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

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: www.phylosoft.org/forester
  26
  27 package org.forester.surfacing;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.text.DecimalFormat;
  35 import java.text.NumberFormat;
  36 import java.util.ArrayList;
  37 import java.util.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.List;
  43 import java.util.Map;
  44 import java.util.PriorityQueue;
  45 import java.util.Set;
  46 import java.util.SortedMap;
  47 import java.util.SortedSet;
  48 import java.util.TreeMap;
  49 import java.util.TreeSet;
  50 import java.util.regex.Matcher;
  51 import java.util.regex.Pattern;
  52
  53 import org.forester.application.surfacing;
  54 import org.forester.evoinference.distance.NeighborJoining;
  55 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  56 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  57 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  58 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  59 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  60 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  61 import org.forester.go.GoId;
  62 import org.forester.go.GoNameSpace;
  63 import org.forester.go.GoTerm;
  64 import org.forester.go.PfamToGoMapping;
  65 import org.forester.io.parsers.nexus.NexusConstants;
  66 import org.forester.io.writers.PhylogenyWriter;
  67 import org.forester.phylogeny.Phylogeny;
  68 import org.forester.phylogeny.PhylogenyMethods;
  69 import org.forester.phylogeny.PhylogenyNode;
  70 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  71 import org.forester.phylogeny.data.BinaryCharacters;
  72 import org.forester.phylogeny.data.Confidence;
  73 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  74 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  75 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  76 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  77 import org.forester.util.AsciiHistogram;
  78 import org.forester.util.BasicDescriptiveStatistics;
  79 import org.forester.util.BasicTable;
  80 import org.forester.util.BasicTableParser;
  81 import org.forester.util.DescriptiveStatistics;
  82 import org.forester.util.ForesterUtil;
  83
  84 public final class SurfacingUtil {
  85
  86     private final static NumberFormat       FORMATTER                        = new DecimalFormat( "0.0E0" );
  87     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  88     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  89
  90                                                                                  @Override
  91                                                                                  public int compare( final Domain d1,
  92                                                                                                      final Domain d2 ) {
  93                                                                                      if ( d1.getPerSequenceEvalue() < d2
  94                                                                                              .getPerSequenceEvalue() ) {
  95                                                                                          return -1;
  96                                                                                      }
  97                                                                                      else if ( d1
  98                                                                                              .getPerSequenceEvalue() > d2
  99                                                                                              .getPerSequenceEvalue() ) {
 100                                                                                          return 1;
 101                                                                                      }
 102                                                                                      else {
 103                                                                                          return d1.compareTo( d2 );
 104                                                                                      }
 105                                                                                  }
 106                                                                              };
 107     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 108     private static final boolean USE_LAST = true;
 109
 110     private SurfacingUtil() {
 111         // Hidden constructor.
 112     }
 113
 114     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 115                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 116         final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 117         for( final DomainId domain_id : all_cd.keySet() ) {
 118             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 119         }
 120     }
 121
 122     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 123                                              final SortedSet<DomainId> domain_ids ) {
 124         final SortedSet<DomainId> domains = genome.getAllDomainIds();
 125         for( final DomainId domain : domains ) {
 126             domain_ids.add( domain );
 127         }
 128     }
 129
 130     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 131         w.write( SurfacingConstants.NL );
 132         w.write( "<head>" );
 133         w.write( "<title>" );
 134         w.write( title );
 135         w.write( "</title>" );
 136         w.write( SurfacingConstants.NL );
 137         w.write( "<style>" );
 138         w.write( SurfacingConstants.NL );
 139         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 140         w.write( SurfacingConstants.NL );
 141         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 142         w.write( SurfacingConstants.NL );
 143         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 144         w.write( SurfacingConstants.NL );
 145         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 146         w.write( SurfacingConstants.NL );
 147         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 148         w.write( SurfacingConstants.NL );
 149         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 150         w.write( SurfacingConstants.NL );
 151         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 152         w.write( SurfacingConstants.NL );
 153         w.write( "</style>" );
 154         w.write( SurfacingConstants.NL );
 155         w.write( "</head>" );
 156         w.write( SurfacingConstants.NL );
 157     }
 158
 159     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 160         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 161         for( final DomainSimilarity similarity : similarities ) {
 162             stats.addValue( similarity.getMeanSimilarityScore() );
 163         }
 164         return stats;
 165     }
 166
 167     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
 168                                                                     final String outfilename_for_counts,
 169                                                                     final String outfilename_for_dc,
 170                                                                     final String outfilename_for_dc_for_go_mapping,
 171                                                                     final String outfilename_for_dc_for_go_mapping_unique,
 172                                                                     final String outfilename_for_rank_counts,
 173                                                                     final String outfilename_for_ancestor_species_counts ) {
 174         try {
 175             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
 176             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
 177             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
 178             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
 179             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
 180             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
 181                 final PhylogenyNode n = it.next();
 182                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
 183                 for( final String dc : gained_dc ) {
 184                     if ( dc_gain_counts.containsKey( dc ) ) {
 185                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
 186                     }
 187                     else {
 188                         dc_gain_counts.put( dc, 1 );
 189                     }
 190                 }
 191             }
 192             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
 193             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
 194             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
 195             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
 196             final Set<String> dcs = dc_gain_counts.keySet();
 197             final SortedSet<String> more_than_once = new TreeSet<String>();
 198             for( final String dc : dcs ) {
 199                 final int count = dc_gain_counts.get( dc );
 200                 if ( histogram.containsKey( count ) ) {
 201                     histogram.put( count, histogram.get( count ) + 1 );
 202                     domain_lists.get( count ).append( ", " + dc );
 203                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
 204                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
 205                 }
 206                 else {
 207                     histogram.put( count, 1 );
 208                     domain_lists.put( count, new StringBuilder( dc ) );
 209                     final PriorityQueue<String> q = new PriorityQueue<String>();
 210                     q.addAll( splitDomainCombination( dc ) );
 211                     domain_lists_go.put( count, q );
 212                     final SortedSet<String> set = new TreeSet<String>();
 213                     set.addAll( splitDomainCombination( dc ) );
 214                     domain_lists_go_unique.put( count, set );
 215                 }
 216                 if ( count > 1 ) {
 217                     more_than_once.add( dc );
 218                 }
 219             }
 220             final Set<Integer> histogram_keys = histogram.keySet();
 221             for( final Integer histogram_key : histogram_keys ) {
 222                 final int count = histogram.get( histogram_key );
 223                 final StringBuilder dc = domain_lists.get( histogram_key );
 224                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 225                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
 226                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 227                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
 228                 Arrays.sort( sorted );
 229                 for( final Object domain : sorted ) {
 230                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
 231                 }
 232                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 233                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
 234                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
 235                 }
 236             }
 237             out_counts.close();
 238             out_dc.close();
 239             out_dc_for_go_mapping.close();
 240             out_dc_for_go_mapping_unique.close();
 241             //
 242             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
 243             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
 244             for( final String dc : more_than_once ) {
 245                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
 246                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
 247                     final PhylogenyNode n = it.next();
 248                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
 249                         nodes.add( n );
 250                     }
 251                 }
 252                 for( int i = 0; i < nodes.size() - 1; ++i ) {
 253                     for( int j = i + 1; j < nodes.size(); ++j ) {
 254                         final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
 255                                                                                             nodes.get( j ) );
 256                         String rank = "unknown";
 257                         if ( lca.getNodeData().isHasTaxonomy()
 258                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
 259                             rank = lca.getNodeData().getTaxonomy().getRank();
 260                         }
 261                         addToCountMap( lca_rank_counts, rank );
 262                         String lca_species;
 263                         if ( lca.getNodeData().isHasTaxonomy()
 264                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
 265                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
 266                         }
 267                         else if ( lca.getNodeData().isHasTaxonomy()
 268                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
 269                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
 270                         }
 271                         else {
 272                             lca_species = lca.getName();
 273                         }
 274                         addToCountMap( lca_ancestor_species_counts, lca_species );
 275                     }
 276                 }
 277             }
 278             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
 279             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
 280             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
 281             ForesterUtil.map2writer( out_for_ancestor_species_counts,
 282                                      lca_ancestor_species_counts,
 283                                      "\t",
 284                                      ForesterUtil.LINE_SEPARATOR );
 285             out_for_rank_counts.close();
 286             out_for_ancestor_species_counts.close();
 287         }
 288         catch ( final IOException e ) {
 289             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
 290         }
 291         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
 292                 + outfilename_for_counts + "]" );
 293         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
 294                 + outfilename_for_dc + "]" );
 295         ForesterUtil.programMessage( surfacing.PRG_NAME,
 296                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
 297                                              + outfilename_for_dc_for_go_mapping + "]" );
 298         ForesterUtil.programMessage( surfacing.PRG_NAME,
 299                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
 300                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
 301     }
 302
 303     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
 304         if ( map.containsKey( s ) ) {
 305             map.put( s, map.get( s ) + 1 );
 306         }
 307         else {
 308             map.put( s, 1 );
 309         }
 310     }
 311
 312     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 313         int overlap_count = 0;
 314         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 315             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 316                 ++overlap_count;
 317             }
 318         }
 319         return overlap_count;
 320     }
 321
 322     public static void checkForOutputFileWriteability( final File outfile ) {
 323         final String error = ForesterUtil.isWritableFile( outfile );
 324         if ( !ForesterUtil.isEmpty( error ) ) {
 325             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 326         }
 327     }
 328
 329     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
 330                                                                         final boolean get_gains ) {
 331         final SortedSet<String> domains = new TreeSet<String>();
 332         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
 333             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
 334             if ( get_gains ) {
 335                 domains.addAll( chars.getGainedCharacters() );
 336             }
 337             else {
 338                 domains.addAll( chars.getLostCharacters() );
 339             }
 340         }
 341         return domains;
 342     }
 343
 344     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 345                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 346                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 347                                                                                            final boolean get_gains ) {
 348         final SortedSet<String> sorted_ids = new TreeSet<String>();
 349         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 350             sorted_ids.add( matrix.getIdentifier( i ) );
 351         }
 352         for( final String id : sorted_ids ) {
 353             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 354                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 355                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 356                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 357                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 358                                 .createInstance( matrix.getCharacter( c ) ) );
 359                     }
 360                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 361                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 362                                 .createInstance( matrix.getCharacter( c ) ) );
 363                     }
 364                     else {
 365                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 366                                 .getCharacter( c ) ) );
 367                     }
 368                 }
 369             }
 370         }
 371     }
 372
 373     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
 374                                                             final boolean domain_combinations,
 375                                                             final CharacterStateMatrix.GainLossStates state,
 376                                                             final String outfile ) {
 377         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
 378                 + ForesterUtil.FILE_SEPARATOR + base_dir );
 379         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 380             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 381         }
 382         if ( domain_combinations ) {
 383             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 384                     + ForesterUtil.FILE_SEPARATOR + "DC" );
 385         }
 386         else {
 387             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 388                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
 389         }
 390         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 391             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 392         }
 393         if ( state == GainLossStates.GAIN ) {
 394             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 395                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
 396         }
 397         else if ( state == GainLossStates.LOSS ) {
 398             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 399                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
 400         }
 401         else {
 402             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 403                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
 404         }
 405         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 406             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 407         }
 408         return per_node_go_mapped_domain_gain_loss_files_base_dir;
 409     }
 410
 411     public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 412         final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
 413                 .size() );
 414         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 415             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 416                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 417             }
 418             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 419         }
 420         return domain_id_to_go_ids_map;
 421     }
 422
 423     public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 424             throws IOException {
 425         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
 426         final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
 427         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 428             final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
 429             if ( !map.containsKey( domain_id ) ) {
 430                 map.put( domain_id, new HashSet<String>() );
 431             }
 432             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 433         }
 434         return map;
 435     }
 436
 437     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 438         checkForOutputFileWriteability( nj_tree_outfile );
 439         final NeighborJoining nj = NeighborJoining.createInstance();
 440         final Phylogeny phylogeny = nj.execute( distance );
 441         phylogeny.setName( nj_tree_outfile.getName() );
 442         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 443         return phylogeny;
 444     }
 445
 446     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
 447         final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
 448         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
 449         for( final DomainId domain_id : cds.keySet() ) {
 450             final CombinableDomains cd = cds.get( domain_id );
 451             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
 452         }
 453         return binary_combinations;
 454     }
 455
 456     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 457                                                             final Detailedness detailedness,
 458                                                             final GoAnnotationOutput go_annotation_output,
 459                                                             final Map<GoId, GoTerm> go_id_to_term_map,
 460                                                             final GoNameSpace go_namespace_limit ) {
 461         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
 462             throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
 463         }
 464         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 465             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 466                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 467                 printable_domain_similarity.setDetailedness( detailedness );
 468                 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
 469                 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
 470                 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
 471             }
 472         }
 473     }
 474
 475     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 476                                                     final int number_of_genomes,
 477                                                     final DomainLengthsTable domain_lengths_table,
 478                                                     final File outfile ) throws IOException {
 479         final DecimalFormat df = new DecimalFormat( "#.00" );
 480         checkForOutputFileWriteability( outfile );
 481         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 482         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 483         out.write( ForesterUtil.LINE_SEPARATOR );
 484         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 485         out.write( ForesterUtil.LINE_SEPARATOR );
 486         out.write( ForesterUtil.LINE_SEPARATOR );
 487         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 488         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 489         out.write( ForesterUtil.LINE_SEPARATOR );
 490         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 491             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 492             if ( species_list.size() > 0 ) {
 493                 out.write( domain_lengths.getDomainId() + "\t" );
 494                 for( final Species species : species_list ) {
 495                     out.write( species + "\t" );
 496                 }
 497                 out.write( ForesterUtil.LINE_SEPARATOR );
 498                 // DescriptiveStatistics stats_for_domain = domain_lengths
 499                 //         .calculateMeanBasedStatistics();
 500                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 501                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 502             }
 503         }
 504         out.write( ForesterUtil.LINE_SEPARATOR );
 505         out.write( ForesterUtil.LINE_SEPARATOR );
 506         out.write( "OUTLIER SPECIES (Z 1.0)" );
 507         out.write( ForesterUtil.LINE_SEPARATOR );
 508         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 509                 .calculateMeanBasedStatisticsForAllSpecies();
 510         out.write( stats_for_all_species.asSummary() );
 511         out.write( ForesterUtil.LINE_SEPARATOR );
 512         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 513         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 514         out.write( ForesterUtil.LINE_SEPARATOR );
 515         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 516         final double population_mean = stats_for_all_species.arithmeticMean();
 517         for( final Species species : domain_lengths_table.getSpecies() ) {
 518             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 519             final double z = ( x - population_mean ) / population_sd;
 520             out.write( species + "\t" + z );
 521             out.write( ForesterUtil.LINE_SEPARATOR );
 522         }
 523         out.write( ForesterUtil.LINE_SEPARATOR );
 524         for( final Species species : domain_lengths_table.getSpecies() ) {
 525             final DescriptiveStatistics stats_for_species = domain_lengths_table
 526                     .calculateMeanBasedStatisticsForSpecies( species );
 527             final double x = stats_for_species.arithmeticMean();
 528             final double z = ( x - population_mean ) / population_sd;
 529             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 530                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 531                 out.write( ForesterUtil.LINE_SEPARATOR );
 532             }
 533         }
 534         out.close();
 535         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 536         //        for( int i = 0; i < number_of_genomes; ++i ) {
 537         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 538         //            histogram_datas
 539         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 540         //                            .calculateMeanBasedStatisticsForSpecies( species )
 541         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 542         //        }
 543         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 544         //        hf.setVisible( true );
 545         System.gc();
 546     }
 547
 548     /**
 549      *
 550      * @param all_binary_domains_combination_lost_fitch
 551      * @param consider_directedness_and_adjacency_for_bin_combinations
 552      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 553      * which were gained under unweighted (Fitch) parsimony.
 554      */
 555     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 556                                                  final boolean radomize_fitch_parsimony,
 557                                                  final String outfile_name,
 558                                                  final DomainParsimonyCalculator domain_parsimony,
 559                                                  final Phylogeny phylogeny,
 560                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 561                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 562                                                  final GoNameSpace go_namespace_limit,
 563                                                  final String parameters_str,
 564                                                  final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
 565                                                  final SortedSet<DomainId> positive_filter,
 566                                                  final boolean output_binary_domain_combinations_for_graphs,
 567                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 568                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 569                                                  final BinaryDomainCombination.DomainCombinationType dc_type ) {
 570         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 571         final String date_time = ForesterUtil.getCurrentDateTime();
 572         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 573         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 574         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 575         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 576         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 577         writeToNexus( outfile_name, domain_parsimony, phylogeny );
 578         // DOLLO DOMAINS
 579         // -------------
 580         Phylogeny local_phylogeny_l = phylogeny.copy();
 581         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 582             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 583         }
 584         else {
 585             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 586         }
 587         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 588                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 589         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 590                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 591         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 592                                                            CharacterStateMatrix.GainLossStates.GAIN,
 593                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 594                                                            sep,
 595                                                            ForesterUtil.LINE_SEPARATOR,
 596                                                            null );
 597         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 598                                                            CharacterStateMatrix.GainLossStates.LOSS,
 599                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 600                                                            sep,
 601                                                            ForesterUtil.LINE_SEPARATOR,
 602                                                            null );
 603         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 604                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 605         //HTML:
 606         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 607                                        go_id_to_term_map,
 608                                        go_namespace_limit,
 609                                        false,
 610                                        domain_parsimony.getGainLossMatrix(),
 611                                        CharacterStateMatrix.GainLossStates.GAIN,
 612                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 613                                        sep,
 614                                        ForesterUtil.LINE_SEPARATOR,
 615                                        "Dollo Parsimony | Gains | Domains",
 616                                        "+",
 617                                        domain_id_to_secondary_features_maps,
 618                                        all_pfams_encountered,
 619                                        all_pfams_gained_as_domains,
 620                                        "_dollo_gains_d" );
 621         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 622                                        go_id_to_term_map,
 623                                        go_namespace_limit,
 624                                        false,
 625                                        domain_parsimony.getGainLossMatrix(),
 626                                        CharacterStateMatrix.GainLossStates.LOSS,
 627                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 628                                        sep,
 629                                        ForesterUtil.LINE_SEPARATOR,
 630                                        "Dollo Parsimony | Losses | Domains",
 631                                        "-",
 632                                        domain_id_to_secondary_features_maps,
 633                                        all_pfams_encountered,
 634                                        all_pfams_lost_as_domains,
 635                                        "_dollo_losses_d" );
 636         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 637                                        go_id_to_term_map,
 638                                        go_namespace_limit,
 639                                        false,
 640                                        domain_parsimony.getGainLossMatrix(),
 641                                        null,
 642                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 643                                        sep,
 644                                        ForesterUtil.LINE_SEPARATOR,
 645                                        "Dollo Parsimony | Present | Domains",
 646                                        "",
 647                                        domain_id_to_secondary_features_maps,
 648                                        all_pfams_encountered,
 649                                        null,
 650                                        "_dollo_present_d" );
 651         preparePhylogeny( local_phylogeny_l,
 652                           domain_parsimony,
 653                           date_time,
 654                           "Dollo parsimony on domain presence/absence",
 655                           "dollo_on_domains_" + outfile_name,
 656                           parameters_str );
 657         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 658                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 659         try {
 660             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 661             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 662         }
 663         catch ( final IOException e ) {
 664             e.printStackTrace();
 665             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 666         }
 667         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 668             // FITCH DOMAIN COMBINATIONS
 669             // -------------------------
 670             local_phylogeny_l = phylogeny.copy();
 671             String randomization = "no";
 672             if ( radomize_fitch_parsimony ) {
 673                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 674                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 675             }
 676             else {
 677                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
 678             }
 679             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 680                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 681             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 682                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 683             SurfacingUtil
 684                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 685                                                           CharacterStateMatrix.GainLossStates.GAIN,
 686                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 687                                                           sep,
 688                                                           ForesterUtil.LINE_SEPARATOR,
 689                                                           null );
 690             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 691                                                                CharacterStateMatrix.GainLossStates.LOSS,
 692                                                                outfile_name
 693                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 694                                                                sep,
 695                                                                ForesterUtil.LINE_SEPARATOR,
 696                                                                null );
 697             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 698                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 699             if ( all_binary_domains_combination_gained_fitch != null ) {
 700                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 701                                                                                     dc_type,
 702                                                                                     all_binary_domains_combination_gained_fitch,
 703                                                                                     true );
 704             }
 705             if ( all_binary_domains_combination_lost_fitch != null ) {
 706                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 707                                                                                     dc_type,
 708                                                                                     all_binary_domains_combination_lost_fitch,
 709                                                                                     false );
 710             }
 711             if ( output_binary_domain_combinations_for_graphs ) {
 712                 SurfacingUtil
 713                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 714                                                                                                            .getGainLossMatrix(),
 715                                                                                                    null,
 716                                                                                                    outfile_name
 717                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 718                                                                                                    sep,
 719                                                                                                    ForesterUtil.LINE_SEPARATOR,
 720                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 721             }
 722             // HTML:
 723             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 724                                            go_id_to_term_map,
 725                                            go_namespace_limit,
 726                                            true,
 727                                            domain_parsimony.getGainLossMatrix(),
 728                                            CharacterStateMatrix.GainLossStates.GAIN,
 729                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 730                                            sep,
 731                                            ForesterUtil.LINE_SEPARATOR,
 732                                            "Fitch Parsimony | Gains | Domain Combinations",
 733                                            "+",
 734                                            null,
 735                                            all_pfams_encountered,
 736                                            all_pfams_gained_as_dom_combinations,
 737                                            "_fitch_gains_dc" );
 738             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 739                                            go_id_to_term_map,
 740                                            go_namespace_limit,
 741                                            true,
 742                                            domain_parsimony.getGainLossMatrix(),
 743                                            CharacterStateMatrix.GainLossStates.LOSS,
 744                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 745                                            sep,
 746                                            ForesterUtil.LINE_SEPARATOR,
 747                                            "Fitch Parsimony | Losses | Domain Combinations",
 748                                            "-",
 749                                            null,
 750                                            all_pfams_encountered,
 751                                            all_pfams_lost_as_dom_combinations,
 752                                            "_fitch_losses_dc" );
 753             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 754                                            go_id_to_term_map,
 755                                            go_namespace_limit,
 756                                            true,
 757                                            domain_parsimony.getGainLossMatrix(),
 758                                            null,
 759                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 760                                            sep,
 761                                            ForesterUtil.LINE_SEPARATOR,
 762                                            "Fitch Parsimony | Present | Domain Combinations",
 763                                            "",
 764                                            null,
 765                                            all_pfams_encountered,
 766                                            null,
 767                                            "_fitch_present_dc" );
 768             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 769                                             go_id_to_term_map,
 770                                             outfile_name,
 771                                             all_pfams_encountered );
 772             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 773             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 774             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 775                               all_pfams_gained_as_dom_combinations );
 776             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 777             preparePhylogeny( local_phylogeny_l,
 778                               domain_parsimony,
 779                               date_time,
 780                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 781                                       + randomization,
 782                               "fitch_on_binary_domain_combinations_" + outfile_name,
 783                               parameters_str );
 784             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 785                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 786             calculateIndependentDomainCombinationGains( local_phylogeny_l, outfile_name
 787                     + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name
 788                     + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX, outfile_name
 789                     + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX, outfile_name
 790                     + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX, outfile_name
 791                     + "_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt" );
 792         }
 793     }
 794
 795     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 796                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 797                                                                      final Phylogeny phylogeny,
 798                                                                      final String parameters_str,
 799                                                                      final Map<Species, MappingResults> mapping_results_map ) {
 800         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 801         final String date_time = ForesterUtil.getCurrentDateTime();
 802         System.out.println();
 803         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 804                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 805                       phylogeny );
 806         Phylogeny local_phylogeny_copy = phylogeny.copy();
 807         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 808         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 809                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 810         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 811                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 812         SurfacingUtil
 813                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 814                                                       CharacterStateMatrix.GainLossStates.GAIN,
 815                                                       outfile_name
 816                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 817                                                       sep,
 818                                                       ForesterUtil.LINE_SEPARATOR,
 819                                                       null );
 820         SurfacingUtil
 821                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 822                                                       CharacterStateMatrix.GainLossStates.LOSS,
 823                                                       outfile_name
 824                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 825                                                       sep,
 826                                                       ForesterUtil.LINE_SEPARATOR,
 827                                                       null );
 828         SurfacingUtil
 829                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 830                                                       null,
 831                                                       outfile_name
 832                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 833                                                       sep,
 834                                                       ForesterUtil.LINE_SEPARATOR,
 835                                                       null );
 836         preparePhylogeny( local_phylogeny_copy,
 837                           secondary_features_parsimony,
 838                           date_time,
 839                           "Dollo parsimony on secondary feature presence/absence",
 840                           "dollo_on_secondary_features_" + outfile_name,
 841                           parameters_str );
 842         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 843                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 844
 845
 846         // FITCH DOMAIN COMBINATIONS
 847         // -------------------------
 848          local_phylogeny_copy = phylogeny.copy();
 849         String randomization = "no";
 850
 851         secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
 852
 853
 854
 855
 856         preparePhylogeny( local_phylogeny_copy,
 857                           secondary_features_parsimony,
 858                           date_time,
 859                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
 860                                   + randomization,
 861                           "fitch_on_binary_domain_combinations_" + outfile_name,
 862                           parameters_str );
 863         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 864                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
 865         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
 866                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
 867                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
 868                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
 869                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
 870                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt" );
 871
 872
 873     }
 874
 875     public static void extractProteinNames( final List<Protein> proteins,
 876                                             final List<DomainId> query_domain_ids_nc_order,
 877                                             final Writer out,
 878                                             final String separator,
 879                                             final String limit_to_species ) throws IOException {
 880         for( final Protein protein : proteins ) {
 881             if ( ForesterUtil.isEmpty( limit_to_species )
 882                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 883                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 884                     out.write( protein.getSpecies().getSpeciesId() );
 885                     out.write( separator );
 886                     out.write( protein.getProteinId().getId() );
 887                     out.write( separator );
 888                     out.write( "[" );
 889                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
 890                     boolean first = true;
 891                     for( final Domain domain : protein.getProteinDomains() ) {
 892                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 893                             visited_domain_ids.add( domain.getDomainId() );
 894                             if ( first ) {
 895                                 first = false;
 896                             }
 897                             else {
 898                                 out.write( " " );
 899                             }
 900                             out.write( domain.getDomainId().getId() );
 901                             out.write( " {" );
 902                             out.write( "" + domain.getTotalCount() );
 903                             out.write( "}" );
 904                         }
 905                     }
 906                     out.write( "]" );
 907                     out.write( separator );
 908                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 909                             .equals( SurfacingConstants.NONE ) ) ) {
 910                         out.write( protein.getDescription() );
 911                     }
 912                     out.write( separator );
 913                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 914                             .equals( SurfacingConstants.NONE ) ) ) {
 915                         out.write( protein.getAccession() );
 916                     }
 917                     out.write( SurfacingConstants.NL );
 918                 }
 919             }
 920         }
 921         out.flush();
 922     }
 923
 924     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
 925                                             final DomainId domain_id,
 926                                             final Writer out,
 927                                             final String separator,
 928                                             final String limit_to_species ) throws IOException {
 929         for( final Species species : protein_lists_per_species.keySet() ) {
 930             for( final Protein protein : protein_lists_per_species.get( species ) ) {
 931                 if ( ForesterUtil.isEmpty( limit_to_species )
 932                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 933                     final List<Domain> domains = protein.getProteinDomains( domain_id );
 934                     if ( domains.size() > 0 ) {
 935                         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 936                         for( final Domain domain : domains ) {
 937                             stats.addValue( domain.getPerSequenceEvalue() );
 938                         }
 939                         out.write( protein.getSpecies().getSpeciesId() );
 940                         out.write( separator );
 941                         out.write( protein.getProteinId().getId() );
 942                         out.write( separator );
 943                         out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
 944                         out.write( separator );
 945                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 946                                 .equals( SurfacingConstants.NONE ) ) ) {
 947                             out.write( protein.getDescription() );
 948                         }
 949                         out.write( separator );
 950                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 951                                 .equals( SurfacingConstants.NONE ) ) ) {
 952                             out.write( protein.getAccession() );
 953                         }
 954                         out.write( SurfacingConstants.NL );
 955                     }
 956                 }
 957             }
 958         }
 959         out.flush();
 960     }
 961
 962     public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
 963         final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
 964         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
 965             final Set<DomainId> all_domains = gwcd.getAllDomainIds();
 966             //    for( final Domain domain : all_domains ) {
 967             all_domains_ids.addAll( all_domains );
 968             //    }
 969         }
 970         return all_domains_ids;
 971     }
 972
 973     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
 974         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
 975         for( final Protein protein_domain_collection : protein_domain_collections ) {
 976             for( final Object name : protein_domain_collection.getProteinDomains() ) {
 977                 final BasicDomain protein_domain = ( BasicDomain ) name;
 978                 final String id = protein_domain.getDomainId().getId();
 979                 if ( map.containsKey( id ) ) {
 980                     map.put( id, map.get( id ) + 1 );
 981                 }
 982                 else {
 983                     map.put( id, 1 );
 984                 }
 985             }
 986         }
 987         return map;
 988     }
 989
 990     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
 991         final PhylogenyNodeIterator it = p.iteratorPostorder();
 992         int c = 0;
 993         while ( it.hasNext() ) {
 994             final PhylogenyNode n = it.next();
 995             if ( ForesterUtil.isEmpty( n.getName() )
 996                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
 997                             .getScientificName() ) )
 998                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
 999                             .getCommonName() ) ) ) {
1000                 if ( n.getParent() != null ) {
1001                     names.append( " " );
1002                     names.append( n.getParent().getName() );
1003                 }
1004                 final List l = n.getAllExternalDescendants();
1005                 for( final Object object : l ) {
1006                     System.out.println( l.toString() );
1007                 }
1008                 ++c;
1009             }
1010         }
1011         return c;
1012     }
1013
1014     /**
1015      * Returns true is Domain domain falls in an uninterrupted stretch of
1016      * covered positions.
1017      *
1018      * @param domain
1019      * @param covered_positions
1020      * @return
1021      */
1022     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1023         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1024             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1025                 return false;
1026             }
1027         }
1028         return true;
1029     }
1030
1031     public static void preparePhylogeny( final Phylogeny p,
1032                                          final DomainParsimonyCalculator domain_parsimony,
1033                                          final String date_time,
1034                                          final String method,
1035                                          final String name,
1036                                          final String parameters_str ) {
1037         domain_parsimony.decoratePhylogenyWithDomains( p );
1038         final StringBuilder desc = new StringBuilder();
1039         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1040         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1041         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1042         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1043         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1044         desc.append( "[Parameters: " + parameters_str + "]" );
1045         p.setName( name );
1046         p.setDescription( desc.toString() );
1047         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1048         p.setRerootable( false );
1049         p.setRooted( true );
1050     }
1051
1052     /*
1053      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1054      *
1055      *
1056      */
1057     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1058                                                             final String protein_id,
1059                                                             final String separator ) {
1060         final StringBuffer sb = new StringBuffer();
1061         if ( protein.getSpecies() == null ) {
1062             throw new IllegalArgumentException( "species must not be null" );
1063         }
1064         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1065             throw new IllegalArgumentException( "species id must not be empty" );
1066         }
1067         final List<Domain> domains = protein.getProteinDomains();
1068         if ( domains.size() > 1 ) {
1069             final Map<String, Integer> counts = new HashMap<String, Integer>();
1070             for( final Domain domain : domains ) {
1071                 final String id = domain.getDomainId().getId();
1072                 if ( counts.containsKey( id ) ) {
1073                     counts.put( id, counts.get( id ) + 1 );
1074                 }
1075                 else {
1076                     counts.put( id, 1 );
1077                 }
1078             }
1079             final Set<String> dcs = new HashSet<String>();
1080             for( int i = 1; i < domains.size(); ++i ) {
1081                 for( int j = 0; j < i; ++j ) {
1082                     Domain domain_n = domains.get( i );
1083                     Domain domain_c = domains.get( j );
1084                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1085                         domain_n = domains.get( j );
1086                         domain_c = domains.get( i );
1087                     }
1088                     final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
1089                     if ( !dcs.contains( dc ) ) {
1090                         dcs.add( dc );
1091                         sb.append( protein.getSpecies() );
1092                         sb.append( separator );
1093                         sb.append( protein_id );
1094                         sb.append( separator );
1095                         sb.append( domain_n.getDomainId().getId() );
1096                         sb.append( separator );
1097                         sb.append( domain_c.getDomainId().getId() );
1098                         sb.append( separator );
1099                         sb.append( domain_n.getPerDomainEvalue() );
1100                         sb.append( separator );
1101                         sb.append( domain_c.getPerDomainEvalue() );
1102                         sb.append( separator );
1103                         sb.append( counts.get( domain_n.getDomainId().getId() ) );
1104                         sb.append( separator );
1105                         sb.append( counts.get( domain_c.getDomainId().getId() ) );
1106                         sb.append( ForesterUtil.LINE_SEPARATOR );
1107                     }
1108                 }
1109             }
1110         }
1111         else if ( domains.size() == 1 ) {
1112             sb.append( protein.getSpecies() );
1113             sb.append( separator );
1114             sb.append( protein_id );
1115             sb.append( separator );
1116             sb.append( domains.get( 0 ).getDomainId().getId() );
1117             sb.append( separator );
1118             sb.append( separator );
1119             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1120             sb.append( separator );
1121             sb.append( separator );
1122             sb.append( 1 );
1123             sb.append( separator );
1124             sb.append( ForesterUtil.LINE_SEPARATOR );
1125         }
1126         else {
1127             sb.append( protein.getSpecies() );
1128             sb.append( separator );
1129             sb.append( protein_id );
1130             sb.append( separator );
1131             sb.append( separator );
1132             sb.append( separator );
1133             sb.append( separator );
1134             sb.append( separator );
1135             sb.append( separator );
1136             sb.append( ForesterUtil.LINE_SEPARATOR );
1137         }
1138         return sb;
1139     }
1140
1141     /**
1142      *
1143      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1144      * domain with 0.3 is ignored
1145      *
1146      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1147      *
1148      *
1149      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1150      * ignored
1151      *
1152      * @param max_allowed_overlap
1153      *            maximal allowed overlap (inclusive) to be still considered not
1154      *            overlapping (zero or negative value to allow any overlap)
1155      * @param remove_engulfed_domains
1156      *            to remove domains which are completely engulfed by coverage of
1157      *            domains with better support
1158      * @param protein
1159      * @return
1160      */
1161     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1162                                                     final boolean remove_engulfed_domains,
1163                                                     final Protein protein ) {
1164         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1165                 .getSpeciesId() );
1166         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1167         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1168         for( final Domain domain : sorted ) {
1169             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1170                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1171                 final int covered_positions_size = covered_positions.size();
1172                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1173                     covered_positions.add( false );
1174                 }
1175                 final int new_covered_positions_size = covered_positions.size();
1176                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1177                     if ( i < new_covered_positions_size ) {
1178                         covered_positions.set( i, true );
1179                     }
1180                     else {
1181                         covered_positions.add( true );
1182                     }
1183                 }
1184                 pruned_protein.addProteinDomain( domain );
1185             }
1186         }
1187         return pruned_protein;
1188     }
1189
1190     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1191         final List<Domain> domains = new ArrayList<Domain>();
1192         for( final Domain d : protein.getProteinDomains() ) {
1193             domains.add( d );
1194         }
1195         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1196         return domains;
1197     }
1198
1199     private static List<String> splitDomainCombination( final String dc ) {
1200         final String[] s = dc.split( "=" );
1201         if ( s.length != 2 ) {
1202             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
1203                     + dc );
1204             System.exit( -1 );
1205         }
1206         final List<String> l = new ArrayList<String>( 2 );
1207         l.add( s[ 0 ] );
1208         l.add( s[ 1 ] );
1209         return l;
1210     }
1211
1212     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1213                                                             final boolean get_gains,
1214                                                             final String outdir,
1215                                                             final String suffix_for_filename ) throws IOException {
1216         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1217         if ( !get_gains ) {
1218             state = CharacterStateMatrix.GainLossStates.LOSS;
1219         }
1220         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1221                                                                   false,
1222                                                                   state,
1223                                                                   outdir );
1224         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1225             final PhylogenyNode node = it.next();
1226             if ( !node.isExternal() ) {
1227                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1228                 if ( domains.size() > 0 ) {
1229                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1230                             + node.getName() + suffix_for_filename );
1231                     for( final String domain : domains ) {
1232                         writer.write( domain );
1233                         writer.write( ForesterUtil.LINE_SEPARATOR );
1234                     }
1235                     writer.close();
1236                 }
1237             }
1238         }
1239     }
1240
1241     private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1242                                                         final Map<GoId, GoTerm> go_id_to_term_map,
1243                                                         final String outfile_name,
1244                                                         final SortedSet<String> all_pfams_encountered ) {
1245         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
1246         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
1247                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
1248         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
1249         int biological_process_counter = 0;
1250         int cellular_component_counter = 0;
1251         int molecular_function_counter = 0;
1252         int pfams_with_mappings_counter = 0;
1253         int pfams_without_mappings_counter = 0;
1254         int pfams_without_mappings_to_bp_or_mf_counter = 0;
1255         int pfams_with_mappings_to_bp_or_mf_counter = 0;
1256         try {
1257             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
1258             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
1259             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
1260             summary_writer.write( "# Pfam to GO mapping summary" );
1261             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1262             summary_writer.write( "# Actual summary is at the end of this file." );
1263             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1264             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
1265             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1266             for( final String pfam : all_pfams_encountered ) {
1267                 all_pfams_encountered_writer.write( pfam );
1268                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
1269                 final DomainId domain_id = new DomainId( pfam );
1270                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1271                     ++pfams_with_mappings_counter;
1272                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
1273                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
1274                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
1275                     boolean maps_to_bp = false;
1276                     boolean maps_to_cc = false;
1277                     boolean maps_to_mf = false;
1278                     for( final GoId go_id : go_ids ) {
1279                         final GoTerm go_term = go_id_to_term_map.get( go_id );
1280                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
1281                             maps_to_bp = true;
1282                         }
1283                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
1284                             maps_to_cc = true;
1285                         }
1286                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
1287                             maps_to_mf = true;
1288                         }
1289                     }
1290                     if ( maps_to_bp ) {
1291                         ++biological_process_counter;
1292                     }
1293                     if ( maps_to_cc ) {
1294                         ++cellular_component_counter;
1295                     }
1296                     if ( maps_to_mf ) {
1297                         ++molecular_function_counter;
1298                     }
1299                     if ( maps_to_bp || maps_to_mf ) {
1300                         ++pfams_with_mappings_to_bp_or_mf_counter;
1301                     }
1302                     else {
1303                         ++pfams_without_mappings_to_bp_or_mf_counter;
1304                     }
1305                 }
1306                 else {
1307                     ++pfams_without_mappings_to_bp_or_mf_counter;
1308                     ++pfams_without_mappings_counter;
1309                     summary_writer.write( pfam );
1310                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1311                 }
1312             }
1313             all_pfams_encountered_writer.close();
1314             all_pfams_encountered_with_go_annotation_writer.close();
1315             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
1316                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
1317             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
1318                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
1319                     + "\"" );
1320             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
1321                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
1322                     + encountered_pfams_summary_file + "\"" );
1323             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
1324                     + all_pfams_encountered.size() );
1325             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
1326                     + pfams_without_mappings_counter + " ["
1327                     + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1328             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
1329                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1330                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1331             ForesterUtil.programMessage( surfacing.PRG_NAME,
1332                                          "Pfams with a mapping                    : " + pfams_with_mappings_counter
1333                                                  + " ["
1334                                                  + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
1335                                                  + "%]" );
1336             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
1337                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1338                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1339             ForesterUtil.programMessage( surfacing.PRG_NAME,
1340                                          "Pfams with mapping to biological process: " + biological_process_counter
1341                                                  + " ["
1342                                                  + ( 100 * biological_process_counter / all_pfams_encountered.size() )
1343                                                  + "%]" );
1344             ForesterUtil.programMessage( surfacing.PRG_NAME,
1345                                          "Pfams with mapping to molecular function: " + molecular_function_counter
1346                                                  + " ["
1347                                                  + ( 100 * molecular_function_counter / all_pfams_encountered.size() )
1348                                                  + "%]" );
1349             ForesterUtil.programMessage( surfacing.PRG_NAME,
1350                                          "Pfams with mapping to cellular component: " + cellular_component_counter
1351                                                  + " ["
1352                                                  + ( 100 * cellular_component_counter / all_pfams_encountered.size() )
1353                                                  + "%]" );
1354             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1355             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
1356             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1357             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
1358                     + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1359             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1360             summary_writer.write( "# Pfams without mapping to proc. or func. : "
1361                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1362                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1363             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1364             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
1365                     + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1366             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1367             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
1368                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1369                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1370             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1371             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
1372                     + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
1373             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1374             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
1375                     + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
1376             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1377             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
1378                     + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
1379             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1380             summary_writer.close();
1381         }
1382         catch ( final IOException e ) {
1383             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
1384         }
1385     }
1386
1387     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1388                                                                           final File output_dir,
1389                                                                           final GenomeWideCombinableDomains gwcd,
1390                                                                           final int i,
1391                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1392         File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
1393                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1394         if ( output_dir != null ) {
1395             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1396         }
1397         checkForOutputFileWriteability( dc_outfile_dot );
1398         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1399         try {
1400             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1401             for( final BinaryDomainCombination bdc : binary_combinations ) {
1402                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1403                         .toString() );
1404                 out_dot.write( SurfacingConstants.NL );
1405             }
1406             out_dot.close();
1407         }
1408         catch ( final IOException e ) {
1409             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1410         }
1411         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1412                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1413                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1414     }
1415
1416     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1417                                                             final CharacterStateMatrix.GainLossStates state,
1418                                                             final String filename,
1419                                                             final String indentifier_characters_separator,
1420                                                             final String character_separator,
1421                                                             final Map<String, String> descriptions ) {
1422         final File outfile = new File( filename );
1423         checkForOutputFileWriteability( outfile );
1424         final SortedSet<String> sorted_ids = new TreeSet<String>();
1425         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1426             sorted_ids.add( matrix.getIdentifier( i ) );
1427         }
1428         try {
1429             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1430             for( final String id : sorted_ids ) {
1431                 out.write( indentifier_characters_separator );
1432                 out.write( "#" + id );
1433                 out.write( indentifier_characters_separator );
1434                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1435                     // Not nice:
1436                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1437                     if ( ( matrix.getState( id, c ) == state )
1438                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1439                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1440                         out.write( matrix.getCharacter( c ) );
1441                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1442                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1443                             out.write( "\t" );
1444                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1445                         }
1446                         out.write( character_separator );
1447                     }
1448                 }
1449             }
1450             out.flush();
1451             out.close();
1452         }
1453         catch ( final IOException e ) {
1454             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1455         }
1456         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1457     }
1458
1459     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1460                                                                                                  final CharacterStateMatrix.GainLossStates state,
1461                                                                                                  final String filename,
1462                                                                                                  final String indentifier_characters_separator,
1463                                                                                                  final String character_separator,
1464                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1465         final File outfile = new File( filename );
1466         checkForOutputFileWriteability( outfile );
1467         final SortedSet<String> sorted_ids = new TreeSet<String>();
1468         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1469             sorted_ids.add( matrix.getIdentifier( i ) );
1470         }
1471         try {
1472             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1473             for( final String id : sorted_ids ) {
1474                 out.write( indentifier_characters_separator );
1475                 out.write( "#" + id );
1476                 out.write( indentifier_characters_separator );
1477                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1478                     // Not nice:
1479                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1480                     if ( ( matrix.getState( id, c ) == state )
1481                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1482                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1483                         BinaryDomainCombination bdc = null;
1484                         try {
1485                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1486                         }
1487                         catch ( final Exception e ) {
1488                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1489                         }
1490                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1491                         out.write( character_separator );
1492                     }
1493                 }
1494             }
1495             out.flush();
1496             out.close();
1497         }
1498         catch ( final IOException e ) {
1499             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1500         }
1501         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1502     }
1503
1504     public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1505                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1506                                                       final GoNameSpace go_namespace_limit,
1507                                                       final boolean domain_combinations,
1508                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1509                                                       final CharacterStateMatrix.GainLossStates state,
1510                                                       final String filename,
1511                                                       final String indentifier_characters_separator,
1512                                                       final String character_separator,
1513                                                       final String title_for_html,
1514                                                       final String prefix_for_html,
1515                                                       final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1516                                                       final SortedSet<String> all_pfams_encountered,
1517                                                       final SortedSet<String> pfams_gained_or_lost,
1518                                                       final String suffix_for_per_node_events_file ) {
1519         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1520             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1521         }
1522         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1523             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1524         }
1525         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1526             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1527         }
1528         final File outfile = new File( filename );
1529         checkForOutputFileWriteability( outfile );
1530         final SortedSet<String> sorted_ids = new TreeSet<String>();
1531         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1532             sorted_ids.add( matrix.getIdentifier( i ) );
1533         }
1534         try {
1535             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1536             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1537                                                                                                                 domain_combinations,
1538                                                                                                                 state,
1539                                                                                                                 filename );
1540             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1541             File per_node_go_mapped_domain_gain_loss_outfile = null;
1542             int per_node_counter = 0;
1543             out.write( "<html>" );
1544             out.write( SurfacingConstants.NL );
1545             addHtmlHead( out, title_for_html );
1546             out.write( SurfacingConstants.NL );
1547             out.write( "<body>" );
1548             out.write( SurfacingConstants.NL );
1549             out.write( "<h1>" );
1550             out.write( SurfacingConstants.NL );
1551             out.write( title_for_html );
1552             out.write( SurfacingConstants.NL );
1553             out.write( "</h1>" );
1554             out.write( SurfacingConstants.NL );
1555             out.write( "<table>" );
1556             out.write( SurfacingConstants.NL );
1557             for( final String id : sorted_ids ) {
1558                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1559                 if ( matcher.matches() ) {
1560                     continue;
1561                 }
1562                 out.write( "<tr>" );
1563                 out.write( "<td>" );
1564                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1565                 out.write( "</td>" );
1566                 out.write( "</tr>" );
1567                 out.write( SurfacingConstants.NL );
1568             }
1569             out.write( "</table>" );
1570             out.write( SurfacingConstants.NL );
1571             for( final String id : sorted_ids ) {
1572                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1573                 if ( matcher.matches() ) {
1574                     continue;
1575                 }
1576                 out.write( SurfacingConstants.NL );
1577                 out.write( "<h2>" );
1578                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1579                 writeTaxonomyLinks( out, id );
1580                 out.write( "</h2>" );
1581                 out.write( SurfacingConstants.NL );
1582                 out.write( "<table>" );
1583                 out.write( SurfacingConstants.NL );
1584                 out.write( "<tr>" );
1585                 out.write( "<td><b>" );
1586                 out.write( "Pfam domain(s)" );
1587                 out.write( "</b></td><td><b>" );
1588                 out.write( "GO term acc" );
1589                 out.write( "</b></td><td><b>" );
1590                 out.write( "GO term" );
1591                 out.write( "</b></td><td><b>" );
1592                 out.write( "GO namespace" );
1593                 out.write( "</b></td>" );
1594                 out.write( "</tr>" );
1595                 out.write( SurfacingConstants.NL );
1596                 out.write( "</tr>" );
1597                 out.write( SurfacingConstants.NL );
1598                 per_node_counter = 0;
1599                 if ( matrix.getNumberOfCharacters() > 0 ) {
1600                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1601                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1602                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1603                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1604                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1605                 }
1606                 else {
1607                     per_node_go_mapped_domain_gain_loss_outfile = null;
1608                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1609                 }
1610                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1611                     // Not nice:
1612                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1613                     if ( ( matrix.getState( id, c ) == state )
1614                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1615                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1616                         final String character = matrix.getCharacter( c );
1617                         String domain_0 = "";
1618                         String domain_1 = "";
1619                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1620                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1621                             if ( s.length != 2 ) {
1622                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1623                                         + character + "]" );
1624                             }
1625                             domain_0 = s[ 0 ];
1626                             domain_1 = s[ 1 ];
1627                         }
1628                         else {
1629                             domain_0 = character;
1630                         }
1631                         writeDomainData( domain_id_to_go_ids_map,
1632                                          go_id_to_term_map,
1633                                          go_namespace_limit,
1634                                          out,
1635                                          domain_0,
1636                                          domain_1,
1637                                          prefix_for_html,
1638                                          character_separator,
1639                                          domain_id_to_secondary_features_maps,
1640                                          null );
1641                         all_pfams_encountered.add( domain_0 );
1642                         if ( pfams_gained_or_lost != null ) {
1643                             pfams_gained_or_lost.add( domain_0 );
1644                         }
1645                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1646                             all_pfams_encountered.add( domain_1 );
1647                             if ( pfams_gained_or_lost != null ) {
1648                                 pfams_gained_or_lost.add( domain_1 );
1649                             }
1650                         }
1651                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1652                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1653                                                                      domain_0,
1654                                                                      domain_1 );
1655                             per_node_counter++;
1656                         }
1657                     }
1658                 }
1659                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1660                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1661                     if ( per_node_counter < 1 ) {
1662                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1663                     }
1664                     per_node_counter = 0;
1665                 }
1666                 out.write( "</table>" );
1667                 out.write( SurfacingConstants.NL );
1668                 out.write( "<hr>" );
1669                 out.write( SurfacingConstants.NL );
1670             } // for( final String id : sorted_ids ) {
1671             out.write( "</body>" );
1672             out.write( SurfacingConstants.NL );
1673             out.write( "</html>" );
1674             out.write( SurfacingConstants.NL );
1675             out.flush();
1676             out.close();
1677         }
1678         catch ( final IOException e ) {
1679             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1680         }
1681         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1682     }
1683
1684     public static void writeBinaryStatesMatrixToListORIGIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1685                                                             final Map<GoId, GoTerm> go_id_to_term_map,
1686                                                             final GoNameSpace go_namespace_limit,
1687                                                             final boolean domain_combinations,
1688                                                             final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1689                                                             final CharacterStateMatrix.GainLossStates state,
1690                                                             final String filename,
1691                                                             final String indentifier_characters_separator,
1692                                                             final String character_separator,
1693                                                             final String title_for_html,
1694                                                             final String prefix_for_html,
1695                                                             final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1696                                                             final SortedSet<String> all_pfams_encountered,
1697                                                             final SortedSet<String> pfams_gained_or_lost,
1698                                                             final String suffix_for_per_node_events_file ) {
1699         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1700             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1701         }
1702         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1703             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1704         }
1705         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1706             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1707         }
1708         final File outfile = new File( filename );
1709         checkForOutputFileWriteability( outfile );
1710         final SortedSet<String> sorted_ids = new TreeSet<String>();
1711         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1712             sorted_ids.add( matrix.getIdentifier( i ) );
1713         }
1714         try {
1715             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1716             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1717                                                                                                                 domain_combinations,
1718                                                                                                                 state,
1719                                                                                                                 filename );
1720             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1721             File per_node_go_mapped_domain_gain_loss_outfile = null;
1722             int per_node_counter = 0;
1723             out.write( "<html>" );
1724             out.write( SurfacingConstants.NL );
1725             addHtmlHead( out, title_for_html );
1726             out.write( SurfacingConstants.NL );
1727             out.write( "<body>" );
1728             out.write( SurfacingConstants.NL );
1729             out.write( "<h1>" );
1730             out.write( SurfacingConstants.NL );
1731             out.write( title_for_html );
1732             out.write( SurfacingConstants.NL );
1733             out.write( "</h1>" );
1734             out.write( SurfacingConstants.NL );
1735             out.write( "<table>" );
1736             out.write( SurfacingConstants.NL );
1737             for( final String id : sorted_ids ) {
1738                 out.write( "<tr>" );
1739                 out.write( "<td>" );
1740                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1741                 writeTaxonomyLinks( out, id );
1742                 out.write( "</td>" );
1743                 out.write( "</tr>" );
1744                 out.write( SurfacingConstants.NL );
1745             }
1746             out.write( "</table>" );
1747             out.write( SurfacingConstants.NL );
1748             for( final String id : sorted_ids ) {
1749                 out.write( SurfacingConstants.NL );
1750                 out.write( "<h2>" );
1751                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1752                 writeTaxonomyLinks( out, id );
1753                 out.write( "</h2>" );
1754                 out.write( SurfacingConstants.NL );
1755                 out.write( "<table>" );
1756                 out.write( SurfacingConstants.NL );
1757                 out.write( "<tr>" );
1758                 out.write( "<td><b>" );
1759                 out.write( "Pfam domain(s)" );
1760                 out.write( "</b></td><td><b>" );
1761                 out.write( "GO term acc" );
1762                 out.write( "</b></td><td><b>" );
1763                 out.write( "GO term" );
1764                 out.write( "</b></td><td><b>" );
1765                 out.write( "Penultimate GO term" );
1766                 out.write( "</b></td><td><b>" );
1767                 out.write( "GO namespace" );
1768                 out.write( "</b></td>" );
1769                 out.write( "</tr>" );
1770                 out.write( SurfacingConstants.NL );
1771                 out.write( "</tr>" );
1772                 out.write( SurfacingConstants.NL );
1773                 per_node_counter = 0;
1774                 if ( matrix.getNumberOfCharacters() > 0 ) {
1775                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1776                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1777                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1778                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1779                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1780                 }
1781                 else {
1782                     per_node_go_mapped_domain_gain_loss_outfile = null;
1783                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1784                 }
1785                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1786                     // Not nice:
1787                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1788                     if ( ( matrix.getState( id, c ) == state )
1789                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1790                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1791                         final String character = matrix.getCharacter( c );
1792                         String domain_0 = "";
1793                         String domain_1 = "";
1794                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1795                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1796                             if ( s.length != 2 ) {
1797                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1798                                         + character + "]" );
1799                             }
1800                             domain_0 = s[ 0 ];
1801                             domain_1 = s[ 1 ];
1802                         }
1803                         else {
1804                             domain_0 = character;
1805                         }
1806                         writeDomainData( domain_id_to_go_ids_map,
1807                                          go_id_to_term_map,
1808                                          go_namespace_limit,
1809                                          out,
1810                                          domain_0,
1811                                          domain_1,
1812                                          prefix_for_html,
1813                                          character_separator,
1814                                          domain_id_to_secondary_features_maps,
1815                                          null );
1816                         all_pfams_encountered.add( domain_0 );
1817                         if ( pfams_gained_or_lost != null ) {
1818                             pfams_gained_or_lost.add( domain_0 );
1819                         }
1820                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1821                             all_pfams_encountered.add( domain_1 );
1822                             if ( pfams_gained_or_lost != null ) {
1823                                 pfams_gained_or_lost.add( domain_1 );
1824                             }
1825                         }
1826                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1827                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1828                                                                      domain_0,
1829                                                                      domain_1 );
1830                             per_node_counter++;
1831                         }
1832                     }
1833                 }
1834                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1835                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1836                     if ( per_node_counter < 1 ) {
1837                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1838                     }
1839                     per_node_counter = 0;
1840                 }
1841                 out.write( "</table>" );
1842                 out.write( SurfacingConstants.NL );
1843                 out.write( "<hr>" );
1844                 out.write( SurfacingConstants.NL );
1845             } // for( final String id : sorted_ids ) {
1846             out.write( "</body>" );
1847             out.write( SurfacingConstants.NL );
1848             out.write( "</html>" );
1849             out.write( SurfacingConstants.NL );
1850             out.flush();
1851             out.close();
1852         }
1853         catch ( final IOException e ) {
1854             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1855         }
1856         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1857     }
1858
1859     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1860                                                           final File output_dir,
1861                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1862                                                           final GenomeWideCombinableDomains gwcd,
1863                                                           final int i,
1864                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1865         File dc_outfile = new File( input_file_properties[ i ][ 0 ]
1866                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1867         if ( output_dir != null ) {
1868             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1869         }
1870         checkForOutputFileWriteability( dc_outfile );
1871         try {
1872             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1873             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1874             out.close();
1875         }
1876         catch ( final IOException e ) {
1877             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1878         }
1879         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1880         try {
1881             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
1882             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1883             if ( stats.getN() < 2 ) {
1884                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1885             }
1886             else {
1887                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1888                         .sampleStandardDeviation() ) + "\t" );
1889             }
1890             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1891             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1892             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1893             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1894             final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
1895             for( final DomainId mpd : mpds ) {
1896                 per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
1897             }
1898             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1899         }
1900         catch ( final IOException e ) {
1901             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1902         }
1903         if ( input_file_properties[ i ].length == 3 ) {
1904             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1905                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1906                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1907         }
1908         else {
1909             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1910                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1911                     + dc_outfile + "\"" );
1912         }
1913     }
1914
1915     private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1916                                          final Map<GoId, GoTerm> go_id_to_term_map,
1917                                          final GoNameSpace go_namespace_limit,
1918                                          final Writer out,
1919                                          final String domain_0,
1920                                          final String domain_1,
1921                                          final String prefix_for_html,
1922                                          final String character_separator_for_non_html_output,
1923                                          final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1924                                          final Set<GoId> all_go_ids ) throws IOException {
1925         boolean any_go_annotation_present = false;
1926         boolean first_has_no_go = false;
1927         int domain_count = 2; // To distinguish between domains and binary domain combinations.
1928         if ( ForesterUtil.isEmpty( domain_1 ) ) {
1929             domain_count = 1;
1930         }
1931         // The following has a difficult to understand logic.
1932         for( int d = 0; d < domain_count; ++d ) {
1933             List<GoId> go_ids = null;
1934             boolean go_annotation_present = false;
1935             if ( d == 0 ) {
1936                 final DomainId domain_id = new DomainId( domain_0 );
1937                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1938                     go_annotation_present = true;
1939                     any_go_annotation_present = true;
1940                     go_ids = domain_id_to_go_ids_map.get( domain_id );
1941                 }
1942                 else {
1943                     first_has_no_go = true;
1944                 }
1945             }
1946             else {
1947                 final DomainId domain_id = new DomainId( domain_1 );
1948                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1949                     go_annotation_present = true;
1950                     any_go_annotation_present = true;
1951                     go_ids = domain_id_to_go_ids_map.get( domain_id );
1952                 }
1953             }
1954             if ( go_annotation_present ) {
1955                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
1956                 for( final GoId go_id : go_ids ) {
1957                     out.write( "<tr>" );
1958                     if ( first ) {
1959                         first = false;
1960                         writeDomainIdsToHtml( out,
1961                                               domain_0,
1962                                               domain_1,
1963                                               prefix_for_html,
1964                                               domain_id_to_secondary_features_maps );
1965                     }
1966                     else {
1967                         out.write( "<td></td>" );
1968                     }
1969                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
1970                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
1971                     }
1972                     final GoTerm go_term = go_id_to_term_map.get( go_id );
1973                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
1974                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
1975                         final String go_id_str = go_id.getId();
1976                         out.write( "<td>" );
1977                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
1978                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
1979                         out.write( "</td><td>" );
1980                         out.write( go_term.getName() );
1981                         if ( domain_count == 2 ) {
1982                             out.write( " (" + d + ")" );
1983                         }
1984                         out.write( "</td><td>" );
1985                         // out.write( top );
1986                         // out.write( "</td><td>" );
1987                         out.write( "[" );
1988                         out.write( go_term.getGoNameSpace().toShortString() );
1989                         out.write( "]" );
1990                         out.write( "</td>" );
1991                         if ( all_go_ids != null ) {
1992                             all_go_ids.add( go_id );
1993                         }
1994                     }
1995                     else {
1996                         out.write( "<td>" );
1997                         out.write( "</td><td>" );
1998                         out.write( "</td><td>" );
1999                         out.write( "</td><td>" );
2000                         out.write( "</td>" );
2001                     }
2002                     out.write( "</tr>" );
2003                     out.write( SurfacingConstants.NL );
2004                 }
2005             }
2006         } //  for( int d = 0; d < domain_count; ++d )
2007         if ( !any_go_annotation_present ) {
2008             out.write( "<tr>" );
2009             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2010             out.write( "<td>" );
2011             out.write( "</td><td>" );
2012             out.write( "</td><td>" );
2013             out.write( "</td><td>" );
2014             out.write( "</td>" );
2015             out.write( "</tr>" );
2016             out.write( SurfacingConstants.NL );
2017         }
2018     }
2019
2020     private static void writeDomainIdsToHtml( final Writer out,
2021                                               final String domain_0,
2022                                               final String domain_1,
2023                                               final String prefix_for_detailed_html,
2024                                               final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
2025             throws IOException {
2026         out.write( "<td>" );
2027         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2028             out.write( prefix_for_detailed_html );
2029             out.write( " " );
2030         }
2031         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2032         out.write( "</td>" );
2033     }
2034
2035     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2036                                                                        final StringBuilder html_title,
2037                                                                        final Writer single_writer,
2038                                                                        Map<Character, Writer> split_writers,
2039                                                                        final SortedSet<DomainSimilarity> similarities,
2040                                                                        final boolean treat_as_binary,
2041                                                                        final List<Species> species_order,
2042                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
2043                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
2044                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
2045                                                                        final boolean verbose ) throws IOException {
2046         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2047         String histogram_title = null;
2048         switch ( sort_field ) {
2049             case ABS_MAX_COUNTS_DIFFERENCE:
2050                 if ( treat_as_binary ) {
2051                     histogram_title = "absolute counts difference:";
2052                 }
2053                 else {
2054                     histogram_title = "absolute (maximal) counts difference:";
2055                 }
2056                 break;
2057             case MAX_COUNTS_DIFFERENCE:
2058                 if ( treat_as_binary ) {
2059                     histogram_title = "counts difference:";
2060                 }
2061                 else {
2062                     histogram_title = "(maximal) counts difference:";
2063                 }
2064                 break;
2065             case DOMAIN_ID:
2066                 histogram_title = "score mean:";
2067                 break;
2068             case MIN:
2069                 histogram_title = "score minimum:";
2070                 break;
2071             case MAX:
2072                 histogram_title = "score maximum:";
2073                 break;
2074             case MAX_DIFFERENCE:
2075                 if ( treat_as_binary ) {
2076                     histogram_title = "difference:";
2077                 }
2078                 else {
2079                     histogram_title = "(maximal) difference:";
2080                 }
2081                 break;
2082             case MEAN:
2083                 histogram_title = "score mean:";
2084                 break;
2085             case SD:
2086                 histogram_title = "score standard deviation:";
2087                 break;
2088             case SPECIES_COUNT:
2089                 histogram_title = "species number:";
2090                 break;
2091             default:
2092                 throw new AssertionError( "Unknown sort field: " + sort_field );
2093         }
2094         for( final DomainSimilarity similarity : similarities ) {
2095             switch ( sort_field ) {
2096                 case ABS_MAX_COUNTS_DIFFERENCE:
2097                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
2098                     break;
2099                 case MAX_COUNTS_DIFFERENCE:
2100                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
2101                     break;
2102                 case DOMAIN_ID:
2103                     stats.addValue( similarity.getMeanSimilarityScore() );
2104                     break;
2105                 case MIN:
2106                     stats.addValue( similarity.getMinimalSimilarityScore() );
2107                     break;
2108                 case MAX:
2109                     stats.addValue( similarity.getMaximalSimilarityScore() );
2110                     break;
2111                 case MAX_DIFFERENCE:
2112                     stats.addValue( similarity.getMaximalDifference() );
2113                     break;
2114                 case MEAN:
2115                     stats.addValue( similarity.getMeanSimilarityScore() );
2116                     break;
2117                 case SD:
2118                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
2119                     break;
2120                 case SPECIES_COUNT:
2121                     stats.addValue( similarity.getSpecies().size() );
2122                     break;
2123                 default:
2124                     throw new AssertionError( "Unknown sort field: " + sort_field );
2125             }
2126         }
2127         //
2128         // final HistogramData[] hists = new HistogramData[ 1 ];
2129         //
2130         //
2131         // List<HistogramDataItem> data_items = new
2132         // ArrayList<HistogramDataItem>();
2133         // double[] values = stats.getDataAsDoubleArray();
2134         // for( int i = 0; i < values.length; i++ ) {
2135         // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
2136         // i ] );
2137         // data_items.add( data_item );
2138         // }
2139         //
2140         //
2141         // HistogramData hd0 = new HistogramData( "name",
2142         // data_items,
2143         // null, 20,
2144         // 40 );
2145         //
2146         //
2147         //
2148         //
2149         // hists[ 0 ] = hd0;
2150         //
2151         // final HistogramsFrame hf = new HistogramsFrame( hists );
2152         // hf.setVisible( true );
2153         //
2154         AsciiHistogram histo = null;
2155         if ( stats.getMin() < stats.getMin() ) {
2156             histo = new AsciiHistogram( stats, histogram_title );
2157         }
2158         if ( verbose ) {
2159             if ( histo != null ) {
2160                 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
2161             }
2162             System.out.println();
2163             System.out.println( "N                   : " + stats.getN() );
2164             System.out.println( "Min                 : " + stats.getMin() );
2165             System.out.println( "Max                 : " + stats.getMax() );
2166             System.out.println( "Mean                : " + stats.arithmeticMean() );
2167             if ( stats.getN() > 1 ) {
2168                 System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
2169             }
2170             else {
2171                 System.out.println( "SD                  : n/a" );
2172             }
2173             System.out.println( "Median              : " + stats.median() );
2174             if ( stats.getN() > 1 ) {
2175                 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
2176             }
2177             else {
2178                 System.out.println( "Pearsonian skewness : n/a" );
2179             }
2180         }
2181         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2182             split_writers = new HashMap<Character, Writer>();
2183             split_writers.put( '_', single_writer );
2184         }
2185         switch ( print_option ) {
2186             case SIMPLE_TAB_DELIMITED:
2187                 break;
2188             case HTML:
2189                 for( final Character key : split_writers.keySet() ) {
2190                     final Writer w = split_writers.get( key );
2191                     w.write( "<html>" );
2192                     w.write( SurfacingConstants.NL );
2193                     if ( key != '_' ) {
2194                         addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
2195                     }
2196                     else {
2197                         addHtmlHead( w, "DCs (" + html_title + ")" );
2198                     }
2199                     w.write( SurfacingConstants.NL );
2200                     w.write( "<body>" );
2201                     w.write( SurfacingConstants.NL );
2202                     w.write( html_desc.toString() );
2203                     w.write( SurfacingConstants.NL );
2204                     w.write( "<hr>" );
2205                     w.write( "<br>" );
2206                     w.write( SurfacingConstants.NL );
2207                     w.write( "<tt><pre>" );
2208                     w.write( SurfacingConstants.NL );
2209                     if ( histo != null ) {
2210                         w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2211                         w.write( SurfacingConstants.NL );
2212                     }
2213                     w.write( "</pre></tt>" );
2214                     w.write( SurfacingConstants.NL );
2215                     w.write( "<table>" );
2216                     w.write( SurfacingConstants.NL );
2217                     w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2218                     w.write( SurfacingConstants.NL );
2219                     w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2220                     w.write( SurfacingConstants.NL );
2221                     w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2222                     w.write( SurfacingConstants.NL );
2223                     w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2224                     w.write( SurfacingConstants.NL );
2225                     if ( stats.getN() > 1 ) {
2226                         w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2227                     }
2228                     else {
2229                         w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2230                     }
2231                     w.write( SurfacingConstants.NL );
2232                     w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
2233                     w.write( SurfacingConstants.NL );
2234                     if ( stats.getN() > 1 ) {
2235                         w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
2236                     }
2237                     else {
2238                         w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
2239                     }
2240                     w.write( SurfacingConstants.NL );
2241                     w.write( "</table>" );
2242                     w.write( SurfacingConstants.NL );
2243                     w.write( "<br>" );
2244                     w.write( SurfacingConstants.NL );
2245                     w.write( "<hr>" );
2246                     w.write( SurfacingConstants.NL );
2247                     w.write( "<br>" );
2248                     w.write( SurfacingConstants.NL );
2249                     w.write( "<table>" );
2250                     w.write( SurfacingConstants.NL );
2251                 }
2252                 break;
2253         }
2254         for( final Writer w : split_writers.values() ) {
2255             w.write( SurfacingConstants.NL );
2256         }
2257         for( final DomainSimilarity similarity : similarities ) {
2258             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2259                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2260             }
2261             if ( single_writer != null ) {
2262                 single_writer.write( similarity.toStringBuffer( print_option ).toString() );
2263             }
2264             else {
2265                 Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
2266                         .toLowerCase().charAt( 0 ) );
2267                 if ( local_writer == null ) {
2268                     local_writer = split_writers.get( '0' );
2269                 }
2270                 local_writer.write( similarity.toStringBuffer( print_option ).toString() );
2271             }
2272             for( final Writer w : split_writers.values() ) {
2273                 w.write( SurfacingConstants.NL );
2274             }
2275         }
2276         switch ( print_option ) {
2277             case HTML:
2278                 for( final Writer w : split_writers.values() ) {
2279                     w.write( SurfacingConstants.NL );
2280                     w.write( "</table>" );
2281                     w.write( SurfacingConstants.NL );
2282                     w.write( "</font>" );
2283                     w.write( SurfacingConstants.NL );
2284                     w.write( "</body>" );
2285                     w.write( SurfacingConstants.NL );
2286                     w.write( "</html>" );
2287                     w.write( SurfacingConstants.NL );
2288                 }
2289                 break;
2290         }
2291         for( final Writer w : split_writers.values() ) {
2292             w.close();
2293         }
2294         return stats;
2295     }
2296
2297     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2298                                                                  final String domain_0,
2299                                                                  final String domain_1 ) throws IOException {
2300         individual_files_writer.write( domain_0 );
2301         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2302         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2303             individual_files_writer.write( domain_1 );
2304             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2305         }
2306     }
2307
2308     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2309                                           final String filename,
2310                                           final Format format ) {
2311         final File outfile = new File( filename );
2312         checkForOutputFileWriteability( outfile );
2313         try {
2314             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2315             matrix.toWriter( out, format );
2316             out.flush();
2317             out.close();
2318         }
2319         catch ( final IOException e ) {
2320             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2321         }
2322         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2323     }
2324
2325     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2326         checkForOutputFileWriteability( matrix_outfile );
2327         try {
2328             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2329             for( final DistanceMatrix distance_matrix : matrices ) {
2330                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2331                 out.write( ForesterUtil.LINE_SEPARATOR );
2332                 out.flush();
2333             }
2334             out.close();
2335         }
2336         catch ( final IOException e ) {
2337             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2338         }
2339         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2340     }
2341
2342     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2343         try {
2344             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2345             for( final String pfam : pfams ) {
2346                 writer.write( pfam );
2347                 writer.write( ForesterUtil.LINE_SEPARATOR );
2348             }
2349             writer.close();
2350             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2351                     + "]" );
2352         }
2353         catch ( final IOException e ) {
2354             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2355         }
2356     }
2357
2358     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2359         final PhylogenyWriter writer = new PhylogenyWriter();
2360         try {
2361             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2362         }
2363         catch ( final IOException e ) {
2364             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2365                     + e );
2366         }
2367         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2368     }
2369
2370     public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
2371         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2372             final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2373             writer.write( " [" );
2374             if ( matcher.matches() ) {
2375                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2376                         + "\" target=\"taxonomy_window\">uniprot</a>" );
2377             }
2378             else {
2379                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2380                         + "\" target=\"taxonomy_window\">eol</a>" );
2381                 writer.write( "|" );
2382                 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2383                         + "\" target=\"taxonomy_window\">tol</a>" );
2384             }
2385             writer.write( "]" );
2386         }
2387     }
2388
2389     private static void writeToNexus( final String outfile_name,
2390                                       final CharacterStateMatrix<BinaryStates> matrix,
2391                                       final Phylogeny phylogeny ) {
2392         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2393             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2394                     + "] to nexus" );
2395         }
2396         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2397         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2398         phylogenies.add( phylogeny );
2399         try {
2400             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2401             w.write( NexusConstants.NEXUS );
2402             w.write( ForesterUtil.LINE_SEPARATOR );
2403             my_matrix.writeNexusTaxaBlock( w );
2404             my_matrix.writeNexusBinaryChractersBlock( w );
2405             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2406             w.flush();
2407             w.close();
2408             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2409         }
2410         catch ( final IOException e ) {
2411             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2412         }
2413     }
2414
2415     private static void writeToNexus( final String outfile_name,
2416                                       final DomainParsimonyCalculator domain_parsimony,
2417                                       final Phylogeny phylogeny ) {
2418         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2419                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2420                       phylogeny );
2421         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2422                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2423                       phylogeny );
2424     }
2425
2426     public static void domainsPerProteinsStatistics( final String genome,
2427                                                      final List<Protein> protein_list,
2428                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
2429                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2430                                                      final SortedSet<String> domains_which_are_always_single,
2431                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
2432                                                      final SortedSet<String> domains_which_never_single,
2433                                                      final Writer writer ) {
2434         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2435         for( final Protein protein : protein_list ) {
2436             final int domains = protein.getNumberOfProteinDomains();
2437             //System.out.println( domains );
2438             stats.addValue( domains );
2439             all_genomes_domains_per_potein_stats.addValue( domains );
2440             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
2441                 all_genomes_domains_per_potein_histo.put( domains, 1 );
2442             }
2443             else {
2444                 all_genomes_domains_per_potein_histo.put( domains,
2445                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
2446             }
2447             if ( domains == 1 ) {
2448                 final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
2449                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2450                     if ( domains_which_never_single.contains( domain ) ) {
2451                         domains_which_never_single.remove( domain );
2452                         domains_which_are_sometimes_single_sometimes_not.add( domain );
2453                     }
2454                     else {
2455                         domains_which_are_always_single.add( domain );
2456                     }
2457                 }
2458             }
2459             else if ( domains > 1 ) {
2460                 for( final Domain d : protein.getProteinDomains() ) {
2461                     final String domain = d.getDomainId().getId();
2462                     // System.out.println( domain );
2463                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2464                         if ( domains_which_are_always_single.contains( domain ) ) {
2465                             domains_which_are_always_single.remove( domain );
2466                             domains_which_are_sometimes_single_sometimes_not.add( domain );
2467                         }
2468                         else {
2469                             domains_which_never_single.add( domain );
2470                         }
2471                     }
2472                 }
2473             }
2474         }
2475         try {
2476             writer.write( genome );
2477             writer.write( "\t" );
2478             if ( stats.getN() >= 1 ) {
2479                 writer.write( stats.arithmeticMean() + "" );
2480                 writer.write( "\t" );
2481                 if ( stats.getN() >= 2 ) {
2482                     writer.write( stats.sampleStandardDeviation() + "" );
2483                 }
2484                 else {
2485                     writer.write( "" );
2486                 }
2487                 writer.write( "\t" );
2488                 writer.write( stats.median() + "" );
2489                 writer.write( "\t" );
2490                 writer.write( stats.getN() + "" );
2491                 writer.write( "\t" );
2492                 writer.write( stats.getMin() + "" );
2493                 writer.write( "\t" );
2494                 writer.write( stats.getMax() + "" );
2495             }
2496             else {
2497                 writer.write( "\t" );
2498                 writer.write( "\t" );
2499                 writer.write( "\t" );
2500                 writer.write( "0" );
2501                 writer.write( "\t" );
2502                 writer.write( "\t" );
2503             }
2504             writer.write( "\n" );
2505         }
2506         catch ( final IOException e ) {
2507             e.printStackTrace();
2508         }
2509     }
2510 }