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

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.surfacing;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.text.DecimalFormat;
  35 import java.text.NumberFormat;
  36 import java.util.ArrayList;
  37 import java.util.Arrays;
  38 import java.util.Collections;
  39 import java.util.Comparator;
  40 import java.util.HashMap;
  41 import java.util.HashSet;
  42 import java.util.Iterator;
  43 import java.util.List;
  44 import java.util.Map;
  45 import java.util.Map.Entry;
  46 import java.util.PriorityQueue;
  47 import java.util.Set;
  48 import java.util.SortedMap;
  49 import java.util.SortedSet;
  50 import java.util.TreeMap;
  51 import java.util.TreeSet;
  52 import java.util.regex.Matcher;
  53 import java.util.regex.Pattern;
  54
  55 import org.forester.application.surfacing;
  56 import org.forester.evoinference.distance.NeighborJoining;
  57 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  58 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  59 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  61 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  62 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  63 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  64 import org.forester.go.GoId;
  65 import org.forester.go.GoNameSpace;
  66 import org.forester.go.GoTerm;
  67 import org.forester.go.PfamToGoMapping;
  68 import org.forester.io.parsers.nexus.NexusConstants;
  69 import org.forester.io.writers.PhylogenyWriter;
  70 import org.forester.phylogeny.Phylogeny;
  71 import org.forester.phylogeny.PhylogenyMethods;
  72 import org.forester.phylogeny.PhylogenyNode;
  73 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  74 import org.forester.phylogeny.data.BinaryCharacters;
  75 import org.forester.phylogeny.data.Confidence;
  76 import org.forester.phylogeny.data.Taxonomy;
  77 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  78 import org.forester.protein.BasicDomain;
  79 import org.forester.protein.BasicProtein;
  80 import org.forester.protein.BinaryDomainCombination;
  81 import org.forester.protein.Domain;
  82 import org.forester.protein.Protein;
  83 import org.forester.species.Species;
  84 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  85 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  86 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  87 import org.forester.util.AsciiHistogram;
  88 import org.forester.util.BasicDescriptiveStatistics;
  89 import org.forester.util.BasicTable;
  90 import org.forester.util.BasicTableParser;
  91 import org.forester.util.DescriptiveStatistics;
  92 import org.forester.util.ForesterUtil;
  93
  94 public final class SurfacingUtil {
  95
  96     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  97     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  98
  99                                                                                  @Override
 100                                                                                  public int compare( final Domain d1,
 101                                                                                                      final Domain d2 ) {
 102                                                                                      if ( d1.getPerSequenceEvalue() < d2
 103                                                                                              .getPerSequenceEvalue() ) {
 104                                                                                          return -1;
 105                                                                                      }
 106                                                                                      else if ( d1
 107                                                                                              .getPerSequenceEvalue() > d2
 108                                                                                              .getPerSequenceEvalue() ) {
 109                                                                                          return 1;
 110                                                                                      }
 111                                                                                      else {
 112                                                                                          return d1.compareTo( d2 );
 113                                                                                      }
 114                                                                                  }
 115                                                                              };
 116     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 117     private static final boolean            USE_LAST                         = true;
 118
 119     private SurfacingUtil() {
 120         // Hidden constructor.
 121     }
 122
 123     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 124                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 125         final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 126         for( final String domain_id : all_cd.keySet() ) {
 127             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 128         }
 129     }
 130
 131     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 132                                              final SortedSet<String> domain_ids ) {
 133         final SortedSet<String> domains = genome.getAllDomainIds();
 134         for( final String domain : domains ) {
 135             domain_ids.add( domain );
 136         }
 137     }
 138
 139     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 140         w.write( SurfacingConstants.NL );
 141         w.write( "<head>" );
 142         w.write( "<title>" );
 143         w.write( title );
 144         w.write( "</title>" );
 145         w.write( SurfacingConstants.NL );
 146         w.write( "<style>" );
 147         w.write( SurfacingConstants.NL );
 148         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 149         w.write( SurfacingConstants.NL );
 150         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 151         w.write( SurfacingConstants.NL );
 152         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 153         w.write( SurfacingConstants.NL );
 154         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 155         w.write( SurfacingConstants.NL );
 156         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 157         w.write( SurfacingConstants.NL );
 158         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 159         w.write( SurfacingConstants.NL );
 160         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 161         w.write( SurfacingConstants.NL );
 162         w.write( "</style>" );
 163         w.write( SurfacingConstants.NL );
 164         w.write( "</head>" );
 165         w.write( SurfacingConstants.NL );
 166     }
 167
 168     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 169         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 170         for( final DomainSimilarity similarity : similarities ) {
 171             stats.addValue( similarity.getMeanSimilarityScore() );
 172         }
 173         return stats;
 174     }
 175
 176     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 177         int overlap_count = 0;
 178         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 179             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 180                 ++overlap_count;
 181             }
 182         }
 183         return overlap_count;
 184     }
 185
 186     public static void checkForOutputFileWriteability( final File outfile ) {
 187         final String error = ForesterUtil.isWritableFile( outfile );
 188         if ( !ForesterUtil.isEmpty( error ) ) {
 189             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 190         }
 191     }
 192
 193     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 194                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 195                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 196                                                                                            final boolean get_gains ) {
 197         final SortedSet<String> sorted_ids = new TreeSet<String>();
 198         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 199             sorted_ids.add( matrix.getIdentifier( i ) );
 200         }
 201         for( final String id : sorted_ids ) {
 202             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 203                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 204                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 205                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 206                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 207                                 .createInstance( matrix.getCharacter( c ) ) );
 208                     }
 209                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 210                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 211                                 .createInstance( matrix.getCharacter( c ) ) );
 212                     }
 213                     else {
 214                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 215                                 .getCharacter( c ) ) );
 216                     }
 217                 }
 218             }
 219         }
 220     }
 221
 222     public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 223         final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
 224         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 225             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 226                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 227             }
 228             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 229         }
 230         return domain_id_to_go_ids_map;
 231     }
 232
 233     public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 234             throws IOException {
 235         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
 236         final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
 237         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 238             final String domain_id = primary_table.getValue( 0, r );
 239             if ( !map.containsKey( domain_id ) ) {
 240                 map.put( domain_id, new HashSet<String>() );
 241             }
 242             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 243         }
 244         return map;
 245     }
 246
 247     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 248         checkForOutputFileWriteability( nj_tree_outfile );
 249         final NeighborJoining nj = NeighborJoining.createInstance();
 250         final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
 251         phylogeny.setName( nj_tree_outfile.getName() );
 252         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 253         return phylogeny;
 254     }
 255
 256     public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
 257         final Map<String, Integer> m = new HashMap<String, Integer>();
 258         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 259             final PhylogenyNode n = iter.next();
 260             if ( n.getNodeData().isHasTaxonomy() ) {
 261                 final Taxonomy t = n.getNodeData().getTaxonomy();
 262                 final String c = t.getTaxonomyCode();
 263                 if ( !ForesterUtil.isEmpty( c ) ) {
 264                     if ( n.getNodeData().getTaxonomy() == null ) {
 265                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 266                     }
 267                     final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
 268                     if ( ForesterUtil.isEmpty( id ) ) {
 269                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 270                     }
 271                     if ( m.containsKey( c ) ) {
 272                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
 273                     }
 274                     final int iid = Integer.valueOf( id );
 275                     if ( m.containsValue( iid ) ) {
 276                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
 277                     }
 278                     m.put( c, iid );
 279                 }
 280             }
 281             else {
 282                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
 283             }
 284         }
 285         return m;
 286     }
 287
 288     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 289                                                             final Detailedness detailedness,
 290                                                             final GoAnnotationOutput go_annotation_output,
 291                                                             final Map<GoId, GoTerm> go_id_to_term_map,
 292                                                             final GoNameSpace go_namespace_limit ) {
 293         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
 294             throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
 295         }
 296         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 297             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 298                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 299                 printable_domain_similarity.setDetailedness( detailedness );
 300                 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
 301                 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
 302                 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
 303             }
 304         }
 305     }
 306
 307     public static void doit( final List<Protein> proteins,
 308                              final List<String> query_domain_ids_nc_order,
 309                              final Writer out,
 310                              final String separator,
 311                              final String limit_to_species,
 312                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
 313         for( final Protein protein : proteins ) {
 314             if ( ForesterUtil.isEmpty( limit_to_species )
 315                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 316                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 317                     out.write( protein.getSpecies().getSpeciesId() );
 318                     out.write( separator );
 319                     out.write( protein.getProteinId().getId() );
 320                     out.write( separator );
 321                     out.write( "[" );
 322                     final Set<String> visited_domain_ids = new HashSet<String>();
 323                     boolean first = true;
 324                     for( final Domain domain : protein.getProteinDomains() ) {
 325                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 326                             visited_domain_ids.add( domain.getDomainId() );
 327                             if ( first ) {
 328                                 first = false;
 329                             }
 330                             else {
 331                                 out.write( " " );
 332                             }
 333                             out.write( domain.getDomainId() );
 334                             out.write( " {" );
 335                             out.write( "" + domain.getTotalCount() );
 336                             out.write( "}" );
 337                         }
 338                     }
 339                     out.write( "]" );
 340                     out.write( separator );
 341                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 342                             .equals( SurfacingConstants.NONE ) ) ) {
 343                         out.write( protein.getDescription() );
 344                     }
 345                     out.write( separator );
 346                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 347                             .equals( SurfacingConstants.NONE ) ) ) {
 348                         out.write( protein.getAccession() );
 349                     }
 350                     out.write( SurfacingConstants.NL );
 351                 }
 352             }
 353         }
 354         out.flush();
 355     }
 356
 357     public static void domainsPerProteinsStatistics( final String genome,
 358                                                      final List<Protein> protein_list,
 359                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
 360                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
 361                                                      final SortedSet<String> domains_which_are_always_single,
 362                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
 363                                                      final SortedSet<String> domains_which_never_single,
 364                                                      final Writer writer ) {
 365         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 366         for( final Protein protein : protein_list ) {
 367             final int domains = protein.getNumberOfProteinDomains();
 368             //System.out.println( domains );
 369             stats.addValue( domains );
 370             all_genomes_domains_per_potein_stats.addValue( domains );
 371             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
 372                 all_genomes_domains_per_potein_histo.put( domains, 1 );
 373             }
 374             else {
 375                 all_genomes_domains_per_potein_histo.put( domains,
 376                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
 377             }
 378             if ( domains == 1 ) {
 379                 final String domain = protein.getProteinDomain( 0 ).getDomainId();
 380                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 381                     if ( domains_which_never_single.contains( domain ) ) {
 382                         domains_which_never_single.remove( domain );
 383                         domains_which_are_sometimes_single_sometimes_not.add( domain );
 384                     }
 385                     else {
 386                         domains_which_are_always_single.add( domain );
 387                     }
 388                 }
 389             }
 390             else if ( domains > 1 ) {
 391                 for( final Domain d : protein.getProteinDomains() ) {
 392                     final String domain = d.getDomainId();
 393                     // System.out.println( domain );
 394                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 395                         if ( domains_which_are_always_single.contains( domain ) ) {
 396                             domains_which_are_always_single.remove( domain );
 397                             domains_which_are_sometimes_single_sometimes_not.add( domain );
 398                         }
 399                         else {
 400                             domains_which_never_single.add( domain );
 401                         }
 402                     }
 403                 }
 404             }
 405         }
 406         try {
 407             writer.write( genome );
 408             writer.write( "\t" );
 409             if ( stats.getN() >= 1 ) {
 410                 writer.write( stats.arithmeticMean() + "" );
 411                 writer.write( "\t" );
 412                 if ( stats.getN() >= 2 ) {
 413                     writer.write( stats.sampleStandardDeviation() + "" );
 414                 }
 415                 else {
 416                     writer.write( "" );
 417                 }
 418                 writer.write( "\t" );
 419                 writer.write( stats.median() + "" );
 420                 writer.write( "\t" );
 421                 writer.write( stats.getN() + "" );
 422                 writer.write( "\t" );
 423                 writer.write( stats.getMin() + "" );
 424                 writer.write( "\t" );
 425                 writer.write( stats.getMax() + "" );
 426             }
 427             else {
 428                 writer.write( "\t" );
 429                 writer.write( "\t" );
 430                 writer.write( "\t" );
 431                 writer.write( "0" );
 432                 writer.write( "\t" );
 433                 writer.write( "\t" );
 434             }
 435             writer.write( "\n" );
 436         }
 437         catch ( final IOException e ) {
 438             e.printStackTrace();
 439         }
 440     }
 441
 442     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 443                                                     final int number_of_genomes,
 444                                                     final DomainLengthsTable domain_lengths_table,
 445                                                     final File outfile ) throws IOException {
 446         final DecimalFormat df = new DecimalFormat( "#.00" );
 447         checkForOutputFileWriteability( outfile );
 448         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 449         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 450         out.write( ForesterUtil.LINE_SEPARATOR );
 451         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 452         out.write( ForesterUtil.LINE_SEPARATOR );
 453         out.write( ForesterUtil.LINE_SEPARATOR );
 454         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 455         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 456         out.write( ForesterUtil.LINE_SEPARATOR );
 457         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 458             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 459             if ( species_list.size() > 0 ) {
 460                 out.write( domain_lengths.getDomainId() + "\t" );
 461                 for( final Species species : species_list ) {
 462                     out.write( species + "\t" );
 463                 }
 464                 out.write( ForesterUtil.LINE_SEPARATOR );
 465                 // DescriptiveStatistics stats_for_domain = domain_lengths
 466                 //         .calculateMeanBasedStatistics();
 467                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 468                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 469             }
 470         }
 471         out.write( ForesterUtil.LINE_SEPARATOR );
 472         out.write( ForesterUtil.LINE_SEPARATOR );
 473         out.write( "OUTLIER SPECIES (Z 1.0)" );
 474         out.write( ForesterUtil.LINE_SEPARATOR );
 475         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 476                 .calculateMeanBasedStatisticsForAllSpecies();
 477         out.write( stats_for_all_species.asSummary() );
 478         out.write( ForesterUtil.LINE_SEPARATOR );
 479         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 480         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 481         out.write( ForesterUtil.LINE_SEPARATOR );
 482         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 483         final double population_mean = stats_for_all_species.arithmeticMean();
 484         for( final Species species : domain_lengths_table.getSpecies() ) {
 485             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 486             final double z = ( x - population_mean ) / population_sd;
 487             out.write( species + "\t" + z );
 488             out.write( ForesterUtil.LINE_SEPARATOR );
 489         }
 490         out.write( ForesterUtil.LINE_SEPARATOR );
 491         for( final Species species : domain_lengths_table.getSpecies() ) {
 492             final DescriptiveStatistics stats_for_species = domain_lengths_table
 493                     .calculateMeanBasedStatisticsForSpecies( species );
 494             final double x = stats_for_species.arithmeticMean();
 495             final double z = ( x - population_mean ) / population_sd;
 496             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 497                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 498                 out.write( ForesterUtil.LINE_SEPARATOR );
 499             }
 500         }
 501         out.close();
 502         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 503         //        for( int i = 0; i < number_of_genomes; ++i ) {
 504         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 505         //            histogram_datas
 506         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 507         //                            .calculateMeanBasedStatisticsForSpecies( species )
 508         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 509         //        }
 510         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 511         //        hf.setVisible( true );
 512         System.gc();
 513     }
 514
 515     /**
 516      *
 517      * @param all_binary_domains_combination_lost_fitch
 518      * @param consider_directedness_and_adjacency_for_bin_combinations
 519      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 520      * which were gained under unweighted (Fitch) parsimony.
 521      */
 522     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 523                                                  final boolean radomize_fitch_parsimony,
 524                                                  final String outfile_name,
 525                                                  final DomainParsimonyCalculator domain_parsimony,
 526                                                  final Phylogeny phylogeny,
 527                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
 528                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 529                                                  final GoNameSpace go_namespace_limit,
 530                                                  final String parameters_str,
 531                                                  final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
 532                                                  final SortedSet<String> positive_filter,
 533                                                  final boolean output_binary_domain_combinations_for_graphs,
 534                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 535                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 536                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 537                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 538                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 539                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
 540                                                  final Map<String, Integer> tax_code_to_id_map,
 541                                                  final boolean write_to_nexus ) {
 542         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 543         final String date_time = ForesterUtil.getCurrentDateTime();
 544         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 545         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 546         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 547         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 548         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 549         if ( write_to_nexus ) {
 550             writeToNexus( outfile_name, domain_parsimony, phylogeny );
 551         }
 552         // DOLLO DOMAINS
 553         // -------------
 554         Phylogeny local_phylogeny_l = phylogeny.copy();
 555         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 556             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 557         }
 558         else {
 559             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 560         }
 561         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 562                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 563         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 564                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 565         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 566                                                            CharacterStateMatrix.GainLossStates.GAIN,
 567                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 568                                                            sep,
 569                                                            ForesterUtil.LINE_SEPARATOR,
 570                                                            null );
 571         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 572                                                            CharacterStateMatrix.GainLossStates.LOSS,
 573                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 574                                                            sep,
 575                                                            ForesterUtil.LINE_SEPARATOR,
 576                                                            null );
 577         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 578                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 579         //HTML:
 580         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 581                                        go_id_to_term_map,
 582                                        go_namespace_limit,
 583                                        false,
 584                                        domain_parsimony.getGainLossMatrix(),
 585                                        CharacterStateMatrix.GainLossStates.GAIN,
 586                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 587                                        sep,
 588                                        ForesterUtil.LINE_SEPARATOR,
 589                                        "Dollo Parsimony | Gains | Domains",
 590                                        "+",
 591                                        domain_id_to_secondary_features_maps,
 592                                        all_pfams_encountered,
 593                                        all_pfams_gained_as_domains,
 594                                        "_dollo_gains_d",
 595                                        tax_code_to_id_map );
 596         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 597                                        go_id_to_term_map,
 598                                        go_namespace_limit,
 599                                        false,
 600                                        domain_parsimony.getGainLossMatrix(),
 601                                        CharacterStateMatrix.GainLossStates.LOSS,
 602                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 603                                        sep,
 604                                        ForesterUtil.LINE_SEPARATOR,
 605                                        "Dollo Parsimony | Losses | Domains",
 606                                        "-",
 607                                        domain_id_to_secondary_features_maps,
 608                                        all_pfams_encountered,
 609                                        all_pfams_lost_as_domains,
 610                                        "_dollo_losses_d",
 611                                        tax_code_to_id_map );
 612         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 613                                        go_id_to_term_map,
 614                                        go_namespace_limit,
 615                                        false,
 616                                        domain_parsimony.getGainLossMatrix(),
 617                                        null,
 618                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 619                                        sep,
 620                                        ForesterUtil.LINE_SEPARATOR,
 621                                        "Dollo Parsimony | Present | Domains",
 622                                        "",
 623                                        domain_id_to_secondary_features_maps,
 624                                        all_pfams_encountered,
 625                                        null,
 626                                        "_dollo_present_d",
 627                                        tax_code_to_id_map );
 628         preparePhylogeny( local_phylogeny_l,
 629                           domain_parsimony,
 630                           date_time,
 631                           "Dollo parsimony on domain presence/absence",
 632                           "dollo_on_domains_" + outfile_name,
 633                           parameters_str );
 634         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 635                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 636         try {
 637             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 638             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 639         }
 640         catch ( final IOException e ) {
 641             e.printStackTrace();
 642             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 643         }
 644         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 645             // FITCH DOMAIN COMBINATIONS
 646             // -------------------------
 647             local_phylogeny_l = phylogeny.copy();
 648             String randomization = "no";
 649             if ( radomize_fitch_parsimony ) {
 650                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 651                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 652             }
 653             else {
 654                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
 655             }
 656             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 657                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 658             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 659                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 660             SurfacingUtil
 661                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 662                                                           CharacterStateMatrix.GainLossStates.GAIN,
 663                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 664                                                           sep,
 665                                                           ForesterUtil.LINE_SEPARATOR,
 666                                                           null );
 667             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 668                                                                CharacterStateMatrix.GainLossStates.LOSS,
 669                                                                outfile_name
 670                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 671                                                                sep,
 672                                                                ForesterUtil.LINE_SEPARATOR,
 673                                                                null );
 674             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 675                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 676             if ( all_binary_domains_combination_gained_fitch != null ) {
 677                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 678                                                                                     dc_type,
 679                                                                                     all_binary_domains_combination_gained_fitch,
 680                                                                                     true );
 681             }
 682             if ( all_binary_domains_combination_lost_fitch != null ) {
 683                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 684                                                                                     dc_type,
 685                                                                                     all_binary_domains_combination_lost_fitch,
 686                                                                                     false );
 687             }
 688             if ( output_binary_domain_combinations_for_graphs ) {
 689                 SurfacingUtil
 690                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 691                                                                                                            .getGainLossMatrix(),
 692                                                                                                    null,
 693                                                                                                    outfile_name
 694                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 695                                                                                                    sep,
 696                                                                                                    ForesterUtil.LINE_SEPARATOR,
 697                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 698             }
 699             // HTML:
 700             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 701                                            go_id_to_term_map,
 702                                            go_namespace_limit,
 703                                            true,
 704                                            domain_parsimony.getGainLossMatrix(),
 705                                            CharacterStateMatrix.GainLossStates.GAIN,
 706                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 707                                            sep,
 708                                            ForesterUtil.LINE_SEPARATOR,
 709                                            "Fitch Parsimony | Gains | Domain Combinations",
 710                                            "+",
 711                                            null,
 712                                            all_pfams_encountered,
 713                                            all_pfams_gained_as_dom_combinations,
 714                                            "_fitch_gains_dc",
 715                                            tax_code_to_id_map );
 716             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 717                                            go_id_to_term_map,
 718                                            go_namespace_limit,
 719                                            true,
 720                                            domain_parsimony.getGainLossMatrix(),
 721                                            CharacterStateMatrix.GainLossStates.LOSS,
 722                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 723                                            sep,
 724                                            ForesterUtil.LINE_SEPARATOR,
 725                                            "Fitch Parsimony | Losses | Domain Combinations",
 726                                            "-",
 727                                            null,
 728                                            all_pfams_encountered,
 729                                            all_pfams_lost_as_dom_combinations,
 730                                            "_fitch_losses_dc",
 731                                            tax_code_to_id_map );
 732             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 733                                            go_id_to_term_map,
 734                                            go_namespace_limit,
 735                                            true,
 736                                            domain_parsimony.getGainLossMatrix(),
 737                                            null,
 738                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 739                                            sep,
 740                                            ForesterUtil.LINE_SEPARATOR,
 741                                            "Fitch Parsimony | Present | Domain Combinations",
 742                                            "",
 743                                            null,
 744                                            all_pfams_encountered,
 745                                            null,
 746                                            "_fitch_present_dc",
 747                                            tax_code_to_id_map );
 748             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 749                                             go_id_to_term_map,
 750                                             outfile_name,
 751                                             all_pfams_encountered );
 752             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 753             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 754             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 755                               all_pfams_gained_as_dom_combinations );
 756             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 757             preparePhylogeny( local_phylogeny_l,
 758                               domain_parsimony,
 759                               date_time,
 760                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 761                                       + randomization,
 762                               "fitch_on_binary_domain_combinations_" + outfile_name,
 763                               parameters_str );
 764             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 765                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 766             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 767                                                         outfile_name
 768                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 769                                                         outfile_name
 770                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 771                                                         outfile_name
 772                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 773                                                         outfile_name
 774                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
 775                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
 776                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
 777                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
 778                                                         protein_length_stats_by_dc,
 779                                                         domain_number_stats_by_dc,
 780                                                         domain_length_stats_by_domain );
 781         }
 782     }
 783
 784     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 785                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 786                                                                      final Phylogeny phylogeny,
 787                                                                      final String parameters_str,
 788                                                                      final Map<Species, MappingResults> mapping_results_map ) {
 789         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 790         final String date_time = ForesterUtil.getCurrentDateTime();
 791         System.out.println();
 792         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 793                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 794                       phylogeny );
 795         Phylogeny local_phylogeny_copy = phylogeny.copy();
 796         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 797         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 798                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 799         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 800                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 801         SurfacingUtil
 802                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 803                                                       CharacterStateMatrix.GainLossStates.GAIN,
 804                                                       outfile_name
 805                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 806                                                       sep,
 807                                                       ForesterUtil.LINE_SEPARATOR,
 808                                                       null );
 809         SurfacingUtil
 810                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 811                                                       CharacterStateMatrix.GainLossStates.LOSS,
 812                                                       outfile_name
 813                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 814                                                       sep,
 815                                                       ForesterUtil.LINE_SEPARATOR,
 816                                                       null );
 817         SurfacingUtil
 818                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 819                                                       null,
 820                                                       outfile_name
 821                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 822                                                       sep,
 823                                                       ForesterUtil.LINE_SEPARATOR,
 824                                                       null );
 825         preparePhylogeny( local_phylogeny_copy,
 826                           secondary_features_parsimony,
 827                           date_time,
 828                           "Dollo parsimony on secondary feature presence/absence",
 829                           "dollo_on_secondary_features_" + outfile_name,
 830                           parameters_str );
 831         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 832                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 833         // FITCH DOMAIN COMBINATIONS
 834         // -------------------------
 835         local_phylogeny_copy = phylogeny.copy();
 836         final String randomization = "no";
 837         secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
 838         preparePhylogeny( local_phylogeny_copy,
 839                           secondary_features_parsimony,
 840                           date_time,
 841                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
 842                                   + randomization,
 843                           "fitch_on_binary_domain_combinations_" + outfile_name,
 844                           parameters_str );
 845         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 846                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
 847         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
 848                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
 849                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
 850                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
 851                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
 852                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
 853                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
 854     }
 855
 856     public static void extractProteinNames( final List<Protein> proteins,
 857                                             final List<String> query_domain_ids_nc_order,
 858                                             final Writer out,
 859                                             final String separator,
 860                                             final String limit_to_species ) throws IOException {
 861         for( final Protein protein : proteins ) {
 862             if ( ForesterUtil.isEmpty( limit_to_species )
 863                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 864                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 865                     out.write( protein.getSpecies().getSpeciesId() );
 866                     out.write( separator );
 867                     out.write( protein.getProteinId().getId() );
 868                     out.write( separator );
 869                     out.write( "[" );
 870                     final Set<String> visited_domain_ids = new HashSet<String>();
 871                     boolean first = true;
 872                     for( final Domain domain : protein.getProteinDomains() ) {
 873                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 874                             visited_domain_ids.add( domain.getDomainId() );
 875                             if ( first ) {
 876                                 first = false;
 877                             }
 878                             else {
 879                                 out.write( " " );
 880                             }
 881                             out.write( domain.getDomainId() );
 882                             out.write( " {" );
 883                             out.write( "" + domain.getTotalCount() );
 884                             out.write( "}" );
 885                         }
 886                     }
 887                     out.write( "]" );
 888                     out.write( separator );
 889                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 890                             .equals( SurfacingConstants.NONE ) ) ) {
 891                         out.write( protein.getDescription() );
 892                     }
 893                     out.write( separator );
 894                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 895                             .equals( SurfacingConstants.NONE ) ) ) {
 896                         out.write( protein.getAccession() );
 897                     }
 898                     out.write( SurfacingConstants.NL );
 899                 }
 900             }
 901         }
 902         out.flush();
 903     }
 904
 905     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
 906                                             final String domain_id,
 907                                             final Writer out,
 908                                             final String separator,
 909                                             final String limit_to_species,
 910                                             final double domain_e_cutoff ) throws IOException {
 911         System.out.println( "Per domain E-value: " + domain_e_cutoff );
 912         for( final Species species : protein_lists_per_species.keySet() ) {
 913             System.out.println( species + ":" );
 914             for( final Protein protein : protein_lists_per_species.get( species ) ) {
 915                 if ( ForesterUtil.isEmpty( limit_to_species )
 916                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 917                     final List<Domain> domains = protein.getProteinDomains( domain_id );
 918                     if ( domains.size() > 0 ) {
 919                         out.write( protein.getSpecies().getSpeciesId() );
 920                         out.write( separator );
 921                         out.write( protein.getProteinId().getId() );
 922                         out.write( separator );
 923                         out.write( domain_id.toString() );
 924                         out.write( separator );
 925                         int prev_to = -1;
 926                         for( final Domain domain : domains ) {
 927                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 928                                 out.write( "/" );
 929                                 out.write( domain.getFrom() + "-" + domain.getTo() );
 930                                 if ( prev_to >= 0 ) {
 931                                     final int l = domain.getFrom() - prev_to;
 932                                     System.out.println( l );
 933                                 }
 934                                 prev_to = domain.getTo();
 935                             }
 936                         }
 937                         out.write( "/" );
 938                         out.write( separator );
 939                         final List<Domain> domain_list = new ArrayList<Domain>();
 940                         for( final Domain domain : protein.getProteinDomains() ) {
 941                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
 942                                 domain_list.add( domain );
 943                             }
 944                         }
 945                         final Domain domain_ary[] = new Domain[ domain_list.size() ];
 946                         for( int i = 0; i < domain_list.size(); ++i ) {
 947                             domain_ary[ i ] = domain_list.get( i );
 948                         }
 949                         Arrays.sort( domain_ary, new DomainComparator( true ) );
 950                         out.write( "{" );
 951                         boolean first = true;
 952                         for( final Domain domain : domain_ary ) {
 953                             if ( first ) {
 954                                 first = false;
 955                             }
 956                             else {
 957                                 out.write( "," );
 958                             }
 959                             out.write( domain.getDomainId().toString() );
 960                             out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
 961                             out.write( ":" + domain.getPerDomainEvalue() );
 962                         }
 963                         out.write( "}" );
 964                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 965                                 .equals( SurfacingConstants.NONE ) ) ) {
 966                             out.write( protein.getDescription() );
 967                         }
 968                         out.write( separator );
 969                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 970                                 .equals( SurfacingConstants.NONE ) ) ) {
 971                             out.write( protein.getAccession() );
 972                         }
 973                         out.write( SurfacingConstants.NL );
 974                     }
 975                 }
 976             }
 977         }
 978         out.flush();
 979     }
 980
 981     public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
 982         final SortedSet<String> all_domains_ids = new TreeSet<String>();
 983         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 984             final Set<String> all_domains = gwcd.getAllDomainIds();
 985             //    for( final Domain domain : all_domains ) {
 986             all_domains_ids.addAll( all_domains );
 987             //    }
 988         }
 989         return all_domains_ids;
 990     }
 991
 992     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
 993         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
 994         for( final Protein protein_domain_collection : protein_domain_collections ) {
 995             for( final Object name : protein_domain_collection.getProteinDomains() ) {
 996                 final BasicDomain protein_domain = ( BasicDomain ) name;
 997                 final String id = protein_domain.getDomainId();
 998                 if ( map.containsKey( id ) ) {
 999                     map.put( id, map.get( id ) + 1 );
1000                 }
1001                 else {
1002                     map.put( id, 1 );
1003                 }
1004             }
1005         }
1006         return map;
1007     }
1008
1009     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1010         final PhylogenyNodeIterator it = p.iteratorPostorder();
1011         int c = 0;
1012         while ( it.hasNext() ) {
1013             final PhylogenyNode n = it.next();
1014             if ( ForesterUtil.isEmpty( n.getName() )
1015                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1016                             .getScientificName() ) )
1017                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1018                             .getCommonName() ) ) ) {
1019                 if ( n.getParent() != null ) {
1020                     names.append( " " );
1021                     names.append( n.getParent().getName() );
1022                 }
1023                 final List l = n.getAllExternalDescendants();
1024                 for( final Object object : l ) {
1025                     System.out.println( l.toString() );
1026                 }
1027                 ++c;
1028             }
1029         }
1030         return c;
1031     }
1032
1033     /**
1034      * Returns true is Domain domain falls in an uninterrupted stretch of
1035      * covered positions.
1036      *
1037      * @param domain
1038      * @param covered_positions
1039      * @return
1040      */
1041     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1042         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1043             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1044                 return false;
1045             }
1046         }
1047         return true;
1048     }
1049
1050     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
1051                                                           final SortedMap<String, Integer> domain_architecuture_counts,
1052                                                           final int min_count,
1053                                                           final File da_counts_outfile,
1054                                                           final File unique_da_outfile ) {
1055         checkForOutputFileWriteability( da_counts_outfile );
1056         checkForOutputFileWriteability( unique_da_outfile );
1057         try {
1058             final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
1059             final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
1060             final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
1061             while ( it.hasNext() ) {
1062                 final Map.Entry<String, Integer> e = it.next();
1063                 final String da = e.getKey();
1064                 final int count = e.getValue();
1065                 if ( count >= min_count ) {
1066                     da_counts_out.write( da );
1067                     da_counts_out.write( "\t" );
1068                     da_counts_out.write( String.valueOf( count ) );
1069                     da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
1070                 }
1071                 if ( count == 1 ) {
1072                     final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
1073                     while ( it2.hasNext() ) {
1074                         final Map.Entry<String, Set<String>> e2 = it2.next();
1075                         final String genome = e2.getKey();
1076                         final Set<String> das = e2.getValue();
1077                         if ( das.contains( da ) ) {
1078                             unique_da_out.write( genome );
1079                             unique_da_out.write( "\t" );
1080                             unique_da_out.write( da );
1081                             unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
1082                         }
1083                     }
1084                 }
1085             }
1086             unique_da_out.close();
1087             da_counts_out.close();
1088         }
1089         catch ( final IOException e ) {
1090             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1091         }
1092         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
1093         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
1094         //
1095     }
1096
1097     public static void preparePhylogeny( final Phylogeny p,
1098                                          final DomainParsimonyCalculator domain_parsimony,
1099                                          final String date_time,
1100                                          final String method,
1101                                          final String name,
1102                                          final String parameters_str ) {
1103         domain_parsimony.decoratePhylogenyWithDomains( p );
1104         final StringBuilder desc = new StringBuilder();
1105         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1106         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1107         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1108         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1109         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1110         desc.append( "[Parameters: " + parameters_str + "]" );
1111         p.setName( name );
1112         p.setDescription( desc.toString() );
1113         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1114         p.setRerootable( false );
1115         p.setRooted( true );
1116     }
1117
1118     /*
1119      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1120      *
1121      *
1122      */
1123     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1124                                                             final String protein_id,
1125                                                             final String separator ) {
1126         final StringBuffer sb = new StringBuffer();
1127         if ( protein.getSpecies() == null ) {
1128             throw new IllegalArgumentException( "species must not be null" );
1129         }
1130         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1131             throw new IllegalArgumentException( "species id must not be empty" );
1132         }
1133         final List<Domain> domains = protein.getProteinDomains();
1134         if ( domains.size() > 1 ) {
1135             final Map<String, Integer> counts = new HashMap<String, Integer>();
1136             for( final Domain domain : domains ) {
1137                 final String id = domain.getDomainId();
1138                 if ( counts.containsKey( id ) ) {
1139                     counts.put( id, counts.get( id ) + 1 );
1140                 }
1141                 else {
1142                     counts.put( id, 1 );
1143                 }
1144             }
1145             final Set<String> dcs = new HashSet<String>();
1146             for( int i = 1; i < domains.size(); ++i ) {
1147                 for( int j = 0; j < i; ++j ) {
1148                     Domain domain_n = domains.get( i );
1149                     Domain domain_c = domains.get( j );
1150                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1151                         domain_n = domains.get( j );
1152                         domain_c = domains.get( i );
1153                     }
1154                     final String dc = domain_n.getDomainId() + domain_c.getDomainId();
1155                     if ( !dcs.contains( dc ) ) {
1156                         dcs.add( dc );
1157                         sb.append( protein.getSpecies() );
1158                         sb.append( separator );
1159                         sb.append( protein_id );
1160                         sb.append( separator );
1161                         sb.append( domain_n.getDomainId() );
1162                         sb.append( separator );
1163                         sb.append( domain_c.getDomainId() );
1164                         sb.append( separator );
1165                         sb.append( domain_n.getPerDomainEvalue() );
1166                         sb.append( separator );
1167                         sb.append( domain_c.getPerDomainEvalue() );
1168                         sb.append( separator );
1169                         sb.append( counts.get( domain_n.getDomainId() ) );
1170                         sb.append( separator );
1171                         sb.append( counts.get( domain_c.getDomainId() ) );
1172                         sb.append( ForesterUtil.LINE_SEPARATOR );
1173                     }
1174                 }
1175             }
1176         }
1177         else if ( domains.size() == 1 ) {
1178             sb.append( protein.getSpecies() );
1179             sb.append( separator );
1180             sb.append( protein_id );
1181             sb.append( separator );
1182             sb.append( domains.get( 0 ).getDomainId() );
1183             sb.append( separator );
1184             sb.append( separator );
1185             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1186             sb.append( separator );
1187             sb.append( separator );
1188             sb.append( 1 );
1189             sb.append( separator );
1190             sb.append( ForesterUtil.LINE_SEPARATOR );
1191         }
1192         else {
1193             sb.append( protein.getSpecies() );
1194             sb.append( separator );
1195             sb.append( protein_id );
1196             sb.append( separator );
1197             sb.append( separator );
1198             sb.append( separator );
1199             sb.append( separator );
1200             sb.append( separator );
1201             sb.append( separator );
1202             sb.append( ForesterUtil.LINE_SEPARATOR );
1203         }
1204         return sb;
1205     }
1206
1207     /**
1208      *
1209      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1210      * domain with 0.3 is ignored
1211      *
1212      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1213      *
1214      *
1215      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1216      * ignored
1217      *
1218      * @param max_allowed_overlap
1219      *            maximal allowed overlap (inclusive) to be still considered not
1220      *            overlapping (zero or negative value to allow any overlap)
1221      * @param remove_engulfed_domains
1222      *            to remove domains which are completely engulfed by coverage of
1223      *            domains with better support
1224      * @param protein
1225      * @return
1226      */
1227     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1228                                                     final boolean remove_engulfed_domains,
1229                                                     final Protein protein ) {
1230         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1231                 .getSpeciesId(), protein.getLength() );
1232         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1233         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1234         for( final Domain domain : sorted ) {
1235             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1236                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1237                 final int covered_positions_size = covered_positions.size();
1238                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1239                     covered_positions.add( false );
1240                 }
1241                 final int new_covered_positions_size = covered_positions.size();
1242                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1243                     if ( i < new_covered_positions_size ) {
1244                         covered_positions.set( i, true );
1245                     }
1246                     else {
1247                         covered_positions.add( true );
1248                     }
1249                 }
1250                 pruned_protein.addProteinDomain( domain );
1251             }
1252         }
1253         return pruned_protein;
1254     }
1255
1256     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1257         final List<Domain> domains = new ArrayList<Domain>();
1258         for( final Domain d : protein.getProteinDomains() ) {
1259             domains.add( d );
1260         }
1261         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1262         return domains;
1263     }
1264
1265     public static int storeDomainArchitectures( final String genome,
1266                                                 final SortedMap<String, Set<String>> domain_architecutures,
1267                                                 final List<Protein> protein_list,
1268                                                 final Map<String, Integer> distinct_domain_architecuture_counts ) {
1269         final Set<String> da = new HashSet<String>();
1270         domain_architecutures.put( genome, da );
1271         for( final Protein protein : protein_list ) {
1272             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
1273             if ( !da.contains( da_str ) ) {
1274                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
1275                     distinct_domain_architecuture_counts.put( da_str, 1 );
1276                 }
1277                 else {
1278                     distinct_domain_architecuture_counts.put( da_str,
1279                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
1280                 }
1281                 da.add( da_str );
1282             }
1283         }
1284         return da.size();
1285     }
1286
1287     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1288                                                             final boolean get_gains,
1289                                                             final String outdir,
1290                                                             final String suffix_for_filename ) throws IOException {
1291         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1292         if ( !get_gains ) {
1293             state = CharacterStateMatrix.GainLossStates.LOSS;
1294         }
1295         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1296                                                                   false,
1297                                                                   state,
1298                                                                   outdir );
1299         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1300             final PhylogenyNode node = it.next();
1301             if ( !node.isExternal() ) {
1302                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1303                 if ( domains.size() > 0 ) {
1304                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1305                             + node.getName() + suffix_for_filename );
1306                     for( final String domain : domains ) {
1307                         writer.write( domain );
1308                         writer.write( ForesterUtil.LINE_SEPARATOR );
1309                     }
1310                     writer.close();
1311                 }
1312             }
1313         }
1314     }
1315
1316     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1317                                                                           final File output_dir,
1318                                                                           final GenomeWideCombinableDomains gwcd,
1319                                                                           final int i,
1320                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1321         File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
1322                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1323         if ( output_dir != null ) {
1324             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1325         }
1326         checkForOutputFileWriteability( dc_outfile_dot );
1327         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1328         try {
1329             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1330             for( final BinaryDomainCombination bdc : binary_combinations ) {
1331                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1332                         .toString() );
1333                 out_dot.write( SurfacingConstants.NL );
1334             }
1335             out_dot.close();
1336         }
1337         catch ( final IOException e ) {
1338             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1339         }
1340         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1341                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1342                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1343     }
1344
1345     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1346                                                             final CharacterStateMatrix.GainLossStates state,
1347                                                             final String filename,
1348                                                             final String indentifier_characters_separator,
1349                                                             final String character_separator,
1350                                                             final Map<String, String> descriptions ) {
1351         final File outfile = new File( filename );
1352         checkForOutputFileWriteability( outfile );
1353         final SortedSet<String> sorted_ids = new TreeSet<String>();
1354         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1355             sorted_ids.add( matrix.getIdentifier( i ) );
1356         }
1357         try {
1358             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1359             for( final String id : sorted_ids ) {
1360                 out.write( indentifier_characters_separator );
1361                 out.write( "#" + id );
1362                 out.write( indentifier_characters_separator );
1363                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1364                     // Not nice:
1365                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1366                     if ( ( matrix.getState( id, c ) == state )
1367                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1368                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1369                         out.write( matrix.getCharacter( c ) );
1370                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1371                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1372                             out.write( "\t" );
1373                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1374                         }
1375                         out.write( character_separator );
1376                     }
1377                 }
1378             }
1379             out.flush();
1380             out.close();
1381         }
1382         catch ( final IOException e ) {
1383             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1384         }
1385         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1386     }
1387
1388     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1389                                                                                                  final CharacterStateMatrix.GainLossStates state,
1390                                                                                                  final String filename,
1391                                                                                                  final String indentifier_characters_separator,
1392                                                                                                  final String character_separator,
1393                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1394         final File outfile = new File( filename );
1395         checkForOutputFileWriteability( outfile );
1396         final SortedSet<String> sorted_ids = new TreeSet<String>();
1397         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1398             sorted_ids.add( matrix.getIdentifier( i ) );
1399         }
1400         try {
1401             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1402             for( final String id : sorted_ids ) {
1403                 out.write( indentifier_characters_separator );
1404                 out.write( "#" + id );
1405                 out.write( indentifier_characters_separator );
1406                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1407                     // Not nice:
1408                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1409                     if ( ( matrix.getState( id, c ) == state )
1410                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1411                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1412                         BinaryDomainCombination bdc = null;
1413                         try {
1414                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1415                         }
1416                         catch ( final Exception e ) {
1417                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1418                         }
1419                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1420                         out.write( character_separator );
1421                     }
1422                 }
1423             }
1424             out.flush();
1425             out.close();
1426         }
1427         catch ( final IOException e ) {
1428             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1429         }
1430         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1431     }
1432
1433     public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
1434                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1435                                                       final GoNameSpace go_namespace_limit,
1436                                                       final boolean domain_combinations,
1437                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1438                                                       final CharacterStateMatrix.GainLossStates state,
1439                                                       final String filename,
1440                                                       final String indentifier_characters_separator,
1441                                                       final String character_separator,
1442                                                       final String title_for_html,
1443                                                       final String prefix_for_html,
1444                                                       final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
1445                                                       final SortedSet<String> all_pfams_encountered,
1446                                                       final SortedSet<String> pfams_gained_or_lost,
1447                                                       final String suffix_for_per_node_events_file,
1448                                                       final Map<String, Integer> tax_code_to_id_map ) {
1449         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1450             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1451         }
1452         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1453             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1454         }
1455         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1456             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1457         }
1458         final File outfile = new File( filename );
1459         checkForOutputFileWriteability( outfile );
1460         final SortedSet<String> sorted_ids = new TreeSet<String>();
1461         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1462             sorted_ids.add( matrix.getIdentifier( i ) );
1463         }
1464         try {
1465             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1466             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1467                                                                                                                 domain_combinations,
1468                                                                                                                 state,
1469                                                                                                                 filename );
1470             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1471             File per_node_go_mapped_domain_gain_loss_outfile = null;
1472             int per_node_counter = 0;
1473             out.write( "<html>" );
1474             out.write( SurfacingConstants.NL );
1475             addHtmlHead( out, title_for_html );
1476             out.write( SurfacingConstants.NL );
1477             out.write( "<body>" );
1478             out.write( SurfacingConstants.NL );
1479             out.write( "<h1>" );
1480             out.write( SurfacingConstants.NL );
1481             out.write( title_for_html );
1482             out.write( SurfacingConstants.NL );
1483             out.write( "</h1>" );
1484             out.write( SurfacingConstants.NL );
1485             out.write( "<table>" );
1486             out.write( SurfacingConstants.NL );
1487             for( final String id : sorted_ids ) {
1488                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1489                 if ( matcher.matches() ) {
1490                     continue;
1491                 }
1492                 out.write( "<tr>" );
1493                 out.write( "<td>" );
1494                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1495                 out.write( "</td>" );
1496                 out.write( "</tr>" );
1497                 out.write( SurfacingConstants.NL );
1498             }
1499             out.write( "</table>" );
1500             out.write( SurfacingConstants.NL );
1501             for( final String id : sorted_ids ) {
1502                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1503                 if ( matcher.matches() ) {
1504                     continue;
1505                 }
1506                 out.write( SurfacingConstants.NL );
1507                 out.write( "<h2>" );
1508                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1509                 writeTaxonomyLinks( out, id, tax_code_to_id_map );
1510                 out.write( "</h2>" );
1511                 out.write( SurfacingConstants.NL );
1512                 out.write( "<table>" );
1513                 out.write( SurfacingConstants.NL );
1514                 out.write( "<tr>" );
1515                 out.write( "<td><b>" );
1516                 out.write( "Pfam domain(s)" );
1517                 out.write( "</b></td><td><b>" );
1518                 out.write( "GO term acc" );
1519                 out.write( "</b></td><td><b>" );
1520                 out.write( "GO term" );
1521                 out.write( "</b></td><td><b>" );
1522                 out.write( "GO namespace" );
1523                 out.write( "</b></td>" );
1524                 out.write( "</tr>" );
1525                 out.write( SurfacingConstants.NL );
1526                 out.write( "</tr>" );
1527                 out.write( SurfacingConstants.NL );
1528                 per_node_counter = 0;
1529                 if ( matrix.getNumberOfCharacters() > 0 ) {
1530                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1531                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1532                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1533                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1534                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1535                 }
1536                 else {
1537                     per_node_go_mapped_domain_gain_loss_outfile = null;
1538                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1539                 }
1540                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1541                     // Not nice:
1542                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1543                     if ( ( matrix.getState( id, c ) == state )
1544                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1545                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1546                         final String character = matrix.getCharacter( c );
1547                         String domain_0 = "";
1548                         String domain_1 = "";
1549                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1550                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1551                             if ( s.length != 2 ) {
1552                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1553                                         + character + "]" );
1554                             }
1555                             domain_0 = s[ 0 ];
1556                             domain_1 = s[ 1 ];
1557                         }
1558                         else {
1559                             domain_0 = character;
1560                         }
1561                         writeDomainData( domain_id_to_go_ids_map,
1562                                          go_id_to_term_map,
1563                                          go_namespace_limit,
1564                                          out,
1565                                          domain_0,
1566                                          domain_1,
1567                                          prefix_for_html,
1568                                          character_separator,
1569                                          domain_id_to_secondary_features_maps,
1570                                          null );
1571                         all_pfams_encountered.add( domain_0 );
1572                         if ( pfams_gained_or_lost != null ) {
1573                             pfams_gained_or_lost.add( domain_0 );
1574                         }
1575                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1576                             all_pfams_encountered.add( domain_1 );
1577                             if ( pfams_gained_or_lost != null ) {
1578                                 pfams_gained_or_lost.add( domain_1 );
1579                             }
1580                         }
1581                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1582                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1583                                                                      domain_0,
1584                                                                      domain_1 );
1585                             per_node_counter++;
1586                         }
1587                     }
1588                 }
1589                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1590                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1591                     if ( per_node_counter < 1 ) {
1592                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1593                     }
1594                     per_node_counter = 0;
1595                 }
1596                 out.write( "</table>" );
1597                 out.write( SurfacingConstants.NL );
1598                 out.write( "<hr>" );
1599                 out.write( SurfacingConstants.NL );
1600             } // for( final String id : sorted_ids ) {
1601             out.write( "</body>" );
1602             out.write( SurfacingConstants.NL );
1603             out.write( "</html>" );
1604             out.write( SurfacingConstants.NL );
1605             out.flush();
1606             out.close();
1607         }
1608         catch ( final IOException e ) {
1609             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1610         }
1611         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1612     }
1613
1614     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1615                                                           final File output_dir,
1616                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1617                                                           final GenomeWideCombinableDomains gwcd,
1618                                                           final int i,
1619                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1620         File dc_outfile = new File( input_file_properties[ i ][ 1 ]
1621                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1622         if ( output_dir != null ) {
1623             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1624         }
1625         checkForOutputFileWriteability( dc_outfile );
1626         try {
1627             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1628             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1629             out.close();
1630         }
1631         catch ( final IOException e ) {
1632             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1633         }
1634         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1635         try {
1636             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
1637             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1638             if ( stats.getN() < 2 ) {
1639                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1640             }
1641             else {
1642                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1643                         .sampleStandardDeviation() ) + "\t" );
1644             }
1645             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1646             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1647             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1648             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1649             final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
1650             for( final String mpd : mpds ) {
1651                 per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
1652             }
1653             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1654         }
1655         catch ( final IOException e ) {
1656             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1657         }
1658         if ( input_file_properties[ i ].length == 3 ) {
1659             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1660                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1661                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1662         }
1663         else {
1664             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1665                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1666                     + dc_outfile + "\"" );
1667         }
1668     }
1669
1670     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
1671                                                                        final StringBuilder html_title,
1672                                                                        final Writer single_writer,
1673                                                                        Map<Character, Writer> split_writers,
1674                                                                        final SortedSet<DomainSimilarity> similarities,
1675                                                                        final boolean treat_as_binary,
1676                                                                        final List<Species> species_order,
1677                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
1678                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
1679                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
1680                                                                        final boolean verbose,
1681                                                                        final Map<String, Integer> tax_code_to_id_map )
1682             throws IOException {
1683         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1684         String histogram_title = null;
1685         switch ( sort_field ) {
1686             case ABS_MAX_COUNTS_DIFFERENCE:
1687                 if ( treat_as_binary ) {
1688                     histogram_title = "absolute counts difference:";
1689                 }
1690                 else {
1691                     histogram_title = "absolute (maximal) counts difference:";
1692                 }
1693                 break;
1694             case MAX_COUNTS_DIFFERENCE:
1695                 if ( treat_as_binary ) {
1696                     histogram_title = "counts difference:";
1697                 }
1698                 else {
1699                     histogram_title = "(maximal) counts difference:";
1700                 }
1701                 break;
1702             case DOMAIN_ID:
1703                 histogram_title = "score mean:";
1704                 break;
1705             case MIN:
1706                 histogram_title = "score minimum:";
1707                 break;
1708             case MAX:
1709                 histogram_title = "score maximum:";
1710                 break;
1711             case MAX_DIFFERENCE:
1712                 if ( treat_as_binary ) {
1713                     histogram_title = "difference:";
1714                 }
1715                 else {
1716                     histogram_title = "(maximal) difference:";
1717                 }
1718                 break;
1719             case MEAN:
1720                 histogram_title = "score mean:";
1721                 break;
1722             case SD:
1723                 histogram_title = "score standard deviation:";
1724                 break;
1725             case SPECIES_COUNT:
1726                 histogram_title = "species number:";
1727                 break;
1728             default:
1729                 throw new AssertionError( "Unknown sort field: " + sort_field );
1730         }
1731         for( final DomainSimilarity similarity : similarities ) {
1732             switch ( sort_field ) {
1733                 case ABS_MAX_COUNTS_DIFFERENCE:
1734                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
1735                     break;
1736                 case MAX_COUNTS_DIFFERENCE:
1737                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
1738                     break;
1739                 case DOMAIN_ID:
1740                     stats.addValue( similarity.getMeanSimilarityScore() );
1741                     break;
1742                 case MIN:
1743                     stats.addValue( similarity.getMinimalSimilarityScore() );
1744                     break;
1745                 case MAX:
1746                     stats.addValue( similarity.getMaximalSimilarityScore() );
1747                     break;
1748                 case MAX_DIFFERENCE:
1749                     stats.addValue( similarity.getMaximalDifference() );
1750                     break;
1751                 case MEAN:
1752                     stats.addValue( similarity.getMeanSimilarityScore() );
1753                     break;
1754                 case SD:
1755                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
1756                     break;
1757                 case SPECIES_COUNT:
1758                     stats.addValue( similarity.getSpecies().size() );
1759                     break;
1760                 default:
1761                     throw new AssertionError( "Unknown sort field: " + sort_field );
1762             }
1763         }
1764         AsciiHistogram histo = null;
1765         if ( stats.getMin() < stats.getMin() ) {
1766             histo = new AsciiHistogram( stats, histogram_title );
1767         }
1768         if ( verbose ) {
1769             if ( histo != null ) {
1770                 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
1771             }
1772             System.out.println();
1773             System.out.println( "N                   : " + stats.getN() );
1774             System.out.println( "Min                 : " + stats.getMin() );
1775             System.out.println( "Max                 : " + stats.getMax() );
1776             System.out.println( "Mean                : " + stats.arithmeticMean() );
1777             if ( stats.getN() > 1 ) {
1778                 System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
1779             }
1780             else {
1781                 System.out.println( "SD                  : n/a" );
1782             }
1783             System.out.println( "Median              : " + stats.median() );
1784             if ( stats.getN() > 1 ) {
1785                 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
1786             }
1787             else {
1788                 System.out.println( "Pearsonian skewness : n/a" );
1789             }
1790         }
1791         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
1792             split_writers = new HashMap<Character, Writer>();
1793             split_writers.put( '_', single_writer );
1794         }
1795         switch ( print_option ) {
1796             case SIMPLE_TAB_DELIMITED:
1797                 break;
1798             case HTML:
1799                 for( final Character key : split_writers.keySet() ) {
1800                     final Writer w = split_writers.get( key );
1801                     w.write( "<html>" );
1802                     w.write( SurfacingConstants.NL );
1803                     if ( key != '_' ) {
1804                         addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
1805                     }
1806                     else {
1807                         addHtmlHead( w, "DCs (" + html_title + ")" );
1808                     }
1809                     w.write( SurfacingConstants.NL );
1810                     w.write( "<body>" );
1811                     w.write( SurfacingConstants.NL );
1812                     w.write( html_desc.toString() );
1813                     w.write( SurfacingConstants.NL );
1814                     w.write( "<hr>" );
1815                     w.write( "<br>" );
1816                     w.write( SurfacingConstants.NL );
1817                     w.write( "<tt><pre>" );
1818                     w.write( SurfacingConstants.NL );
1819                     if ( histo != null ) {
1820                         w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
1821                         w.write( SurfacingConstants.NL );
1822                     }
1823                     w.write( "</pre></tt>" );
1824                     w.write( SurfacingConstants.NL );
1825                     w.write( "<table>" );
1826                     w.write( SurfacingConstants.NL );
1827                     w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
1828                     w.write( SurfacingConstants.NL );
1829                     w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
1830                     w.write( SurfacingConstants.NL );
1831                     w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
1832                     w.write( SurfacingConstants.NL );
1833                     w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
1834                     w.write( SurfacingConstants.NL );
1835                     if ( stats.getN() > 1 ) {
1836                         w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
1837                     }
1838                     else {
1839                         w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
1840                     }
1841                     w.write( SurfacingConstants.NL );
1842                     w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
1843                     w.write( SurfacingConstants.NL );
1844                     if ( stats.getN() > 1 ) {
1845                         w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
1846                     }
1847                     else {
1848                         w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
1849                     }
1850                     w.write( SurfacingConstants.NL );
1851                     w.write( "</table>" );
1852                     w.write( SurfacingConstants.NL );
1853                     w.write( "<br>" );
1854                     w.write( SurfacingConstants.NL );
1855                     w.write( "<hr>" );
1856                     w.write( SurfacingConstants.NL );
1857                     w.write( "<br>" );
1858                     w.write( SurfacingConstants.NL );
1859                     w.write( "<table>" );
1860                     w.write( SurfacingConstants.NL );
1861                 }
1862                 break;
1863         }
1864         for( final Writer w : split_writers.values() ) {
1865             w.write( SurfacingConstants.NL );
1866         }
1867         for( final DomainSimilarity similarity : similarities ) {
1868             if ( ( species_order != null ) && !species_order.isEmpty() ) {
1869                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
1870             }
1871             if ( single_writer != null ) {
1872                 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1873                 single_writer.write( SurfacingConstants.NL );
1874             }
1875             else {
1876                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
1877                         .charAt( 0 ) );
1878                 if ( local_writer == null ) {
1879                     local_writer = split_writers.get( '0' );
1880                 }
1881                 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
1882                 local_writer.write( SurfacingConstants.NL );
1883             }
1884             // for( final Writer w : split_writers.values() ) {
1885             //w.write( SurfacingConstants.NL );
1886             // }
1887         }
1888         switch ( print_option ) {
1889             case HTML:
1890                 for( final Writer w : split_writers.values() ) {
1891                     w.write( SurfacingConstants.NL );
1892                     w.write( "</table>" );
1893                     w.write( SurfacingConstants.NL );
1894                     w.write( "</font>" );
1895                     w.write( SurfacingConstants.NL );
1896                     w.write( "</body>" );
1897                     w.write( SurfacingConstants.NL );
1898                     w.write( "</html>" );
1899                     w.write( SurfacingConstants.NL );
1900                 }
1901                 break;
1902         }
1903         for( final Writer w : split_writers.values() ) {
1904             w.close();
1905         }
1906         return stats;
1907     }
1908
1909     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
1910                                           final String filename,
1911                                           final Format format ) {
1912         final File outfile = new File( filename );
1913         checkForOutputFileWriteability( outfile );
1914         try {
1915             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1916             matrix.toWriter( out, format );
1917             out.flush();
1918             out.close();
1919         }
1920         catch ( final IOException e ) {
1921             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1922         }
1923         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
1924     }
1925
1926     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
1927         checkForOutputFileWriteability( matrix_outfile );
1928         try {
1929             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
1930             for( final DistanceMatrix distance_matrix : matrices ) {
1931                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
1932                 out.write( ForesterUtil.LINE_SEPARATOR );
1933                 out.flush();
1934             }
1935             out.close();
1936         }
1937         catch ( final IOException e ) {
1938             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1939         }
1940         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
1941     }
1942
1943     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
1944         final PhylogenyWriter writer = new PhylogenyWriter();
1945         try {
1946             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
1947         }
1948         catch ( final IOException e ) {
1949             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
1950                     + e );
1951         }
1952         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
1953     }
1954
1955     public static void writeTaxonomyLinks( final Writer writer,
1956                                            final String species,
1957                                            final Map<String, Integer> tax_code_to_id_map ) throws IOException {
1958         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
1959             writer.write( " [" );
1960             if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
1961                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
1962                         + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
1963             }
1964             else {
1965                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
1966                         + "\" target=\"taxonomy_window\">eol</a>" );
1967                 writer.write( "|" );
1968                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
1969                         + "\" target=\"taxonomy_window\">scholar</a>" );
1970                 writer.write( "|" );
1971                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
1972                         + "\" target=\"taxonomy_window\">google</a>" );
1973             }
1974             writer.write( "]" );
1975         }
1976     }
1977
1978     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
1979         if ( map.containsKey( s ) ) {
1980             map.put( s, map.get( s ) + 1 );
1981         }
1982         else {
1983             map.put( s, 1 );
1984         }
1985     }
1986
1987     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
1988                                                                     final String outfilename_for_counts,
1989                                                                     final String outfilename_for_dc,
1990                                                                     final String outfilename_for_dc_for_go_mapping,
1991                                                                     final String outfilename_for_dc_for_go_mapping_unique,
1992                                                                     final String outfilename_for_rank_counts,
1993                                                                     final String outfilename_for_ancestor_species_counts,
1994                                                                     final String outfilename_for_protein_stats,
1995                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
1996                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
1997                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
1998         try {
1999             //
2000             //            if ( protein_length_stats_by_dc != null ) {
2001             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
2002             //                    System.out.print( entry.getKey().toString() );
2003             //                    System.out.print( ": " );
2004             //                    double[] a = entry.getValue().getDataAsDoubleArray();
2005             //                    for( int i = 0; i < a.length; i++ ) {
2006             //                        System.out.print( a[ i ] + " " );
2007             //                    }
2008             //                    System.out.println();
2009             //                }
2010             //            }
2011             //            if ( domain_number_stats_by_dc != null ) {
2012             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
2013             //                    System.out.print( entry.getKey().toString() );
2014             //                    System.out.print( ": " );
2015             //                    double[] a = entry.getValue().getDataAsDoubleArray();
2016             //                    for( int i = 0; i < a.length; i++ ) {
2017             //                        System.out.print( a[ i ] + " " );
2018             //                    }
2019             //                    System.out.println();
2020             //                }
2021             //            }
2022             //
2023             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
2024             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
2025             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
2026             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
2027             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
2028             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
2029                 final PhylogenyNode n = it.next();
2030                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
2031                 for( final String dc : gained_dc ) {
2032                     if ( dc_gain_counts.containsKey( dc ) ) {
2033                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
2034                     }
2035                     else {
2036                         dc_gain_counts.put( dc, 1 );
2037                     }
2038                 }
2039             }
2040             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
2041             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
2042             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
2043             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
2044             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
2045             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
2046             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
2047             final Set<String> dcs = dc_gain_counts.keySet();
2048             final SortedSet<String> more_than_once = new TreeSet<String>();
2049             final DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
2050             final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
2051             final DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
2052             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
2053             long gained_multiple_times_domain_length_sum = 0;
2054             long gained_once_domain_length_sum = 0;
2055             long gained_multiple_times_domain_length_count = 0;
2056             long gained_once_domain_length_count = 0;
2057             for( final String dc : dcs ) {
2058                 final int count = dc_gain_counts.get( dc );
2059                 if ( histogram.containsKey( count ) ) {
2060                     histogram.put( count, histogram.get( count ) + 1 );
2061                     domain_lists.get( count ).append( ", " + dc );
2062                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
2063                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
2064                 }
2065                 else {
2066                     histogram.put( count, 1 );
2067                     domain_lists.put( count, new StringBuilder( dc ) );
2068                     final PriorityQueue<String> q = new PriorityQueue<String>();
2069                     q.addAll( splitDomainCombination( dc ) );
2070                     domain_lists_go.put( count, q );
2071                     final SortedSet<String> set = new TreeSet<String>();
2072                     set.addAll( splitDomainCombination( dc ) );
2073                     domain_lists_go_unique.put( count, set );
2074                 }
2075                 if ( protein_length_stats_by_dc != null ) {
2076                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
2077                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
2078                     }
2079                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
2080                             .arithmeticMean() );
2081                 }
2082                 if ( domain_number_stats_by_dc != null ) {
2083                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
2084                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
2085                     }
2086                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
2087                             .arithmeticMean() );
2088                 }
2089                 if ( domain_length_stats_by_domain != null ) {
2090                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
2091                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
2092                     }
2093                     final String[] ds = dc.split( "=" );
2094                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2095                             .get( ds[ 0 ] ).arithmeticMean() );
2096                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2097                             .get( ds[ 1 ] ).arithmeticMean() );
2098                 }
2099                 if ( count > 1 ) {
2100                     more_than_once.add( dc );
2101                     if ( protein_length_stats_by_dc != null ) {
2102                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2103                         for( final double element : s.getData() ) {
2104                             gained_multiple_times_lengths_stats.addValue( element );
2105                         }
2106                     }
2107                     if ( domain_number_stats_by_dc != null ) {
2108                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2109                         for( final double element : s.getData() ) {
2110                             gained_multiple_times_domain_count_stats.addValue( element );
2111                         }
2112                     }
2113                     if ( domain_length_stats_by_domain != null ) {
2114                         final String[] ds = dc.split( "=" );
2115                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2116                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2117                         for( final double element : s0.getData() ) {
2118                             gained_multiple_times_domain_length_sum += element;
2119                             ++gained_multiple_times_domain_length_count;
2120                         }
2121                         for( final double element : s1.getData() ) {
2122                             gained_multiple_times_domain_length_sum += element;
2123                             ++gained_multiple_times_domain_length_count;
2124                         }
2125                     }
2126                 }
2127                 else {
2128                     if ( protein_length_stats_by_dc != null ) {
2129                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2130                         for( final double element : s.getData() ) {
2131                             gained_once_lengths_stats.addValue( element );
2132                         }
2133                     }
2134                     if ( domain_number_stats_by_dc != null ) {
2135                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2136                         for( final double element : s.getData() ) {
2137                             gained_once_domain_count_stats.addValue( element );
2138                         }
2139                     }
2140                     if ( domain_length_stats_by_domain != null ) {
2141                         final String[] ds = dc.split( "=" );
2142                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2143                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2144                         for( final double element : s0.getData() ) {
2145                             gained_once_domain_length_sum += element;
2146                             ++gained_once_domain_length_count;
2147                         }
2148                         for( final double element : s1.getData() ) {
2149                             gained_once_domain_length_sum += element;
2150                             ++gained_once_domain_length_count;
2151                         }
2152                     }
2153                 }
2154             }
2155             final Set<Integer> histogram_keys = histogram.keySet();
2156             for( final Integer histogram_key : histogram_keys ) {
2157                 final int count = histogram.get( histogram_key );
2158                 final StringBuilder dc = domain_lists.get( histogram_key );
2159                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
2160                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
2161                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2162                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
2163                 Arrays.sort( sorted );
2164                 for( final Object domain : sorted ) {
2165                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
2166                 }
2167                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2168                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
2169                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
2170                 }
2171             }
2172             out_counts.close();
2173             out_dc.close();
2174             out_dc_for_go_mapping.close();
2175             out_dc_for_go_mapping_unique.close();
2176             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
2177             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
2178             for( final String dc : more_than_once ) {
2179                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
2180                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
2181                     final PhylogenyNode n = it.next();
2182                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
2183                         nodes.add( n );
2184                     }
2185                 }
2186                 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
2187                     for( int j = i + 1; j < nodes.size(); ++j ) {
2188                         final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
2189                         String rank = "unknown";
2190                         if ( lca.getNodeData().isHasTaxonomy()
2191                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
2192                             rank = lca.getNodeData().getTaxonomy().getRank();
2193                         }
2194                         addToCountMap( lca_rank_counts, rank );
2195                         String lca_species;
2196                         if ( lca.getNodeData().isHasTaxonomy()
2197                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
2198                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
2199                         }
2200                         else if ( lca.getNodeData().isHasTaxonomy()
2201                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
2202                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
2203                         }
2204                         else {
2205                             lca_species = lca.getName();
2206                         }
2207                         addToCountMap( lca_ancestor_species_counts, lca_species );
2208                     }
2209                 }
2210             }
2211             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
2212             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
2213             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
2214             ForesterUtil.map2writer( out_for_ancestor_species_counts,
2215                                      lca_ancestor_species_counts,
2216                                      "\t",
2217                                      ForesterUtil.LINE_SEPARATOR );
2218             out_for_rank_counts.close();
2219             out_for_ancestor_species_counts.close();
2220             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
2221                     && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
2222                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
2223                 w.write( "Domain Lengths: " );
2224                 w.write( "\n" );
2225                 if ( domain_length_stats_by_domain != null ) {
2226                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
2227                             .entrySet() ) {
2228                         w.write( entry.getKey().toString() );
2229                         w.write( "\t" + entry.getValue().arithmeticMean() );
2230                         w.write( "\t" + entry.getValue().median() );
2231                         w.write( "\n" );
2232                     }
2233                 }
2234                 w.flush();
2235                 w.write( "\n" );
2236                 w.write( "\n" );
2237                 w.write( "Protein Lengths: " );
2238                 w.write( "\n" );
2239                 if ( protein_length_stats_by_dc != null ) {
2240                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
2241                             .entrySet() ) {
2242                         w.write( entry.getKey().toString() );
2243                         w.write( "\t" + entry.getValue().arithmeticMean() );
2244                         w.write( "\t" + entry.getValue().median() );
2245                         w.write( "\n" );
2246                     }
2247                 }
2248                 w.flush();
2249                 w.write( "\n" );
2250                 w.write( "\n" );
2251                 w.write( "Number of domains: " );
2252                 w.write( "\n" );
2253                 if ( domain_number_stats_by_dc != null ) {
2254                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
2255                             .entrySet() ) {
2256                         w.write( entry.getKey().toString() );
2257                         w.write( "\t" + entry.getValue().arithmeticMean() );
2258                         w.write( "\t" + entry.getValue().median() );
2259                         w.write( "\n" );
2260                     }
2261                 }
2262                 w.flush();
2263                 w.write( "\n" );
2264                 w.write( "\n" );
2265                 w.write( "Gained once, domain lengths:" );
2266                 w.write( "\n" );
2267                 w.write( "N: " + gained_once_domain_length_count );
2268                 w.write( "\n" );
2269                 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
2270                 w.write( "\n" );
2271                 w.write( "\n" );
2272                 w.write( "Gained multiple times, domain lengths:" );
2273                 w.write( "\n" );
2274                 w.write( "N: " + gained_multiple_times_domain_length_count );
2275                 w.write( "\n" );
2276                 w.write( "Avg: "
2277                         + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
2278                 w.write( "\n" );
2279                 w.write( "\n" );
2280                 w.write( "\n" );
2281                 w.write( "\n" );
2282                 w.write( "Gained once, protein lengths:" );
2283                 w.write( "\n" );
2284                 w.write( gained_once_lengths_stats.toString() );
2285                 w.write( "\n" );
2286                 w.write( "\n" );
2287                 w.write( "Gained once, domain counts:" );
2288                 w.write( "\n" );
2289                 w.write( gained_once_domain_count_stats.toString() );
2290                 w.write( "\n" );
2291                 w.write( "\n" );
2292                 w.write( "Gained multiple times, protein lengths:" );
2293                 w.write( "\n" );
2294                 w.write( gained_multiple_times_lengths_stats.toString() );
2295                 w.write( "\n" );
2296                 w.write( "\n" );
2297                 w.write( "Gained multiple times, domain counts:" );
2298                 w.write( "\n" );
2299                 w.write( gained_multiple_times_domain_count_stats.toString() );
2300                 w.flush();
2301                 w.close();
2302             }
2303         }
2304         catch ( final IOException e ) {
2305             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2306         }
2307         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
2308                 + outfilename_for_counts + "]" );
2309         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
2310                 + outfilename_for_dc + "]" );
2311         ForesterUtil.programMessage( surfacing.PRG_NAME,
2312                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
2313                                              + outfilename_for_dc_for_go_mapping + "]" );
2314         ForesterUtil.programMessage( surfacing.PRG_NAME,
2315                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
2316                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
2317     }
2318
2319     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
2320                                                                         final boolean get_gains ) {
2321         final SortedSet<String> domains = new TreeSet<String>();
2322         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
2323             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
2324             if ( get_gains ) {
2325                 domains.addAll( chars.getGainedCharacters() );
2326             }
2327             else {
2328                 domains.addAll( chars.getLostCharacters() );
2329             }
2330         }
2331         return domains;
2332     }
2333
2334     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
2335                                                             final boolean domain_combinations,
2336                                                             final CharacterStateMatrix.GainLossStates state,
2337                                                             final String outfile ) {
2338         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
2339                 + ForesterUtil.FILE_SEPARATOR + base_dir );
2340         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2341             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2342         }
2343         if ( domain_combinations ) {
2344             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2345                     + ForesterUtil.FILE_SEPARATOR + "DC" );
2346         }
2347         else {
2348             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2349                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
2350         }
2351         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2352             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2353         }
2354         if ( state == GainLossStates.GAIN ) {
2355             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2356                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
2357         }
2358         else if ( state == GainLossStates.LOSS ) {
2359             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2360                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
2361         }
2362         else {
2363             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2364                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
2365         }
2366         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2367             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2368         }
2369         return per_node_go_mapped_domain_gain_loss_files_base_dir;
2370     }
2371
2372     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
2373         final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
2374         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
2375         for( final String domain_id : cds.keySet() ) {
2376             final CombinableDomains cd = cds.get( domain_id );
2377             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
2378         }
2379         return binary_combinations;
2380     }
2381
2382     private static List<String> splitDomainCombination( final String dc ) {
2383         final String[] s = dc.split( "=" );
2384         if ( s.length != 2 ) {
2385             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
2386                     + dc );
2387             System.exit( -1 );
2388         }
2389         final List<String> l = new ArrayList<String>( 2 );
2390         l.add( s[ 0 ] );
2391         l.add( s[ 1 ] );
2392         return l;
2393     }
2394
2395     private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2396                                                         final Map<GoId, GoTerm> go_id_to_term_map,
2397                                                         final String outfile_name,
2398                                                         final SortedSet<String> all_pfams_encountered ) {
2399         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
2400         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
2401                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
2402         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
2403         int biological_process_counter = 0;
2404         int cellular_component_counter = 0;
2405         int molecular_function_counter = 0;
2406         int pfams_with_mappings_counter = 0;
2407         int pfams_without_mappings_counter = 0;
2408         int pfams_without_mappings_to_bp_or_mf_counter = 0;
2409         int pfams_with_mappings_to_bp_or_mf_counter = 0;
2410         try {
2411             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
2412             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
2413             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
2414             summary_writer.write( "# Pfam to GO mapping summary" );
2415             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2416             summary_writer.write( "# Actual summary is at the end of this file." );
2417             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2418             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
2419             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2420             for( final String pfam : all_pfams_encountered ) {
2421                 all_pfams_encountered_writer.write( pfam );
2422                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
2423                 final String domain_id = new String( pfam );
2424                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2425                     ++pfams_with_mappings_counter;
2426                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
2427                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
2428                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
2429                     boolean maps_to_bp = false;
2430                     boolean maps_to_cc = false;
2431                     boolean maps_to_mf = false;
2432                     for( final GoId go_id : go_ids ) {
2433                         final GoTerm go_term = go_id_to_term_map.get( go_id );
2434                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
2435                             maps_to_bp = true;
2436                         }
2437                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
2438                             maps_to_cc = true;
2439                         }
2440                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
2441                             maps_to_mf = true;
2442                         }
2443                     }
2444                     if ( maps_to_bp ) {
2445                         ++biological_process_counter;
2446                     }
2447                     if ( maps_to_cc ) {
2448                         ++cellular_component_counter;
2449                     }
2450                     if ( maps_to_mf ) {
2451                         ++molecular_function_counter;
2452                     }
2453                     if ( maps_to_bp || maps_to_mf ) {
2454                         ++pfams_with_mappings_to_bp_or_mf_counter;
2455                     }
2456                     else {
2457                         ++pfams_without_mappings_to_bp_or_mf_counter;
2458                     }
2459                 }
2460                 else {
2461                     ++pfams_without_mappings_to_bp_or_mf_counter;
2462                     ++pfams_without_mappings_counter;
2463                     summary_writer.write( pfam );
2464                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2465                 }
2466             }
2467             all_pfams_encountered_writer.close();
2468             all_pfams_encountered_with_go_annotation_writer.close();
2469             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
2470                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
2471             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
2472                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
2473                     + "\"" );
2474             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
2475                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
2476                     + encountered_pfams_summary_file + "\"" );
2477             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
2478                     + all_pfams_encountered.size() );
2479             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
2480                     + pfams_without_mappings_counter + " ["
2481                     + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2482             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
2483                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2484                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2485             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
2486                     + pfams_with_mappings_counter + " ["
2487                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2488             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
2489                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2490                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2491             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
2492                     + biological_process_counter + " ["
2493                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2494             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
2495                     + molecular_function_counter + " ["
2496                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2497             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
2498                     + cellular_component_counter + " ["
2499                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2500             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2501             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
2502             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2503             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
2504                     + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2505             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2506             summary_writer.write( "# Pfams without mapping to proc. or func. : "
2507                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
2508                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2509             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2510             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
2511                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
2512             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2513             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
2514                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
2515                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
2516             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2517             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
2518                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
2519             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2520             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
2521                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
2522             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2523             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
2524                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
2525             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
2526             summary_writer.close();
2527         }
2528         catch ( final IOException e ) {
2529             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2530         }
2531     }
2532
2533     private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
2534                                          final Map<GoId, GoTerm> go_id_to_term_map,
2535                                          final GoNameSpace go_namespace_limit,
2536                                          final Writer out,
2537                                          final String domain_0,
2538                                          final String domain_1,
2539                                          final String prefix_for_html,
2540                                          final String character_separator_for_non_html_output,
2541                                          final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
2542                                          final Set<GoId> all_go_ids ) throws IOException {
2543         boolean any_go_annotation_present = false;
2544         boolean first_has_no_go = false;
2545         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2546         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2547             domain_count = 1;
2548         }
2549         // The following has a difficult to understand logic.
2550         for( int d = 0; d < domain_count; ++d ) {
2551             List<GoId> go_ids = null;
2552             boolean go_annotation_present = false;
2553             if ( d == 0 ) {
2554                 if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
2555                     go_annotation_present = true;
2556                     any_go_annotation_present = true;
2557                     go_ids = domain_id_to_go_ids_map.get( domain_0 );
2558                 }
2559                 else {
2560                     first_has_no_go = true;
2561                 }
2562             }
2563             else {
2564                 if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
2565                     go_annotation_present = true;
2566                     any_go_annotation_present = true;
2567                     go_ids = domain_id_to_go_ids_map.get( domain_1 );
2568                 }
2569             }
2570             if ( go_annotation_present ) {
2571                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2572                 for( final GoId go_id : go_ids ) {
2573                     out.write( "<tr>" );
2574                     if ( first ) {
2575                         first = false;
2576                         writeDomainIdsToHtml( out,
2577                                               domain_0,
2578                                               domain_1,
2579                                               prefix_for_html,
2580                                               domain_id_to_secondary_features_maps );
2581                     }
2582                     else {
2583                         out.write( "<td></td>" );
2584                     }
2585                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2586                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2587                     }
2588                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2589                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2590                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2591                         final String go_id_str = go_id.getId();
2592                         out.write( "<td>" );
2593                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2594                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2595                         out.write( "</td><td>" );
2596                         out.write( go_term.getName() );
2597                         if ( domain_count == 2 ) {
2598                             out.write( " (" + d + ")" );
2599                         }
2600                         out.write( "</td><td>" );
2601                         // out.write( top );
2602                         // out.write( "</td><td>" );
2603                         out.write( "[" );
2604                         out.write( go_term.getGoNameSpace().toShortString() );
2605                         out.write( "]" );
2606                         out.write( "</td>" );
2607                         if ( all_go_ids != null ) {
2608                             all_go_ids.add( go_id );
2609                         }
2610                     }
2611                     else {
2612                         out.write( "<td>" );
2613                         out.write( "</td><td>" );
2614                         out.write( "</td><td>" );
2615                         out.write( "</td><td>" );
2616                         out.write( "</td>" );
2617                     }
2618                     out.write( "</tr>" );
2619                     out.write( SurfacingConstants.NL );
2620                 }
2621             }
2622         } //  for( int d = 0; d < domain_count; ++d )
2623         if ( !any_go_annotation_present ) {
2624             out.write( "<tr>" );
2625             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2626             out.write( "<td>" );
2627             out.write( "</td><td>" );
2628             out.write( "</td><td>" );
2629             out.write( "</td><td>" );
2630             out.write( "</td>" );
2631             out.write( "</tr>" );
2632             out.write( SurfacingConstants.NL );
2633         }
2634     }
2635
2636     private static void writeDomainIdsToHtml( final Writer out,
2637                                               final String domain_0,
2638                                               final String domain_1,
2639                                               final String prefix_for_detailed_html,
2640                                               final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
2641             throws IOException {
2642         out.write( "<td>" );
2643         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2644             out.write( prefix_for_detailed_html );
2645             out.write( " " );
2646         }
2647         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2648         out.write( "</td>" );
2649     }
2650
2651     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2652                                                                  final String domain_0,
2653                                                                  final String domain_1 ) throws IOException {
2654         individual_files_writer.write( domain_0 );
2655         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2656         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2657             individual_files_writer.write( domain_1 );
2658             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2659         }
2660     }
2661
2662     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2663         try {
2664             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2665             for( final String pfam : pfams ) {
2666                 writer.write( pfam );
2667                 writer.write( ForesterUtil.LINE_SEPARATOR );
2668             }
2669             writer.close();
2670             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2671                     + "]" );
2672         }
2673         catch ( final IOException e ) {
2674             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2675         }
2676     }
2677
2678     private static void writeToNexus( final String outfile_name,
2679                                       final CharacterStateMatrix<BinaryStates> matrix,
2680                                       final Phylogeny phylogeny ) {
2681         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2682             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2683                     + "] to nexus" );
2684         }
2685         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2686         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2687         phylogenies.add( phylogeny );
2688         try {
2689             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2690             w.write( NexusConstants.NEXUS );
2691             w.write( ForesterUtil.LINE_SEPARATOR );
2692             my_matrix.writeNexusTaxaBlock( w );
2693             my_matrix.writeNexusBinaryChractersBlock( w );
2694             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2695             w.flush();
2696             w.close();
2697             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2698         }
2699         catch ( final IOException e ) {
2700             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2701         }
2702     }
2703
2704     private static void writeToNexus( final String outfile_name,
2705                                       final DomainParsimonyCalculator domain_parsimony,
2706                                       final Phylogeny phylogeny ) {
2707         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2708                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2709                       phylogeny );
2710         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2711                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2712                       phylogeny );
2713     }
2714
2715     final static class DomainComparator implements Comparator<Domain> {
2716
2717         final private boolean _ascending;
2718
2719         public DomainComparator( final boolean ascending ) {
2720             _ascending = ascending;
2721         }
2722
2723         @Override
2724         public final int compare( final Domain d0, final Domain d1 ) {
2725             if ( d0.getFrom() < d1.getFrom() ) {
2726                 return _ascending ? -1 : 1;
2727             }
2728             else if ( d0.getFrom() > d1.getFrom() ) {
2729                 return _ascending ? 1 : -1;
2730             }
2731             return 0;
2732         }
2733     }
2734 }