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.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  87 import org.forester.util.AsciiHistogram;
  88 import org.forester.util.BasicDescriptiveStatistics;
  89 import org.forester.util.BasicTable;
  90 import org.forester.util.BasicTableParser;
  91 import org.forester.util.DescriptiveStatistics;
  92 import org.forester.util.ForesterUtil;
  93
  94 public final class SurfacingUtil {
  95
  96     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  97     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  98
  99                                                                                  @Override
 100                                                                                  public int compare( final Domain d1,
 101                                                                                                      final Domain d2 ) {
 102                                                                                      if ( d1.getPerSequenceEvalue() < d2
 103                                                                                              .getPerSequenceEvalue() ) {
 104                                                                                          return -1;
 105                                                                                      }
 106                                                                                      else if ( d1
 107                                                                                              .getPerSequenceEvalue() > d2
 108                                                                                              .getPerSequenceEvalue() ) {
 109                                                                                          return 1;
 110                                                                                      }
 111                                                                                      else {
 112                                                                                          return d1.compareTo( d2 );
 113                                                                                      }
 114                                                                                  }
 115                                                                              };
 116     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 117
 118     private SurfacingUtil() {
 119         // Hidden constructor.
 120     }
 121
 122     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 123                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 124         final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 125         for( final String domain_id : all_cd.keySet() ) {
 126             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 127         }
 128     }
 129
 130     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 131                                              final SortedSet<String> domain_ids ) {
 132         final SortedSet<String> domains = genome.getAllDomainIds();
 133         for( final String domain : domains ) {
 134             domain_ids.add( domain );
 135         }
 136     }
 137
 138     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 139         w.write( SurfacingConstants.NL );
 140         w.write( "<head>" );
 141         w.write( "<title>" );
 142         w.write( title );
 143         w.write( "</title>" );
 144         w.write( SurfacingConstants.NL );
 145         w.write( "<style>" );
 146         w.write( SurfacingConstants.NL );
 147         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 148         w.write( SurfacingConstants.NL );
 149         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 150         w.write( SurfacingConstants.NL );
 151         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 152         w.write( SurfacingConstants.NL );
 153         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 154         w.write( SurfacingConstants.NL );
 155         //
 156         w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7pt;}" );
 157         w.write( SurfacingConstants.NL );
 158         w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7pt;}" );
 159         w.write( SurfacingConstants.NL );
 160         w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7pt;}" );
 161         w.write( SurfacingConstants.NL );
 162         w.write( "a.pl:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
 163         w.write( SurfacingConstants.NL );
 164         //
 165         w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7pt;}" );
 166         w.write( SurfacingConstants.NL );
 167         w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7pt;}" );
 168         w.write( SurfacingConstants.NL );
 169         w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7pt;}" );
 170         w.write( SurfacingConstants.NL );
 171         w.write( "a.ps:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
 172         w.write( SurfacingConstants.NL );
 173         //
 174         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 175         w.write( SurfacingConstants.NL );
 176         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 177         w.write( SurfacingConstants.NL );
 178         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 179         w.write( SurfacingConstants.NL );
 180         w.write( "</style>" );
 181         w.write( SurfacingConstants.NL );
 182         w.write( "</head>" );
 183         w.write( SurfacingConstants.NL );
 184     }
 185
 186     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 187         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 188         for( final DomainSimilarity similarity : similarities ) {
 189             stats.addValue( similarity.getMeanSimilarityScore() );
 190         }
 191         return stats;
 192     }
 193
 194     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 195         int overlap_count = 0;
 196         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 197             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 198                 ++overlap_count;
 199             }
 200         }
 201         return overlap_count;
 202     }
 203
 204     public static void checkForOutputFileWriteability( final File outfile ) {
 205         final String error = ForesterUtil.isWritableFile( outfile );
 206         if ( !ForesterUtil.isEmpty( error ) ) {
 207             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 208         }
 209     }
 210
 211     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 212                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 213                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 214                                                                                            final boolean get_gains ) {
 215         final SortedSet<String> sorted_ids = new TreeSet<String>();
 216         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 217             sorted_ids.add( matrix.getIdentifier( i ) );
 218         }
 219         for( final String id : sorted_ids ) {
 220             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 221                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 222                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 223                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 224                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 225                                 .createInstance( matrix.getCharacter( c ) ) );
 226                     }
 227                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 228                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 229                                 .createInstance( matrix.getCharacter( c ) ) );
 230                     }
 231                     else {
 232                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 233                                 .getCharacter( c ) ) );
 234                     }
 235                 }
 236             }
 237         }
 238     }
 239
 240     public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 241         final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
 242         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 243             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 244                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 245             }
 246             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 247         }
 248         return domain_id_to_go_ids_map;
 249     }
 250
 251     public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 252             throws IOException {
 253         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
 254         final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
 255         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 256             final String domain_id = primary_table.getValue( 0, r );
 257             if ( !map.containsKey( domain_id ) ) {
 258                 map.put( domain_id, new HashSet<String>() );
 259             }
 260             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 261         }
 262         return map;
 263     }
 264
 265     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 266         checkForOutputFileWriteability( nj_tree_outfile );
 267         final NeighborJoining nj = NeighborJoining.createInstance();
 268         final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
 269         phylogeny.setName( nj_tree_outfile.getName() );
 270         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 271         return phylogeny;
 272     }
 273
 274     public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
 275         final Map<String, Integer> m = new HashMap<String, Integer>();
 276         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 277             final PhylogenyNode n = iter.next();
 278             if ( n.getNodeData().isHasTaxonomy() ) {
 279                 final Taxonomy t = n.getNodeData().getTaxonomy();
 280                 final String c = t.getTaxonomyCode();
 281                 if ( !ForesterUtil.isEmpty( c ) ) {
 282                     if ( n.getNodeData().getTaxonomy() == null ) {
 283                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 284                     }
 285                     final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
 286                     if ( ForesterUtil.isEmpty( id ) ) {
 287                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 288                     }
 289                     if ( m.containsKey( c ) ) {
 290                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
 291                     }
 292                     final int iid = Integer.valueOf( id );
 293                     if ( m.containsValue( iid ) ) {
 294                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
 295                     }
 296                     m.put( c, iid );
 297                 }
 298             }
 299             else {
 300                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
 301             }
 302         }
 303         return m;
 304     }
 305
 306     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 307                                                             final Detailedness detailedness ) {
 308         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 309             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 310                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 311                 printable_domain_similarity.setDetailedness( detailedness );
 312             }
 313         }
 314     }
 315
 316     public static void doit( final List<Protein> proteins,
 317                              final List<String> query_domain_ids_nc_order,
 318                              final Writer out,
 319                              final String separator,
 320                              final String limit_to_species,
 321                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
 322         for( final Protein protein : proteins ) {
 323             if ( ForesterUtil.isEmpty( limit_to_species )
 324                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 325                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 326                     out.write( protein.getSpecies().getSpeciesId() );
 327                     out.write( separator );
 328                     out.write( protein.getProteinId().getId() );
 329                     out.write( separator );
 330                     out.write( "[" );
 331                     final Set<String> visited_domain_ids = new HashSet<String>();
 332                     boolean first = true;
 333                     for( final Domain domain : protein.getProteinDomains() ) {
 334                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 335                             visited_domain_ids.add( domain.getDomainId() );
 336                             if ( first ) {
 337                                 first = false;
 338                             }
 339                             else {
 340                                 out.write( " " );
 341                             }
 342                             out.write( domain.getDomainId() );
 343                             out.write( " {" );
 344                             out.write( "" + domain.getTotalCount() );
 345                             out.write( "}" );
 346                         }
 347                     }
 348                     out.write( "]" );
 349                     out.write( separator );
 350                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 351                             .equals( SurfacingConstants.NONE ) ) ) {
 352                         out.write( protein.getDescription() );
 353                     }
 354                     out.write( separator );
 355                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 356                             .equals( SurfacingConstants.NONE ) ) ) {
 357                         out.write( protein.getAccession() );
 358                     }
 359                     out.write( SurfacingConstants.NL );
 360                 }
 361             }
 362         }
 363         out.flush();
 364     }
 365
 366     public static void domainsPerProteinsStatistics( final String genome,
 367                                                      final List<Protein> protein_list,
 368                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
 369                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
 370                                                      final SortedSet<String> domains_which_are_always_single,
 371                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
 372                                                      final SortedSet<String> domains_which_never_single,
 373                                                      final Writer writer ) {
 374         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 375         for( final Protein protein : protein_list ) {
 376             final int domains = protein.getNumberOfProteinDomains();
 377             //System.out.println( domains );
 378             stats.addValue( domains );
 379             all_genomes_domains_per_potein_stats.addValue( domains );
 380             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
 381                 all_genomes_domains_per_potein_histo.put( domains, 1 );
 382             }
 383             else {
 384                 all_genomes_domains_per_potein_histo.put( domains,
 385                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
 386             }
 387             if ( domains == 1 ) {
 388                 final String domain = protein.getProteinDomain( 0 ).getDomainId();
 389                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 390                     if ( domains_which_never_single.contains( domain ) ) {
 391                         domains_which_never_single.remove( domain );
 392                         domains_which_are_sometimes_single_sometimes_not.add( domain );
 393                     }
 394                     else {
 395                         domains_which_are_always_single.add( domain );
 396                     }
 397                 }
 398             }
 399             else if ( domains > 1 ) {
 400                 for( final Domain d : protein.getProteinDomains() ) {
 401                     final String domain = d.getDomainId();
 402                     // System.out.println( domain );
 403                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 404                         if ( domains_which_are_always_single.contains( domain ) ) {
 405                             domains_which_are_always_single.remove( domain );
 406                             domains_which_are_sometimes_single_sometimes_not.add( domain );
 407                         }
 408                         else {
 409                             domains_which_never_single.add( domain );
 410                         }
 411                     }
 412                 }
 413             }
 414         }
 415         try {
 416             writer.write( genome );
 417             writer.write( "\t" );
 418             if ( stats.getN() >= 1 ) {
 419                 writer.write( stats.arithmeticMean() + "" );
 420                 writer.write( "\t" );
 421                 if ( stats.getN() >= 2 ) {
 422                     writer.write( stats.sampleStandardDeviation() + "" );
 423                 }
 424                 else {
 425                     writer.write( "" );
 426                 }
 427                 writer.write( "\t" );
 428                 writer.write( stats.median() + "" );
 429                 writer.write( "\t" );
 430                 writer.write( stats.getN() + "" );
 431                 writer.write( "\t" );
 432                 writer.write( stats.getMin() + "" );
 433                 writer.write( "\t" );
 434                 writer.write( stats.getMax() + "" );
 435             }
 436             else {
 437                 writer.write( "\t" );
 438                 writer.write( "\t" );
 439                 writer.write( "\t" );
 440                 writer.write( "0" );
 441                 writer.write( "\t" );
 442                 writer.write( "\t" );
 443             }
 444             writer.write( "\n" );
 445         }
 446         catch ( final IOException e ) {
 447             e.printStackTrace();
 448         }
 449     }
 450
 451     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 452                                                     final int number_of_genomes,
 453                                                     final DomainLengthsTable domain_lengths_table,
 454                                                     final File outfile ) throws IOException {
 455         final DecimalFormat df = new DecimalFormat( "#.00" );
 456         checkForOutputFileWriteability( outfile );
 457         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 458         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 459         out.write( ForesterUtil.LINE_SEPARATOR );
 460         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 461         out.write( ForesterUtil.LINE_SEPARATOR );
 462         out.write( ForesterUtil.LINE_SEPARATOR );
 463         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 464         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 465         out.write( ForesterUtil.LINE_SEPARATOR );
 466         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 467             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 468             if ( species_list.size() > 0 ) {
 469                 out.write( domain_lengths.getDomainId() + "\t" );
 470                 for( final Species species : species_list ) {
 471                     out.write( species + "\t" );
 472                 }
 473                 out.write( ForesterUtil.LINE_SEPARATOR );
 474             }
 475         }
 476         out.write( ForesterUtil.LINE_SEPARATOR );
 477         out.write( ForesterUtil.LINE_SEPARATOR );
 478         out.write( "OUTLIER SPECIES (Z 1.0)" );
 479         out.write( ForesterUtil.LINE_SEPARATOR );
 480         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 481                 .calculateMeanBasedStatisticsForAllSpecies();
 482         out.write( stats_for_all_species.asSummary() );
 483         out.write( ForesterUtil.LINE_SEPARATOR );
 484         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 485         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 486         out.write( ForesterUtil.LINE_SEPARATOR );
 487         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 488         final double population_mean = stats_for_all_species.arithmeticMean();
 489         for( final Species species : domain_lengths_table.getSpecies() ) {
 490             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 491             final double z = ( x - population_mean ) / population_sd;
 492             out.write( species + "\t" + z );
 493             out.write( ForesterUtil.LINE_SEPARATOR );
 494         }
 495         out.write( ForesterUtil.LINE_SEPARATOR );
 496         for( final Species species : domain_lengths_table.getSpecies() ) {
 497             final DescriptiveStatistics stats_for_species = domain_lengths_table
 498                     .calculateMeanBasedStatisticsForSpecies( species );
 499             final double x = stats_for_species.arithmeticMean();
 500             final double z = ( x - population_mean ) / population_sd;
 501             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 502                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 503                 out.write( ForesterUtil.LINE_SEPARATOR );
 504             }
 505         }
 506         out.close();
 507         System.gc();
 508     }
 509
 510     /**
 511      *
 512      * @param all_binary_domains_combination_lost_fitch
 513      * @param use_last_in_fitch_parsimony
 514      * @param consider_directedness_and_adjacency_for_bin_combinations
 515      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 516      * which were gained under unweighted (Fitch) parsimony.
 517      */
 518     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 519                                                  final boolean radomize_fitch_parsimony,
 520                                                  final String outfile_name,
 521                                                  final DomainParsimonyCalculator domain_parsimony,
 522                                                  final Phylogeny phylogeny,
 523                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
 524                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 525                                                  final GoNameSpace go_namespace_limit,
 526                                                  final String parameters_str,
 527                                                  final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
 528                                                  final SortedSet<String> positive_filter,
 529                                                  final boolean output_binary_domain_combinations_for_graphs,
 530                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 531                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 532                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 533                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 534                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 535                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
 536                                                  final Map<String, Integer> tax_code_to_id_map,
 537                                                  final boolean write_to_nexus,
 538                                                  final boolean use_last_in_fitch_parsimony ) {
 539         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 540         final String date_time = ForesterUtil.getCurrentDateTime();
 541         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 542         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 543         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 544         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 545         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 546         if ( write_to_nexus ) {
 547             writeToNexus( outfile_name, domain_parsimony, phylogeny );
 548         }
 549         // DOLLO DOMAINS
 550         // -------------
 551         Phylogeny local_phylogeny_l = phylogeny.copy();
 552         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 553             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 554         }
 555         else {
 556             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 557         }
 558         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 559                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 560         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 561                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 562         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 563                                                            CharacterStateMatrix.GainLossStates.GAIN,
 564                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 565                                                            sep,
 566                                                            ForesterUtil.LINE_SEPARATOR,
 567                                                            null );
 568         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 569                                                            CharacterStateMatrix.GainLossStates.LOSS,
 570                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 571                                                            sep,
 572                                                            ForesterUtil.LINE_SEPARATOR,
 573                                                            null );
 574         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 575                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 576         //HTML:
 577         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 578                                        go_id_to_term_map,
 579                                        go_namespace_limit,
 580                                        false,
 581                                        domain_parsimony.getGainLossMatrix(),
 582                                        CharacterStateMatrix.GainLossStates.GAIN,
 583                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 584                                        sep,
 585                                        ForesterUtil.LINE_SEPARATOR,
 586                                        "Dollo Parsimony | Gains | Domains",
 587                                        "+",
 588                                        domain_id_to_secondary_features_maps,
 589                                        all_pfams_encountered,
 590                                        all_pfams_gained_as_domains,
 591                                        "_dollo_gains_d",
 592                                        tax_code_to_id_map );
 593         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 594                                        go_id_to_term_map,
 595                                        go_namespace_limit,
 596                                        false,
 597                                        domain_parsimony.getGainLossMatrix(),
 598                                        CharacterStateMatrix.GainLossStates.LOSS,
 599                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 600                                        sep,
 601                                        ForesterUtil.LINE_SEPARATOR,
 602                                        "Dollo Parsimony | Losses | Domains",
 603                                        "-",
 604                                        domain_id_to_secondary_features_maps,
 605                                        all_pfams_encountered,
 606                                        all_pfams_lost_as_domains,
 607                                        "_dollo_losses_d",
 608                                        tax_code_to_id_map );
 609         //        writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 610         //                                       go_id_to_term_map,
 611         //                                       go_namespace_limit,
 612         //                                       false,
 613         //                                       domain_parsimony.getGainLossMatrix(),
 614         //                                       null,
 615         //                                       outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 616         //                                       sep,
 617         //                                       ForesterUtil.LINE_SEPARATOR,
 618         //                                       "Dollo Parsimony | Present | Domains",
 619         //                                       "",
 620         //                                       domain_id_to_secondary_features_maps,
 621         //                                       all_pfams_encountered,
 622         //                                       null,
 623         //                                       "_dollo_present_d",
 624         //                                       tax_code_to_id_map );
 625         preparePhylogeny( local_phylogeny_l,
 626                           domain_parsimony,
 627                           date_time,
 628                           "Dollo parsimony on domain presence/absence",
 629                           "dollo_on_domains_" + outfile_name,
 630                           parameters_str );
 631         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 632                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 633         try {
 634             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 635             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 636         }
 637         catch ( final IOException e ) {
 638             e.printStackTrace();
 639             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 640         }
 641         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 642             // FITCH DOMAIN COMBINATIONS
 643             // -------------------------
 644             local_phylogeny_l = phylogeny.copy();
 645             String randomization = "no";
 646             if ( radomize_fitch_parsimony ) {
 647                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 648                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 649             }
 650             else {
 651                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
 652             }
 653             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 654                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 655             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 656                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 657             SurfacingUtil
 658                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 659                                                           CharacterStateMatrix.GainLossStates.GAIN,
 660                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 661                                                           sep,
 662                                                           ForesterUtil.LINE_SEPARATOR,
 663                                                           null );
 664             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 665                                                                CharacterStateMatrix.GainLossStates.LOSS,
 666                                                                outfile_name
 667                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 668                                                                sep,
 669                                                                ForesterUtil.LINE_SEPARATOR,
 670                                                                null );
 671             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 672                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 673             if ( all_binary_domains_combination_gained_fitch != null ) {
 674                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 675                                                                                     dc_type,
 676                                                                                     all_binary_domains_combination_gained_fitch,
 677                                                                                     true );
 678             }
 679             if ( all_binary_domains_combination_lost_fitch != null ) {
 680                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 681                                                                                     dc_type,
 682                                                                                     all_binary_domains_combination_lost_fitch,
 683                                                                                     false );
 684             }
 685             if ( output_binary_domain_combinations_for_graphs ) {
 686                 SurfacingUtil
 687                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 688                                                                                                            .getGainLossMatrix(),
 689                                                                                                    null,
 690                                                                                                    outfile_name
 691                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 692                                                                                                    sep,
 693                                                                                                    ForesterUtil.LINE_SEPARATOR,
 694                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 695             }
 696             // HTML:
 697             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 698                                            go_id_to_term_map,
 699                                            go_namespace_limit,
 700                                            true,
 701                                            domain_parsimony.getGainLossMatrix(),
 702                                            CharacterStateMatrix.GainLossStates.GAIN,
 703                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 704                                            sep,
 705                                            ForesterUtil.LINE_SEPARATOR,
 706                                            "Fitch Parsimony | Gains | Domain Combinations",
 707                                            "+",
 708                                            null,
 709                                            all_pfams_encountered,
 710                                            all_pfams_gained_as_dom_combinations,
 711                                            "_fitch_gains_dc",
 712                                            tax_code_to_id_map );
 713             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 714                                            go_id_to_term_map,
 715                                            go_namespace_limit,
 716                                            true,
 717                                            domain_parsimony.getGainLossMatrix(),
 718                                            CharacterStateMatrix.GainLossStates.LOSS,
 719                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 720                                            sep,
 721                                            ForesterUtil.LINE_SEPARATOR,
 722                                            "Fitch Parsimony | Losses | Domain Combinations",
 723                                            "-",
 724                                            null,
 725                                            all_pfams_encountered,
 726                                            all_pfams_lost_as_dom_combinations,
 727                                            "_fitch_losses_dc",
 728                                            tax_code_to_id_map );
 729             //            writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 730             //                                           go_id_to_term_map,
 731             //                                           go_namespace_limit,
 732             //                                           true,
 733             //                                           domain_parsimony.getGainLossMatrix(),
 734             //                                           null,
 735             //                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 736             //                                           sep,
 737             //                                           ForesterUtil.LINE_SEPARATOR,
 738             //                                           "Fitch Parsimony | Present | Domain Combinations",
 739             //                                           "",
 740             //                                           null,
 741             //                                           all_pfams_encountered,
 742             //                                           null,
 743             //                                           "_fitch_present_dc",
 744             //                                           tax_code_to_id_map );
 745             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 746                                             go_id_to_term_map,
 747                                             outfile_name,
 748                                             all_pfams_encountered );
 749             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 750             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 751             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 752                               all_pfams_gained_as_dom_combinations );
 753             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 754             preparePhylogeny( local_phylogeny_l,
 755                               domain_parsimony,
 756                               date_time,
 757                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 758                                       + randomization,
 759                               "fitch_on_binary_domain_combinations_" + outfile_name,
 760                               parameters_str );
 761             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 762                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 763             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 764                                                         outfile_name
 765                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 766                                                         outfile_name
 767                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 768                                                         outfile_name
 769                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 770                                                         outfile_name
 771                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
 772                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
 773                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
 774                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
 775                                                         protein_length_stats_by_dc,
 776                                                         domain_number_stats_by_dc,
 777                                                         domain_length_stats_by_domain );
 778         }
 779     }
 780
 781     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 782                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 783                                                                      final Phylogeny phylogeny,
 784                                                                      final String parameters_str,
 785                                                                      final Map<Species, MappingResults> mapping_results_map,
 786                                                                      final boolean use_last_in_fitch_parsimony ) {
 787         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 788         final String date_time = ForesterUtil.getCurrentDateTime();
 789         System.out.println();
 790         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 791                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 792                       phylogeny );
 793         Phylogeny local_phylogeny_copy = phylogeny.copy();
 794         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 795         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 796                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 797         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 798                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 799         SurfacingUtil
 800                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 801                                                       CharacterStateMatrix.GainLossStates.GAIN,
 802                                                       outfile_name
 803                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 804                                                       sep,
 805                                                       ForesterUtil.LINE_SEPARATOR,
 806                                                       null );
 807         SurfacingUtil
 808                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 809                                                       CharacterStateMatrix.GainLossStates.LOSS,
 810                                                       outfile_name
 811                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 812                                                       sep,
 813                                                       ForesterUtil.LINE_SEPARATOR,
 814                                                       null );
 815         SurfacingUtil
 816                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 817                                                       null,
 818                                                       outfile_name
 819                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 820                                                       sep,
 821                                                       ForesterUtil.LINE_SEPARATOR,
 822                                                       null );
 823         preparePhylogeny( local_phylogeny_copy,
 824                           secondary_features_parsimony,
 825                           date_time,
 826                           "Dollo parsimony on secondary feature presence/absence",
 827                           "dollo_on_secondary_features_" + outfile_name,
 828                           parameters_str );
 829         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 830                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 831         // FITCH DOMAIN COMBINATIONS
 832         // -------------------------
 833         local_phylogeny_copy = phylogeny.copy();
 834         final String randomization = "no";
 835         secondary_features_parsimony
 836                 .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
 837         preparePhylogeny( local_phylogeny_copy,
 838                           secondary_features_parsimony,
 839                           date_time,
 840                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
 841                                   + randomization,
 842                           "fitch_on_binary_domain_combinations_" + outfile_name,
 843                           parameters_str );
 844         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 845                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
 846         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
 847                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
 848                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
 849                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
 850                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
 851                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
 852                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
 853     }
 854
 855     public static void extractProteinNames( final List<Protein> proteins,
 856                                             final List<String> query_domain_ids_nc_order,
 857                                             final Writer out,
 858                                             final String separator,
 859                                             final String limit_to_species ) throws IOException {
 860         for( final Protein protein : proteins ) {
 861             if ( ForesterUtil.isEmpty( limit_to_species )
 862                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 863                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 864                     out.write( protein.getSpecies().getSpeciesId() );
 865                     out.write( separator );
 866                     out.write( protein.getProteinId().getId() );
 867                     out.write( separator );
 868                     out.write( "[" );
 869                     final Set<String> visited_domain_ids = new HashSet<String>();
 870                     boolean first = true;
 871                     for( final Domain domain : protein.getProteinDomains() ) {
 872                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 873                             visited_domain_ids.add( domain.getDomainId() );
 874                             if ( first ) {
 875                                 first = false;
 876                             }
 877                             else {
 878                                 out.write( " " );
 879                             }
 880                             out.write( domain.getDomainId() );
 881                             out.write( " {" );
 882                             out.write( "" + domain.getTotalCount() );
 883                             out.write( "}" );
 884                         }
 885                     }
 886                     out.write( "]" );
 887                     out.write( separator );
 888                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 889                             .equals( SurfacingConstants.NONE ) ) ) {
 890                         out.write( protein.getDescription() );
 891                     }
 892                     out.write( separator );
 893                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 894                             .equals( SurfacingConstants.NONE ) ) ) {
 895                         out.write( protein.getAccession() );
 896                     }
 897                     out.write( SurfacingConstants.NL );
 898                 }
 899             }
 900         }
 901         out.flush();
 902     }
 903
 904     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
 905                                             final String domain_id,
 906                                             final Writer out,
 907                                             final String separator,
 908                                             final String limit_to_species,
 909                                             final double domain_e_cutoff ) throws IOException {
 910         System.out.println( "Per domain E-value: " + domain_e_cutoff );
 911         for( final Species species : protein_lists_per_species.keySet() ) {
 912             System.out.println( species + ":" );
 913             for( final Protein protein : protein_lists_per_species.get( species ) ) {
 914                 if ( ForesterUtil.isEmpty( limit_to_species )
 915                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 916                     final List<Domain> domains = protein.getProteinDomains( domain_id );
 917                     if ( domains.size() > 0 ) {
 918                         out.write( protein.getSpecies().getSpeciesId() );
 919                         out.write( separator );
 920                         out.write( protein.getProteinId().getId() );
 921                         out.write( separator );
 922                         out.write( domain_id.toString() );
 923                         out.write( separator );
 924                         int prev_to = -1;
 925                         for( final Domain domain : domains ) {
 926                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 927                                 out.write( "/" );
 928                                 out.write( domain.getFrom() + "-" + domain.getTo() );
 929                                 if ( prev_to >= 0 ) {
 930                                     final int l = domain.getFrom() - prev_to;
 931                                     System.out.println( l );
 932                                 }
 933                                 prev_to = domain.getTo();
 934                             }
 935                         }
 936                         out.write( "/" );
 937                         out.write( separator );
 938                         final List<Domain> domain_list = new ArrayList<Domain>();
 939                         for( final Domain domain : protein.getProteinDomains() ) {
 940                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 941                                 domain_list.add( domain );
 942                             }
 943                         }
 944                         final Domain domain_ary[] = new Domain[ domain_list.size() ];
 945                         for( int i = 0; i < domain_list.size(); ++i ) {
 946                             domain_ary[ i ] = domain_list.get( i );
 947                         }
 948                         Arrays.sort( domain_ary, new DomainComparator( true ) );
 949                         out.write( "{" );
 950                         boolean first = true;
 951                         for( final Domain domain : domain_ary ) {
 952                             if ( first ) {
 953                                 first = false;
 954                             }
 955                             else {
 956                                 out.write( "," );
 957                             }
 958                             out.write( domain.getDomainId().toString() );
 959                             out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
 960                             out.write( ":" + domain.getPerDomainEvalue() );
 961                         }
 962                         out.write( "}" );
 963                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 964                                 .equals( SurfacingConstants.NONE ) ) ) {
 965                             out.write( protein.getDescription() );
 966                         }
 967                         out.write( separator );
 968                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 969                                 .equals( SurfacingConstants.NONE ) ) ) {
 970                             out.write( protein.getAccession() );
 971                         }
 972                         out.write( SurfacingConstants.NL );
 973                     }
 974                 }
 975             }
 976         }
 977         out.flush();
 978     }
 979
 980     public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
 981         final SortedSet<String> all_domains_ids = new TreeSet<String>();
 982         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 983             final Set<String> all_domains = gwcd.getAllDomainIds();
 984             //    for( final Domain domain : all_domains ) {
 985             all_domains_ids.addAll( all_domains );
 986             //    }
 987         }
 988         return all_domains_ids;
 989     }
 990
 991     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
 992         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
 993         for( final Protein protein_domain_collection : protein_domain_collections ) {
 994             for( final Object name : protein_domain_collection.getProteinDomains() ) {
 995                 final BasicDomain protein_domain = ( BasicDomain ) name;
 996                 final String id = protein_domain.getDomainId();
 997                 if ( map.containsKey( id ) ) {
 998                     map.put( id, map.get( id ) + 1 );
 999                 }
1000                 else {
1001                     map.put( id, 1 );
1002                 }
1003             }
1004         }
1005         return map;
1006     }
1007
1008     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1009         final PhylogenyNodeIterator it = p.iteratorPostorder();
1010         int c = 0;
1011         while ( it.hasNext() ) {
1012             final PhylogenyNode n = it.next();
1013             if ( ForesterUtil.isEmpty( n.getName() )
1014                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1015                             .getScientificName() ) )
1016                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1017                             .getCommonName() ) ) ) {
1018                 if ( n.getParent() != null ) {
1019                     names.append( " " );
1020                     names.append( n.getParent().getName() );
1021                 }
1022                 final List l = n.getAllExternalDescendants();
1023                 for( final Object object : l ) {
1024                     System.out.println( l.toString() );
1025                 }
1026                 ++c;
1027             }
1028         }
1029         return c;
1030     }
1031
1032     /**
1033      * Returns true is Domain domain falls in an uninterrupted stretch of
1034      * covered positions.
1035      *
1036      * @param domain
1037      * @param covered_positions
1038      * @return
1039      */
1040     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1041         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1042             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1043                 return false;
1044             }
1045         }
1046         return true;
1047     }
1048
1049     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
1050                                                           final SortedMap<String, Integer> domain_architecuture_counts,
1051                                                           final int min_count,
1052                                                           final File da_counts_outfile,
1053                                                           final File unique_da_outfile ) {
1054         checkForOutputFileWriteability( da_counts_outfile );
1055         checkForOutputFileWriteability( unique_da_outfile );
1056         try {
1057             final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
1058             final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
1059             final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
1060             while ( it.hasNext() ) {
1061                 final Map.Entry<String, Integer> e = it.next();
1062                 final String da = e.getKey();
1063                 final int count = e.getValue();
1064                 if ( count >= min_count ) {
1065                     da_counts_out.write( da );
1066                     da_counts_out.write( "\t" );
1067                     da_counts_out.write( String.valueOf( count ) );
1068                     da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
1069                 }
1070                 if ( count == 1 ) {
1071                     final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
1072                     while ( it2.hasNext() ) {
1073                         final Map.Entry<String, Set<String>> e2 = it2.next();
1074                         final String genome = e2.getKey();
1075                         final Set<String> das = e2.getValue();
1076                         if ( das.contains( da ) ) {
1077                             unique_da_out.write( genome );
1078                             unique_da_out.write( "\t" );
1079                             unique_da_out.write( da );
1080                             unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
1081                         }
1082                     }
1083                 }
1084             }
1085             unique_da_out.close();
1086             da_counts_out.close();
1087         }
1088         catch ( final IOException e ) {
1089             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1090         }
1091         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
1092         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
1093         //
1094     }
1095
1096     public static void preparePhylogeny( final Phylogeny p,
1097                                          final DomainParsimonyCalculator domain_parsimony,
1098                                          final String date_time,
1099                                          final String method,
1100                                          final String name,
1101                                          final String parameters_str ) {
1102         domain_parsimony.decoratePhylogenyWithDomains( p );
1103         final StringBuilder desc = new StringBuilder();
1104         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1105         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1106         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1107         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1108         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1109         desc.append( "[Parameters: " + parameters_str + "]" );
1110         p.setName( name );
1111         p.setDescription( desc.toString() );
1112         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1113         p.setRerootable( false );
1114         p.setRooted( true );
1115     }
1116
1117     /*
1118      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1119      *
1120      *
1121      */
1122     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1123                                                             final String protein_id,
1124                                                             final String separator ) {
1125         final StringBuffer sb = new StringBuffer();
1126         if ( protein.getSpecies() == null ) {
1127             throw new IllegalArgumentException( "species must not be null" );
1128         }
1129         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1130             throw new IllegalArgumentException( "species id must not be empty" );
1131         }
1132         final List<Domain> domains = protein.getProteinDomains();
1133         if ( domains.size() > 1 ) {
1134             final Map<String, Integer> counts = new HashMap<String, Integer>();
1135             for( final Domain domain : domains ) {
1136                 final String id = domain.getDomainId();
1137                 if ( counts.containsKey( id ) ) {
1138                     counts.put( id, counts.get( id ) + 1 );
1139                 }
1140                 else {
1141                     counts.put( id, 1 );
1142                 }
1143             }
1144             final Set<String> dcs = new HashSet<String>();
1145             for( int i = 1; i < domains.size(); ++i ) {
1146                 for( int j = 0; j < i; ++j ) {
1147                     Domain domain_n = domains.get( i );
1148                     Domain domain_c = domains.get( j );
1149                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1150                         domain_n = domains.get( j );
1151                         domain_c = domains.get( i );
1152                     }
1153                     final String dc = domain_n.getDomainId() + domain_c.getDomainId();
1154                     if ( !dcs.contains( dc ) ) {
1155                         dcs.add( dc );
1156                         sb.append( protein.getSpecies() );
1157                         sb.append( separator );
1158                         sb.append( protein_id );
1159                         sb.append( separator );
1160                         sb.append( domain_n.getDomainId() );
1161                         sb.append( separator );
1162                         sb.append( domain_c.getDomainId() );
1163                         sb.append( separator );
1164                         sb.append( domain_n.getPerDomainEvalue() );
1165                         sb.append( separator );
1166                         sb.append( domain_c.getPerDomainEvalue() );
1167                         sb.append( separator );
1168                         sb.append( counts.get( domain_n.getDomainId() ) );
1169                         sb.append( separator );
1170                         sb.append( counts.get( domain_c.getDomainId() ) );
1171                         sb.append( ForesterUtil.LINE_SEPARATOR );
1172                     }
1173                 }
1174             }
1175         }
1176         else if ( domains.size() == 1 ) {
1177             sb.append( protein.getSpecies() );
1178             sb.append( separator );
1179             sb.append( protein_id );
1180             sb.append( separator );
1181             sb.append( domains.get( 0 ).getDomainId() );
1182             sb.append( separator );
1183             sb.append( separator );
1184             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1185             sb.append( separator );
1186             sb.append( separator );
1187             sb.append( 1 );
1188             sb.append( separator );
1189             sb.append( ForesterUtil.LINE_SEPARATOR );
1190         }
1191         else {
1192             sb.append( protein.getSpecies() );
1193             sb.append( separator );
1194             sb.append( protein_id );
1195             sb.append( separator );
1196             sb.append( separator );
1197             sb.append( separator );
1198             sb.append( separator );
1199             sb.append( separator );
1200             sb.append( separator );
1201             sb.append( ForesterUtil.LINE_SEPARATOR );
1202         }
1203         return sb;
1204     }
1205
1206     /**
1207      *
1208      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1209      * domain with 0.3 is ignored
1210      *
1211      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1212      *
1213      *
1214      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1215      * ignored
1216      *
1217      * @param max_allowed_overlap
1218      *            maximal allowed overlap (inclusive) to be still considered not
1219      *            overlapping (zero or negative value to allow any overlap)
1220      * @param remove_engulfed_domains
1221      *            to remove domains which are completely engulfed by coverage of
1222      *            domains with better support
1223      * @param protein
1224      * @return
1225      */
1226     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1227                                                     final boolean remove_engulfed_domains,
1228                                                     final Protein protein ) {
1229         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1230                 .getSpeciesId(), protein.getLength() );
1231         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1232         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1233         for( final Domain domain : sorted ) {
1234             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1235                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1236                 final int covered_positions_size = covered_positions.size();
1237                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1238                     covered_positions.add( false );
1239                 }
1240                 final int new_covered_positions_size = covered_positions.size();
1241                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1242                     if ( i < new_covered_positions_size ) {
1243                         covered_positions.set( i, true );
1244                     }
1245                     else {
1246                         covered_positions.add( true );
1247                     }
1248                 }
1249                 pruned_protein.addProteinDomain( domain );
1250             }
1251         }
1252         return pruned_protein;
1253     }
1254
1255     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1256         final List<Domain> domains = new ArrayList<Domain>();
1257         for( final Domain d : protein.getProteinDomains() ) {
1258             domains.add( d );
1259         }
1260         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1261         return domains;
1262     }
1263
1264     public static int storeDomainArchitectures( final String genome,
1265                                                 final SortedMap<String, Set<String>> domain_architecutures,
1266                                                 final List<Protein> protein_list,
1267                                                 final Map<String, Integer> distinct_domain_architecuture_counts ) {
1268         final Set<String> da = new HashSet<String>();
1269         domain_architecutures.put( genome, da );
1270         for( final Protein protein : protein_list ) {
1271             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
1272             if ( !da.contains( da_str ) ) {
1273                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
1274                     distinct_domain_architecuture_counts.put( da_str, 1 );
1275                 }
1276                 else {
1277                     distinct_domain_architecuture_counts.put( da_str,
1278                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
1279                 }
1280                 da.add( da_str );
1281             }
1282         }
1283         return da.size();
1284     }
1285
1286     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1287                                                             final boolean get_gains,
1288                                                             final String outdir,
1289                                                             final String suffix_for_filename ) throws IOException {
1290         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1291         if ( !get_gains ) {
1292             state = CharacterStateMatrix.GainLossStates.LOSS;
1293         }
1294         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1295                                                                   false,
1296                                                                   state,
1297                                                                   outdir );
1298         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1299             final PhylogenyNode node = it.next();
1300             if ( !node.isExternal() ) {
1301                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1302                 if ( domains.size() > 0 ) {
1303                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1304                             + node.getName() + suffix_for_filename );
1305                     for( final String domain : domains ) {
1306                         writer.write( domain );
1307                         writer.write( ForesterUtil.LINE_SEPARATOR );
1308                     }
1309                     writer.close();
1310                 }
1311             }
1312         }
1313     }
1314
1315     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1316                                                                           final File output_dir,
1317                                                                           final GenomeWideCombinableDomains gwcd,
1318                                                                           final int i,
1319                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1320         File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
1321                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1322         if ( output_dir != null ) {
1323             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1324         }
1325         checkForOutputFileWriteability( dc_outfile_dot );
1326         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1327         try {
1328             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1329             for( final BinaryDomainCombination bdc : binary_combinations ) {
1330                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1331                         .toString() );
1332                 out_dot.write( SurfacingConstants.NL );
1333             }
1334             out_dot.close();
1335         }
1336         catch ( final IOException e ) {
1337             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1338         }
1339         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1340                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1341                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1342     }
1343
1344     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1345                                                             final CharacterStateMatrix.GainLossStates state,
1346                                                             final String filename,
1347                                                             final String indentifier_characters_separator,
1348                                                             final String character_separator,
1349                                                             final Map<String, String> descriptions ) {
1350         final File outfile = new File( filename );
1351         checkForOutputFileWriteability( outfile );
1352         final SortedSet<String> sorted_ids = new TreeSet<String>();
1353         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1354             sorted_ids.add( matrix.getIdentifier( i ) );
1355         }
1356         try {
1357             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1358             for( final String id : sorted_ids ) {
1359                 out.write( indentifier_characters_separator );
1360                 out.write( "#" + id );
1361                 out.write( indentifier_characters_separator );
1362                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1363                     // Not nice:
1364                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1365                     if ( ( matrix.getState( id, c ) == state )
1366                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1367                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1368                         out.write( matrix.getCharacter( c ) );
1369                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1370                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1371                             out.write( "\t" );
1372                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1373                         }
1374                         out.write( character_separator );
1375                     }
1376                 }
1377             }
1378             out.flush();
1379             out.close();
1380         }
1381         catch ( final IOException e ) {
1382             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1383         }
1384         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1385     }
1386
1387     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1388                                                                                                  final CharacterStateMatrix.GainLossStates state,
1389                                                                                                  final String filename,
1390                                                                                                  final String indentifier_characters_separator,
1391                                                                                                  final String character_separator,
1392                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1393         final File outfile = new File( filename );
1394         checkForOutputFileWriteability( outfile );
1395         final SortedSet<String> sorted_ids = new TreeSet<String>();
1396         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1397             sorted_ids.add( matrix.getIdentifier( i ) );
1398         }
1399         try {
1400             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1401             for( final String id : sorted_ids ) {
1402                 out.write( indentifier_characters_separator );
1403                 out.write( "#" + id );
1404                 out.write( indentifier_characters_separator );
1405                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1406                     // Not nice:
1407                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1408                     if ( ( matrix.getState( id, c ) == state )
1409                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1410                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1411                         BinaryDomainCombination bdc = null;
1412                         try {
1413                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1414                         }
1415                         catch ( final Exception e ) {
1416                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1417                         }
1418                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1419                         out.write( character_separator );
1420                     }
1421                 }
1422             }
1423             out.flush();
1424             out.close();
1425         }
1426         catch ( final IOException e ) {
1427             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1428         }
1429         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1430     }
1431
1432     public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
1433                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1434                                                       final GoNameSpace go_namespace_limit,
1435                                                       final boolean domain_combinations,
1436                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1437                                                       final CharacterStateMatrix.GainLossStates state,
1438                                                       final String filename,
1439                                                       final String indentifier_characters_separator,
1440                                                       final String character_separator,
1441                                                       final String title_for_html,
1442                                                       final String prefix_for_html,
1443                                                       final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
1444                                                       final SortedSet<String> all_pfams_encountered,
1445                                                       final SortedSet<String> pfams_gained_or_lost,
1446                                                       final String suffix_for_per_node_events_file,
1447                                                       final Map<String, Integer> tax_code_to_id_map ) {
1448         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1449             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1450         }
1451         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1452             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1453         }
1454         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1455             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1456         }
1457         final File outfile = new File( filename );
1458         checkForOutputFileWriteability( outfile );
1459         final SortedSet<String> sorted_ids = new TreeSet<String>();
1460         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1461             sorted_ids.add( matrix.getIdentifier( i ) );
1462         }
1463         try {
1464             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1465             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1466                                                                                                                 domain_combinations,
1467                                                                                                                 state,
1468                                                                                                                 filename );
1469             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1470             File per_node_go_mapped_domain_gain_loss_outfile = null;
1471             int per_node_counter = 0;
1472             out.write( "<html>" );
1473             out.write( SurfacingConstants.NL );
1474             addHtmlHead( out, title_for_html );
1475             out.write( SurfacingConstants.NL );
1476             out.write( "<body>" );
1477             out.write( SurfacingConstants.NL );
1478             out.write( "<h1>" );
1479             out.write( SurfacingConstants.NL );
1480             out.write( title_for_html );
1481             out.write( SurfacingConstants.NL );
1482             out.write( "</h1>" );
1483             out.write( SurfacingConstants.NL );
1484             out.write( "<table>" );
1485             out.write( SurfacingConstants.NL );
1486             for( final String id : sorted_ids ) {
1487                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1488                 if ( matcher.matches() ) {
1489                     continue;
1490                 }
1491                 out.write( "<tr>" );
1492                 out.write( "<td>" );
1493                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1494                 out.write( "</td>" );
1495                 out.write( "</tr>" );
1496                 out.write( SurfacingConstants.NL );
1497             }
1498             out.write( "</table>" );
1499             out.write( SurfacingConstants.NL );
1500             for( final String id : sorted_ids ) {
1501                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1502                 if ( matcher.matches() ) {
1503                     continue;
1504                 }
1505                 out.write( SurfacingConstants.NL );
1506                 out.write( "<h2>" );
1507                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1508                 writeTaxonomyLinks( out, id, tax_code_to_id_map );
1509                 out.write( "</h2>" );
1510                 out.write( SurfacingConstants.NL );
1511                 out.write( "<table>" );
1512                 out.write( SurfacingConstants.NL );
1513                 out.write( "<tr>" );
1514                 out.write( "<td><b>" );
1515                 out.write( "Pfam domain(s)" );
1516                 out.write( "</b></td><td><b>" );
1517                 out.write( "GO term acc" );
1518                 out.write( "</b></td><td><b>" );
1519                 out.write( "GO term" );
1520                 out.write( "</b></td><td><b>" );
1521                 out.write( "GO namespace" );
1522                 out.write( "</b></td>" );
1523                 out.write( "</tr>" );
1524                 out.write( SurfacingConstants.NL );
1525                 out.write( "</tr>" );
1526                 out.write( SurfacingConstants.NL );
1527                 per_node_counter = 0;
1528                 if ( matrix.getNumberOfCharacters() > 0 ) {
1529                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1530                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1531                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1532                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1533                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1534                 }
1535                 else {
1536                     per_node_go_mapped_domain_gain_loss_outfile = null;
1537                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1538                 }
1539                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1540                     // Not nice:
1541                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1542                     if ( ( matrix.getState( id, c ) == state )
1543                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1544                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1545                         final String character = matrix.getCharacter( c );
1546                         String domain_0 = "";
1547                         String domain_1 = "";
1548                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1549                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1550                             if ( s.length != 2 ) {
1551                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1552                                         + character + "]" );
1553                             }
1554                             domain_0 = s[ 0 ];
1555                             domain_1 = s[ 1 ];
1556                         }
1557                         else {
1558                             domain_0 = character;
1559                         }
1560                         writeDomainData( domain_id_to_go_ids_map,
1561                                          go_id_to_term_map,
1562                                          go_namespace_limit,
1563                                          out,
1564                                          domain_0,
1565                                          domain_1,
1566                                          prefix_for_html,
1567                                          character_separator,
1568                                          domain_id_to_secondary_features_maps,
1569                                          null );
1570                         all_pfams_encountered.add( domain_0 );
1571                         if ( pfams_gained_or_lost != null ) {
1572                             pfams_gained_or_lost.add( domain_0 );
1573                         }
1574                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1575                             all_pfams_encountered.add( domain_1 );
1576                             if ( pfams_gained_or_lost != null ) {
1577                                 pfams_gained_or_lost.add( domain_1 );
1578                             }
1579                         }
1580                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1581                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1582                                                                      domain_0,
1583                                                                      domain_1 );
1584                             per_node_counter++;
1585                         }
1586                     }
1587                 }
1588                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1589                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1590                     if ( per_node_counter < 1 ) {
1591                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1592                     }
1593                     per_node_counter = 0;
1594                 }
1595                 out.write( "</table>" );
1596                 out.write( SurfacingConstants.NL );
1597                 out.write( "<hr>" );
1598                 out.write( SurfacingConstants.NL );
1599             } // for( final String id : sorted_ids ) {
1600             out.write( "</body>" );
1601             out.write( SurfacingConstants.NL );
1602             out.write( "</html>" );
1603             out.write( SurfacingConstants.NL );
1604             out.flush();
1605             out.close();
1606         }
1607         catch ( final IOException e ) {
1608             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1609         }
1610         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1611     }
1612
1613     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1614                                                           final File output_dir,
1615                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1616                                                           final GenomeWideCombinableDomains gwcd,
1617                                                           final int i,
1618                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1619         File dc_outfile = new File( input_file_properties[ i ][ 1 ]
1620                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1621         if ( output_dir != null ) {
1622             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1623         }
1624         checkForOutputFileWriteability( dc_outfile );
1625         try {
1626             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1627             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1628             out.close();
1629         }
1630         catch ( final IOException e ) {
1631             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1632         }
1633         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1634         try {
1635             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
1636             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1637             if ( stats.getN() < 2 ) {
1638                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1639             }
1640             else {
1641                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1642                         .sampleStandardDeviation() ) + "\t" );
1643             }
1644             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1645             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1646             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1647             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1648             final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
1649             for( final String mpd : mpds ) {
1650                 per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
1651             }
1652             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1653         }
1654         catch ( final IOException e ) {
1655             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1656         }
1657         if ( input_file_properties[ i ].length == 3 ) {
1658             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1659                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1660                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1661         }
1662         else {
1663             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1664                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1665                     + dc_outfile + "\"" );
1666         }
1667     }
1668
1669     public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
1670                                                       final StringBuilder html_title,
1671                                                       final Writer simple_tab_writer,
1672                                                       final Writer single_writer,
1673                                                       Map<Character, Writer> split_writers,
1674                                                       final SortedSet<DomainSimilarity> similarities,
1675                                                       final boolean treat_as_binary,
1676                                                       final List<Species> species_order,
1677                                                       final PrintableDomainSimilarity.PRINT_OPTION print_option,
1678                                                       final DomainSimilarity.DomainSimilarityScoring scoring,
1679                                                       final boolean verbose,
1680                                                       final Map<String, Integer> tax_code_to_id_map )
1681             throws IOException {
1682         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
1683             split_writers = new HashMap<Character, Writer>();
1684             split_writers.put( '_', single_writer );
1685         }
1686         switch ( print_option ) {
1687             case SIMPLE_TAB_DELIMITED:
1688                 break;
1689             case HTML:
1690                 for( final Character key : split_writers.keySet() ) {
1691                     final Writer w = split_writers.get( key );
1692                     w.write( "<html>" );
1693                     w.write( SurfacingConstants.NL );
1694                     if ( key != '_' ) {
1695                         addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
1696                     }
1697                     else {
1698                         addHtmlHead( w, "DC analysis (" + html_title + ")" );
1699                     }
1700                     w.write( SurfacingConstants.NL );
1701                     w.write( "<body>" );
1702                     w.write( SurfacingConstants.NL );
1703                     w.write( html_desc.toString() );
1704                     w.write( SurfacingConstants.NL );
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 ( simple_tab_writer != null ) {
1751                 simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
1752                                                                     tax_code_to_id_map ).toString() );
1753             }
1754             if ( single_writer != null ) {
1755                 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1756                 single_writer.write( SurfacingConstants.NL );
1757             }
1758             else {
1759                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
1760                         .charAt( 0 ) );
1761                 if ( local_writer == null ) {
1762                     local_writer = split_writers.get( '0' );
1763                 }
1764                 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1765                 local_writer.write( SurfacingConstants.NL );
1766             }
1767         }
1768         switch ( print_option ) {
1769             case HTML:
1770                 for( final Writer w : split_writers.values() ) {
1771                     w.write( SurfacingConstants.NL );
1772                     w.write( "</table>" );
1773                     w.write( SurfacingConstants.NL );
1774                     w.write( "</font>" );
1775                     w.write( SurfacingConstants.NL );
1776                     w.write( "</body>" );
1777                     w.write( SurfacingConstants.NL );
1778                     w.write( "</html>" );
1779                     w.write( SurfacingConstants.NL );
1780                 }
1781                 break;
1782         }
1783         for( final Writer w : split_writers.values() ) {
1784             w.close();
1785         }
1786     }
1787
1788     private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
1789             throws IOException {
1790         w.write( "<hr>" );
1791         w.write( "<br>" );
1792         w.write( SurfacingConstants.NL );
1793         w.write( "<tt><pre>" );
1794         w.write( SurfacingConstants.NL );
1795         if ( histo != null ) {
1796             w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
1797             w.write( SurfacingConstants.NL );
1798         }
1799         w.write( "</pre></tt>" );
1800         w.write( SurfacingConstants.NL );
1801         w.write( "<table>" );
1802         w.write( SurfacingConstants.NL );
1803         w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
1804         w.write( SurfacingConstants.NL );
1805         w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
1806         w.write( SurfacingConstants.NL );
1807         w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
1808         w.write( SurfacingConstants.NL );
1809         w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
1810         w.write( SurfacingConstants.NL );
1811         if ( stats.getN() > 1 ) {
1812             w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
1813         }
1814         else {
1815             w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
1816         }
1817         w.write( SurfacingConstants.NL );
1818         w.write( "</table>" );
1819         w.write( SurfacingConstants.NL );
1820         w.write( "<br>" );
1821         w.write( SurfacingConstants.NL );
1822     }
1823
1824     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
1825                                           final String filename,
1826                                           final Format format ) {
1827         final File outfile = new File( filename );
1828         checkForOutputFileWriteability( outfile );
1829         try {
1830             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1831             matrix.toWriter( out, format );
1832             out.flush();
1833             out.close();
1834         }
1835         catch ( final IOException e ) {
1836             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1837         }
1838         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
1839     }
1840
1841     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
1842         checkForOutputFileWriteability( matrix_outfile );
1843         try {
1844             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
1845             for( final DistanceMatrix distance_matrix : matrices ) {
1846                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
1847                 out.write( ForesterUtil.LINE_SEPARATOR );
1848                 out.flush();
1849             }
1850             out.close();
1851         }
1852         catch ( final IOException e ) {
1853             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1854         }
1855         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
1856     }
1857
1858     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
1859         final PhylogenyWriter writer = new PhylogenyWriter();
1860         try {
1861             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
1862         }
1863         catch ( final IOException e ) {
1864             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
1865                     + e );
1866         }
1867         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
1868     }
1869
1870     public static void writeTaxonomyLinks( final Writer writer,
1871                                            final String species,
1872                                            final Map<String, Integer> tax_code_to_id_map ) throws IOException {
1873         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
1874             writer.write( " [" );
1875             if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
1876                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
1877                         + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
1878             }
1879             else {
1880                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
1881                         + "\" target=\"taxonomy_window\">eol</a>" );
1882                 writer.write( "|" );
1883                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
1884                         + "\" target=\"taxonomy_window\">scholar</a>" );
1885                 writer.write( "|" );
1886                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
1887                         + "\" target=\"taxonomy_window\">google</a>" );
1888             }
1889             writer.write( "]" );
1890         }
1891     }
1892
1893     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
1894         if ( map.containsKey( s ) ) {
1895             map.put( s, map.get( s ) + 1 );
1896         }
1897         else {
1898             map.put( s, 1 );
1899         }
1900     }
1901
1902     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
1903                                                                     final String outfilename_for_counts,
1904                                                                     final String outfilename_for_dc,
1905                                                                     final String outfilename_for_dc_for_go_mapping,
1906                                                                     final String outfilename_for_dc_for_go_mapping_unique,
1907                                                                     final String outfilename_for_rank_counts,
1908                                                                     final String outfilename_for_ancestor_species_counts,
1909                                                                     final String outfilename_for_protein_stats,
1910                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
1911                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
1912                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
1913         try {
1914             //
1915             //            if ( protein_length_stats_by_dc != null ) {
1916             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
1917             //                    System.out.print( entry.getKey().toString() );
1918             //                    System.out.print( ": " );
1919             //                    double[] a = entry.getValue().getDataAsDoubleArray();
1920             //                    for( int i = 0; i < a.length; i++ ) {
1921             //                        System.out.print( a[ i ] + " " );
1922             //                    }
1923             //                    System.out.println();
1924             //                }
1925             //            }
1926             //            if ( domain_number_stats_by_dc != null ) {
1927             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
1928             //                    System.out.print( entry.getKey().toString() );
1929             //                    System.out.print( ": " );
1930             //                    double[] a = entry.getValue().getDataAsDoubleArray();
1931             //                    for( int i = 0; i < a.length; i++ ) {
1932             //                        System.out.print( a[ i ] + " " );
1933             //                    }
1934             //                    System.out.println();
1935             //                }
1936             //            }
1937             //
1938             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
1939             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
1940             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
1941             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
1942             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
1943             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
1944                 final PhylogenyNode n = it.next();
1945                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
1946                 for( final String dc : gained_dc ) {
1947                     if ( dc_gain_counts.containsKey( dc ) ) {
1948                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
1949                     }
1950                     else {
1951                         dc_gain_counts.put( dc, 1 );
1952                     }
1953                 }
1954             }
1955             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
1956             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
1957             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
1958             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
1959             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
1960             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
1961             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
1962             final Set<String> dcs = dc_gain_counts.keySet();
1963             final SortedSet<String> more_than_once = new TreeSet<String>();
1964             DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
1965             DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
1966             DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
1967             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
1968             long gained_multiple_times_domain_length_sum = 0;
1969             long gained_once_domain_length_sum = 0;
1970             long gained_multiple_times_domain_length_count = 0;
1971             long gained_once_domain_length_count = 0;
1972             for( final String dc : dcs ) {
1973                 final int count = dc_gain_counts.get( dc );
1974                 if ( histogram.containsKey( count ) ) {
1975                     histogram.put( count, histogram.get( count ) + 1 );
1976                     domain_lists.get( count ).append( ", " + dc );
1977                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
1978                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
1979                 }
1980                 else {
1981                     histogram.put( count, 1 );
1982                     domain_lists.put( count, new StringBuilder( dc ) );
1983                     final PriorityQueue<String> q = new PriorityQueue<String>();
1984                     q.addAll( splitDomainCombination( dc ) );
1985                     domain_lists_go.put( count, q );
1986                     final SortedSet<String> set = new TreeSet<String>();
1987                     set.addAll( splitDomainCombination( dc ) );
1988                     domain_lists_go_unique.put( count, set );
1989                 }
1990                 if ( protein_length_stats_by_dc != null ) {
1991                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
1992                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
1993                     }
1994                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
1995                             .arithmeticMean() );
1996                 }
1997                 if ( domain_number_stats_by_dc != null ) {
1998                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
1999                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
2000                     }
2001                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
2002                             .arithmeticMean() );
2003                 }
2004                 if ( domain_length_stats_by_domain != null ) {
2005                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
2006                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
2007                     }
2008                     final String[] ds = dc.split( "=" );
2009                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2010                             .get( ds[ 0 ] ).arithmeticMean() );
2011                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2012                             .get( ds[ 1 ] ).arithmeticMean() );
2013                 }
2014                 if ( count > 1 ) {
2015                     more_than_once.add( dc );
2016                     if ( protein_length_stats_by_dc != null ) {
2017                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2018                         for( final double element : s.getData() ) {
2019                             gained_multiple_times_lengths_stats.addValue( element );
2020                         }
2021                     }
2022                     if ( domain_number_stats_by_dc != null ) {
2023                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2024                         for( final double element : s.getData() ) {
2025                             gained_multiple_times_domain_count_stats.addValue( element );
2026                         }
2027                     }
2028                     if ( domain_length_stats_by_domain != null ) {
2029                         final String[] ds = dc.split( "=" );
2030                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2031                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2032                         for( final double element : s0.getData() ) {
2033                             gained_multiple_times_domain_length_sum += element;
2034                             ++gained_multiple_times_domain_length_count;
2035                         }
2036                         for( final double element : s1.getData() ) {
2037                             gained_multiple_times_domain_length_sum += element;
2038                             ++gained_multiple_times_domain_length_count;
2039                         }
2040                     }
2041                 }
2042                 else {
2043                     if ( protein_length_stats_by_dc != null ) {
2044                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2045                         for( final double element : s.getData() ) {
2046                             gained_once_lengths_stats.addValue( element );
2047                         }
2048                     }
2049                     if ( domain_number_stats_by_dc != null ) {
2050                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2051                         for( final double element : s.getData() ) {
2052                             gained_once_domain_count_stats.addValue( element );
2053                         }
2054                     }
2055                     if ( domain_length_stats_by_domain != null ) {
2056                         final String[] ds = dc.split( "=" );
2057                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2058                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2059                         for( final double element : s0.getData() ) {
2060                             gained_once_domain_length_sum += element;
2061                             ++gained_once_domain_length_count;
2062                         }
2063                         for( final double element : s1.getData() ) {
2064                             gained_once_domain_length_sum += element;
2065                             ++gained_once_domain_length_count;
2066                         }
2067                     }
2068                 }
2069             }
2070             final Set<Integer> histogram_keys = histogram.keySet();
2071             for( final Integer histogram_key : histogram_keys ) {
2072                 final int count = histogram.get( histogram_key );
2073                 final StringBuilder dc = domain_lists.get( histogram_key );
2074                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
2075                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
2076                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2077                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
2078                 Arrays.sort( sorted );
2079                 for( final Object domain : sorted ) {
2080                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
2081                 }
2082                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2083                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
2084                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
2085                 }
2086             }
2087             out_counts.close();
2088             out_dc.close();
2089             out_dc_for_go_mapping.close();
2090             out_dc_for_go_mapping_unique.close();
2091             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
2092             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
2093             for( final String dc : more_than_once ) {
2094                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
2095                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
2096                     final PhylogenyNode n = it.next();
2097                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
2098                         nodes.add( n );
2099                     }
2100                 }
2101                 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
2102                     for( int j = i + 1; j < nodes.size(); ++j ) {
2103                         final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
2104                         String rank = "unknown";
2105                         if ( lca.getNodeData().isHasTaxonomy()
2106                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
2107                             rank = lca.getNodeData().getTaxonomy().getRank();
2108                         }
2109                         addToCountMap( lca_rank_counts, rank );
2110                         String lca_species;
2111                         if ( lca.getNodeData().isHasTaxonomy()
2112                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
2113                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
2114                         }
2115                         else if ( lca.getNodeData().isHasTaxonomy()
2116                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
2117                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
2118                         }
2119                         else {
2120                             lca_species = lca.getName();
2121                         }
2122                         addToCountMap( lca_ancestor_species_counts, lca_species );
2123                     }
2124                 }
2125             }
2126             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
2127             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
2128             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
2129             ForesterUtil.map2writer( out_for_ancestor_species_counts,
2130                                      lca_ancestor_species_counts,
2131                                      "\t",
2132                                      ForesterUtil.LINE_SEPARATOR );
2133             out_for_rank_counts.close();
2134             out_for_ancestor_species_counts.close();
2135             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
2136                     && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
2137                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
2138                 w.write( "Domain Lengths: " );
2139                 w.write( "\n" );
2140                 if ( domain_length_stats_by_domain != null ) {
2141                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
2142                             .entrySet() ) {
2143                         w.write( entry.getKey().toString() );
2144                         w.write( "\t" + entry.getValue().arithmeticMean() );
2145                         w.write( "\t" + entry.getValue().median() );
2146                         w.write( "\n" );
2147                     }
2148                 }
2149                 w.flush();
2150                 w.write( "\n" );
2151                 w.write( "\n" );
2152                 w.write( "Protein Lengths: " );
2153                 w.write( "\n" );
2154                 if ( protein_length_stats_by_dc != null ) {
2155                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
2156                             .entrySet() ) {
2157                         w.write( entry.getKey().toString() );
2158                         w.write( "\t" + entry.getValue().arithmeticMean() );
2159                         w.write( "\t" + entry.getValue().median() );
2160                         w.write( "\n" );
2161                     }
2162                 }
2163                 w.flush();
2164                 w.write( "\n" );
2165                 w.write( "\n" );
2166                 w.write( "Number of domains: " );
2167                 w.write( "\n" );
2168                 if ( domain_number_stats_by_dc != null ) {
2169                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
2170                             .entrySet() ) {
2171                         w.write( entry.getKey().toString() );
2172                         w.write( "\t" + entry.getValue().arithmeticMean() );
2173                         w.write( "\t" + entry.getValue().median() );
2174                         w.write( "\n" );
2175                     }
2176                 }
2177                 w.flush();
2178                 w.write( "\n" );
2179                 w.write( "\n" );
2180                 w.write( "Gained once, domain lengths:" );
2181                 w.write( "\n" );
2182                 w.write( "N: " + gained_once_domain_length_count );
2183                 w.write( "\n" );
2184                 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
2185                 w.write( "\n" );
2186                 w.write( "\n" );
2187                 w.write( "Gained multiple times, domain lengths:" );
2188                 w.write( "\n" );
2189                 w.write( "N: " + gained_multiple_times_domain_length_count );
2190                 w.write( "\n" );
2191                 w.write( "Avg: "
2192                         + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
2193                 w.write( "\n" );
2194                 w.write( "\n" );
2195                 w.write( "\n" );
2196                 w.write( "\n" );
2197                 w.write( "Gained once, protein lengths:" );
2198                 w.write( "\n" );
2199                 w.write( gained_once_lengths_stats.toString() );
2200                 gained_once_lengths_stats = null;
2201                 w.write( "\n" );
2202                 w.write( "\n" );
2203                 w.write( "Gained once, domain counts:" );
2204                 w.write( "\n" );
2205                 w.write( gained_once_domain_count_stats.toString() );
2206                 gained_once_domain_count_stats = null;
2207                 w.write( "\n" );
2208                 w.write( "\n" );
2209                 w.write( "Gained multiple times, protein lengths:" );
2210                 w.write( "\n" );
2211                 w.write( gained_multiple_times_lengths_stats.toString() );
2212                 gained_multiple_times_lengths_stats = null;
2213                 w.write( "\n" );
2214                 w.write( "\n" );
2215                 w.write( "Gained multiple times, domain counts:" );
2216                 w.write( "\n" );
2217                 w.write( gained_multiple_times_domain_count_stats.toString() );
2218                 w.flush();
2219                 w.close();
2220             }
2221         }
2222         catch ( final IOException e ) {
2223             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2224         }
2225         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
2226                 + outfilename_for_counts + "]" );
2227         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
2228                 + outfilename_for_dc + "]" );
2229         ForesterUtil.programMessage( surfacing.PRG_NAME,
2230                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
2231                                              + outfilename_for_dc_for_go_mapping + "]" );
2232         ForesterUtil.programMessage( surfacing.PRG_NAME,
2233                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
2234                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
2235     }
2236
2237     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
2238                                                                         final boolean get_gains ) {
2239         final SortedSet<String> domains = new TreeSet<String>();
2240         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
2241             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
2242             if ( get_gains ) {
2243                 domains.addAll( chars.getGainedCharacters() );
2244             }
2245             else {
2246                 domains.addAll( chars.getLostCharacters() );
2247             }
2248         }
2249         return domains;
2250     }
2251
2252     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
2253                                                             final boolean domain_combinations,
2254                                                             final CharacterStateMatrix.GainLossStates state,
2255                                                             final String outfile ) {
2256         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
2257                 + ForesterUtil.FILE_SEPARATOR + base_dir );
2258         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2259             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2260         }
2261         if ( domain_combinations ) {
2262             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2263                     + ForesterUtil.FILE_SEPARATOR + "DC" );
2264         }
2265         else {
2266             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2267                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
2268         }
2269         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2270             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2271         }
2272         if ( state == GainLossStates.GAIN ) {
2273             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2274                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
2275         }
2276         else if ( state == GainLossStates.LOSS ) {
2277             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2278                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
2279         }
2280         else {
2281             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2282                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
2283         }
2284         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2285             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2286         }
2287         return per_node_go_mapped_domain_gain_loss_files_base_dir;
2288     }
2289
2290     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
2291         final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
2292         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
2293         for( final String domain_id : cds.keySet() ) {
2294             final CombinableDomains cd = cds.get( domain_id );
2295             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
2296         }
2297         return binary_combinations;
2298     }
2299
2300     private static List<String> splitDomainCombination( final String dc ) {
2301         final String[] s = dc.split( "=" );
2302         if ( s.length != 2 ) {
2303             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
2304                     + dc );
2305             System.exit( -1 );
2306         }
2307         final List<String> l = new ArrayList<String>( 2 );
2308         l.add( s[ 0 ] );
2309         l.add( s[ 1 ] );
2310         return l;
2311     }
2312
2313     private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2314                                                         final Map<GoId, GoTerm> go_id_to_term_map,
2315                                                         final String outfile_name,
2316                                                         final SortedSet<String> all_pfams_encountered ) {
2317         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
2318         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
2319                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
2320         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
2321         int biological_process_counter = 0;
2322         int cellular_component_counter = 0;
2323         int molecular_function_counter = 0;
2324         int pfams_with_mappings_counter = 0;
2325         int pfams_without_mappings_counter = 0;
2326         int pfams_without_mappings_to_bp_or_mf_counter = 0;
2327         int pfams_with_mappings_to_bp_or_mf_counter = 0;
2328         try {
2329             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
2330             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
2331             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
2332             summary_writer.write( "# Pfam to GO mapping summary" );
2333             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2334             summary_writer.write( "# Actual summary is at the end of this file." );
2335             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2336             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
2337             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2338             for( final String pfam : all_pfams_encountered ) {
2339                 all_pfams_encountered_writer.write( pfam );
2340                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
2341                 final String domain_id = new String( pfam );
2342                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2343                     ++pfams_with_mappings_counter;
2344                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
2345                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
2346                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
2347                     boolean maps_to_bp = false;
2348                     boolean maps_to_cc = false;
2349                     boolean maps_to_mf = false;
2350                     for( final GoId go_id : go_ids ) {
2351                         final GoTerm go_term = go_id_to_term_map.get( go_id );
2352                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
2353                             maps_to_bp = true;
2354                         }
2355                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
2356                             maps_to_cc = true;
2357                         }
2358                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
2359                             maps_to_mf = true;
2360                         }
2361                     }
2362                     if ( maps_to_bp ) {
2363                         ++biological_process_counter;
2364                     }
2365                     if ( maps_to_cc ) {
2366                         ++cellular_component_counter;
2367                     }
2368                     if ( maps_to_mf ) {
2369                         ++molecular_function_counter;
2370                     }
2371                     if ( maps_to_bp || maps_to_mf ) {
2372                         ++pfams_with_mappings_to_bp_or_mf_counter;
2373                     }
2374                     else {
2375                         ++pfams_without_mappings_to_bp_or_mf_counter;
2376                     }
2377                 }
2378                 else {
2379                     ++pfams_without_mappings_to_bp_or_mf_counter;
2380                     ++pfams_without_mappings_counter;
2381                     summary_writer.write( pfam );
2382                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2383                 }
2384             }
2385             all_pfams_encountered_writer.close();
2386             all_pfams_encountered_with_go_annotation_writer.close();
2387             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
2388                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
2389             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
2390                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
2391                     + "\"" );
2392             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
2393                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
2394                     + encountered_pfams_summary_file + "\"" );
2395             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
2396                     + all_pfams_encountered.size() );
2397             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
2398                     + pfams_without_mappings_counter + " ["
2399                     + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2400             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
2401                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2402                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2403             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
2404                     + pfams_with_mappings_counter + " ["
2405                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2406             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
2407                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2408                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2409             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
2410                     + biological_process_counter + " ["
2411                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2412             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
2413                     + molecular_function_counter + " ["
2414                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2415             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
2416                     + cellular_component_counter + " ["
2417                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2418             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2419             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
2420             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2421             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
2422                     + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2423             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2424             summary_writer.write( "# Pfams without mapping to proc. or func. : "
2425                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2426                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2427             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2428             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
2429                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2430             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2431             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
2432                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2433                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2434             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2435             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
2436                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2437             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2438             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
2439                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2440             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2441             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
2442                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2443             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2444             summary_writer.close();
2445         }
2446         catch ( final IOException e ) {
2447             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2448         }
2449     }
2450
2451     private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2452                                          final Map<GoId, GoTerm> go_id_to_term_map,
2453                                          final GoNameSpace go_namespace_limit,
2454                                          final Writer out,
2455                                          final String domain_0,
2456                                          final String domain_1,
2457                                          final String prefix_for_html,
2458                                          final String character_separator_for_non_html_output,
2459                                          final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
2460                                          final Set<GoId> all_go_ids ) throws IOException {
2461         boolean any_go_annotation_present = false;
2462         boolean first_has_no_go = false;
2463         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2464         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2465             domain_count = 1;
2466         }
2467         // The following has a difficult to understand logic.
2468         for( int d = 0; d < domain_count; ++d ) {
2469             List<GoId> go_ids = null;
2470             boolean go_annotation_present = false;
2471             if ( d == 0 ) {
2472                 if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
2473                     go_annotation_present = true;
2474                     any_go_annotation_present = true;
2475                     go_ids = domain_id_to_go_ids_map.get( domain_0 );
2476                 }
2477                 else {
2478                     first_has_no_go = true;
2479                 }
2480             }
2481             else {
2482                 if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
2483                     go_annotation_present = true;
2484                     any_go_annotation_present = true;
2485                     go_ids = domain_id_to_go_ids_map.get( domain_1 );
2486                 }
2487             }
2488             if ( go_annotation_present ) {
2489                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2490                 for( final GoId go_id : go_ids ) {
2491                     out.write( "<tr>" );
2492                     if ( first ) {
2493                         first = false;
2494                         writeDomainIdsToHtml( out,
2495                                               domain_0,
2496                                               domain_1,
2497                                               prefix_for_html,
2498                                               domain_id_to_secondary_features_maps );
2499                     }
2500                     else {
2501                         out.write( "<td></td>" );
2502                     }
2503                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2504                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2505                     }
2506                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2507                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2508                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2509                         final String go_id_str = go_id.getId();
2510                         out.write( "<td>" );
2511                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2512                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2513                         out.write( "</td><td>" );
2514                         out.write( go_term.getName() );
2515                         if ( domain_count == 2 ) {
2516                             out.write( " (" + d + ")" );
2517                         }
2518                         out.write( "</td><td>" );
2519                         // out.write( top );
2520                         // out.write( "</td><td>" );
2521                         out.write( "[" );
2522                         out.write( go_term.getGoNameSpace().toShortString() );
2523                         out.write( "]" );
2524                         out.write( "</td>" );
2525                         if ( all_go_ids != null ) {
2526                             all_go_ids.add( go_id );
2527                         }
2528                     }
2529                     else {
2530                         out.write( "<td>" );
2531                         out.write( "</td><td>" );
2532                         out.write( "</td><td>" );
2533                         out.write( "</td><td>" );
2534                         out.write( "</td>" );
2535                     }
2536                     out.write( "</tr>" );
2537                     out.write( SurfacingConstants.NL );
2538                 }
2539             }
2540         } //  for( int d = 0; d < domain_count; ++d )
2541         if ( !any_go_annotation_present ) {
2542             out.write( "<tr>" );
2543             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2544             out.write( "<td>" );
2545             out.write( "</td><td>" );
2546             out.write( "</td><td>" );
2547             out.write( "</td><td>" );
2548             out.write( "</td>" );
2549             out.write( "</tr>" );
2550             out.write( SurfacingConstants.NL );
2551         }
2552     }
2553
2554     private static void writeDomainIdsToHtml( final Writer out,
2555                                               final String domain_0,
2556                                               final String domain_1,
2557                                               final String prefix_for_detailed_html,
2558                                               final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
2559             throws IOException {
2560         out.write( "<td>" );
2561         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2562             out.write( prefix_for_detailed_html );
2563             out.write( " " );
2564         }
2565         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2566         out.write( "</td>" );
2567     }
2568
2569     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2570                                                                  final String domain_0,
2571                                                                  final String domain_1 ) throws IOException {
2572         individual_files_writer.write( domain_0 );
2573         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2574         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2575             individual_files_writer.write( domain_1 );
2576             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2577         }
2578     }
2579
2580     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2581         try {
2582             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2583             for( final String pfam : pfams ) {
2584                 writer.write( pfam );
2585                 writer.write( ForesterUtil.LINE_SEPARATOR );
2586             }
2587             writer.close();
2588             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2589                     + "]" );
2590         }
2591         catch ( final IOException e ) {
2592             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2593         }
2594     }
2595
2596     private static void writeToNexus( final String outfile_name,
2597                                       final CharacterStateMatrix<BinaryStates> matrix,
2598                                       final Phylogeny phylogeny ) {
2599         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2600             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2601                     + "] to nexus" );
2602         }
2603         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2604         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2605         phylogenies.add( phylogeny );
2606         try {
2607             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2608             w.write( NexusConstants.NEXUS );
2609             w.write( ForesterUtil.LINE_SEPARATOR );
2610             my_matrix.writeNexusTaxaBlock( w );
2611             my_matrix.writeNexusBinaryChractersBlock( w );
2612             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2613             w.flush();
2614             w.close();
2615             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2616         }
2617         catch ( final IOException e ) {
2618             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2619         }
2620     }
2621
2622     private static void writeToNexus( final String outfile_name,
2623                                       final DomainParsimonyCalculator domain_parsimony,
2624                                       final Phylogeny phylogeny ) {
2625         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2626                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2627                       phylogeny );
2628         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2629                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2630                       phylogeny );
2631     }
2632
2633     final static class DomainComparator implements Comparator<Domain> {
2634
2635         final private boolean _ascending;
2636
2637         public DomainComparator( final boolean ascending ) {
2638             _ascending = ascending;
2639         }
2640
2641         @Override
2642         public final int compare( final Domain d0, final Domain d1 ) {
2643             if ( d0.getFrom() < d1.getFrom() ) {
2644                 return _ascending ? -1 : 1;
2645             }
2646             else if ( d0.getFrom() > d1.getFrom() ) {
2647                 return _ascending ? 1 : -1;
2648             }
2649             return 0;
2650         }
2651     }
2652 }