                                             final String indentifier_characters_separator,
1328                                                             final String character_separator,
1329                                                             final Map<String, String> descriptions ) {
1330         final File outfile = new File( filename );
1331         checkForOutputFileWriteability( outfile );
1332         final SortedSet<String> sorted_ids = new TreeSet<String>();
1333         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1334             sorted_ids.add( matrix.getIdentifier( i ) );
1335         }
1336         try {
1337             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1338             for( final String id : sorted_ids ) {
1339                 out.write( indentifier_characters_separator );
1340                 out.write( "#" + id );
1341                 out.write( indentifier_characters_separator );
1342                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1343                     // Not nice:
1344                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1345                     if ( ( matrix.getState( id, c ) == state )
1346                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1347                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1348                         out.write( matrix.getCharacter( c ) );
1349                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1350                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1351                             out.write( "\t" );
1352                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1353                         }
1354                         out.write( character_separator );
1355                     }
1356                 }
1357             }
1358             out.flush();
1359             out.close();
1360         }
1361         catch ( final IOException e ) {
1362             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1363         }
1364         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1365     }
1366
1367     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1368                                                                                                  final CharacterStateMatrix.GainLossStates state,
1369                                                                                                  final String filename,
1370                                                                                                  final String indentifier_characters_separator,
1371                                                                                                  final String character_separator,
1372                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1373         final File outfile = new File( filename );
1374         checkForOutputFileWriteability( outfile );
1375         final SortedSet<String> sorted_ids = new TreeSet<String>();
1376         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1377             sorted_ids.add( matrix.getIdentifier( i ) );
1378         }
1379         try {
1380             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1381             for( final String id : sorted_ids ) {
1382                 out.write( indentifier_characters_separator );
1383                 out.write( "#" + id );
1384                 out.write( indentifier_characters_separator );
1385                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1386                     // Not nice:
1387                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1388                     if ( ( matrix.getState( id, c ) == state )
1389                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1390                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1391                         BinaryDomainCombination bdc = null;
1392                         try {
1393                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1394                         }
1395                         catch ( final Exception e ) {
1396                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1397                         }
1398                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1399                         out.write( character_separator );
1400                     }
1401                 }
1402             }
1403             out.flush();
1404             out.close();
1405         }
1406         catch ( final IOException e ) {
1407             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1408         }
1409         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1410     }
1411
1412     public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
1413                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1414                                                       final GoNameSpace go_namespace_limit,
1415                                                       final boolean domain_combinations,
1416                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1417                                                       final CharacterStateMatrix.GainLossStates state,
1418                                                       final String filename,
1419                                                       final String indentifier_characters_separator,
1420                                                       final String character_separator,
1421                                                       final String title_for_html,
1422                                                       final String prefix_for_html,
1423                                                       final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
1424                                                       final SortedSet<String> all_pfams_encountered,
1425                                                       final SortedSet<String> pfams_gained_or_lost,
1426                                                       final String suffix_for_per_node_events_file,
1427                                                       final Map<String, Integer> tax_code_to_id_map ) {
1428         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1429             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1430         }
1431         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1432             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1433         }
1434         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1435             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1436         }
1437         final File outfile = new File( filename );
1438         checkForOutputFileWriteability( outfile );
1439         final SortedSet<String> sorted_ids = new TreeSet<String>();
1440         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1441             sorted_ids.add( matrix.getIdentifier( i ) );
1442         }
1443         try {
1444             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1445             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1446                                                                                                                 domain_combinations,
1447                                                                                                                 state,
1448                                                                                                                 filename );
1449             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1450             File per_node_go_mapped_domain_gain_loss_outfile = null;
1451             int per_node_counter = 0;
1452             out.write( "<html>" );
1453             out.write( SurfacingConstants.NL );
1454             addHtmlHead( out, title_for_html );
1455             out.write( SurfacingConstants.NL );
1456             out.write( "<body>" );
1457             out.write( SurfacingConstants.NL );
1458             out.write( "<h1>" );
1459             out.write( SurfacingConstants.NL );
1460             out.write( title_for_html );
1461             out.write( SurfacingConstants.NL );
1462             out.write( "</h1>" );
1463             out.write( SurfacingConstants.NL );
1464             out.write( "<table>" );
1465             out.write( SurfacingConstants.NL );
1466             for( final String id : sorted_ids ) {
1467                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1468                 if ( matcher.matches() ) {
1469                     continue;
1470                 }
1471                 out.write( "<tr>" );
1472                 out.write( "<td>" );
1473                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1474                 out.write( "</td>" );
1475                 out.write( "</tr>" );
1476                 out.write( SurfacingConstants.NL );
1477             }
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( SurfacingConstants.NL );
1486                 out.write( "<h2>" );
1487                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1488                 writeTaxonomyLinks( out, id, tax_code_to_id_map );
1489                 out.write( "</h2>" );
1490                 out.write( SurfacingConstants.NL );
1491                 out.write( "<table>" );
1492                 out.write( SurfacingConstants.NL );
1493                 out.write( "<tr>" );
1494                 out.write( "<td><b>" );
1495                 out.write( "Pfam domain(s)" );
1496                 out.write( "</b></td><td><b>" );
1497                 out.write( "GO term acc" );
1498                 out.write( "</b></td><td><b>" );
1499                 out.write( "GO term" );
1500                 out.write( "</b></td><td><b>" );
1501                 out.write( "GO namespace" );
1502                 out.write( "</b></td>" );
1503                 out.write( "</tr>" );
1504                 out.write( SurfacingConstants.NL );
1505                 out.write( "</tr>" );
1506                 out.write( SurfacingConstants.NL );
1507                 per_node_counter = 0;
1508                 if ( matrix.getNumberOfCharacters() > 0 ) {
1509                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1510                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1511                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1512                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1513                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1514                 }
1515                 else {
1516                     per_node_go_mapped_domain_gain_loss_outfile = null;
1517                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1518                 }
1519                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1520                     // Not nice:
1521                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1522                     if ( ( matrix.getState( id, c ) == state )
1523                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1524                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1525                         final String character = matrix.getCharacter( c );
1526                         String domain_0 = "";
1527                         String domain_1 = "";
1528                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1529                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1530                             if ( s.length != 2 ) {
1531                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1532                                         + character + "]" );
1533                             }
1534                             domain_0 = s[ 0 ];
1535                             domain_1 = s[ 1 ];
1536                         }
1537                         else {
1538                             domain_0 = character;
1539                         }
1540                         writeDomainData( domain_id_to_go_ids_map,
1541                                          go_id_to_term_map,
1542                                          go_namespace_limit,
1543                                          out,
1544                                          domain_0,
1545                                          domain_1,
1546                                          prefix_for_html,
1547                                          character_separator,
1548                                          domain_id_to_secondary_features_maps,
1549                                          null );
1550                         all_pfams_encountered.add( domain_0 );
1551                         if ( pfams_gained_or_lost != null ) {
1552                             pfams_gained_or_lost.add( domain_0 );
1553                         }
1554                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1555                             all_pfams_encountered.add( domain_1 );
1556                             if ( pfams_gained_or_lost != null ) {
1557                                 pfams_gained_or_lost.add( domain_1 );
1558                             }
1559                         }
1560                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1561                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1562                                                                      domain_0,
1563                                                                      domain_1 );
1564                             per_node_counter++;
1565                         }
1566                     }
1567                 }
1568                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1569                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1570                     if ( per_node_counter < 1 ) {
1571                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1572                     }
1573                     per_node_counter = 0;
1574                 }
1575                 out.write( "</table>" );
1576                 out.write( SurfacingConstants.NL );
1577                 out.write( "<hr>" );
1578                 out.write( SurfacingConstants.NL );
1579             } // for( final String id : sorted_ids ) {
1580             out.write( "</body>" );
1581             out.write( SurfacingConstants.NL );
1582             out.write( "</html>" );
1583             out.write( SurfacingConstants.NL );
1584             out.flush();
1585             out.close();
1586         }
1587         catch ( final IOException e ) {
1588             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1589         }
1590         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1591     }
1592
1593     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1594                                                           final File output_dir,
1595                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1596                                                           final GenomeWideCombinableDomains gwcd,
1597                                                           final int i,
1598                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1599         File dc_outfile = new File( input_file_properties[ i ][ 1 ]
1600                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1601         if ( output_dir != null ) {
1602             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1603         }
1604         checkForOutputFileWriteability( dc_outfile );
1605         try {
1606             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1607             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1608             out.close();
1609         }
1610         catch ( final IOException e ) {
1611             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1612         }
1613         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1614         try {
1615             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
1616             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1617             if ( stats.getN() < 2 ) {
1618                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1619             }
1620             else {
1621                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1622                         .sampleStandardDeviation() ) + "\t" );
1623             }
1624             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1625             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1626             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1627             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1628             final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
1629             for( final String mpd : mpds ) {
1630                 per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
1631             }
1632             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1633         }
1634         catch ( final IOException e ) {
1635             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1636         }
1637         if ( input_file_properties[ i ].length == 3 ) {
1638             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1639                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1640                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1641         }
1642         else {
1643             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1644                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1645                     + dc_outfile + "\"" );
1646         }
1647     }
1648
1649     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
1650                                                                        final StringBuilder html_title,
1651                                                                        final Writer single_writer,
1652                                                                        Map<Character, Writer> split_writers,
1653                                                                        final SortedSet<DomainSimilarity> similarities,
1654                                                                        final boolean treat_as_binary,
1655                                                                        final List<Species> species_order,
1656                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
1657                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
1658                                                                        final boolean verbose,
1659                                                                        final Map<String, Integer> tax_code_to_id_map,
1660                                                                        final boolean print_some_stats )
1661             throws IOException {
1662         DescriptiveStatistics stats = null;
1663         AsciiHistogram histo = null;
1664         if ( print_some_stats ) {
1665             stats = new BasicDescriptiveStatistics();
1666             final String histogram_title = "score mean distribution:";
1667             for( final DomainSimilarity similarity : similarities ) {
1668                 stats.addValue( similarity.getMeanSimilarityScore() );
1669             }
1670             try {
1671                 if ( stats.getMin() < stats.getMax() ) {
1672                     histo = new AsciiHistogram( stats, histogram_title );
1673                 }
1674             }
1675             catch ( final Exception e ) {
1676                 histo = null;
1677             }
1678         }
1679         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
1680             split_writers = new HashMap<Character, Writer>();
1681             split_writers.put( '_', single_writer );
1682         }
1683         switch ( print_option ) {
1684             case SIMPLE_TAB_DELIMITED:
1685                 break;
1686             case HTML:
1687                 for( final Character key : split_writers.keySet() ) {
1688                     final Writer w = split_writers.get( key );
1689                     w.write( "<html>" );
1690                     w.write( SurfacingConstants.NL );
1691                     if ( key != '_' ) {
1692                         addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
1693                     }
1694                     else {
1695                         addHtmlHead( w, "DC analysis (" + html_title + ")" );
1696                     }
1697                     w.write( SurfacingConstants.NL );
1698                     w.write( "<body>" );
1699                     w.write( SurfacingConstants.NL );
1700                     w.write( html_desc.toString() );
1701                     w.write( SurfacingConstants.NL );
1702                     if ( print_some_stats ) {
1703                         printSomeStats( stats, histo, w );
1704                     }
1705                     w.write( "<hr>" );
1706                     w.write( SurfacingConstants.NL );
1707                     w.write( "<br>" );
1708                     w.write( SurfacingConstants.NL );
1709                     w.write( "<table>" );
1710                     w.write( SurfacingConstants.NL );
1711                     w.write( "<tr><td><b>Domains:</b></td></tr>" );
1712                     w.write( SurfacingConstants.NL );
1713                 }
1714                 break;
1715         }
1716         //
1717         for( final DomainSimilarity similarity : similarities ) {
1718             if ( ( species_order != null ) && !species_order.isEmpty() ) {
1719                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
1720             }
1721             if ( single_writer != null ) {
1722                 single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
1723                         + similarity.getDomainId() + "</a></b></td></tr>" );
1724                 single_writer.write( SurfacingConstants.NL );
1725             }
1726             else {
1727                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
1728                         .charAt( 0 ) );
1729                 if ( local_writer == null ) {
1730                     local_writer = split_writers.get( '0' );
1731                 }
1732                 local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
1733                         + similarity.getDomainId() + "</a></b></td></tr>" );
1734                 local_writer.write( SurfacingConstants.NL );
1735             }
1736         }
1737         for( final Writer w : split_writers.values() ) {
1738             w.write( "</table>" );
1739             w.write( SurfacingConstants.NL );
1740             w.write( "<hr>" );
1741             w.write( SurfacingConstants.NL );
1742             w.write( "<table>" );
1743             w.write( SurfacingConstants.NL );
1744         }
1745         //
1746         for( final DomainSimilarity similarity : similarities ) {
1747             if ( ( species_order != null ) && !species_order.isEmpty() ) {
1748                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
1749             }
1750             if ( single_writer != null ) {
1751                 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1752                 single_writer.write( SurfacingConstants.NL );
1753             }
1754             else {
1755                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
1756                         .charAt( 0 ) );
1757                 if ( local_writer == null ) {
1758                     local_writer = split_writers.get( '0' );
1759                 }
1760                 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1761                 local_writer.write( SurfacingConstants.NL );
1762             }
1763         }
1764         switch ( print_option ) {
1765             case HTML:
1766                 for( final Writer w : split_writers.values() ) {
1767                     w.write( SurfacingConstants.NL );
1768                     w.write( "</table>" );
1769                     w.write( SurfacingConstants.NL );
1770                     w.write( "</font>" );
1771                     w.write( SurfacingConstants.NL );
1772                     w.write( "</body>" );
1773                     w.write( SurfacingConstants.NL );
1774                     w.write( "</html>" );
1775                     w.write( SurfacingConstants.NL );
1776                 }
1777                 break;
1778         }
1779         for( final Writer w : split_writers.values() ) {
1780             w.close();
1781         }
1782         return stats;
1783     }
1784
1785     private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
1786             throws IOException {
1787         w.write( "<hr>" );
1788         w.write( "<br>" );
1789         w.write( SurfacingConstants.NL );
1790         w.write( "<tt><pre>" );
1791         w.write( SurfacingConstants.NL );
1792         if ( histo != null ) {
1793             w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
1794             w.write( SurfacingConstants.NL );
1795         }
1796         w.write( "</pre></tt>" );
1797         w.write( SurfacingConstants.NL );
1798         w.write( "<table>" );
1799         w.write( SurfacingConstants.NL );
1800         w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
1801         w.write( SurfacingConstants.NL );
1802         w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
1803         w.write( SurfacingConstants.NL );
1804         w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
1805         w.write( SurfacingConstants.NL );
1806         w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
1807         w.write( SurfacingConstants.NL );
1808         if ( stats.getN() > 1 ) {
1809             w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
1810         }
1811         else {
1812             w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
1813         }
1814         w.write( SurfacingConstants.NL );
1815         w.write( "</table>" );
1816         w.write( SurfacingConstants.NL );
1817         w.write( "<br>" );
1818         w.write( SurfacingConstants.NL );
1819     }
1820
1821     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
1822                                           final String filename,
1823                                           final Format format ) {
1824         final File outfile = new File( filename );
1825         checkForOutputFileWriteability( outfile );
1826         try {
1827             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1828             matrix.toWriter( out, format );
1829             out.flush();
1830             out.close();
1831         }
1832         catch ( final IOException e ) {
1833             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1834         }
1835         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
1836     }
1837
1838     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
1839         checkForOutputFileWriteability( matrix_outfile );
1840         try {
1841             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
1842             for( final DistanceMatrix distance_matrix : matrices ) {
1843                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
1844                 out.write( ForesterUtil.LINE_SEPARATOR );
1845                 out.flush();
1846             }
1847             out.close();
1848         }
1849         catch ( final IOException e ) {
1850             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1851         }
1852         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
1853     }
1854
1855     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
1856         final PhylogenyWriter writer = new PhylogenyWriter();
1857         try {
1858             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
1859         }
1860         catch ( final IOException e ) {
1861             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
1862                     + e );
1863         }
1864         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
1865     }
1866
1867     public static void writeTaxonomyLinks( final Writer writer,
1868                                            final String species,
1869                                            final Map<String, Integer> tax_code_to_id_map ) throws IOException {
1870         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
1871             writer.write( " [" );
1872             if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
1873                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
1874                         + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
1875             }
1876             else {
1877                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
1878                         + "\" target=\"taxonomy_window\">eol</a>" );
1879                 writer.write( "|" );
1880                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
1881                         + "\" target=\"taxonomy_window\">scholar</a>" );
1882                 writer.write( "|" );
1883                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
1884                         + "\" target=\"taxonomy_window\">google</a>" );
1885             }
1886             writer.write( "]" );
1887         }
1888     }
1889
1890     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
1891         if ( map.containsKey( s ) ) {
1892             map.put( s, map.get( s ) + 1 );
1893         }
1894         else {
1895             map.put( s, 1 );
1896         }
1897     }
1898
1899     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
1900                                                                     final String outfilename_for_counts,
1901                                                                     final String outfilename_for_dc,
1902                                                                     final String outfilename_for_dc_for_go_mapping,
1903                                                                     final String outfilename_for_dc_for_go_mapping_unique,
1904                                                                     final String outfilename_for_rank_counts,
1905                                                                     final String outfilename_for_ancestor_species_counts,
1906                                                                     final String outfilename_for_protein_stats,
1907                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
1908                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
1909                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
1910         try {
1911             //
1912             //            if ( protein_length_stats_by_dc != null ) {
1913             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
1914             //                    System.out.print( entry.getKey().toString() );
1915             //                    System.out.print( ": " );
1916             //                    double[] a = entry.getValue().getDataAsDoubleArray();
1917             //                    for( int i = 0; i < a.length; i++ ) {
1918             //                        System.out.print( a[ i ] + " " );
1919             //                    }
1920             //                    System.out.println();
1921             //                }
1922             //            }
1923             //            if ( domain_number_stats_by_dc != null ) {
1924             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
1925             //                    System.out.print( entry.getKey().toString() );
1926             //                    System.out.print( ": " );
1927             //                    double[] a = entry.getValue().getDataAsDoubleArray();
1928             //                    for( int i = 0; i < a.length; i++ ) {
1929             //                        System.out.print( a[ i ] + " " );
1930             //                    }
1931             //                    System.out.println();
1932             //                }
1933             //            }
1934             //
1935             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
1936             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
1937             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
1938             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
1939             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
1940             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
1941                 final PhylogenyNode n = it.next();
1942                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
1943                 for( final String dc : gained_dc ) {
1944                     if ( dc_gain_counts.containsKey( dc ) ) {
1945                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
1946                     }
1947                     else {
1948                         dc_gain_counts.put( dc, 1 );
1949                     }
1950                 }
1951             }
1952             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
1953             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
1954             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
1955             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
1956             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
1957             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
1958             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
1959             final Set<String> dcs = dc_gain_counts.keySet();
1960             final SortedSet<String> more_than_once = new TreeSet<String>();
1961             DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
1962             DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
1963             DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
1964             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
1965             long gained_multiple_times_domain_length_sum = 0;
1966             long gained_once_domain_length_sum = 0;
1967             long gained_multiple_times_domain_length_count = 0;
1968             long gained_once_domain_length_count = 0;
1969             for( final String dc : dcs ) {
1970                 final int count = dc_gain_counts.get( dc );
1971                 if ( histogram.containsKey( count ) ) {
1972                     histogram.put( count, histogram.get( count ) + 1 );
1973                     domain_lists.get( count ).append( ", " + dc );
1974                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
1975                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
1976                 }
1977                 else {
1978                     histogram.put( count, 1 );
1979                     domain_lists.put( count, new StringBuilder( dc ) );
1980                     final PriorityQueue<String> q = new PriorityQueue<String>();
1981                     q.addAll( splitDomainCombination( dc ) );
1982                     domain_lists_go.put( count, q );
1983                     final SortedSet<String> set = new TreeSet<String>();
1984                     set.addAll( splitDomainCombination( dc ) );
1985                     domain_lists_go_unique.put( count, set );
1986                 }
1987                 if ( protein_length_stats_by_dc != null ) {
1988                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
1989                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
1990                     }
1991                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
1992                             .arithmeticMean() );
1993                 }
1994                 if ( domain_number_stats_by_dc != null ) {
1995                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
1996                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
1997                     }
1998                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
1999                             .arithmeticMean() );
2000                 }
2001                 if ( domain_length_stats_by_domain != null ) {
2002                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
2003                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
2004                     }
2005                     final String[] ds = dc.split( "=" );
2006                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2007                             .get( ds[ 0 ] ).arithmeticMean() );
2008                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2009                             .get( ds[ 1 ] ).arithmeticMean() );
2010                 }
2011                 if ( count > 1 ) {
2012                     more_than_once.add( dc );
2013                     if ( protein_length_stats_by_dc != null ) {
2014                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2015                         for( final double element : s.getData() ) {
2016                             gained_multiple_times_lengths_stats.addValue( element );
2017                         }
2018                     }
2019                     if ( domain_number_stats_by_dc != null ) {
2020                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2021                         for( final double element : s.getData() ) {
2022                             gained_multiple_times_domain_count_stats.addValue( element );
2023                         }
2024                     }
2025                     if ( domain_length_stats_by_domain != null ) {
2026                         final String[] ds = dc.split( "=" );
2027                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2028                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2029                         for( final double element : s0.getData() ) {
2030                             gained_multiple_times_domain_length_sum += element;
2031                             ++gained_multiple_times_domain_length_count;
2032                         }
2033                         for( final double element : s1.getData() ) {
2034                             gained_multiple_times_domain_length_sum += element;
2035                             ++gained_multiple_times_domain_length_count;
2036                         }
2037                     }
2038                 }
2039                 else {
2040                     if ( protein_length_stats_by_dc != null ) {
2041                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2042                         for( final double element : s.getData() ) {
2043                             gained_once_lengths_stats.addValue( element );
2044                         }
2045                     }
2046                     if ( domain_number_stats_by_dc != null ) {
2047                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2048                         for( final double element : s.getData() ) {
2049                             gained_once_domain_count_stats.addValue( element );
2050                         }
2051                     }
2052                     if ( domain_length_stats_by_domain != null ) {
2053                         final String[] ds = dc.split( "=" );
2054                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2055                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2056                         for( final double element : s0.getData() ) {
2057                             gained_once_domain_length_sum += element;
2058                             ++gained_once_domain_length_count;
2059                         }
2060                         for( final double element : s1.getData() ) {
2061                             gained_once_domain_length_sum += element;
2062                             ++gained_once_domain_length_count;
2063                         }
2064                     }
2065                 }
2066             }
2067             final Set<Integer> histogram_keys = histogram.keySet();
2068             for( final Integer histogram_key : histogram_keys ) {
2069                 final int count = histogram.get( histogram_key );
2070                 final StringBuilder dc = domain_lists.get( histogram_key );
2071                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
2072                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
2073                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2074                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
2075                 Arrays.sort( sorted );
2076                 for( final Object domain : sorted ) {
2077                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
2078                 }
2079                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2080                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
2081                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
2082                 }
2083             }
2084             out_counts.close();
2085             out_dc.close();
2086             out_dc_for_go_mapping.close();
2087             out_dc_for_go_mapping_unique.close();
2088             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
2089             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
2090             for( final String dc : more_than_once ) {
2091                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
2092                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
2093                     final PhylogenyNode n = it.next();
2094                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
2095                         nodes.add( n );
2096                     }
2097                 }
2098                 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
2099                     for( int j = i + 1; j < nodes.size(); ++j ) {
2100                         final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
2101                         String rank = "unknown";
2102                         if ( lca.getNodeData().isHasTaxonomy()
2103                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
2104                             rank = lca.getNodeData().getTaxonomy().getRank();
2105                         }
2106                         addToCountMap( lca_rank_counts, rank );
2107                         String lca_species;
2108                         if ( lca.getNodeData().isHasTaxonomy()
2109                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
2110                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
2111                         }
2112                         else if ( lca.getNodeData().isHasTaxonomy()
2113                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
2114                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
2115                         }
2116                         else {
2117                             lca_species = lca.getName();
2118                         }
2119                         addToCountMap( lca_ancestor_species_counts, lca_species );
2120                     }
2121                 }
2122             }
2123             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
2124             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
2125             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
2126             ForesterUtil.map2writer( out_for_ancestor_species_counts,
2127                                      lca_ancestor_species_counts,
2128                                      "\t",
2129                                      ForesterUtil.LINE_SEPARATOR );
2130             out_for_rank_counts.close();
2131             out_for_ancestor_species_counts.close();
2132             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
2133                     && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
2134                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
2135                 w.write( "Domain Lengths: " );
2136                 w.write( "\n" );
2137                 if ( domain_length_stats_by_domain != null ) {
2138                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
2139                             .entrySet() ) {
2140                         w.write( entry.getKey().toString() );
2141                         w.write( "\t" + entry.getValue().arithmeticMean() );
2142                         w.write( "\t" + entry.getValue().median() );
2143                         w.write( "\n" );
2144                     }
2145                 }
2146                 w.flush();
2147                 w.write( "\n" );
2148                 w.write( "\n" );
2149                 w.write( "Protein Lengths: " );
2150                 w.write( "\n" );
2151                 if ( protein_length_stats_by_dc != null ) {
2152                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
2153                             .entrySet() ) {
2154                         w.write( entry.getKey().toString() );
2155                         w.write( "\t" + entry.getValue().arithmeticMean() );
2156                         w.write( "\t" + entry.getValue().median() );
2157                         w.write( "\n" );
2158                     }
2159                 }
2160                 w.flush();
2161                 w.write( "\n" );
2162                 w.write( "\n" );
2163                 w.write( "Number of domains: " );
2164                 w.write( "\n" );
2165                 if ( domain_number_stats_by_dc != null ) {
2166                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
2167                             .entrySet() ) {
2168                         w.write( entry.getKey().toString() );
2169                         w.write( "\t" + entry.getValue().arithmeticMean() );
2170                         w.write( "\t" + entry.getValue().median() );
2171                         w.write( "\n" );
2172                     }
2173                 }
2174                 w.flush();
2175                 w.write( "\n" );
2176                 w.write( "\n" );
2177                 w.write( "Gained once, domain lengths:" );
2178                 w.write( "\n" );
2179                 w.write( "N: " + gained_once_domain_length_count );
2180                 w.write( "\n" );
2181                 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
2182                 w.write( "\n" );
2183                 w.write( "\n" );
2184                 w.write( "Gained multiple times, domain lengths:" );
2185                 w.write( "\n" );
2186                 w.write( "N: " + gained_multiple_times_domain_length_count );
2187                 w.write( "\n" );
2188                 w.write( "Avg: "
2189                         + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
2190                 w.write( "\n" );
2191                 w.write( "\n" );
2192                 w.write( "\n" );
2193                 w.write( "\n" );
2194                 w.write( "Gained once, protein lengths:" );
2195                 w.write( "\n" );
2196                 w.write( gained_once_lengths_stats.toString() );
2197                 gained_once_lengths_stats = null;
2198                 w.write( "\n" );
2199                 w.write( "\n" );
2200                 w.write( "Gained once, domain counts:" );
2201                 w.write( "\n" );
2202                 w.write( gained_once_domain_count_stats.toString() );
2203                 gained_once_domain_count_stats = null;
2204                 w.write( "\n" );
2205                 w.write( "\n" );
2206                 w.write( "Gained multiple times, protein lengths:" );
2207                 w.write( "\n" );
2208                 w.write( gained_multiple_times_lengths_stats.toString() );
2209                 gained_multiple_times_lengths_stats = null;
2210                 w.write( "\n" );
2211                 w.write( "\n" );
2212                 w.write( "Gained multiple times, domain counts:" );
2213                 w.write( "\n" );
2214                 w.write( gained_multiple_times_domain_count_stats.toString() );
2215                 w.flush();
2216                 w.close();
2217             }
2218         }
2219         catch ( final IOException e ) {
2220             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2221         }
2222         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
2223                 + outfilename_for_counts + "]" );
2224         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
2225                 + outfilename_for_dc + "]" );
2226         ForesterUtil.programMessage( surfacing.PRG_NAME,
2227                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
2228                                              + outfilename_for_dc_for_go_mapping + "]" );
2229         ForesterUtil.programMessage( surfacing.PRG_NAME,
2230                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
2231                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
2232     }
2233
2234     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
2235                                                                         final boolean get_gains ) {
2236         final SortedSet<String> domains = new TreeSet<String>();
2237         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
2238             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
2239             if ( get_gains ) {
2240                 domains.addAll( chars.getGainedCharacters() );
2241             }
2242             else {
2243                 domains.addAll( chars.getLostCharacters() );
2244             }
2245         }
2246         return domains;
2247     }
2248
2249     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
2250                                                             final boolean domain_combinations,
2251                                                             final CharacterStateMatrix.GainLossStates state,
2252                                                             final String outfile ) {
2253         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
2254                 + ForesterUtil.FILE_SEPARATOR + base_dir );
2255         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2256             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2257         }
2258         if ( domain_combinations ) {
2259             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2260                     + ForesterUtil.FILE_SEPARATOR + "DC" );
2261         }
2262         else {
2263             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2264                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
2265         }
2266         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2267             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2268         }
2269         if ( state == GainLossStates.GAIN ) {
2270             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2271                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
2272         }
2273         else if ( state == GainLossStates.LOSS ) {
2274             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2275                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
2276         }
2277         else {
2278             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2279                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
2280         }
2281         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2282             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2283         }
2284         return per_node_go_mapped_domain_gain_loss_files_base_dir;
2285     }
2286
2287     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
2288         final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
2289         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
2290         for( final String domain_id : cds.keySet() ) {
2291             final CombinableDomains cd = cds.get( domain_id );
2292             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
2293         }
2294         return binary_combinations;
2295     }
2296
2297     private static List<String> splitDomainCombination( final String dc ) {
2298         final String[] s = dc.split( "=" );
2299         if ( s.length != 2 ) {
2300             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
2301                     + dc );
2302             System.exit( -1 );
2303         }
2304         final List<String> l = new ArrayList<String>( 2 );
2305         l.add( s[ 0 ] );
2306         l.add( s[ 1 ] );
2307         return l;
2308     }
2309
2310     private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2311                                                         final Map<GoId, GoTerm> go_id_to_term_map,
2312                                                         final String outfile_name,
2313                                                         final SortedSet<String> all_pfams_encountered ) {
2314         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
2315         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
2316                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
2317         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
2318         int biological_process_counter = 0;
2319         int cellular_component_counter = 0;
2320         int molecular_function_counter = 0;
2321         int pfams_with_mappings_counter = 0;
2322         int pfams_without_mappings_counter = 0;
2323         int pfams_without_mappings_to_bp_or_mf_counter = 0;
2324         int pfams_with_mappings_to_bp_or_mf_counter = 0;
2325         try {
2326             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
2327             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
2328             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
2329             summary_writer.write( "# Pfam to GO mapping summary" );
2330             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2331             summary_writer.write( "# Actual summary is at the end of this file." );
2332             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2333             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
2334             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2335             for( final String pfam : all_pfams_encountered ) {
2336                 all_pfams_encountered_writer.write( pfam );
2337                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
2338                 final String domain_id = new String( pfam );
2339                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2340                     ++pfams_with_mappings_counter;
2341                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
2342                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
2343                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
2344                     boolean maps_to_bp = false;
2345                     boolean maps_to_cc = false;
2346                     boolean maps_to_mf = false;
2347                     for( final GoId go_id : go_ids ) {
2348                         final GoTerm go_term = go_id_to_term_map.get( go_id );
2349                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
2350                             maps_to_bp = true;
2351                         }
2352                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
2353                             maps_to_cc = true;
2354                         }
2355                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
2356                             maps_to_mf = true;
2357                         }
2358                     }
2359                     if ( maps_to_bp ) {
2360                         ++biological_process_counter;
2361                     }
2362                     if ( maps_to_cc ) {
2363                         ++cellular_component_counter;
2364                     }
2365                     if ( maps_to_mf ) {
2366                         ++molecular_function_counter;
2367                     }
2368                     if ( maps_to_bp || maps_to_mf ) {
2369                         ++pfams_with_mappings_to_bp_or_mf_counter;
2370                     }
2371                     else {
2372                         ++pfams_without_mappings_to_bp_or_mf_counter;
2373                     }
2374                 }
2375                 else {
2376                     ++pfams_without_mappings_to_bp_or_mf_counter;
2377                     ++pfams_without_mappings_counter;
2378                     summary_writer.write( pfam );
2379                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2380                 }
2381             }
2382             all_pfams_encountered_writer.close();
2383             all_pfams_encountered_with_go_annotation_writer.close();
2384             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
2385                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
2386             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
2387                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
2388                     + "\"" );
2389             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
2390                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
2391                     + encountered_pfams_summary_file + "\"" );
2392             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
2393                     + all_pfams_encountered.size() );
2394             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
2395                     + pfams_without_mappings_counter + " ["
2396                     + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2397             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
2398                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2399                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2400             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
2401                     + pfams_with_mappings_counter + " ["
2402                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2403             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
2404                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2405                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2406             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
2407                     + biological_process_counter + " ["
2408                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2409             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
2410                     + molecular_function_counter + " ["
2411                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2412             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
2413                     + cellular_component_counter + " ["
2414                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2415             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2416             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
2417             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2418             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
2419                     + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2420             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2421             summary_writer.write( "# Pfams without mapping to proc. or func. : "
2422                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2423                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2424             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2425             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
2426                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2427             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2428             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
2429                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2430                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2431             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2432             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
2433                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2434             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2435             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
2436                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2437             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2438             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
2439                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2440             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2441             summary_writer.close();
2442         }
2443         catch ( final IOException e ) {
2444             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2445         }
2446     }
2447
2448     private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2449                                          final Map<GoId, GoTerm> go_id_to_term_map,
2450                                          final GoNameSpace go_namespace_limit,
2451                                          final Writer out,
2452                                          final String domain_0,
2453                                          final String domain_1,
2454                                          final String prefix_for_html,
2455                                          final String character_separator_for_non_html_output,
2456                                          final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
2457                                          final Set<GoId> all_go_ids ) throws IOException {
2458         boolean any_go_annotation_present = false;
2459         boolean first_has_no_go = false;
2460         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2461         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2462             domain_count = 1;
2463         }
2464         // The following has a difficult to understand logic.
2465         for( int d = 0; d < domain_count; ++d ) {
2466             List<GoId> go_ids = null;
2467             boolean go_annotation_present = false;
2468             if ( d == 0 ) {
2469                 if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
2470                     go_annotation_present = true;
2471                     any_go_annotation_present = true;
2472                     go_ids = domain_id_to_go_ids_map.get( domain_0 );
2473                 }
2474                 else {
2475                     first_has_no_go = true;
2476                 }
2477             }
2478             else {
2479                 if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
2480                     go_annotation_present = true;
2481                     any_go_annotation_present = true;
2482                     go_ids = domain_id_to_go_ids_map.get( domain_1 );
2483                 }
2484             }
2485             if ( go_annotation_present ) {
2486                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2487                 for( final GoId go_id : go_ids ) {
2488                     out.write( "<tr>" );
2489                     if ( first ) {
2490                         first = false;
2491                         writeDomainIdsToHtml( out,
2492                                               domain_0,
2493                                               domain_1,
2494                                               prefix_for_html,
2495                                               domain_id_to_secondary_features_maps );
2496                     }
2497                     else {
2498                         out.write( "<td></td>" );
2499                     }
2500                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2501                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2502                     }
2503                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2504                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2505                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2506                         final String go_id_str = go_id.getId();
2507                         out.write( "<td>" );
2508                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2509                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2510                         out.write( "</td><td>" );
2511                         out.write( go_term.getName() );
2512                         if ( domain_count == 2 ) {
2513                             out.write( " (" + d + ")" );
2514                         }
2515                         out.write( "</td><td>" );
2516                         // out.write( top );
2517                         // out.write( "</td><td>" );
2518                         out.write( "[" );
2519                         out.write( go_term.getGoNameSpace().toShortString() );
2520                         out.write( "]" );
2521                         out.write( "</td>" );
2522                         if ( all_go_ids != null ) {
2523                             all_go_ids.add( go_id );
2524                         }
2525                     }
2526                     else {
2527                         out.write( "<td>" );
2528                         out.write( "</td><td>" );
2529                         out.write( "</td><td>" );
2530                         out.write( "</td><td>" );
2531                         out.write( "</td>" );
2532                     }
2533                     out.write( "</tr>" );
2534                     out.write( SurfacingConstants.NL );
2535                 }
2536             }
2537         } //  for( int d = 0; d < domain_count; ++d )
2538         if ( !any_go_annotation_present ) {
2539             out.write( "<tr>" );
2540             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2541             out.write( "<td>" );
2542             out.write( "</td><td>" );
2543             out.write( "</td><td>" );
2544             out.write( "</td><td>" );
2545             out.write( "</td>" );
2546             out.write( "</tr>" );
2547             out.write( SurfacingConstants.NL );
2548         }
2549     }
2550
2551     private static void writeDomainIdsToHtml( final Writer out,
2552                                               final String domain_0,
2553                                               final String domain_1,
2554                                               final String prefix_for_detailed_html,
2555                                               final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
2556             throws IOException {
2557         out.write( "<td>" );
2558         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2559             out.write( prefix_for_detailed_html );
2560             out.write( " " );
2561         }
2562         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2563         out.write( "</td>" );
2564     }
2565
2566     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2567                                                                  final String domain_0,
2568                                                                  final String domain_1 ) throws IOException {
2569         individual_files_writer.write( domain_0 );
2570         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2571         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2572             individual_files_writer.write( domain_1 );
2573             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2574         }
2575     }
2576
2577     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2578         try {
2579             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2580             for( final String pfam : pfams ) {
2581                 writer.write( pfam );
2582                 writer.write( ForesterUtil.LINE_SEPARATOR );
2583             }
2584             writer.close();
2585             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2586                     + "]" );
2587         }
2588         catch ( final IOException e ) {
2589             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2590         }
2591     }
2592
2593     private static void writeToNexus( final String outfile_name,
2594                                       final CharacterStateMatrix<BinaryStates> matrix,
2595                                       final Phylogeny phylogeny ) {
2596         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2597             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2598                     + "] to nexus" );
2599         }
2600         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2601         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2602         phylogenies.add( phylogeny );
2603         try {
2604             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2605             w.write( NexusConstants.NEXUS );
2606             w.write( ForesterUtil.LINE_SEPARATOR );
2607             my_matrix.writeNexusTaxaBlock( w );
2608             my_matrix.writeNexusBinaryChractersBlock( w );
2609             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2610             w.flush();
2611             w.close();
2612             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2613         }
2614         catch ( final IOException e ) {
2615             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2616         }
2617     }
2618
2619     private static void writeToNexus( final String outfile_name,
2620                                       final DomainParsimonyCalculator domain_parsimony,
2621                                       final Phylogeny phylogeny ) {
2622         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2623                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2624                       phylogeny );
2625         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2626                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2627                       phylogeny );
2628     }
2629
2630     final static class DomainComparator implements Comparator<Domain> {
2631
2632         final private boolean _ascending;
2633
2634         public DomainComparator( final boolean ascending ) {
2635             _ascending = ascending;
2636         }
2637
2638         @Override
2639         public final int compare( final Domain d0, final Domain d1 ) {
2640             if ( d0.getFrom() < d1.getFrom() ) {
2641                 return _ascending ? -1 : 1;
2642             }
2643             else if ( d0.getFrom() > d1.getFrom() ) {
2644                 return _ascending ? 1 : -1;
2645             }
2646             return 0;
2647         }
2648     }
2649 }