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: www.phylosoft.org/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.Collections;
  38 import java.util.Comparator;
  39 import java.util.HashMap;
  40 import java.util.HashSet;
  41 import java.util.List;
  42 import java.util.Map;
  43 import java.util.Set;
  44 import java.util.SortedMap;
  45 import java.util.SortedSet;
  46 import java.util.TreeMap;
  47 import java.util.TreeSet;
  48 import java.util.regex.Matcher;
  49 import java.util.regex.Pattern;
  50
  51 import org.forester.application.surfacing_old;
  52 import org.forester.evoinference.distance.NeighborJoining;
  53 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  54 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  55 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  56 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  57 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  58 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  59 import org.forester.go.GoId;
  60 import org.forester.go.GoNameSpace;
  61 import org.forester.go.GoTerm;
  62 import org.forester.go.GoUtils;
  63 import org.forester.go.PfamToGoMapping;
  64 import org.forester.io.parsers.nexus.NexusConstants;
  65 import org.forester.io.writers.PhylogenyWriter;
  66 import org.forester.phylogeny.Phylogeny;
  67 import org.forester.phylogeny.PhylogenyMethods;
  68 import org.forester.phylogeny.PhylogenyNode;
  69 import org.forester.phylogeny.data.BinaryCharacters;
  70 import org.forester.phylogeny.data.Confidence;
  71 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  72 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  73 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  74 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  75 import org.forester.util.AsciiHistogram;
  76 import org.forester.util.BasicDescriptiveStatistics;
  77 import org.forester.util.BasicTable;
  78 import org.forester.util.BasicTableParser;
  79 import org.forester.util.DescriptiveStatistics;
  80 import org.forester.util.ForesterUtil;
  81
  82 public final class SurfacingUtil {
  83
  84     private final static NumberFormat       FORMATTER                        = new DecimalFormat( "0.0E0" );
  85     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  86     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  87
  88                                                                                  public int compare( final Domain d1,
  89                                                                                                      final Domain d2 ) {
  90                                                                                      if ( d1.getPerSequenceEvalue() < d2
  91                                                                                              .getPerSequenceEvalue() ) {
  92                                                                                          return -1;
  93                                                                                      }
  94                                                                                      else if ( d1
  95                                                                                              .getPerSequenceEvalue() > d2
  96                                                                                              .getPerSequenceEvalue() ) {
  97                                                                                          return 1;
  98                                                                                      }
  99                                                                                      else {
 100                                                                                          return d1.compareTo( d2 );
 101                                                                                      }
 102                                                                                  }
 103                                                                              };
 104     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 105
 106     private SurfacingUtil() {
 107         // Hidden constructor.
 108     }
 109
 110     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 111                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 112         final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 113         for( final DomainId domain_id : all_cd.keySet() ) {
 114             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 115         }
 116     }
 117
 118     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 119                                              final SortedSet<DomainId> domain_ids ) {
 120         final SortedSet<DomainId> domains = genome.getAllDomainIds();
 121         for( final DomainId domain : domains ) {
 122             domain_ids.add( domain );
 123         }
 124     }
 125
 126     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 127         w.write( SurfacingConstants.NL );
 128         w.write( "<head>" );
 129         w.write( "<title>" );
 130         w.write( title );
 131         w.write( "</title>" );
 132         w.write( SurfacingConstants.NL );
 133         w.write( "<style>" );
 134         w.write( SurfacingConstants.NL );
 135         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 136         w.write( SurfacingConstants.NL );
 137         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 138         w.write( SurfacingConstants.NL );
 139         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 140         w.write( SurfacingConstants.NL );
 141         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 142         w.write( SurfacingConstants.NL );
 143         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 144         w.write( SurfacingConstants.NL );
 145         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 146         w.write( SurfacingConstants.NL );
 147         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 148         w.write( SurfacingConstants.NL );
 149         w.write( "</style>" );
 150         w.write( SurfacingConstants.NL );
 151         w.write( "</head>" );
 152         w.write( SurfacingConstants.NL );
 153     }
 154
 155     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 156         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 157         for( final DomainSimilarity similarity : similarities ) {
 158             stats.addValue( similarity.getMeanSimilarityScore() );
 159         }
 160         return stats;
 161     }
 162
 163     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 164         int overlap_count = 0;
 165         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 166             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 167                 ++overlap_count;
 168             }
 169         }
 170         return overlap_count;
 171     }
 172
 173     public static void checkForOutputFileWriteability( final File outfile ) {
 174         final String error = ForesterUtil.isWritableFile( outfile );
 175         if ( !ForesterUtil.isEmpty( error ) ) {
 176             ForesterUtil.fatalError( surfacing_old.PRG_NAME, error );
 177         }
 178     }
 179
 180     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
 181                                                                         final boolean get_gains ) {
 182         final SortedSet<String> domains = new TreeSet<String>();
 183         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
 184             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
 185             if ( get_gains ) {
 186                 domains.addAll( chars.getGainedCharacters() );
 187             }
 188             else {
 189                 domains.addAll( chars.getLostCharacters() );
 190             }
 191         }
 192         return domains;
 193     }
 194
 195     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 196                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 197                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 198                                                                                            final boolean get_gains ) {
 199         final SortedSet<String> sorted_ids = new TreeSet<String>();
 200         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 201             sorted_ids.add( matrix.getIdentifier( i ) );
 202         }
 203         for( final String id : sorted_ids ) {
 204             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 205                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 206                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 207                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 208                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 209                                 .createInstance( matrix.getCharacter( c ) ) );
 210                     }
 211                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 212                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 213                                 .createInstance( matrix.getCharacter( c ) ) );
 214                     }
 215                     else {
 216                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 217                                 .getCharacter( c ) ) );
 218                     }
 219                 }
 220             }
 221         }
 222     }
 223
 224     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
 225                                                             final boolean domain_combinations,
 226                                                             final CharacterStateMatrix.GainLossStates state,
 227                                                             final String outfile ) {
 228         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
 229                 + ForesterUtil.FILE_SEPARATOR + base_dir );
 230         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 231             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 232         }
 233         if ( domain_combinations ) {
 234             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 235                     + ForesterUtil.FILE_SEPARATOR + "DC" );
 236         }
 237         else {
 238             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 239                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
 240         }
 241         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 242             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 243         }
 244         if ( state == GainLossStates.GAIN ) {
 245             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 246                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
 247         }
 248         else if ( state == GainLossStates.LOSS ) {
 249             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 250                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
 251         }
 252         else {
 253             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 254                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
 255         }
 256         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 257             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 258         }
 259         return per_node_go_mapped_domain_gain_loss_files_base_dir;
 260     }
 261
 262     public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 263         final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
 264                 .size() );
 265         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 266             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 267                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 268             }
 269             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 270         }
 271         return domain_id_to_go_ids_map;
 272     }
 273
 274     public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 275             throws IOException {
 276         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
 277         final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
 278         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 279             final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
 280             if ( !map.containsKey( domain_id ) ) {
 281                 map.put( domain_id, new HashSet<String>() );
 282             }
 283             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 284         }
 285         return map;
 286     }
 287
 288     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 289         checkForOutputFileWriteability( nj_tree_outfile );
 290         final NeighborJoining nj = NeighborJoining.createInstance();
 291         final Phylogeny phylogeny = nj.execute( distance );
 292         phylogeny.setName( nj_tree_outfile.getName() );
 293         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 294         return phylogeny;
 295     }
 296
 297     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
 298         final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
 299         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
 300         for( final DomainId domain_id : cds.keySet() ) {
 301             final CombinableDomains cd = cds.get( domain_id );
 302             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
 303         }
 304         return binary_combinations;
 305     }
 306
 307     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 308                                                             final Detailedness detailedness,
 309                                                             final GoAnnotationOutput go_annotation_output,
 310                                                             final Map<GoId, GoTerm> go_id_to_term_map,
 311                                                             final GoNameSpace go_namespace_limit ) {
 312         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
 313             throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
 314         }
 315         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 316             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 317                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 318                 printable_domain_similarity.setDetailedness( detailedness );
 319                 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
 320                 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
 321                 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
 322             }
 323         }
 324     }
 325
 326     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 327                                                     final int number_of_genomes,
 328                                                     final DomainLengthsTable domain_lengths_table,
 329                                                     final File outfile ) throws IOException {
 330         final DecimalFormat df = new DecimalFormat( "#.00" );
 331         checkForOutputFileWriteability( outfile );
 332         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 333         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 334         out.write( ForesterUtil.LINE_SEPARATOR );
 335         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 336         out.write( ForesterUtil.LINE_SEPARATOR );
 337         out.write( ForesterUtil.LINE_SEPARATOR );
 338         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 339         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 340         out.write( ForesterUtil.LINE_SEPARATOR );
 341         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 342             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 343             if ( species_list.size() > 0 ) {
 344                 out.write( domain_lengths.getDomainId() + "\t" );
 345                 for( final Species species : species_list ) {
 346                     out.write( species + "\t" );
 347                 }
 348                 out.write( ForesterUtil.LINE_SEPARATOR );
 349                 // DescriptiveStatistics stats_for_domain = domain_lengths
 350                 //         .calculateMeanBasedStatistics();
 351                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 352                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 353             }
 354         }
 355         out.write( ForesterUtil.LINE_SEPARATOR );
 356         out.write( ForesterUtil.LINE_SEPARATOR );
 357         out.write( "OUTLIER SPECIES (Z 1.0)" );
 358         out.write( ForesterUtil.LINE_SEPARATOR );
 359         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 360                 .calculateMeanBasedStatisticsForAllSpecies();
 361         out.write( stats_for_all_species.asSummary() );
 362         out.write( ForesterUtil.LINE_SEPARATOR );
 363         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 364         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 365         out.write( ForesterUtil.LINE_SEPARATOR );
 366         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 367         final double population_mean = stats_for_all_species.arithmeticMean();
 368         for( final Species species : domain_lengths_table.getSpecies() ) {
 369             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 370             final double z = ( x - population_mean ) / population_sd;
 371             out.write( species + "\t" + z );
 372             out.write( ForesterUtil.LINE_SEPARATOR );
 373         }
 374         out.write( ForesterUtil.LINE_SEPARATOR );
 375         for( final Species species : domain_lengths_table.getSpecies() ) {
 376             final DescriptiveStatistics stats_for_species = domain_lengths_table
 377                     .calculateMeanBasedStatisticsForSpecies( species );
 378             final double x = stats_for_species.arithmeticMean();
 379             final double z = ( x - population_mean ) / population_sd;
 380             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 381                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 382                 out.write( ForesterUtil.LINE_SEPARATOR );
 383             }
 384         }
 385         out.close();
 386         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 387         //        for( int i = 0; i < number_of_genomes; ++i ) {
 388         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 389         //            histogram_datas
 390         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 391         //                            .calculateMeanBasedStatisticsForSpecies( species )
 392         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 393         //        }
 394         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 395         //        hf.setVisible( true );
 396         System.gc();
 397     }
 398
 399     /**
 400      *
 401      * @param all_binary_domains_combination_lost_fitch
 402      * @param consider_directedness_and_adjacency_for_bin_combinations
 403      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 404      * which were gained under unweighted (Fitch) parsimony.
 405      */
 406     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 407                                                  final boolean radomize_fitch_parsimony,
 408                                                  final String outfile_name,
 409                                                  final DomainParsimonyCalculator domain_parsimony,
 410                                                  final Phylogeny phylogeny,
 411                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 412                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 413                                                  final GoNameSpace go_namespace_limit,
 414                                                  final String parameters_str,
 415                                                  final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
 416                                                  final SortedSet<DomainId> positive_filter,
 417                                                  final boolean output_binary_domain_combinations_for_graphs,
 418                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 419                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 420                                                  final BinaryDomainCombination.DomainCombinationType dc_type ) {
 421         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 422         final String date_time = ForesterUtil.getCurrentDateTime();
 423         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 424         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 425         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 426         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 427         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 428         writeToNexus( outfile_name, domain_parsimony, phylogeny );
 429         // DOLLO DOMAINS
 430         // -------------
 431         Phylogeny local_phylogeny_l = phylogeny.copy();
 432         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 433             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 434         }
 435         else {
 436             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 437         }
 438         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 439                 + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 440         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 441                 + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 442         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 443                                                            CharacterStateMatrix.GainLossStates.GAIN,
 444                                                            outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 445                                                            sep,
 446                                                            ForesterUtil.LINE_SEPARATOR,
 447                                                            null );
 448         SurfacingUtil
 449                 .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 450                                                       CharacterStateMatrix.GainLossStates.LOSS,
 451                                                       outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 452                                                       sep,
 453                                                       ForesterUtil.LINE_SEPARATOR,
 454                                                       null );
 455         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 456                 + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 457         //HTML:
 458         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 459                                        go_id_to_term_map,
 460                                        go_namespace_limit,
 461                                        false,
 462                                        domain_parsimony.getGainLossMatrix(),
 463                                        CharacterStateMatrix.GainLossStates.GAIN,
 464                                        outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 465                                        sep,
 466                                        ForesterUtil.LINE_SEPARATOR,
 467                                        "Dollo Parsimony | Gains | Domains",
 468                                        "+",
 469                                        domain_id_to_secondary_features_maps,
 470                                        all_pfams_encountered,
 471                                        all_pfams_gained_as_domains,
 472                                        "_dollo_gains_d" );
 473         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 474                                        go_id_to_term_map,
 475                                        go_namespace_limit,
 476                                        false,
 477                                        domain_parsimony.getGainLossMatrix(),
 478                                        CharacterStateMatrix.GainLossStates.LOSS,
 479                                        outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 480                                        sep,
 481                                        ForesterUtil.LINE_SEPARATOR,
 482                                        "Dollo Parsimony | Losses | Domains",
 483                                        "-",
 484                                        domain_id_to_secondary_features_maps,
 485                                        all_pfams_encountered,
 486                                        all_pfams_lost_as_domains,
 487                                        "_dollo_losses_d" );
 488         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 489                                        go_id_to_term_map,
 490                                        go_namespace_limit,
 491                                        false,
 492                                        domain_parsimony.getGainLossMatrix(),
 493                                        null,
 494                                        outfile_name + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 495                                        sep,
 496                                        ForesterUtil.LINE_SEPARATOR,
 497                                        "Dollo Parsimony | Present | Domains",
 498                                        "",
 499                                        domain_id_to_secondary_features_maps,
 500                                        all_pfams_encountered,
 501                                        null,
 502                                        "_dollo_present_d" );
 503         preparePhylogeny( local_phylogeny_l,
 504                           domain_parsimony,
 505                           date_time,
 506                           "Dollo parsimony on domain presence/absence",
 507                           "dollo_on_domains_" + outfile_name,
 508                           parameters_str );
 509         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 510                 + surfacing_old.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 511         try {
 512             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 513             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 514         }
 515         catch ( final IOException e ) {
 516             e.printStackTrace();
 517             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
 518         }
 519         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 520             // FITCH DOMAIN COMBINATIONS
 521             // -------------------------
 522             local_phylogeny_l = phylogeny.copy();
 523             String randomization = "no";
 524             if ( radomize_fitch_parsimony ) {
 525                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 526                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 527             }
 528             else {
 529                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( false );
 530             }
 531             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 532                     + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 533             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 534                     + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 535             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 536                                                                CharacterStateMatrix.GainLossStates.GAIN,
 537                                                                outfile_name
 538                                                                        + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 539                                                                sep,
 540                                                                ForesterUtil.LINE_SEPARATOR,
 541                                                                null );
 542             SurfacingUtil
 543                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 544                                                           CharacterStateMatrix.GainLossStates.LOSS,
 545                                                           outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 546                                                           sep,
 547                                                           ForesterUtil.LINE_SEPARATOR,
 548                                                           null );
 549             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 550                     + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 551             if ( all_binary_domains_combination_gained_fitch != null ) {
 552                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony
 553                         .getGainLossMatrix(), dc_type, all_binary_domains_combination_gained_fitch, true );
 554             }
 555             if ( all_binary_domains_combination_lost_fitch != null ) {
 556                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony
 557                         .getGainLossMatrix(), dc_type, all_binary_domains_combination_lost_fitch, false );
 558             }
 559             if ( output_binary_domain_combinations_for_graphs ) {
 560                 SurfacingUtil
 561                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 562                                                                                                            .getGainLossMatrix(),
 563                                                                                                    null,
 564                                                                                                    outfile_name
 565                                                                                                            + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 566                                                                                                    sep,
 567                                                                                                    ForesterUtil.LINE_SEPARATOR,
 568                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 569             }
 570             // HTML:
 571             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 572                                            go_id_to_term_map,
 573                                            go_namespace_limit,
 574                                            true,
 575                                            domain_parsimony.getGainLossMatrix(),
 576                                            CharacterStateMatrix.GainLossStates.GAIN,
 577                                            outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 578                                            sep,
 579                                            ForesterUtil.LINE_SEPARATOR,
 580                                            "Fitch Parsimony | Gains | Domain Combinations",
 581                                            "+",
 582                                            null,
 583                                            all_pfams_encountered,
 584                                            all_pfams_gained_as_dom_combinations,
 585                                            "_fitch_gains_dc" );
 586             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 587                                            go_id_to_term_map,
 588                                            go_namespace_limit,
 589                                            true,
 590                                            domain_parsimony.getGainLossMatrix(),
 591                                            CharacterStateMatrix.GainLossStates.LOSS,
 592                                            outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 593                                            sep,
 594                                            ForesterUtil.LINE_SEPARATOR,
 595                                            "Fitch Parsimony | Losses | Domain Combinations",
 596                                            "-",
 597                                            null,
 598                                            all_pfams_encountered,
 599                                            all_pfams_lost_as_dom_combinations,
 600                                            "_fitch_losses_dc" );
 601             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 602                                            go_id_to_term_map,
 603                                            go_namespace_limit,
 604                                            true,
 605                                            domain_parsimony.getGainLossMatrix(),
 606                                            null,
 607                                            outfile_name + surfacing_old.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 608                                            sep,
 609                                            ForesterUtil.LINE_SEPARATOR,
 610                                            "Fitch Parsimony | Present | Domain Combinations",
 611                                            "",
 612                                            null,
 613                                            all_pfams_encountered,
 614                                            null,
 615                                            "_fitch_present_dc" );
 616             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 617                                             go_id_to_term_map,
 618                                             outfile_name,
 619                                             all_pfams_encountered );
 620             writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX,
 621                               all_pfams_gained_as_domains );
 622             writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 623             writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 624                               all_pfams_gained_as_dom_combinations );
 625             writePfamsToFile( outfile_name + surfacing_old.ALL_PFAMS_LOST_AS_DC_SUFFIX,
 626                               all_pfams_lost_as_dom_combinations );
 627             preparePhylogeny( local_phylogeny_l,
 628                               domain_parsimony,
 629                               date_time,
 630                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 631                                       + randomization,
 632                               "fitch_on_binary_domain_combinations_" + outfile_name,
 633                               parameters_str );
 634             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 635                     + surfacing_old.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 636         }
 637     }
 638
 639     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 640                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 641                                                                      final Phylogeny phylogeny,
 642                                                                      final String parameters_str,
 643                                                                      final Map<Species, MappingResults> mapping_results_map ) {
 644         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 645         final String date_time = ForesterUtil.getCurrentDateTime();
 646         System.out.println();
 647         writeToNexus( outfile_name + surfacing_old.NEXUS_SECONDARY_FEATURES, secondary_features_parsimony
 648                 .createMatrixOfSecondaryFeaturePresenceOrAbsence( null ), phylogeny );
 649         final Phylogeny local_phylogeny_copy = phylogeny.copy();
 650         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 651         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 652                 + surfacing_old.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 653         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 654                 + surfacing_old.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 655         SurfacingUtil
 656                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 657                                                       CharacterStateMatrix.GainLossStates.GAIN,
 658                                                       outfile_name
 659                                                               + surfacing_old.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 660                                                       sep,
 661                                                       ForesterUtil.LINE_SEPARATOR,
 662                                                       null );
 663         SurfacingUtil
 664                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 665                                                       CharacterStateMatrix.GainLossStates.LOSS,
 666                                                       outfile_name
 667                                                               + surfacing_old.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 668                                                       sep,
 669                                                       ForesterUtil.LINE_SEPARATOR,
 670                                                       null );
 671         SurfacingUtil
 672                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 673                                                       null,
 674                                                       outfile_name
 675                                                               + surfacing_old.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 676                                                       sep,
 677                                                       ForesterUtil.LINE_SEPARATOR,
 678                                                       null );
 679         preparePhylogeny( local_phylogeny_copy,
 680                           secondary_features_parsimony,
 681                           date_time,
 682                           "Dollo parsimony on secondary feature presence/absence",
 683                           "dollo_on_secondary_features_" + outfile_name,
 684                           parameters_str );
 685         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 686                 + surfacing_old.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 687     }
 688
 689     public static void extractProteinNames( final List<Protein> proteins,
 690                                             final List<DomainId> query_domain_ids_nc_order,
 691                                             final Writer out,
 692                                             final String separator ) throws IOException {
 693         for( final Protein protein : proteins ) {
 694             if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 695                 out.write( protein.getSpecies().getSpeciesId() );
 696                 out.write( separator );
 697                 out.write( protein.getProteinId().getId() );
 698                 out.write( separator );
 699                 out.write( "[" );
 700                 final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
 701                 boolean first = true;
 702                 for( final Domain domain : protein.getProteinDomains() ) {
 703                     if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 704                         visited_domain_ids.add( domain.getDomainId() );
 705                         if ( first ) {
 706                             first = false;
 707                         }
 708                         else {
 709                             out.write( " " );
 710                         }
 711                         out.write( domain.getDomainId().getId() );
 712                         out.write( " {" );
 713                         out.write( "" + domain.getTotalCount() );
 714                         out.write( "}" );
 715                     }
 716                 }
 717                 out.write( "]" );
 718                 out.write( separator );
 719                 if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 720                         .equals( SurfacingConstants.NONE ) ) ) {
 721                     out.write( protein.getDescription() );
 722                 }
 723                 out.write( separator );
 724                 if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 725                         .equals( SurfacingConstants.NONE ) ) ) {
 726                     out.write( protein.getAccession() );
 727                 }
 728                 out.write( SurfacingConstants.NL );
 729             }
 730         }
 731         out.flush();
 732     }
 733
 734     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
 735                                             final DomainId domain_id,
 736                                             final Writer out,
 737                                             final String separator ) throws IOException {
 738         for( final Species species : protein_lists_per_species.keySet() ) {
 739             for( final Protein protein : protein_lists_per_species.get( species ) ) {
 740                 final List<Domain> domains = protein.getProteinDomains( domain_id );
 741                 if ( domains.size() > 0 ) {
 742                     final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 743                     for( final Domain domain : domains ) {
 744                         stats.addValue( domain.getPerSequenceEvalue() );
 745                     }
 746                     out.write( protein.getSpecies().getSpeciesId() );
 747                     out.write( separator );
 748                     out.write( protein.getProteinId().getId() );
 749                     out.write( separator );
 750                     out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
 751                     out.write( separator );
 752                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 753                             .equals( SurfacingConstants.NONE ) ) ) {
 754                         out.write( protein.getDescription() );
 755                     }
 756                     out.write( separator );
 757                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 758                             .equals( SurfacingConstants.NONE ) ) ) {
 759                         out.write( protein.getAccession() );
 760                     }
 761                     out.write( SurfacingConstants.NL );
 762                 }
 763             }
 764         }
 765         out.flush();
 766     }
 767
 768     public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
 769         final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
 770         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 771             final Set<DomainId> all_domains = gwcd.getAllDomainIds();
 772             //    for( final Domain domain : all_domains ) {
 773             all_domains_ids.addAll( all_domains );
 774             //    }
 775         }
 776         return all_domains_ids;
 777     }
 778
 779     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
 780         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
 781         for( final Protein protein_domain_collection : protein_domain_collections ) {
 782             for( final Object name : protein_domain_collection.getProteinDomains() ) {
 783                 final BasicDomain protein_domain = ( BasicDomain ) name;
 784                 final String id = protein_domain.getDomainId().getId();
 785                 if ( map.containsKey( id ) ) {
 786                     map.put( id, map.get( id ) + 1 );
 787                 }
 788                 else {
 789                     map.put( id, 1 );
 790                 }
 791             }
 792         }
 793         return map;
 794     }
 795
 796     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
 797         final PhylogenyNodeIterator it = p.iteratorPostorder();
 798         int c = 0;
 799         while ( it.hasNext() ) {
 800             final PhylogenyNode n = it.next();
 801             if ( ForesterUtil.isEmpty( n.getName() )
 802                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
 803                             .getScientificName() ) ) ) {
 804                 if ( n.getParent() != null ) {
 805                     names.append( " " );
 806                     names.append( n.getParent().getName() );
 807                 }
 808                 ++c;
 809             }
 810         }
 811         return c;
 812     }
 813
 814     /**
 815      * Returns true is Domain domain falls in an uninterrupted stretch of
 816      * covered positions.
 817      *
 818      * @param domain
 819      * @param covered_positions
 820      * @return
 821      */
 822     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
 823         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 824             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
 825                 return false;
 826             }
 827         }
 828         return true;
 829     }
 830
 831     public static void preparePhylogeny( final Phylogeny p,
 832                                          final DomainParsimonyCalculator domain_parsimony,
 833                                          final String date_time,
 834                                          final String method,
 835                                          final String name,
 836                                          final String parameters_str ) {
 837         domain_parsimony.decoratePhylogenyWithDomains( p );
 838         final StringBuilder desc = new StringBuilder();
 839         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
 840         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
 841         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
 842         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
 843         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
 844         desc.append( "[Parameters: " + parameters_str + "]" );
 845         p.setName( name );
 846         p.setDescription( desc.toString() );
 847         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
 848         p.setRerootable( false );
 849         p.setRooted( true );
 850     }
 851
 852     /**
 853      *
 854      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
 855      * domain with 0.3 is ignored
 856      *
 857      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
 858      *
 859      *
 860      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
 861      * ignored
 862      *
 863      * @param max_allowed_overlap
 864      *            maximal allowed overlap (inclusive) to be still considered not
 865      *            overlapping (zero or negative value to allow any overlap)
 866      * @param remove_engulfed_domains
 867      *            to remove domains which are completely engulfed by coverage of
 868      *            domains with better support
 869      * @param protein
 870      * @return
 871      */
 872     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
 873                                                     final boolean remove_engulfed_domains,
 874                                                     final Protein protein ) {
 875         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
 876                 .getSpeciesId() );
 877         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
 878         final List<Boolean> covered_positions = new ArrayList<Boolean>();
 879         for( final Domain domain : sorted ) {
 880             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
 881                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
 882                 final int covered_positions_size = covered_positions.size();
 883                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
 884                     covered_positions.add( false );
 885                 }
 886                 final int new_covered_positions_size = covered_positions.size();
 887                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 888                     if ( i < new_covered_positions_size ) {
 889                         covered_positions.set( i, true );
 890                     }
 891                     else {
 892                         covered_positions.add( true );
 893                     }
 894                 }
 895                 pruned_protein.addProteinDomain( domain );
 896             }
 897         }
 898         return pruned_protein;
 899     }
 900
 901     static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
 902         final List<Domain> domains = new ArrayList<Domain>();
 903         for( final Domain d : protein.getProteinDomains() ) {
 904             domains.add( d );
 905         }
 906         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
 907         return domains;
 908     }
 909
 910     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
 911                                                             final boolean get_gains,
 912                                                             final String outdir,
 913                                                             final String suffix_for_filename ) throws IOException {
 914         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
 915         if ( !get_gains ) {
 916             state = CharacterStateMatrix.GainLossStates.LOSS;
 917         }
 918         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
 919                                                                   false,
 920                                                                   state,
 921                                                                   outdir );
 922         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
 923             final PhylogenyNode node = it.next();
 924             if ( !node.isExternal() ) {
 925                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
 926                 if ( domains.size() > 0 ) {
 927                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
 928                             + node.getName() + suffix_for_filename );
 929                     for( final String domain : domains ) {
 930                         writer.write( domain );
 931                         writer.write( ForesterUtil.LINE_SEPARATOR );
 932                     }
 933                     writer.close();
 934                 }
 935             }
 936         }
 937     }
 938
 939     private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 940                                                         final Map<GoId, GoTerm> go_id_to_term_map,
 941                                                         final String outfile_name,
 942                                                         final SortedSet<String> all_pfams_encountered ) {
 943         final File all_pfams_encountered_file = new File( outfile_name + surfacing_old.ALL_PFAMS_ENCOUNTERED_SUFFIX );
 944         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
 945                 + surfacing_old.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
 946         final File encountered_pfams_summary_file = new File( outfile_name
 947                 + surfacing_old.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
 948         int biological_process_counter = 0;
 949         int cellular_component_counter = 0;
 950         int molecular_function_counter = 0;
 951         int pfams_with_mappings_counter = 0;
 952         int pfams_without_mappings_counter = 0;
 953         int pfams_without_mappings_to_bp_or_mf_counter = 0;
 954         int pfams_with_mappings_to_bp_or_mf_counter = 0;
 955         try {
 956             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
 957             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
 958             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
 959             summary_writer.write( "# Pfam to GO mapping summary" );
 960             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
 961             summary_writer.write( "# Actual summary is at the end of this file." );
 962             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
 963             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
 964             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
 965             for( final String pfam : all_pfams_encountered ) {
 966                 all_pfams_encountered_writer.write( pfam );
 967                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
 968                 final DomainId domain_id = new DomainId( pfam );
 969                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
 970                     ++pfams_with_mappings_counter;
 971                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
 972                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
 973                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
 974                     boolean maps_to_bp = false;
 975                     boolean maps_to_cc = false;
 976                     boolean maps_to_mf = false;
 977                     for( final GoId go_id : go_ids ) {
 978                         final GoTerm go_term = go_id_to_term_map.get( go_id );
 979                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
 980                             maps_to_bp = true;
 981                         }
 982                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
 983                             maps_to_cc = true;
 984                         }
 985                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
 986                             maps_to_mf = true;
 987                         }
 988                     }
 989                     if ( maps_to_bp ) {
 990                         ++biological_process_counter;
 991                     }
 992                     if ( maps_to_cc ) {
 993                         ++cellular_component_counter;
 994                     }
 995                     if ( maps_to_mf ) {
 996                         ++molecular_function_counter;
 997                     }
 998                     if ( maps_to_bp || maps_to_mf ) {
 999                         ++pfams_with_mappings_to_bp_or_mf_counter;
1000                     }
1001                     else {
1002                         ++pfams_without_mappings_to_bp_or_mf_counter;
1003                     }
1004                 }
1005                 else {
1006                     ++pfams_without_mappings_to_bp_or_mf_counter;
1007                     ++pfams_without_mappings_counter;
1008                     summary_writer.write( pfam );
1009                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1010                 }
1011             }
1012             all_pfams_encountered_writer.close();
1013             all_pfams_encountered_with_go_annotation_writer.close();
1014             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
1015                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
1016             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
1017                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
1018                     + "\"" );
1019             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote summary (including all ["
1020                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
1021                     + encountered_pfams_summary_file + "\"" );
1022             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Sum of Pfams encountered                : "
1023                     + all_pfams_encountered.size() );
1024             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without a mapping                 : "
1025                     + pfams_without_mappings_counter + " ["
1026                     + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1027             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams without mapping to proc. or func. : "
1028                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1029                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1030             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with a mapping                    : "
1031                     + pfams_with_mappings_counter + " ["
1032                     + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1033             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
1034                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1035                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1036             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with mapping to biological process: "
1037                     + biological_process_counter + " ["
1038                     + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
1039             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with mapping to molecular function: "
1040                     + molecular_function_counter + " ["
1041                     + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
1042             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Pfams with mapping to cellular component: "
1043                     + cellular_component_counter + " ["
1044                     + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
1045             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1046             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
1047             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1048             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
1049                     + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1050             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1051             summary_writer.write( "# Pfams without mapping to proc. or func. : "
1052                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1053                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1054             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1055             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
1056                     + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1057             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1058             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
1059                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1060                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1061             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1062             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
1063                     + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
1064             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1065             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
1066                     + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
1067             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1068             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
1069                     + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
1070             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1071             summary_writer.close();
1072         }
1073         catch ( final IOException e ) {
1074             ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
1075         }
1076     }
1077
1078     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1079                                                                           final File output_dir,
1080                                                                           final GenomeWideCombinableDomains gwcd,
1081                                                                           final int i,
1082                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1083         File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
1084                 + surfacing_old.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1085         if ( output_dir != null ) {
1086             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1087         }
1088         checkForOutputFileWriteability( dc_outfile_dot );
1089         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1090         try {
1091             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1092             for( final BinaryDomainCombination bdc : binary_combinations ) {
1093                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1094                         .toString() );
1095                 out_dot.write( SurfacingConstants.NL );
1096             }
1097             out_dot.close();
1098         }
1099         catch ( final IOException e ) {
1100             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1101         }
1102         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote binary domain combination for \""
1103                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1104                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1105     }
1106
1107     /*
1108      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1109      *
1110      *
1111      */
1112     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1113                                                             final String protein_id,
1114                                                             final String separator ) {
1115         final StringBuffer sb = new StringBuffer();
1116         if ( protein.getSpecies() == null ) {
1117             throw new IllegalArgumentException( "species must not be null" );
1118         }
1119         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1120             throw new IllegalArgumentException( "species id must not be empty" );
1121         }
1122         final List<Domain> domains = protein.getProteinDomains();
1123         if ( domains.size() > 1 ) {
1124             final Map<String, Integer> counts = new HashMap<String, Integer>();
1125             for( final Domain domain : domains ) {
1126                 final String id = domain.getDomainId().getId();
1127                 if ( counts.containsKey( id ) ) {
1128                     counts.put( id, counts.get( id ) + 1 );
1129                 }
1130                 else {
1131                     counts.put( id, 1 );
1132                 }
1133             }
1134             for( int i = 1; i < domains.size(); ++i ) {
1135                 for( int j = 0; j < i; ++j ) {
1136                     Domain domain_n = domains.get( i );
1137                     Domain domain_c = domains.get( j );
1138                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1139                         domain_n = domains.get( j );
1140                         domain_c = domains.get( i );
1141                     }
1142                     sb.append( protein.getSpecies() );
1143                     sb.append( separator );
1144                     sb.append( protein_id );
1145                     sb.append( separator );
1146                     sb.append( domain_n.getDomainId().getId() );
1147                     sb.append( separator );
1148                     sb.append( domain_c.getDomainId().getId() );
1149                     sb.append( separator );
1150                     sb.append( domain_n.getPerDomainEvalue() );
1151                     sb.append( separator );
1152                     sb.append( domain_c.getPerDomainEvalue() );
1153                     sb.append( separator );
1154                     sb.append( counts.get( domain_n.getDomainId().getId() ) );
1155                     sb.append( separator );
1156                     sb.append( counts.get( domain_c.getDomainId().getId() ) );
1157                     sb.append( ForesterUtil.LINE_SEPARATOR );
1158                 }
1159             }
1160         }
1161         else if ( domains.size() == 1 ) {
1162             sb.append( protein.getSpecies() );
1163             sb.append( separator );
1164             sb.append( protein_id );
1165             sb.append( separator );
1166             sb.append( domains.get( 0 ).getDomainId().getId() );
1167             sb.append( separator );
1168             sb.append( separator );
1169             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1170             sb.append( separator );
1171             sb.append( separator );
1172             sb.append( 1 );
1173             sb.append( separator );
1174             sb.append( ForesterUtil.LINE_SEPARATOR );
1175         }
1176         else {
1177             sb.append( protein.getSpecies() );
1178             sb.append( separator );
1179             sb.append( protein_id );
1180             sb.append( separator );
1181             sb.append( separator );
1182             sb.append( separator );
1183             sb.append( separator );
1184             sb.append( separator );
1185             sb.append( separator );
1186             sb.append( ForesterUtil.LINE_SEPARATOR );
1187         }
1188         return sb;
1189     }
1190
1191     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1192                                                             final CharacterStateMatrix.GainLossStates state,
1193                                                             final String filename,
1194                                                             final String indentifier_characters_separator,
1195                                                             final String character_separator,
1196                                                             final Map<String, String> descriptions ) {
1197         final File outfile = new File( filename );
1198         checkForOutputFileWriteability( outfile );
1199         final SortedSet<String> sorted_ids = new TreeSet<String>();
1200         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1201             sorted_ids.add( matrix.getIdentifier( i ) );
1202         }
1203         try {
1204             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1205             for( final String id : sorted_ids ) {
1206                 out.write( indentifier_characters_separator );
1207                 out.write( "#" + id );
1208                 out.write( indentifier_characters_separator );
1209                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1210                     // Not nice:
1211                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1212                     if ( ( matrix.getState( id, c ) == state )
1213                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1214                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1215                         out.write( matrix.getCharacter( c ) );
1216                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1217                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1218                             out.write( "\t" );
1219                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1220                         }
1221                         out.write( character_separator );
1222                     }
1223                 }
1224             }
1225             out.flush();
1226             out.close();
1227         }
1228         catch ( final IOException e ) {
1229             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1230         }
1231         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1232     }
1233
1234     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1235                                                                                                  final CharacterStateMatrix.GainLossStates state,
1236                                                                                                  final String filename,
1237                                                                                                  final String indentifier_characters_separator,
1238                                                                                                  final String character_separator,
1239                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1240         final File outfile = new File( filename );
1241         checkForOutputFileWriteability( outfile );
1242         final SortedSet<String> sorted_ids = new TreeSet<String>();
1243         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1244             sorted_ids.add( matrix.getIdentifier( i ) );
1245         }
1246         try {
1247             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1248             for( final String id : sorted_ids ) {
1249                 out.write( indentifier_characters_separator );
1250                 out.write( "#" + id );
1251                 out.write( indentifier_characters_separator );
1252                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1253                     // Not nice:
1254                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1255                     if ( ( matrix.getState( id, c ) == state )
1256                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1257                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1258                         BinaryDomainCombination bdc = null;
1259                         try {
1260                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1261                         }
1262                         catch ( final Exception e ) {
1263                             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
1264                         }
1265                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1266                         out.write( character_separator );
1267                     }
1268                 }
1269             }
1270             out.flush();
1271             out.close();
1272         }
1273         catch ( final IOException e ) {
1274             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1275         }
1276         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1277     }
1278
1279     public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1280                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1281                                                       final GoNameSpace go_namespace_limit,
1282                                                       final boolean domain_combinations,
1283                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1284                                                       final CharacterStateMatrix.GainLossStates state,
1285                                                       final String filename,
1286                                                       final String indentifier_characters_separator,
1287                                                       final String character_separator,
1288                                                       final String title_for_html,
1289                                                       final String prefix_for_html,
1290                                                       final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1291                                                       final SortedSet<String> all_pfams_encountered,
1292                                                       final SortedSet<String> pfams_gained_or_lost,
1293                                                       final String suffix_for_per_node_events_file ) {
1294         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1295             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1296         }
1297         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1298             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1299         }
1300         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1301             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1302         }
1303         final File outfile = new File( filename );
1304         checkForOutputFileWriteability( outfile );
1305         final SortedSet<String> sorted_ids = new TreeSet<String>();
1306         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1307             sorted_ids.add( matrix.getIdentifier( i ) );
1308         }
1309         try {
1310             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1311             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1312                                                                                                                 domain_combinations,
1313                                                                                                                 state,
1314                                                                                                                 filename );
1315             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1316             File per_node_go_mapped_domain_gain_loss_outfile = null;
1317             int per_node_counter = 0;
1318             out.write( "<html>" );
1319             out.write( SurfacingConstants.NL );
1320             addHtmlHead( out, title_for_html );
1321             out.write( SurfacingConstants.NL );
1322             out.write( "<body>" );
1323             out.write( SurfacingConstants.NL );
1324             out.write( "<h1>" );
1325             out.write( SurfacingConstants.NL );
1326             out.write( title_for_html );
1327             out.write( SurfacingConstants.NL );
1328             out.write( "</h1>" );
1329             out.write( SurfacingConstants.NL );
1330             out.write( "<table>" );
1331             out.write( SurfacingConstants.NL );
1332             for( final String id : sorted_ids ) {
1333                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1334                 if ( matcher.matches() ) {
1335                     continue;
1336                 }
1337                 out.write( "<tr>" );
1338                 out.write( "<td>" );
1339                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1340                 out.write( "</td>" );
1341                 out.write( "</tr>" );
1342                 out.write( SurfacingConstants.NL );
1343             }
1344             out.write( "</table>" );
1345             out.write( SurfacingConstants.NL );
1346             for( final String id : sorted_ids ) {
1347                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1348                 if ( matcher.matches() ) {
1349                     continue;
1350                 }
1351                 out.write( SurfacingConstants.NL );
1352                 out.write( "<h2>" );
1353                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1354                 writeTaxonomyLinks( out, id );
1355                 out.write( "</h2>" );
1356                 out.write( SurfacingConstants.NL );
1357                 out.write( "<table>" );
1358                 out.write( SurfacingConstants.NL );
1359                 out.write( "<tr>" );
1360                 out.write( "<td><b>" );
1361                 out.write( "Pfam domain(s)" );
1362                 out.write( "</b></td><td><b>" );
1363                 out.write( "GO term acc" );
1364                 out.write( "</b></td><td><b>" );
1365                 out.write( "GO term" );
1366                 out.write( "</b></td><td><b>" );
1367                 out.write( "GO namespace" );
1368                 out.write( "</b></td>" );
1369                 out.write( "</tr>" );
1370                 out.write( SurfacingConstants.NL );
1371                 out.write( "</tr>" );
1372                 out.write( SurfacingConstants.NL );
1373                 per_node_counter = 0;
1374                 if ( matrix.getNumberOfCharacters() > 0 ) {
1375                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1376                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1377                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1378                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1379                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1380                 }
1381                 else {
1382                     per_node_go_mapped_domain_gain_loss_outfile = null;
1383                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1384                 }
1385                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1386                     // Not nice:
1387                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1388                     if ( ( matrix.getState( id, c ) == state )
1389                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1390                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1391                         final String character = matrix.getCharacter( c );
1392                         String domain_0 = "";
1393                         String domain_1 = "";
1394                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1395                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1396                             if ( s.length != 2 ) {
1397                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1398                                         + character + "]" );
1399                             }
1400                             domain_0 = s[ 0 ];
1401                             domain_1 = s[ 1 ];
1402                         }
1403                         else {
1404                             domain_0 = character;
1405                         }
1406                         writeDomainData( domain_id_to_go_ids_map,
1407                                          go_id_to_term_map,
1408                                          go_namespace_limit,
1409                                          out,
1410                                          domain_0,
1411                                          domain_1,
1412                                          prefix_for_html,
1413                                          character_separator,
1414                                          domain_id_to_secondary_features_maps,
1415                                          null );
1416                         all_pfams_encountered.add( domain_0 );
1417                         if ( pfams_gained_or_lost != null ) {
1418                             pfams_gained_or_lost.add( domain_0 );
1419                         }
1420                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1421                             all_pfams_encountered.add( domain_1 );
1422                             if ( pfams_gained_or_lost != null ) {
1423                                 pfams_gained_or_lost.add( domain_1 );
1424                             }
1425                         }
1426                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1427                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1428                                                                      domain_0,
1429                                                                      domain_1 );
1430                             per_node_counter++;
1431                         }
1432                     }
1433                 }
1434                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1435                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1436                     if ( per_node_counter < 1 ) {
1437                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1438                     }
1439                     per_node_counter = 0;
1440                 }
1441                 out.write( "</table>" );
1442                 out.write( SurfacingConstants.NL );
1443                 out.write( "<hr>" );
1444                 out.write( SurfacingConstants.NL );
1445             } // for( final String id : sorted_ids ) {
1446             out.write( "</body>" );
1447             out.write( SurfacingConstants.NL );
1448             out.write( "</html>" );
1449             out.write( SurfacingConstants.NL );
1450             out.flush();
1451             out.close();
1452         }
1453         catch ( final IOException e ) {
1454             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1455         }
1456         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
1457                 + "\"" );
1458     }
1459
1460     public static void writeBinaryStatesMatrixToListORIGIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1461                                                             final Map<GoId, GoTerm> go_id_to_term_map,
1462                                                             final GoNameSpace go_namespace_limit,
1463                                                             final boolean domain_combinations,
1464                                                             final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1465                                                             final CharacterStateMatrix.GainLossStates state,
1466                                                             final String filename,
1467                                                             final String indentifier_characters_separator,
1468                                                             final String character_separator,
1469                                                             final String title_for_html,
1470                                                             final String prefix_for_html,
1471                                                             final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1472                                                             final SortedSet<String> all_pfams_encountered,
1473                                                             final SortedSet<String> pfams_gained_or_lost,
1474                                                             final String suffix_for_per_node_events_file ) {
1475         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1476             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1477         }
1478         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1479             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1480         }
1481         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1482             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1483         }
1484         final File outfile = new File( filename );
1485         checkForOutputFileWriteability( outfile );
1486         final SortedSet<String> sorted_ids = new TreeSet<String>();
1487         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1488             sorted_ids.add( matrix.getIdentifier( i ) );
1489         }
1490         try {
1491             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1492             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing_old.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1493                                                                                                                 domain_combinations,
1494                                                                                                                 state,
1495                                                                                                                 filename );
1496             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1497             File per_node_go_mapped_domain_gain_loss_outfile = null;
1498             int per_node_counter = 0;
1499             out.write( "<html>" );
1500             out.write( SurfacingConstants.NL );
1501             addHtmlHead( out, title_for_html );
1502             out.write( SurfacingConstants.NL );
1503             out.write( "<body>" );
1504             out.write( SurfacingConstants.NL );
1505             out.write( "<h1>" );
1506             out.write( SurfacingConstants.NL );
1507             out.write( title_for_html );
1508             out.write( SurfacingConstants.NL );
1509             out.write( "</h1>" );
1510             out.write( SurfacingConstants.NL );
1511             out.write( "<table>" );
1512             out.write( SurfacingConstants.NL );
1513             for( final String id : sorted_ids ) {
1514                 out.write( "<tr>" );
1515                 out.write( "<td>" );
1516                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1517                 writeTaxonomyLinks( out, id );
1518                 out.write( "</td>" );
1519                 out.write( "</tr>" );
1520                 out.write( SurfacingConstants.NL );
1521             }
1522             out.write( "</table>" );
1523             out.write( SurfacingConstants.NL );
1524             for( final String id : sorted_ids ) {
1525                 out.write( SurfacingConstants.NL );
1526                 out.write( "<h2>" );
1527                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1528                 writeTaxonomyLinks( out, id );
1529                 out.write( "</h2>" );
1530                 out.write( SurfacingConstants.NL );
1531                 out.write( "<table>" );
1532                 out.write( SurfacingConstants.NL );
1533                 out.write( "<tr>" );
1534                 out.write( "<td><b>" );
1535                 out.write( "Pfam domain(s)" );
1536                 out.write( "</b></td><td><b>" );
1537                 out.write( "GO term acc" );
1538                 out.write( "</b></td><td><b>" );
1539                 out.write( "GO term" );
1540                 out.write( "</b></td><td><b>" );
1541                 out.write( "Penultimate GO term" );
1542                 out.write( "</b></td><td><b>" );
1543                 out.write( "GO namespace" );
1544                 out.write( "</b></td>" );
1545                 out.write( "</tr>" );
1546                 out.write( SurfacingConstants.NL );
1547                 out.write( "</tr>" );
1548                 out.write( SurfacingConstants.NL );
1549                 per_node_counter = 0;
1550                 if ( matrix.getNumberOfCharacters() > 0 ) {
1551                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1552                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1553                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1554                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1555                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1556                 }
1557                 else {
1558                     per_node_go_mapped_domain_gain_loss_outfile = null;
1559                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1560                 }
1561                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1562                     // Not nice:
1563                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1564                     if ( ( matrix.getState( id, c ) == state )
1565                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1566                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1567                         final String character = matrix.getCharacter( c );
1568                         String domain_0 = "";
1569                         String domain_1 = "";
1570                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1571                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1572                             if ( s.length != 2 ) {
1573                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1574                                         + character + "]" );
1575                             }
1576                             domain_0 = s[ 0 ];
1577                             domain_1 = s[ 1 ];
1578                         }
1579                         else {
1580                             domain_0 = character;
1581                         }
1582                         writeDomainData( domain_id_to_go_ids_map,
1583                                          go_id_to_term_map,
1584                                          go_namespace_limit,
1585                                          out,
1586                                          domain_0,
1587                                          domain_1,
1588                                          prefix_for_html,
1589                                          character_separator,
1590                                          domain_id_to_secondary_features_maps,
1591                                          null );
1592                         all_pfams_encountered.add( domain_0 );
1593                         if ( pfams_gained_or_lost != null ) {
1594                             pfams_gained_or_lost.add( domain_0 );
1595                         }
1596                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1597                             all_pfams_encountered.add( domain_1 );
1598                             if ( pfams_gained_or_lost != null ) {
1599                                 pfams_gained_or_lost.add( domain_1 );
1600                             }
1601                         }
1602                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1603                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1604                                                                      domain_0,
1605                                                                      domain_1 );
1606                             per_node_counter++;
1607                         }
1608                     }
1609                 }
1610                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1611                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1612                     if ( per_node_counter < 1 ) {
1613                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1614                     }
1615                     per_node_counter = 0;
1616                 }
1617                 out.write( "</table>" );
1618                 out.write( SurfacingConstants.NL );
1619                 out.write( "<hr>" );
1620                 out.write( SurfacingConstants.NL );
1621             } // for( final String id : sorted_ids ) {
1622             out.write( "</body>" );
1623             out.write( SurfacingConstants.NL );
1624             out.write( "</html>" );
1625             out.write( SurfacingConstants.NL );
1626             out.flush();
1627             out.close();
1628         }
1629         catch ( final IOException e ) {
1630             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1631         }
1632         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename
1633                 + "\"" );
1634     }
1635
1636     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1637                                                           final File output_dir,
1638                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1639                                                           final GenomeWideCombinableDomains gwcd,
1640                                                           final int i,
1641                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1642         File dc_outfile = new File( input_file_properties[ i ][ 0 ]
1643                 + surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1644         if ( output_dir != null ) {
1645             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1646         }
1647         checkForOutputFileWriteability( dc_outfile );
1648         try {
1649             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1650             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1651             out.close();
1652         }
1653         catch ( final IOException e ) {
1654             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1655         }
1656         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1657         try {
1658             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
1659             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1660             if ( stats.getN() < 2 ) {
1661                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1662             }
1663             else {
1664                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1665                         .sampleStandardDeviation() )
1666                         + "\t" );
1667             }
1668             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1669             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1670             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1671             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1672             final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
1673             for( final DomainId mpd : mpds ) {
1674                 per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
1675             }
1676             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1677         }
1678         catch ( final IOException e ) {
1679             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
1680         }
1681         if ( input_file_properties[ i ].length == 3 ) {
1682             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
1683                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1684                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1685         }
1686         else {
1687             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote domain combination counts for \""
1688                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1689                     + dc_outfile + "\"" );
1690         }
1691     }
1692
1693     private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1694                                          final Map<GoId, GoTerm> go_id_to_term_map,
1695                                          final GoNameSpace go_namespace_limit,
1696                                          final Writer out,
1697                                          final String domain_0,
1698                                          final String domain_1,
1699                                          final String prefix_for_html,
1700                                          final String character_separator_for_non_html_output,
1701                                          final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1702                                          final Set<GoId> all_go_ids ) throws IOException {
1703         boolean any_go_annotation_present = false;
1704         boolean first_has_no_go = false;
1705         int domain_count = 2; // To distinguish between domains and binary domain combinations.
1706         if ( ForesterUtil.isEmpty( domain_1 ) ) {
1707             domain_count = 1;
1708         }
1709         // The following has a difficult to understand logic.
1710         for( int d = 0; d < domain_count; ++d ) {
1711             List<GoId> go_ids = null;
1712             boolean go_annotation_present = false;
1713             if ( d == 0 ) {
1714                 final DomainId domain_id = new DomainId( domain_0 );
1715                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1716                     go_annotation_present = true;
1717                     any_go_annotation_present = true;
1718                     go_ids = domain_id_to_go_ids_map.get( domain_id );
1719                 }
1720                 else {
1721                     first_has_no_go = true;
1722                 }
1723             }
1724             else {
1725                 final DomainId domain_id = new DomainId( domain_1 );
1726                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1727                     go_annotation_present = true;
1728                     any_go_annotation_present = true;
1729                     go_ids = domain_id_to_go_ids_map.get( domain_id );
1730                 }
1731             }
1732             if ( go_annotation_present ) {
1733                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
1734                 for( final GoId go_id : go_ids ) {
1735                     out.write( "<tr>" );
1736                     if ( first ) {
1737                         first = false;
1738                         writeDomainIdsToHtml( out,
1739                                               domain_0,
1740                                               domain_1,
1741                                               prefix_for_html,
1742                                               domain_id_to_secondary_features_maps );
1743                     }
1744                     else {
1745                         out.write( "<td></td>" );
1746                     }
1747                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
1748                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
1749                     }
1750                     final GoTerm go_term = go_id_to_term_map.get( go_id );
1751                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
1752                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
1753                         final String go_id_str = go_id.getId();
1754                         out.write( "<td>" );
1755                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
1756                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
1757                         out.write( "</td><td>" );
1758                         out.write( go_term.getName() );
1759                         if ( domain_count == 2 ) {
1760                             out.write( " (" + d + ")" );
1761                         }
1762                         out.write( "</td><td>" );
1763                         // out.write( top );
1764                         // out.write( "</td><td>" );
1765                         out.write( "[" );
1766                         out.write( go_term.getGoNameSpace().toShortString() );
1767                         out.write( "]" );
1768                         out.write( "</td>" );
1769                         if ( all_go_ids != null ) {
1770                             all_go_ids.add( go_id );
1771                         }
1772                     }
1773                     else {
1774                         out.write( "<td>" );
1775                         out.write( "</td><td>" );
1776                         out.write( "</td><td>" );
1777                         out.write( "</td><td>" );
1778                         out.write( "</td>" );
1779                     }
1780                     out.write( "</tr>" );
1781                     out.write( SurfacingConstants.NL );
1782                 }
1783             }
1784         } //  for( int d = 0; d < domain_count; ++d )
1785         if ( !any_go_annotation_present ) {
1786             out.write( "<tr>" );
1787             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
1788             out.write( "<td>" );
1789             out.write( "</td><td>" );
1790             out.write( "</td><td>" );
1791             out.write( "</td><td>" );
1792             out.write( "</td>" );
1793             out.write( "</tr>" );
1794             out.write( SurfacingConstants.NL );
1795         }
1796     }
1797
1798     private static void writeDomainDataORIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1799                                              final Map<GoId, GoTerm> go_id_to_term_map,
1800                                              final GoNameSpace go_namespace_limit,
1801                                              final Writer out,
1802                                              final String domain_0,
1803                                              final String domain_1,
1804                                              final String prefix_for_html,
1805                                              final String character_separator_for_non_html_output,
1806                                              final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1807                                              final Set<GoId> all_go_ids ) throws IOException {
1808         boolean any_go_annotation_present = false;
1809         boolean first_has_no_go = false;
1810         int domain_count = 2; // To distinguish between domains and binary domain combinations.
1811         if ( ForesterUtil.isEmpty( domain_1 ) ) {
1812             domain_count = 1;
1813         }
1814         // The following has a difficult to understand logic.
1815         for( int d = 0; d < domain_count; ++d ) {
1816             List<GoId> go_ids = null;
1817             boolean go_annotation_present = false;
1818             if ( d == 0 ) {
1819                 final DomainId domain_id = new DomainId( domain_0 );
1820                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1821                     go_annotation_present = true;
1822                     any_go_annotation_present = true;
1823                     go_ids = domain_id_to_go_ids_map.get( domain_id );
1824                 }
1825                 else {
1826                     first_has_no_go = true;
1827                 }
1828             }
1829             else {
1830                 final DomainId domain_id = new DomainId( domain_1 );
1831                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1832                     go_annotation_present = true;
1833                     any_go_annotation_present = true;
1834                     go_ids = domain_id_to_go_ids_map.get( domain_id );
1835                 }
1836             }
1837             if ( go_annotation_present ) {
1838                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
1839                 for( final GoId go_id : go_ids ) {
1840                     out.write( "<tr>" );
1841                     if ( first ) {
1842                         first = false;
1843                         writeDomainIdsToHtml( out,
1844                                               domain_0,
1845                                               domain_1,
1846                                               prefix_for_html,
1847                                               domain_id_to_secondary_features_maps );
1848                     }
1849                     else {
1850                         out.write( "<td></td>" );
1851                     }
1852                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
1853                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
1854                     }
1855                     final GoTerm go_term = go_id_to_term_map.get( go_id );
1856                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
1857                         final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
1858                         final String go_id_str = go_id.getId();
1859                         out.write( "<td>" );
1860                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
1861                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
1862                         out.write( "</td><td>" );
1863                         out.write( go_term.getName() );
1864                         if ( domain_count == 2 ) {
1865                             out.write( " (" + d + ")" );
1866                         }
1867                         out.write( "</td><td>" );
1868                         out.write( top );
1869                         out.write( "</td><td>" );
1870                         out.write( "[" );
1871                         out.write( go_term.getGoNameSpace().toShortString() );
1872                         out.write( "]" );
1873                         out.write( "</td>" );
1874                         if ( all_go_ids != null ) {
1875                             all_go_ids.add( go_id );
1876                         }
1877                     }
1878                     else {
1879                         out.write( "<td>" );
1880                         out.write( "</td><td>" );
1881                         out.write( "</td><td>" );
1882                         out.write( "</td><td>" );
1883                         out.write( "</td>" );
1884                     }
1885                     out.write( "</tr>" );
1886                     out.write( SurfacingConstants.NL );
1887                 }
1888             }
1889         } //  for( int d = 0; d < domain_count; ++d )
1890         if ( !any_go_annotation_present ) {
1891             out.write( "<tr>" );
1892             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
1893             out.write( "<td>" );
1894             out.write( "</td><td>" );
1895             out.write( "</td><td>" );
1896             out.write( "</td><td>" );
1897             out.write( "</td>" );
1898             out.write( "</tr>" );
1899             out.write( SurfacingConstants.NL );
1900         }
1901     }
1902
1903     private static void writeDomainIdsToHtml( final Writer out,
1904                                               final String domain_0,
1905                                               final String domain_1,
1906                                               final String prefix_for_detailed_html,
1907                                               final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
1908             throws IOException {
1909         out.write( "<td>" );
1910         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
1911             out.write( prefix_for_detailed_html );
1912             out.write( " " );
1913         }
1914         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
1915         //if ( ForesterUtil.isEmpty( domain_1 ) ) {
1916         //    out.write( " <a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + domain_0
1917         //            + SurfacingConstants.GOOGLE_SCHOLAR_LIMITS + "\">[gs]</a>" );
1918         //}
1919         // if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1920         //     out.write( "=" );
1921         //    out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_1 + "\">" + domain_1 + "</a>" );
1922         //}
1923         //        else if ( ( domain_id_to_secondary_features_maps != null )
1924         //                && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1925         //            out.write( " [" );
1926         //            boolean first = true;
1927         //            for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
1928         //                final Set<String> sec_features = domain_id_to_secondary_features_map.get( new DomainId( domain_0 ) );
1929         //                if ( ( sec_features != null ) && ( sec_features.size() > 0 ) ) {
1930         //                    for( final String sec_feature : sec_features ) {
1931         //                        if ( first ) {
1932         //                            first = false;
1933         //                        }
1934         //                        else {
1935         //                            out.write( ", " );
1936         //                        }
1937         //                        if ( SurfacingConstants.SECONDARY_FEATURES_ARE_SCOP
1938         //                                && ( SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK != null ) ) {
1939         //                            out.write( "<a href=\"" + SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK + sec_feature
1940         //                                    + "\" target=\"scop_window\">" + sec_feature + "</a>" );
1941         //                        }
1942         //                        else {
1943         //                            out.write( sec_feature );
1944         //                        }
1945         //                    }
1946         //                }
1947         //            }
1948         //            out.write( "]" );
1949         //        }
1950         out.write( "</td>" );
1951     }
1952
1953     private static void writeDomainIdsToHtmlORIG( final Writer out,
1954                                                   final String domain_0,
1955                                                   final String domain_1,
1956                                                   final String prefix_for_detailed_html,
1957                                                   final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
1958             throws IOException {
1959         out.write( "<td>" );
1960         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
1961             out.write( prefix_for_detailed_html );
1962             out.write( " " );
1963         }
1964         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
1965         if ( ForesterUtil.isEmpty( domain_1 ) ) {
1966             out.write( " <a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + domain_0
1967                     + SurfacingConstants.GOOGLE_SCHOLAR_LIMITS + "\">[gs]</a>" );
1968         }
1969         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1970             out.write( "=" );
1971             out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_1 + "\">" + domain_1 + "</a>" );
1972         }
1973         else if ( ( domain_id_to_secondary_features_maps != null )
1974                 && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
1975             out.write( " [" );
1976             boolean first = true;
1977             for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
1978                 final Set<String> sec_features = domain_id_to_secondary_features_map.get( new DomainId( domain_0 ) );
1979                 if ( ( sec_features != null ) && ( sec_features.size() > 0 ) ) {
1980                     for( final String sec_feature : sec_features ) {
1981                         if ( first ) {
1982                             first = false;
1983                         }
1984                         else {
1985                             out.write( ", " );
1986                         }
1987                         if ( SurfacingConstants.SECONDARY_FEATURES_ARE_SCOP
1988                                 && ( SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK != null ) ) {
1989                             out.write( "<a href=\"" + SurfacingConstants.SECONDARY_FEATURES_SCOP_LINK + sec_feature
1990                                     + "\" target=\"scop_window\">" + sec_feature + "</a>" );
1991                         }
1992                         else {
1993                             out.write( sec_feature );
1994                         }
1995                     }
1996                 }
1997             }
1998             out.write( "]" );
1999         }
2000         out.write( "</td>" );
2001     }
2002
2003     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2004                                                                        final StringBuilder html_title,
2005                                                                        final Writer w,
2006                                                                        final SortedSet<DomainSimilarity> similarities,
2007                                                                        final boolean treat_as_binary,
2008                                                                        final List<Species> species_order,
2009                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
2010                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
2011                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
2012                                                                        final boolean verbose ) throws IOException {
2013         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2014         String histogram_title = null;
2015         switch ( sort_field ) {
2016             case ABS_MAX_COUNTS_DIFFERENCE:
2017                 if ( treat_as_binary ) {
2018                     histogram_title = "absolute counts difference:";
2019                 }
2020                 else {
2021                     histogram_title = "absolute (maximal) counts difference:";
2022                 }
2023                 break;
2024             case MAX_COUNTS_DIFFERENCE:
2025                 if ( treat_as_binary ) {
2026                     histogram_title = "counts difference:";
2027                 }
2028                 else {
2029                     histogram_title = "(maximal) counts difference:";
2030                 }
2031                 break;
2032             case DOMAIN_ID:
2033                 histogram_title = "score mean:";
2034                 break;
2035             case MIN:
2036                 histogram_title = "score minimum:";
2037                 break;
2038             case MAX:
2039                 histogram_title = "score maximum:";
2040                 break;
2041             case MAX_DIFFERENCE:
2042                 if ( treat_as_binary ) {
2043                     histogram_title = "difference:";
2044                 }
2045                 else {
2046                     histogram_title = "(maximal) difference:";
2047                 }
2048                 break;
2049             case MEAN:
2050                 histogram_title = "score mean:";
2051                 break;
2052             case SD:
2053                 histogram_title = "score standard deviation:";
2054                 break;
2055             case SPECIES_COUNT:
2056                 histogram_title = "species number:";
2057                 break;
2058             default:
2059                 throw new AssertionError( "Unknown sort field: " + sort_field );
2060         }
2061         for( final DomainSimilarity similarity : similarities ) {
2062             switch ( sort_field ) {
2063                 case ABS_MAX_COUNTS_DIFFERENCE:
2064                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
2065                     break;
2066                 case MAX_COUNTS_DIFFERENCE:
2067                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
2068                     break;
2069                 case DOMAIN_ID:
2070                     stats.addValue( similarity.getMeanSimilarityScore() );
2071                     break;
2072                 case MIN:
2073                     stats.addValue( similarity.getMinimalSimilarityScore() );
2074                     break;
2075                 case MAX:
2076                     stats.addValue( similarity.getMaximalSimilarityScore() );
2077                     break;
2078                 case MAX_DIFFERENCE:
2079                     stats.addValue( similarity.getMaximalDifference() );
2080                     break;
2081                 case MEAN:
2082                     stats.addValue( similarity.getMeanSimilarityScore() );
2083                     break;
2084                 case SD:
2085                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
2086                     break;
2087                 case SPECIES_COUNT:
2088                     stats.addValue( similarity.getSpecies().size() );
2089                     break;
2090                 default:
2091                     throw new AssertionError( "Unknown sort field: " + sort_field );
2092             }
2093         }
2094         //
2095         // final HistogramData[] hists = new HistogramData[ 1 ];
2096         //
2097         //
2098         // List<HistogramDataItem> data_items = new
2099         // ArrayList<HistogramDataItem>();
2100         // double[] values = stats.getDataAsDoubleArray();
2101         // for( int i = 0; i < values.length; i++ ) {
2102         // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
2103         // i ] );
2104         // data_items.add( data_item );
2105         // }
2106         //
2107         //
2108         // HistogramData hd0 = new HistogramData( "name",
2109         // data_items,
2110         // null, 20,
2111         // 40 );
2112         //
2113         //
2114         //
2115         //
2116         // hists[ 0 ] = hd0;
2117         //
2118         // final HistogramsFrame hf = new HistogramsFrame( hists );
2119         // hf.setVisible( true );
2120         //
2121         AsciiHistogram histo = null;
2122         if ( stats.getMin() < stats.getMin() ) {
2123             histo = new AsciiHistogram( stats, histogram_title );
2124         }
2125         if ( verbose ) {
2126             if ( histo != null ) {
2127                 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
2128             }
2129             System.out.println();
2130             System.out.println( "N                   : " + stats.getN() );
2131             System.out.println( "Min                 : " + stats.getMin() );
2132             System.out.println( "Max                 : " + stats.getMax() );
2133             System.out.println( "Mean                : " + stats.arithmeticMean() );
2134             if ( stats.getN() > 1 ) {
2135                 System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
2136             }
2137             else {
2138                 System.out.println( "SD                  : n/a" );
2139             }
2140             System.out.println( "Median              : " + stats.median() );
2141             if ( stats.getN() > 1 ) {
2142                 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
2143             }
2144             else {
2145                 System.out.println( "Pearsonian skewness : n/a" );
2146             }
2147         }
2148         switch ( print_option ) {
2149             case SIMPLE_TAB_DELIMITED:
2150                 break;
2151             case HTML:
2152                 w.write( "<html>" );
2153                 w.write( SurfacingConstants.NL );
2154                 addHtmlHead( w, "SURFACING :: " + html_title );
2155                 w.write( SurfacingConstants.NL );
2156                 w.write( "<body>" );
2157                 w.write( SurfacingConstants.NL );
2158                 w.write( html_desc.toString() );
2159                 w.write( SurfacingConstants.NL );
2160                 w.write( "<hr>" );
2161                 w.write( "<br>" );
2162                 w.write( SurfacingConstants.NL );
2163                 w.write( "<tt><pre>" );
2164                 w.write( SurfacingConstants.NL );
2165                 if ( histo != null ) {
2166                     w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2167                     w.write( SurfacingConstants.NL );
2168                 }
2169                 w.write( "</pre></tt>" );
2170                 w.write( SurfacingConstants.NL );
2171                 w.write( "<table>" );
2172                 w.write( SurfacingConstants.NL );
2173                 w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2174                 w.write( SurfacingConstants.NL );
2175                 w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2176                 w.write( SurfacingConstants.NL );
2177                 w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2178                 w.write( SurfacingConstants.NL );
2179                 w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2180                 w.write( SurfacingConstants.NL );
2181                 if ( stats.getN() > 1 ) {
2182                     w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2183                 }
2184                 else {
2185                     w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2186                 }
2187                 w.write( SurfacingConstants.NL );
2188                 w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
2189                 w.write( SurfacingConstants.NL );
2190                 if ( stats.getN() > 1 ) {
2191                     w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
2192                 }
2193                 else {
2194                     w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
2195                 }
2196                 w.write( SurfacingConstants.NL );
2197                 w.write( "</table>" );
2198                 w.write( SurfacingConstants.NL );
2199                 w.write( "<br>" );
2200                 w.write( SurfacingConstants.NL );
2201                 w.write( "<hr>" );
2202                 w.write( SurfacingConstants.NL );
2203                 w.write( "<br>" );
2204                 w.write( SurfacingConstants.NL );
2205                 w.write( "<table>" );
2206                 w.write( SurfacingConstants.NL );
2207                 break;
2208         }
2209         w.write( SurfacingConstants.NL );
2210         for( final DomainSimilarity similarity : similarities ) {
2211             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2212                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2213             }
2214             w.write( similarity.toStringBuffer( print_option ).toString() );
2215             w.write( SurfacingConstants.NL );
2216         }
2217         switch ( print_option ) {
2218             case HTML:
2219                 w.write( SurfacingConstants.NL );
2220                 w.write( "</table>" );
2221                 w.write( SurfacingConstants.NL );
2222                 w.write( "</font>" );
2223                 w.write( SurfacingConstants.NL );
2224                 w.write( "</body>" );
2225                 w.write( SurfacingConstants.NL );
2226                 w.write( "</html>" );
2227                 w.write( SurfacingConstants.NL );
2228                 break;
2229         }
2230         w.flush();
2231         w.close();
2232         return stats;
2233     }
2234
2235     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2236                                                                  final String domain_0,
2237                                                                  final String domain_1 ) throws IOException {
2238         individual_files_writer.write( domain_0 );
2239         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2240         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2241             individual_files_writer.write( domain_1 );
2242             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2243         }
2244     }
2245
2246     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2247                                           final String filename,
2248                                           final Format format ) {
2249         final File outfile = new File( filename );
2250         checkForOutputFileWriteability( outfile );
2251         try {
2252             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2253             matrix.toWriter( out, format );
2254             out.flush();
2255             out.close();
2256         }
2257         catch ( final IOException e ) {
2258             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
2259         }
2260         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2261     }
2262
2263     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2264         checkForOutputFileWriteability( matrix_outfile );
2265         try {
2266             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2267             for( final DistanceMatrix distance_matrix : matrices ) {
2268                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2269                 out.write( ForesterUtil.LINE_SEPARATOR );
2270                 out.flush();
2271             }
2272             out.close();
2273         }
2274         catch ( final IOException e ) {
2275             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
2276         }
2277         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2278     }
2279
2280     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2281         try {
2282             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2283             for( final String pfam : pfams ) {
2284                 writer.write( pfam );
2285                 writer.write( ForesterUtil.LINE_SEPARATOR );
2286             }
2287             writer.close();
2288             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2289                     + "]" );
2290         }
2291         catch ( final IOException e ) {
2292             ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "Failure to write: " + e );
2293         }
2294     }
2295
2296     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2297         final PhylogenyWriter writer = new PhylogenyWriter();
2298         try {
2299             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2300         }
2301         catch ( final IOException e ) {
2302             ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "failed to write phylogeny to \"" + filename
2303                     + "\": " + e );
2304         }
2305         ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2306     }
2307
2308     public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
2309         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2310             final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2311             writer.write( " [" );
2312             if ( matcher.matches() ) {
2313                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2314                         + "\" target=\"taxonomy_window\">uniprot</a>" );
2315             }
2316             else {
2317                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2318                         + "\" target=\"taxonomy_window\">eol</a>" );
2319                 writer.write( "|" );
2320                 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2321                         + "\" target=\"taxonomy_window\">tol</a>" );
2322             }
2323             writer.write( "]" );
2324         }
2325     }
2326
2327     public static void writeTaxonomyLinksORIG( final Writer writer, final String species ) throws IOException {
2328         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2329             final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2330             writer.write( " [" );
2331             if ( matcher.matches() ) {
2332                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2333                         + "\" target=\"taxonomy_window\">uniprot</a>" );
2334             }
2335             else {
2336                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2337                         + "\" target=\"taxonomy_window\">eol</a>" );
2338                 writer.write( "|" );
2339                 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2340                         + "\" target=\"taxonomy_window\">tol</a>" );
2341                 writer.write( "|" );
2342                 writer.write( "<a href=\"" + SurfacingConstants.WIKIPEDIA_LINK + species
2343                         + "\" target=\"taxonomy_window\">wikipedia</a>" );
2344                 writer.write( "|" );
2345                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_LINK + species
2346                         + "\" target=\"taxonomy_window\">gs</a>" );
2347             }
2348             writer.write( "]" );
2349         }
2350     }
2351
2352     private static void writeToNexus( final String outfile_name, final CharacterStateMatrix<BinaryStates> matrix ) {
2353         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2354             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2355                     + "] to nexus" );
2356         }
2357         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2358         try {
2359             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2360             w.write( NexusConstants.NEXUS );
2361             w.write( ForesterUtil.LINE_SEPARATOR );
2362             my_matrix.writeNexusTaxaBlock( w );
2363             my_matrix.writeNexusBinaryChractersBlock( w );
2364             w.flush();
2365             w.close();
2366             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2367         }
2368         catch ( final IOException e ) {
2369             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
2370         }
2371     }
2372
2373     private static void writeToNexus( final String outfile_name,
2374                                       final CharacterStateMatrix<BinaryStates> matrix,
2375                                       final Phylogeny phylogeny ) {
2376         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2377             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2378                     + "] to nexus" );
2379         }
2380         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2381         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2382         phylogenies.add( phylogeny );
2383         try {
2384             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2385             w.write( NexusConstants.NEXUS );
2386             w.write( ForesterUtil.LINE_SEPARATOR );
2387             my_matrix.writeNexusTaxaBlock( w );
2388             my_matrix.writeNexusBinaryChractersBlock( w );
2389             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies );
2390             w.flush();
2391             w.close();
2392             ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2393         }
2394         catch ( final IOException e ) {
2395             ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
2396         }
2397     }
2398
2399     private static void writeToNexus( final String outfile_name, final DomainParsimonyCalculator domain_parsimony ) {
2400         writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS, domain_parsimony
2401                 .createMatrixOfDomainPresenceOrAbsence() );
2402         writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, domain_parsimony
2403                 .createMatrixOfBinaryDomainCombinationPresenceOrAbsence() );
2404     }
2405
2406     private static void writeToNexus( final String outfile_name,
2407                                       final DomainParsimonyCalculator domain_parsimony,
2408                                       final Phylogeny phylogeny ) {
2409         writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAINS, domain_parsimony
2410                 .createMatrixOfDomainPresenceOrAbsence(), phylogeny );
2411         writeToNexus( outfile_name + surfacing_old.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS, domain_parsimony
2412                 .createMatrixOfBinaryDomainCombinationPresenceOrAbsence(), phylogeny );
2413     }
2414 }