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.Map.Entry;
  45 import java.util.PriorityQueue;
  46 import java.util.Set;
  47 import java.util.SortedMap;
  48 import java.util.SortedSet;
  49 import java.util.TreeMap;
  50 import java.util.TreeSet;
  51 import java.util.regex.Matcher;
  52 import java.util.regex.Pattern;
  53
  54 import org.forester.application.surfacing;
  55 import org.forester.evoinference.distance.NeighborJoining;
  56 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  57 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  58 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  59 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  61 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  62 import org.forester.go.GoId;
  63 import org.forester.go.GoNameSpace;
  64 import org.forester.go.GoTerm;
  65 import org.forester.go.PfamToGoMapping;
  66 import org.forester.io.parsers.nexus.NexusConstants;
  67 import org.forester.io.writers.PhylogenyWriter;
  68 import org.forester.phylogeny.Phylogeny;
  69 import org.forester.phylogeny.PhylogenyMethods;
  70 import org.forester.phylogeny.PhylogenyNode;
  71 import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  72 import org.forester.phylogeny.data.BinaryCharacters;
  73 import org.forester.phylogeny.data.Confidence;
  74 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  75 import org.forester.protein.BasicProtein;
  76 import org.forester.protein.BinaryDomainCombination;
  77 import org.forester.protein.Domain;
  78 import org.forester.protein.DomainId;
  79 import org.forester.protein.Protein;
  80 import org.forester.species.Species;
  81 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  82 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  83 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  84 import org.forester.util.AsciiHistogram;
  85 import org.forester.util.BasicDescriptiveStatistics;
  86 import org.forester.util.BasicTable;
  87 import org.forester.util.BasicTableParser;
  88 import org.forester.util.DescriptiveStatistics;
  89 import org.forester.util.ForesterUtil;
  90
  91 public final class SurfacingUtil {
  92
  93     private final static NumberFormat       FORMATTER                        = new DecimalFormat( "0.0E0" );
  94     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  95     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  96
  97                                                                                  @Override
  98                                                                                  public int compare( final Domain d1,
  99                                                                                                      final Domain d2 ) {
 100                                                                                      if ( d1.getPerSequenceEvalue() < d2
 101                                                                                              .getPerSequenceEvalue() ) {
 102                                                                                          return -1;
 103                                                                                      }
 104                                                                                      else if ( d1
 105                                                                                              .getPerSequenceEvalue() > d2
 106                                                                                              .getPerSequenceEvalue() ) {
 107                                                                                          return 1;
 108                                                                                      }
 109                                                                                      else {
 110                                                                                          return d1.compareTo( d2 );
 111                                                                                      }
 112                                                                                  }
 113                                                                              };
 114     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 115     private static final boolean            USE_LAST                         = true;
 116
 117     private SurfacingUtil() {
 118         // Hidden constructor.
 119     }
 120
 121     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 122                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 123         final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 124         for( final DomainId domain_id : all_cd.keySet() ) {
 125             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 126         }
 127     }
 128
 129     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 130                                              final SortedSet<DomainId> domain_ids ) {
 131         final SortedSet<DomainId> domains = genome.getAllDomainIds();
 132         for( final DomainId domain : domains ) {
 133             domain_ids.add( domain );
 134         }
 135     }
 136
 137     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 138         w.write( SurfacingConstants.NL );
 139         w.write( "<head>" );
 140         w.write( "<title>" );
 141         w.write( title );
 142         w.write( "</title>" );
 143         w.write( SurfacingConstants.NL );
 144         w.write( "<style>" );
 145         w.write( SurfacingConstants.NL );
 146         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 147         w.write( SurfacingConstants.NL );
 148         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 149         w.write( SurfacingConstants.NL );
 150         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 151         w.write( SurfacingConstants.NL );
 152         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 153         w.write( SurfacingConstants.NL );
 154         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 155         w.write( SurfacingConstants.NL );
 156         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 157         w.write( SurfacingConstants.NL );
 158         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 159         w.write( SurfacingConstants.NL );
 160         w.write( "</style>" );
 161         w.write( SurfacingConstants.NL );
 162         w.write( "</head>" );
 163         w.write( SurfacingConstants.NL );
 164     }
 165
 166     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 167         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 168         for( final DomainSimilarity similarity : similarities ) {
 169             stats.addValue( similarity.getMeanSimilarityScore() );
 170         }
 171         return stats;
 172     }
 173
 174     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
 175                                                                     final String outfilename_for_counts,
 176                                                                     final String outfilename_for_dc,
 177                                                                     final String outfilename_for_dc_for_go_mapping,
 178                                                                     final String outfilename_for_dc_for_go_mapping_unique,
 179                                                                     final String outfilename_for_rank_counts,
 180                                                                     final String outfilename_for_ancestor_species_counts,
 181                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 182                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc ) {
 183         try {
 184             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
 185             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
 186             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
 187             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
 188             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
 189             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
 190                 final PhylogenyNode n = it.next();
 191                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
 192                 for( final String dc : gained_dc ) {
 193                     if ( dc_gain_counts.containsKey( dc ) ) {
 194                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
 195                     }
 196                     else {
 197                         dc_gain_counts.put( dc, 1 );
 198                     }
 199                 }
 200             }
 201             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
 202             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
 203             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
 204             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
 205             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
 206             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
 207             final Set<String> dcs = dc_gain_counts.keySet();
 208             final SortedSet<String> more_than_once = new TreeSet<String>();
 209             for( final String dc : dcs ) {
 210                 final int count = dc_gain_counts.get( dc );
 211                 if ( histogram.containsKey( count ) ) {
 212                     histogram.put( count, histogram.get( count ) + 1 );
 213                     domain_lists.get( count ).append( ", " + dc );
 214                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
 215                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
 216                 }
 217                 else {
 218                     histogram.put( count, 1 );
 219                     domain_lists.put( count, new StringBuilder( dc ) );
 220                     final PriorityQueue<String> q = new PriorityQueue<String>();
 221                     q.addAll( splitDomainCombination( dc ) );
 222                     domain_lists_go.put( count, q );
 223                     final SortedSet<String> set = new TreeSet<String>();
 224                     set.addAll( splitDomainCombination( dc ) );
 225                     domain_lists_go_unique.put( count, set );
 226                 }
 227                 if ( protein_length_stats_by_dc != null ) {
 228                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
 229                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
 230                     }
 231                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
 232                             .arithmeticMean() );
 233                 }
 234                 if ( domain_number_stats_by_dc != null ) {
 235                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
 236                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
 237                     }
 238                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
 239                             .arithmeticMean() );
 240                 }
 241                 if ( count > 1 ) {
 242                     more_than_once.add( dc );
 243                 }
 244             }
 245             final Set<Integer> histogram_keys = histogram.keySet();
 246             for( final Integer histogram_key : histogram_keys ) {
 247                 final int count = histogram.get( histogram_key );
 248                 final StringBuilder dc = domain_lists.get( histogram_key );
 249                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 250                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
 251                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 252                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
 253                 Arrays.sort( sorted );
 254                 for( final Object domain : sorted ) {
 255                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
 256                 }
 257                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 258                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
 259                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
 260                 }
 261             }
 262             out_counts.close();
 263             out_dc.close();
 264             out_dc_for_go_mapping.close();
 265             out_dc_for_go_mapping_unique.close();
 266             //
 267             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
 268             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
 269             for( final String dc : more_than_once ) {
 270                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
 271                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
 272                     final PhylogenyNode n = it.next();
 273                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
 274                         nodes.add( n );
 275                     }
 276                 }
 277                 for( int i = 0; i < nodes.size() - 1; ++i ) {
 278                     for( int j = i + 1; j < nodes.size(); ++j ) {
 279                         final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
 280                                                                                             nodes.get( j ) );
 281                         String rank = "unknown";
 282                         if ( lca.getNodeData().isHasTaxonomy()
 283                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
 284                             rank = lca.getNodeData().getTaxonomy().getRank();
 285                         }
 286                         addToCountMap( lca_rank_counts, rank );
 287                         String lca_species;
 288                         if ( lca.getNodeData().isHasTaxonomy()
 289                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
 290                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
 291                         }
 292                         else if ( lca.getNodeData().isHasTaxonomy()
 293                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
 294                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
 295                         }
 296                         else {
 297                             lca_species = lca.getName();
 298                         }
 299                         addToCountMap( lca_ancestor_species_counts, lca_species );
 300                     }
 301                 }
 302             }
 303             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
 304             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
 305             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
 306             ForesterUtil.map2writer( out_for_ancestor_species_counts,
 307                                      lca_ancestor_species_counts,
 308                                      "\t",
 309                                      ForesterUtil.LINE_SEPARATOR );
 310             out_for_rank_counts.close();
 311             out_for_ancestor_species_counts.close();
 312             System.out.println( "Lengths: " );
 313             if ( protein_length_stats_by_dc != null ) {
 314                 for( final Entry<?, ?> entry : dc_reapp_counts_to_protein_length_stats.entrySet() ) {
 315                     System.out.println( entry.getKey().toString() );
 316                     System.out.println( ": " );
 317                     System.out.println( entry.getValue().toString() );
 318                 }
 319             }
 320             System.out.println( "Number of domains: " );
 321             if ( domain_number_stats_by_dc != null ) {
 322                 for( final Entry<?, ?> entry : dc_reapp_counts_to_domain_number_stats.entrySet() ) {
 323                     System.out.println( entry.getKey().toString() );
 324                     System.out.println( ": " );
 325                     System.out.println( entry.getValue().toString() );
 326                 }
 327             }
 328         }
 329         catch ( final IOException e ) {
 330             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
 331         }
 332         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
 333                 + outfilename_for_counts + "]" );
 334         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
 335                 + outfilename_for_dc + "]" );
 336         ForesterUtil.programMessage( surfacing.PRG_NAME,
 337                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
 338                                              + outfilename_for_dc_for_go_mapping + "]" );
 339         ForesterUtil.programMessage( surfacing.PRG_NAME,
 340                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
 341                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
 342     }
 343
 344     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
 345         if ( map.containsKey( s ) ) {
 346             map.put( s, map.get( s ) + 1 );
 347         }
 348         else {
 349             map.put( s, 1 );
 350         }
 351     }
 352
 353     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 354         int overlap_count = 0;
 355         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 356             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 357                 ++overlap_count;
 358             }
 359         }
 360         return overlap_count;
 361     }
 362
 363     public static void checkForOutputFileWriteability( final File outfile ) {
 364         final String error = ForesterUtil.isWritableFile( outfile );
 365         if ( !ForesterUtil.isEmpty( error ) ) {
 366             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 367         }
 368     }
 369
 370     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
 371                                                                         final boolean get_gains ) {
 372         final SortedSet<String> domains = new TreeSet<String>();
 373         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
 374             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
 375             if ( get_gains ) {
 376                 domains.addAll( chars.getGainedCharacters() );
 377             }
 378             else {
 379                 domains.addAll( chars.getLostCharacters() );
 380             }
 381         }
 382         return domains;
 383     }
 384
 385     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 386                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 387                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 388                                                                                            final boolean get_gains ) {
 389         final SortedSet<String> sorted_ids = new TreeSet<String>();
 390         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 391             sorted_ids.add( matrix.getIdentifier( i ) );
 392         }
 393         for( final String id : sorted_ids ) {
 394             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 395                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 396                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 397                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 398                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 399                                 .createInstance( matrix.getCharacter( c ) ) );
 400                     }
 401                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 402                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 403                                 .createInstance( matrix.getCharacter( c ) ) );
 404                     }
 405                     else {
 406                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 407                                 .getCharacter( c ) ) );
 408                     }
 409                 }
 410             }
 411         }
 412     }
 413
 414     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
 415                                                             final boolean domain_combinations,
 416                                                             final CharacterStateMatrix.GainLossStates state,
 417                                                             final String outfile ) {
 418         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
 419                 + ForesterUtil.FILE_SEPARATOR + base_dir );
 420         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 421             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 422         }
 423         if ( domain_combinations ) {
 424             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 425                     + ForesterUtil.FILE_SEPARATOR + "DC" );
 426         }
 427         else {
 428             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 429                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
 430         }
 431         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 432             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 433         }
 434         if ( state == GainLossStates.GAIN ) {
 435             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 436                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
 437         }
 438         else if ( state == GainLossStates.LOSS ) {
 439             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 440                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
 441         }
 442         else {
 443             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 444                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
 445         }
 446         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 447             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 448         }
 449         return per_node_go_mapped_domain_gain_loss_files_base_dir;
 450     }
 451
 452     public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 453         final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
 454                 .size() );
 455         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 456             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 457                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 458             }
 459             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 460         }
 461         return domain_id_to_go_ids_map;
 462     }
 463
 464     public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 465             throws IOException {
 466         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
 467         final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
 468         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 469             final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
 470             if ( !map.containsKey( domain_id ) ) {
 471                 map.put( domain_id, new HashSet<String>() );
 472             }
 473             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 474         }
 475         return map;
 476     }
 477
 478     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 479         checkForOutputFileWriteability( nj_tree_outfile );
 480         final NeighborJoining nj = NeighborJoining.createInstance();
 481         final Phylogeny phylogeny = nj.execute( distance );
 482         phylogeny.setName( nj_tree_outfile.getName() );
 483         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 484         return phylogeny;
 485     }
 486
 487     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
 488         final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
 489         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
 490         for( final DomainId domain_id : cds.keySet() ) {
 491             final CombinableDomains cd = cds.get( domain_id );
 492             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
 493         }
 494         return binary_combinations;
 495     }
 496
 497     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 498                                                             final Detailedness detailedness,
 499                                                             final GoAnnotationOutput go_annotation_output,
 500                                                             final Map<GoId, GoTerm> go_id_to_term_map,
 501                                                             final GoNameSpace go_namespace_limit ) {
 502         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
 503             throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
 504         }
 505         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 506             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 507                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 508                 printable_domain_similarity.setDetailedness( detailedness );
 509                 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
 510                 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
 511                 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
 512             }
 513         }
 514     }
 515
 516     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 517                                                     final int number_of_genomes,
 518                                                     final DomainLengthsTable domain_lengths_table,
 519                                                     final File outfile ) throws IOException {
 520         final DecimalFormat df = new DecimalFormat( "#.00" );
 521         checkForOutputFileWriteability( outfile );
 522         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 523         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 524         out.write( ForesterUtil.LINE_SEPARATOR );
 525         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 526         out.write( ForesterUtil.LINE_SEPARATOR );
 527         out.write( ForesterUtil.LINE_SEPARATOR );
 528         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 529         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 530         out.write( ForesterUtil.LINE_SEPARATOR );
 531         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 532             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 533             if ( species_list.size() > 0 ) {
 534                 out.write( domain_lengths.getDomainId() + "\t" );
 535                 for( final Species species : species_list ) {
 536                     out.write( species + "\t" );
 537                 }
 538                 out.write( ForesterUtil.LINE_SEPARATOR );
 539                 // DescriptiveStatistics stats_for_domain = domain_lengths
 540                 //         .calculateMeanBasedStatistics();
 541                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 542                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 543             }
 544         }
 545         out.write( ForesterUtil.LINE_SEPARATOR );
 546         out.write( ForesterUtil.LINE_SEPARATOR );
 547         out.write( "OUTLIER SPECIES (Z 1.0)" );
 548         out.write( ForesterUtil.LINE_SEPARATOR );
 549         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 550                 .calculateMeanBasedStatisticsForAllSpecies();
 551         out.write( stats_for_all_species.asSummary() );
 552         out.write( ForesterUtil.LINE_SEPARATOR );
 553         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 554         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 555         out.write( ForesterUtil.LINE_SEPARATOR );
 556         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 557         final double population_mean = stats_for_all_species.arithmeticMean();
 558         for( final Species species : domain_lengths_table.getSpecies() ) {
 559             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 560             final double z = ( x - population_mean ) / population_sd;
 561             out.write( species + "\t" + z );
 562             out.write( ForesterUtil.LINE_SEPARATOR );
 563         }
 564         out.write( ForesterUtil.LINE_SEPARATOR );
 565         for( final Species species : domain_lengths_table.getSpecies() ) {
 566             final DescriptiveStatistics stats_for_species = domain_lengths_table
 567                     .calculateMeanBasedStatisticsForSpecies( species );
 568             final double x = stats_for_species.arithmeticMean();
 569             final double z = ( x - population_mean ) / population_sd;
 570             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 571                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 572                 out.write( ForesterUtil.LINE_SEPARATOR );
 573             }
 574         }
 575         out.close();
 576         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 577         //        for( int i = 0; i < number_of_genomes; ++i ) {
 578         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 579         //            histogram_datas
 580         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 581         //                            .calculateMeanBasedStatisticsForSpecies( species )
 582         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 583         //        }
 584         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 585         //        hf.setVisible( true );
 586         System.gc();
 587     }
 588
 589     /**
 590      *
 591      * @param all_binary_domains_combination_lost_fitch
 592      * @param consider_directedness_and_adjacency_for_bin_combinations
 593      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 594      * which were gained under unweighted (Fitch) parsimony.
 595      */
 596     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 597                                                  final boolean radomize_fitch_parsimony,
 598                                                  final String outfile_name,
 599                                                  final DomainParsimonyCalculator domain_parsimony,
 600                                                  final Phylogeny phylogeny,
 601                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 602                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 603                                                  final GoNameSpace go_namespace_limit,
 604                                                  final String parameters_str,
 605                                                  final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
 606                                                  final SortedSet<DomainId> positive_filter,
 607                                                  final boolean output_binary_domain_combinations_for_graphs,
 608                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 609                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 610                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 611                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 612                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc ) {
 613         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 614         final String date_time = ForesterUtil.getCurrentDateTime();
 615         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 616         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 617         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 618         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 619         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 620         writeToNexus( outfile_name, domain_parsimony, phylogeny );
 621         // DOLLO DOMAINS
 622         // -------------
 623         Phylogeny local_phylogeny_l = phylogeny.copy();
 624         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 625             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 626         }
 627         else {
 628             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 629         }
 630         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 631                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 632         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 633                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 634         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 635                                                            CharacterStateMatrix.GainLossStates.GAIN,
 636                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 637                                                            sep,
 638                                                            ForesterUtil.LINE_SEPARATOR,
 639                                                            null );
 640         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 641                                                            CharacterStateMatrix.GainLossStates.LOSS,
 642                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 643                                                            sep,
 644                                                            ForesterUtil.LINE_SEPARATOR,
 645                                                            null );
 646         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 647                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 648         //HTML:
 649         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 650                                        go_id_to_term_map,
 651                                        go_namespace_limit,
 652                                        false,
 653                                        domain_parsimony.getGainLossMatrix(),
 654                                        CharacterStateMatrix.GainLossStates.GAIN,
 655                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 656                                        sep,
 657                                        ForesterUtil.LINE_SEPARATOR,
 658                                        "Dollo Parsimony | Gains | Domains",
 659                                        "+",
 660                                        domain_id_to_secondary_features_maps,
 661                                        all_pfams_encountered,
 662                                        all_pfams_gained_as_domains,
 663                                        "_dollo_gains_d" );
 664         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 665                                        go_id_to_term_map,
 666                                        go_namespace_limit,
 667                                        false,
 668                                        domain_parsimony.getGainLossMatrix(),
 669                                        CharacterStateMatrix.GainLossStates.LOSS,
 670                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 671                                        sep,
 672                                        ForesterUtil.LINE_SEPARATOR,
 673                                        "Dollo Parsimony | Losses | Domains",
 674                                        "-",
 675                                        domain_id_to_secondary_features_maps,
 676                                        all_pfams_encountered,
 677                                        all_pfams_lost_as_domains,
 678                                        "_dollo_losses_d" );
 679         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 680                                        go_id_to_term_map,
 681                                        go_namespace_limit,
 682                                        false,
 683                                        domain_parsimony.getGainLossMatrix(),
 684                                        null,
 685                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 686                                        sep,
 687                                        ForesterUtil.LINE_SEPARATOR,
 688                                        "Dollo Parsimony | Present | Domains",
 689                                        "",
 690                                        domain_id_to_secondary_features_maps,
 691                                        all_pfams_encountered,
 692                                        null,
 693                                        "_dollo_present_d" );
 694         preparePhylogeny( local_phylogeny_l,
 695                           domain_parsimony,
 696                           date_time,
 697                           "Dollo parsimony on domain presence/absence",
 698                           "dollo_on_domains_" + outfile_name,
 699                           parameters_str );
 700         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 701                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 702         try {
 703             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 704             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 705         }
 706         catch ( final IOException e ) {
 707             e.printStackTrace();
 708             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 709         }
 710         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 711             // FITCH DOMAIN COMBINATIONS
 712             // -------------------------
 713             local_phylogeny_l = phylogeny.copy();
 714             String randomization = "no";
 715             if ( radomize_fitch_parsimony ) {
 716                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 717                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 718             }
 719             else {
 720                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
 721             }
 722             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 723                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 724             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 725                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 726             SurfacingUtil
 727                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 728                                                           CharacterStateMatrix.GainLossStates.GAIN,
 729                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 730                                                           sep,
 731                                                           ForesterUtil.LINE_SEPARATOR,
 732                                                           null );
 733             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 734                                                                CharacterStateMatrix.GainLossStates.LOSS,
 735                                                                outfile_name
 736                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 737                                                                sep,
 738                                                                ForesterUtil.LINE_SEPARATOR,
 739                                                                null );
 740             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 741                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 742             if ( all_binary_domains_combination_gained_fitch != null ) {
 743                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 744                                                                                     dc_type,
 745                                                                                     all_binary_domains_combination_gained_fitch,
 746                                                                                     true );
 747             }
 748             if ( all_binary_domains_combination_lost_fitch != null ) {
 749                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 750                                                                                     dc_type,
 751                                                                                     all_binary_domains_combination_lost_fitch,
 752                                                                                     false );
 753             }
 754             if ( output_binary_domain_combinations_for_graphs ) {
 755                 SurfacingUtil
 756                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 757                                                                                                            .getGainLossMatrix(),
 758                                                                                                    null,
 759                                                                                                    outfile_name
 760                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 761                                                                                                    sep,
 762                                                                                                    ForesterUtil.LINE_SEPARATOR,
 763                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 764             }
 765             // HTML:
 766             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 767                                            go_id_to_term_map,
 768                                            go_namespace_limit,
 769                                            true,
 770                                            domain_parsimony.getGainLossMatrix(),
 771                                            CharacterStateMatrix.GainLossStates.GAIN,
 772                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 773                                            sep,
 774                                            ForesterUtil.LINE_SEPARATOR,
 775                                            "Fitch Parsimony | Gains | Domain Combinations",
 776                                            "+",
 777                                            null,
 778                                            all_pfams_encountered,
 779                                            all_pfams_gained_as_dom_combinations,
 780                                            "_fitch_gains_dc" );
 781             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 782                                            go_id_to_term_map,
 783                                            go_namespace_limit,
 784                                            true,
 785                                            domain_parsimony.getGainLossMatrix(),
 786                                            CharacterStateMatrix.GainLossStates.LOSS,
 787                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 788                                            sep,
 789                                            ForesterUtil.LINE_SEPARATOR,
 790                                            "Fitch Parsimony | Losses | Domain Combinations",
 791                                            "-",
 792                                            null,
 793                                            all_pfams_encountered,
 794                                            all_pfams_lost_as_dom_combinations,
 795                                            "_fitch_losses_dc" );
 796             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 797                                            go_id_to_term_map,
 798                                            go_namespace_limit,
 799                                            true,
 800                                            domain_parsimony.getGainLossMatrix(),
 801                                            null,
 802                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 803                                            sep,
 804                                            ForesterUtil.LINE_SEPARATOR,
 805                                            "Fitch Parsimony | Present | Domain Combinations",
 806                                            "",
 807                                            null,
 808                                            all_pfams_encountered,
 809                                            null,
 810                                            "_fitch_present_dc" );
 811             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 812                                             go_id_to_term_map,
 813                                             outfile_name,
 814                                             all_pfams_encountered );
 815             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 816             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 817             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 818                               all_pfams_gained_as_dom_combinations );
 819             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 820             preparePhylogeny( local_phylogeny_l,
 821                               domain_parsimony,
 822                               date_time,
 823                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 824                                       + randomization,
 825                               "fitch_on_binary_domain_combinations_" + outfile_name,
 826                               parameters_str );
 827             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 828                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 829             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 830                                                         outfile_name
 831                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 832                                                         outfile_name
 833                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 834                                                         outfile_name
 835                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 836                                                         outfile_name
 837                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
 838                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
 839                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
 840                                                         protein_length_stats_by_dc,
 841                                                         domain_number_stats_by_dc );
 842         }
 843     }
 844
 845     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 846                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 847                                                                      final Phylogeny phylogeny,
 848                                                                      final String parameters_str,
 849                                                                      final Map<Species, MappingResults> mapping_results_map ) {
 850         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 851         final String date_time = ForesterUtil.getCurrentDateTime();
 852         System.out.println();
 853         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 854                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 855                       phylogeny );
 856         Phylogeny local_phylogeny_copy = phylogeny.copy();
 857         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 858         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 859                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 860         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 861                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 862         SurfacingUtil
 863                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 864                                                       CharacterStateMatrix.GainLossStates.GAIN,
 865                                                       outfile_name
 866                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 867                                                       sep,
 868                                                       ForesterUtil.LINE_SEPARATOR,
 869                                                       null );
 870         SurfacingUtil
 871                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 872                                                       CharacterStateMatrix.GainLossStates.LOSS,
 873                                                       outfile_name
 874                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 875                                                       sep,
 876                                                       ForesterUtil.LINE_SEPARATOR,
 877                                                       null );
 878         SurfacingUtil
 879                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 880                                                       null,
 881                                                       outfile_name
 882                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 883                                                       sep,
 884                                                       ForesterUtil.LINE_SEPARATOR,
 885                                                       null );
 886         preparePhylogeny( local_phylogeny_copy,
 887                           secondary_features_parsimony,
 888                           date_time,
 889                           "Dollo parsimony on secondary feature presence/absence",
 890                           "dollo_on_secondary_features_" + outfile_name,
 891                           parameters_str );
 892         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 893                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 894         // FITCH DOMAIN COMBINATIONS
 895         // -------------------------
 896         local_phylogeny_copy = phylogeny.copy();
 897         final String randomization = "no";
 898         secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
 899         preparePhylogeny( local_phylogeny_copy,
 900                           secondary_features_parsimony,
 901                           date_time,
 902                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
 903                                   + randomization,
 904                           "fitch_on_binary_domain_combinations_" + outfile_name,
 905                           parameters_str );
 906         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 907                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
 908         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
 909                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
 910                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
 911                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
 912                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
 913                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
 914                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null );
 915     }
 916
 917     public static void doit( final List<Protein> proteins,
 918                              final List<DomainId> query_domain_ids_nc_order,
 919                              final Writer out,
 920                              final String separator,
 921                              final String limit_to_species,
 922                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
 923         for( final Protein protein : proteins ) {
 924             if ( ForesterUtil.isEmpty( limit_to_species )
 925                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 926                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 927                     out.write( protein.getSpecies().getSpeciesId() );
 928                     out.write( separator );
 929                     out.write( protein.getProteinId().getId() );
 930                     out.write( separator );
 931                     out.write( "[" );
 932                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
 933                     boolean first = true;
 934                     for( final Domain domain : protein.getProteinDomains() ) {
 935                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 936                             visited_domain_ids.add( domain.getDomainId() );
 937                             if ( first ) {
 938                                 first = false;
 939                             }
 940                             else {
 941                                 out.write( " " );
 942                             }
 943                             out.write( domain.getDomainId().getId() );
 944                             out.write( " {" );
 945                             out.write( "" + domain.getTotalCount() );
 946                             out.write( "}" );
 947                         }
 948                     }
 949                     out.write( "]" );
 950                     out.write( separator );
 951                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 952                             .equals( SurfacingConstants.NONE ) ) ) {
 953                         out.write( protein.getDescription() );
 954                     }
 955                     out.write( separator );
 956                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 957                             .equals( SurfacingConstants.NONE ) ) ) {
 958                         out.write( protein.getAccession() );
 959                     }
 960                     out.write( SurfacingConstants.NL );
 961                 }
 962             }
 963         }
 964         out.flush();
 965     }
 966
 967     public static void extractProteinNames( final List<Protein> proteins,
 968                                             final List<DomainId> query_domain_ids_nc_order,
 969                                             final Writer out,
 970                                             final String separator,
 971                                             final String limit_to_species ) throws IOException {
 972         for( final Protein protein : proteins ) {
 973             if ( ForesterUtil.isEmpty( limit_to_species )
 974                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 975                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 976                     out.write( protein.getSpecies().getSpeciesId() );
 977                     out.write( separator );
 978                     out.write( protein.getProteinId().getId() );
 979                     out.write( separator );
 980                     out.write( "[" );
 981                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
 982                     boolean first = true;
 983                     for( final Domain domain : protein.getProteinDomains() ) {
 984                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 985                             visited_domain_ids.add( domain.getDomainId() );
 986                             if ( first ) {
 987                                 first = false;
 988                             }
 989                             else {
 990                                 out.write( " " );
 991                             }
 992                             out.write( domain.getDomainId().getId() );
 993                             out.write( " {" );
 994                             out.write( "" + domain.getTotalCount() );
 995                             out.write( "}" );
 996                         }
 997                     }
 998                     out.write( "]" );
 999                     out.write( separator );
1000                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1001                             .equals( SurfacingConstants.NONE ) ) ) {
1002                         out.write( protein.getDescription() );
1003                     }
1004                     out.write( separator );
1005                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1006                             .equals( SurfacingConstants.NONE ) ) ) {
1007                         out.write( protein.getAccession() );
1008                     }
1009                     out.write( SurfacingConstants.NL );
1010                 }
1011             }
1012         }
1013         out.flush();
1014     }
1015
1016     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
1017                                             final DomainId domain_id,
1018                                             final Writer out,
1019                                             final String separator,
1020                                             final String limit_to_species ) throws IOException {
1021         for( final Species species : protein_lists_per_species.keySet() ) {
1022             for( final Protein protein : protein_lists_per_species.get( species ) ) {
1023                 if ( ForesterUtil.isEmpty( limit_to_species )
1024                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1025                     final List<Domain> domains = protein.getProteinDomains( domain_id );
1026                     if ( domains.size() > 0 ) {
1027                         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1028                         for( final Domain domain : domains ) {
1029                             stats.addValue( domain.getPerSequenceEvalue() );
1030                         }
1031                         out.write( protein.getSpecies().getSpeciesId() );
1032                         out.write( separator );
1033                         out.write( protein.getProteinId().getId() );
1034                         out.write( separator );
1035                         out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
1036                         out.write( separator );
1037                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1038                                 .equals( SurfacingConstants.NONE ) ) ) {
1039                             out.write( protein.getDescription() );
1040                         }
1041                         out.write( separator );
1042                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1043                                 .equals( SurfacingConstants.NONE ) ) ) {
1044                             out.write( protein.getAccession() );
1045                         }
1046                         out.write( SurfacingConstants.NL );
1047                     }
1048                 }
1049             }
1050         }
1051         out.flush();
1052     }
1053
1054     public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
1055         final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
1056         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1057             final Set<DomainId> all_domains = gwcd.getAllDomainIds();
1058             //    for( final Domain domain : all_domains ) {
1059             all_domains_ids.addAll( all_domains );
1060             //    }
1061         }
1062         return all_domains_ids;
1063     }
1064
1065     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
1066         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
1067         for( final Protein protein_domain_collection : protein_domain_collections ) {
1068             for( final Object name : protein_domain_collection.getProteinDomains() ) {
1069                 final BasicDomain protein_domain = ( BasicDomain ) name;
1070                 final String id = protein_domain.getDomainId().getId();
1071                 if ( map.containsKey( id ) ) {
1072                     map.put( id, map.get( id ) + 1 );
1073                 }
1074                 else {
1075                     map.put( id, 1 );
1076                 }
1077             }
1078         }
1079         return map;
1080     }
1081
1082     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1083         final PhylogenyNodeIterator it = p.iteratorPostorder();
1084         int c = 0;
1085         while ( it.hasNext() ) {
1086             final PhylogenyNode n = it.next();
1087             if ( ForesterUtil.isEmpty( n.getName() )
1088                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1089                             .getScientificName() ) )
1090                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1091                             .getCommonName() ) ) ) {
1092                 if ( n.getParent() != null ) {
1093                     names.append( " " );
1094                     names.append( n.getParent().getName() );
1095                 }
1096                 final List l = n.getAllExternalDescendants();
1097                 for( final Object object : l ) {
1098                     System.out.println( l.toString() );
1099                 }
1100                 ++c;
1101             }
1102         }
1103         return c;
1104     }
1105
1106     /**
1107      * Returns true is Domain domain falls in an uninterrupted stretch of
1108      * covered positions.
1109      *
1110      * @param domain
1111      * @param covered_positions
1112      * @return
1113      */
1114     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1115         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1116             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1117                 return false;
1118             }
1119         }
1120         return true;
1121     }
1122
1123     public static void preparePhylogeny( final Phylogeny p,
1124                                          final DomainParsimonyCalculator domain_parsimony,
1125                                          final String date_time,
1126                                          final String method,
1127                                          final String name,
1128                                          final String parameters_str ) {
1129         domain_parsimony.decoratePhylogenyWithDomains( p );
1130         final StringBuilder desc = new StringBuilder();
1131         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1132         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1133         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1134         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1135         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1136         desc.append( "[Parameters: " + parameters_str + "]" );
1137         p.setName( name );
1138         p.setDescription( desc.toString() );
1139         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1140         p.setRerootable( false );
1141         p.setRooted( true );
1142     }
1143
1144     /*
1145      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1146      *
1147      *
1148      */
1149     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1150                                                             final String protein_id,
1151                                                             final String separator ) {
1152         final StringBuffer sb = new StringBuffer();
1153         if ( protein.getSpecies() == null ) {
1154             throw new IllegalArgumentException( "species must not be null" );
1155         }
1156         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1157             throw new IllegalArgumentException( "species id must not be empty" );
1158         }
1159         final List<Domain> domains = protein.getProteinDomains();
1160         if ( domains.size() > 1 ) {
1161             final Map<String, Integer> counts = new HashMap<String, Integer>();
1162             for( final Domain domain : domains ) {
1163                 final String id = domain.getDomainId().getId();
1164                 if ( counts.containsKey( id ) ) {
1165                     counts.put( id, counts.get( id ) + 1 );
1166                 }
1167                 else {
1168                     counts.put( id, 1 );
1169                 }
1170             }
1171             final Set<String> dcs = new HashSet<String>();
1172             for( int i = 1; i < domains.size(); ++i ) {
1173                 for( int j = 0; j < i; ++j ) {
1174                     Domain domain_n = domains.get( i );
1175                     Domain domain_c = domains.get( j );
1176                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1177                         domain_n = domains.get( j );
1178                         domain_c = domains.get( i );
1179                     }
1180                     final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
1181                     if ( !dcs.contains( dc ) ) {
1182                         dcs.add( dc );
1183                         sb.append( protein.getSpecies() );
1184                         sb.append( separator );
1185                         sb.append( protein_id );
1186                         sb.append( separator );
1187                         sb.append( domain_n.getDomainId().getId() );
1188                         sb.append( separator );
1189                         sb.append( domain_c.getDomainId().getId() );
1190                         sb.append( separator );
1191                         sb.append( domain_n.getPerDomainEvalue() );
1192                         sb.append( separator );
1193                         sb.append( domain_c.getPerDomainEvalue() );
1194                         sb.append( separator );
1195                         sb.append( counts.get( domain_n.getDomainId().getId() ) );
1196                         sb.append( separator );
1197                         sb.append( counts.get( domain_c.getDomainId().getId() ) );
1198                         sb.append( ForesterUtil.LINE_SEPARATOR );
1199                     }
1200                 }
1201             }
1202         }
1203         else if ( domains.size() == 1 ) {
1204             sb.append( protein.getSpecies() );
1205             sb.append( separator );
1206             sb.append( protein_id );
1207             sb.append( separator );
1208             sb.append( domains.get( 0 ).getDomainId().getId() );
1209             sb.append( separator );
1210             sb.append( separator );
1211             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1212             sb.append( separator );
1213             sb.append( separator );
1214             sb.append( 1 );
1215             sb.append( separator );
1216             sb.append( ForesterUtil.LINE_SEPARATOR );
1217         }
1218         else {
1219             sb.append( protein.getSpecies() );
1220             sb.append( separator );
1221             sb.append( protein_id );
1222             sb.append( separator );
1223             sb.append( separator );
1224             sb.append( separator );
1225             sb.append( separator );
1226             sb.append( separator );
1227             sb.append( separator );
1228             sb.append( ForesterUtil.LINE_SEPARATOR );
1229         }
1230         return sb;
1231     }
1232
1233     /**
1234      *
1235      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1236      * domain with 0.3 is ignored
1237      *
1238      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1239      *
1240      *
1241      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1242      * ignored
1243      *
1244      * @param max_allowed_overlap
1245      *            maximal allowed overlap (inclusive) to be still considered not
1246      *            overlapping (zero or negative value to allow any overlap)
1247      * @param remove_engulfed_domains
1248      *            to remove domains which are completely engulfed by coverage of
1249      *            domains with better support
1250      * @param protein
1251      * @return
1252      */
1253     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1254                                                     final boolean remove_engulfed_domains,
1255                                                     final Protein protein ) {
1256         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1257                 .getSpeciesId(), protein.getLength() );
1258         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1259         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1260         for( final Domain domain : sorted ) {
1261             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1262                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1263                 final int covered_positions_size = covered_positions.size();
1264                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1265                     covered_positions.add( false );
1266                 }
1267                 final int new_covered_positions_size = covered_positions.size();
1268                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1269                     if ( i < new_covered_positions_size ) {
1270                         covered_positions.set( i, true );
1271                     }
1272                     else {
1273                         covered_positions.add( true );
1274                     }
1275                 }
1276                 pruned_protein.addProteinDomain( domain );
1277             }
1278         }
1279         return pruned_protein;
1280     }
1281
1282     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1283         final List<Domain> domains = new ArrayList<Domain>();
1284         for( final Domain d : protein.getProteinDomains() ) {
1285             domains.add( d );
1286         }
1287         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1288         return domains;
1289     }
1290
1291     private static List<String> splitDomainCombination( final String dc ) {
1292         final String[] s = dc.split( "=" );
1293         if ( s.length != 2 ) {
1294             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
1295                     + dc );
1296             System.exit( -1 );
1297         }
1298         final List<String> l = new ArrayList<String>( 2 );
1299         l.add( s[ 0 ] );
1300         l.add( s[ 1 ] );
1301         return l;
1302     }
1303
1304     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1305                                                             final boolean get_gains,
1306                                                             final String outdir,
1307                                                             final String suffix_for_filename ) throws IOException {
1308         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1309         if ( !get_gains ) {
1310             state = CharacterStateMatrix.GainLossStates.LOSS;
1311         }
1312         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1313                                                                   false,
1314                                                                   state,
1315                                                                   outdir );
1316         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1317             final PhylogenyNode node = it.next();
1318             if ( !node.isExternal() ) {
1319                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1320                 if ( domains.size() > 0 ) {
1321                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1322                             + node.getName() + suffix_for_filename );
1323                     for( final String domain : domains ) {
1324                         writer.write( domain );
1325                         writer.write( ForesterUtil.LINE_SEPARATOR );
1326                     }
1327                     writer.close();
1328                 }
1329             }
1330         }
1331     }
1332
1333     private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1334                                                         final Map<GoId, GoTerm> go_id_to_term_map,
1335                                                         final String outfile_name,
1336                                                         final SortedSet<String> all_pfams_encountered ) {
1337         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
1338         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
1339                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
1340         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
1341         int biological_process_counter = 0;
1342         int cellular_component_counter = 0;
1343         int molecular_function_counter = 0;
1344         int pfams_with_mappings_counter = 0;
1345         int pfams_without_mappings_counter = 0;
1346         int pfams_without_mappings_to_bp_or_mf_counter = 0;
1347         int pfams_with_mappings_to_bp_or_mf_counter = 0;
1348         try {
1349             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
1350             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
1351             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
1352             summary_writer.write( "# Pfam to GO mapping summary" );
1353             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1354             summary_writer.write( "# Actual summary is at the end of this file." );
1355             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1356             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
1357             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1358             for( final String pfam : all_pfams_encountered ) {
1359                 all_pfams_encountered_writer.write( pfam );
1360                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
1361                 final DomainId domain_id = new DomainId( pfam );
1362                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1363                     ++pfams_with_mappings_counter;
1364                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
1365                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
1366                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
1367                     boolean maps_to_bp = false;
1368                     boolean maps_to_cc = false;
1369                     boolean maps_to_mf = false;
1370                     for( final GoId go_id : go_ids ) {
1371                         final GoTerm go_term = go_id_to_term_map.get( go_id );
1372                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
1373                             maps_to_bp = true;
1374                         }
1375                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
1376                             maps_to_cc = true;
1377                         }
1378                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
1379                             maps_to_mf = true;
1380                         }
1381                     }
1382                     if ( maps_to_bp ) {
1383                         ++biological_process_counter;
1384                     }
1385                     if ( maps_to_cc ) {
1386                         ++cellular_component_counter;
1387                     }
1388                     if ( maps_to_mf ) {
1389                         ++molecular_function_counter;
1390                     }
1391                     if ( maps_to_bp || maps_to_mf ) {
1392                         ++pfams_with_mappings_to_bp_or_mf_counter;
1393                     }
1394                     else {
1395                         ++pfams_without_mappings_to_bp_or_mf_counter;
1396                     }
1397                 }
1398                 else {
1399                     ++pfams_without_mappings_to_bp_or_mf_counter;
1400                     ++pfams_without_mappings_counter;
1401                     summary_writer.write( pfam );
1402                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1403                 }
1404             }
1405             all_pfams_encountered_writer.close();
1406             all_pfams_encountered_with_go_annotation_writer.close();
1407             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
1408                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
1409             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
1410                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
1411                     + "\"" );
1412             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
1413                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
1414                     + encountered_pfams_summary_file + "\"" );
1415             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
1416                     + all_pfams_encountered.size() );
1417             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
1418                     + pfams_without_mappings_counter + " ["
1419                     + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1420             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
1421                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1422                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1423             ForesterUtil.programMessage( surfacing.PRG_NAME,
1424                                          "Pfams with a mapping                    : " + pfams_with_mappings_counter
1425                                                  + " ["
1426                                                  + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
1427                                                  + "%]" );
1428             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
1429                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1430                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1431             ForesterUtil.programMessage( surfacing.PRG_NAME,
1432                                          "Pfams with mapping to biological process: " + biological_process_counter
1433                                                  + " ["
1434                                                  + ( 100 * biological_process_counter / all_pfams_encountered.size() )
1435                                                  + "%]" );
1436             ForesterUtil.programMessage( surfacing.PRG_NAME,
1437                                          "Pfams with mapping to molecular function: " + molecular_function_counter
1438                                                  + " ["
1439                                                  + ( 100 * molecular_function_counter / all_pfams_encountered.size() )
1440                                                  + "%]" );
1441             ForesterUtil.programMessage( surfacing.PRG_NAME,
1442                                          "Pfams with mapping to cellular component: " + cellular_component_counter
1443                                                  + " ["
1444                                                  + ( 100 * cellular_component_counter / all_pfams_encountered.size() )
1445                                                  + "%]" );
1446             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1447             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
1448             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1449             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
1450                     + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1451             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1452             summary_writer.write( "# Pfams without mapping to proc. or func. : "
1453                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1454                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1455             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1456             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
1457                     + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1458             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1459             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
1460                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1461                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1462             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1463             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
1464                     + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
1465             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1466             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
1467                     + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
1468             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1469             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
1470                     + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
1471             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1472             summary_writer.close();
1473         }
1474         catch ( final IOException e ) {
1475             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
1476         }
1477     }
1478
1479     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1480                                                                           final File output_dir,
1481                                                                           final GenomeWideCombinableDomains gwcd,
1482                                                                           final int i,
1483                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1484         File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
1485                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1486         if ( output_dir != null ) {
1487             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1488         }
1489         checkForOutputFileWriteability( dc_outfile_dot );
1490         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1491         try {
1492             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1493             for( final BinaryDomainCombination bdc : binary_combinations ) {
1494                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1495                         .toString() );
1496                 out_dot.write( SurfacingConstants.NL );
1497             }
1498             out_dot.close();
1499         }
1500         catch ( final IOException e ) {
1501             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1502         }
1503         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1504                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1505                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1506     }
1507
1508     public static void writeBinaryStatesMatrixAsListToFile( 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 Map<String, String> descriptions ) {
1514         final File outfile = new File( filename );
1515         checkForOutputFileWriteability( outfile );
1516         final SortedSet<String> sorted_ids = new TreeSet<String>();
1517         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1518             sorted_ids.add( matrix.getIdentifier( i ) );
1519         }
1520         try {
1521             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1522             for( final String id : sorted_ids ) {
1523                 out.write( indentifier_characters_separator );
1524                 out.write( "#" + id );
1525                 out.write( indentifier_characters_separator );
1526                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1527                     // Not nice:
1528                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1529                     if ( ( matrix.getState( id, c ) == state )
1530                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1531                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1532                         out.write( matrix.getCharacter( c ) );
1533                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1534                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1535                             out.write( "\t" );
1536                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1537                         }
1538                         out.write( character_separator );
1539                     }
1540                 }
1541             }
1542             out.flush();
1543             out.close();
1544         }
1545         catch ( final IOException e ) {
1546             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1547         }
1548         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1549     }
1550
1551     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1552                                                                                                  final CharacterStateMatrix.GainLossStates state,
1553                                                                                                  final String filename,
1554                                                                                                  final String indentifier_characters_separator,
1555                                                                                                  final String character_separator,
1556                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1557         final File outfile = new File( filename );
1558         checkForOutputFileWriteability( outfile );
1559         final SortedSet<String> sorted_ids = new TreeSet<String>();
1560         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1561             sorted_ids.add( matrix.getIdentifier( i ) );
1562         }
1563         try {
1564             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1565             for( final String id : sorted_ids ) {
1566                 out.write( indentifier_characters_separator );
1567                 out.write( "#" + id );
1568                 out.write( indentifier_characters_separator );
1569                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1570                     // Not nice:
1571                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1572                     if ( ( matrix.getState( id, c ) == state )
1573                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1574                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1575                         BinaryDomainCombination bdc = null;
1576                         try {
1577                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1578                         }
1579                         catch ( final Exception e ) {
1580                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1581                         }
1582                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1583                         out.write( character_separator );
1584                     }
1585                 }
1586             }
1587             out.flush();
1588             out.close();
1589         }
1590         catch ( final IOException e ) {
1591             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1592         }
1593         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1594     }
1595
1596     public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1597                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1598                                                       final GoNameSpace go_namespace_limit,
1599                                                       final boolean domain_combinations,
1600                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1601                                                       final CharacterStateMatrix.GainLossStates state,
1602                                                       final String filename,
1603                                                       final String indentifier_characters_separator,
1604                                                       final String character_separator,
1605                                                       final String title_for_html,
1606                                                       final String prefix_for_html,
1607                                                       final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1608                                                       final SortedSet<String> all_pfams_encountered,
1609                                                       final SortedSet<String> pfams_gained_or_lost,
1610                                                       final String suffix_for_per_node_events_file ) {
1611         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1612             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1613         }
1614         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1615             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1616         }
1617         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1618             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1619         }
1620         final File outfile = new File( filename );
1621         checkForOutputFileWriteability( outfile );
1622         final SortedSet<String> sorted_ids = new TreeSet<String>();
1623         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1624             sorted_ids.add( matrix.getIdentifier( i ) );
1625         }
1626         try {
1627             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1628             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1629                                                                                                                 domain_combinations,
1630                                                                                                                 state,
1631                                                                                                                 filename );
1632             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1633             File per_node_go_mapped_domain_gain_loss_outfile = null;
1634             int per_node_counter = 0;
1635             out.write( "<html>" );
1636             out.write( SurfacingConstants.NL );
1637             addHtmlHead( out, title_for_html );
1638             out.write( SurfacingConstants.NL );
1639             out.write( "<body>" );
1640             out.write( SurfacingConstants.NL );
1641             out.write( "<h1>" );
1642             out.write( SurfacingConstants.NL );
1643             out.write( title_for_html );
1644             out.write( SurfacingConstants.NL );
1645             out.write( "</h1>" );
1646             out.write( SurfacingConstants.NL );
1647             out.write( "<table>" );
1648             out.write( SurfacingConstants.NL );
1649             for( final String id : sorted_ids ) {
1650                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1651                 if ( matcher.matches() ) {
1652                     continue;
1653                 }
1654                 out.write( "<tr>" );
1655                 out.write( "<td>" );
1656                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1657                 out.write( "</td>" );
1658                 out.write( "</tr>" );
1659                 out.write( SurfacingConstants.NL );
1660             }
1661             out.write( "</table>" );
1662             out.write( SurfacingConstants.NL );
1663             for( final String id : sorted_ids ) {
1664                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1665                 if ( matcher.matches() ) {
1666                     continue;
1667                 }
1668                 out.write( SurfacingConstants.NL );
1669                 out.write( "<h2>" );
1670                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1671                 writeTaxonomyLinks( out, id );
1672                 out.write( "</h2>" );
1673                 out.write( SurfacingConstants.NL );
1674                 out.write( "<table>" );
1675                 out.write( SurfacingConstants.NL );
1676                 out.write( "<tr>" );
1677                 out.write( "<td><b>" );
1678                 out.write( "Pfam domain(s)" );
1679                 out.write( "</b></td><td><b>" );
1680                 out.write( "GO term acc" );
1681                 out.write( "</b></td><td><b>" );
1682                 out.write( "GO term" );
1683                 out.write( "</b></td><td><b>" );
1684                 out.write( "GO namespace" );
1685                 out.write( "</b></td>" );
1686                 out.write( "</tr>" );
1687                 out.write( SurfacingConstants.NL );
1688                 out.write( "</tr>" );
1689                 out.write( SurfacingConstants.NL );
1690                 per_node_counter = 0;
1691                 if ( matrix.getNumberOfCharacters() > 0 ) {
1692                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1693                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1694                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1695                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1696                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1697                 }
1698                 else {
1699                     per_node_go_mapped_domain_gain_loss_outfile = null;
1700                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1701                 }
1702                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1703                     // Not nice:
1704                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1705                     if ( ( matrix.getState( id, c ) == state )
1706                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1707                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1708                         final String character = matrix.getCharacter( c );
1709                         String domain_0 = "";
1710                         String domain_1 = "";
1711                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1712                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1713                             if ( s.length != 2 ) {
1714                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1715                                         + character + "]" );
1716                             }
1717                             domain_0 = s[ 0 ];
1718                             domain_1 = s[ 1 ];
1719                         }
1720                         else {
1721                             domain_0 = character;
1722                         }
1723                         writeDomainData( domain_id_to_go_ids_map,
1724                                          go_id_to_term_map,
1725                                          go_namespace_limit,
1726                                          out,
1727                                          domain_0,
1728                                          domain_1,
1729                                          prefix_for_html,
1730                                          character_separator,
1731                                          domain_id_to_secondary_features_maps,
1732                                          null );
1733                         all_pfams_encountered.add( domain_0 );
1734                         if ( pfams_gained_or_lost != null ) {
1735                             pfams_gained_or_lost.add( domain_0 );
1736                         }
1737                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1738                             all_pfams_encountered.add( domain_1 );
1739                             if ( pfams_gained_or_lost != null ) {
1740                                 pfams_gained_or_lost.add( domain_1 );
1741                             }
1742                         }
1743                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1744                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1745                                                                      domain_0,
1746                                                                      domain_1 );
1747                             per_node_counter++;
1748                         }
1749                     }
1750                 }
1751                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1752                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1753                     if ( per_node_counter < 1 ) {
1754                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1755                     }
1756                     per_node_counter = 0;
1757                 }
1758                 out.write( "</table>" );
1759                 out.write( SurfacingConstants.NL );
1760                 out.write( "<hr>" );
1761                 out.write( SurfacingConstants.NL );
1762             } // for( final String id : sorted_ids ) {
1763             out.write( "</body>" );
1764             out.write( SurfacingConstants.NL );
1765             out.write( "</html>" );
1766             out.write( SurfacingConstants.NL );
1767             out.flush();
1768             out.close();
1769         }
1770         catch ( final IOException e ) {
1771             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1772         }
1773         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1774     }
1775
1776     public static void writeBinaryStatesMatrixToListORIGIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1777                                                             final Map<GoId, GoTerm> go_id_to_term_map,
1778                                                             final GoNameSpace go_namespace_limit,
1779                                                             final boolean domain_combinations,
1780                                                             final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1781                                                             final CharacterStateMatrix.GainLossStates state,
1782                                                             final String filename,
1783                                                             final String indentifier_characters_separator,
1784                                                             final String character_separator,
1785                                                             final String title_for_html,
1786                                                             final String prefix_for_html,
1787                                                             final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1788                                                             final SortedSet<String> all_pfams_encountered,
1789                                                             final SortedSet<String> pfams_gained_or_lost,
1790                                                             final String suffix_for_per_node_events_file ) {
1791         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1792             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1793         }
1794         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1795             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1796         }
1797         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1798             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1799         }
1800         final File outfile = new File( filename );
1801         checkForOutputFileWriteability( outfile );
1802         final SortedSet<String> sorted_ids = new TreeSet<String>();
1803         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1804             sorted_ids.add( matrix.getIdentifier( i ) );
1805         }
1806         try {
1807             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1808             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1809                                                                                                                 domain_combinations,
1810                                                                                                                 state,
1811                                                                                                                 filename );
1812             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1813             File per_node_go_mapped_domain_gain_loss_outfile = null;
1814             int per_node_counter = 0;
1815             out.write( "<html>" );
1816             out.write( SurfacingConstants.NL );
1817             addHtmlHead( out, title_for_html );
1818             out.write( SurfacingConstants.NL );
1819             out.write( "<body>" );
1820             out.write( SurfacingConstants.NL );
1821             out.write( "<h1>" );
1822             out.write( SurfacingConstants.NL );
1823             out.write( title_for_html );
1824             out.write( SurfacingConstants.NL );
1825             out.write( "</h1>" );
1826             out.write( SurfacingConstants.NL );
1827             out.write( "<table>" );
1828             out.write( SurfacingConstants.NL );
1829             for( final String id : sorted_ids ) {
1830                 out.write( "<tr>" );
1831                 out.write( "<td>" );
1832                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1833                 writeTaxonomyLinks( out, id );
1834                 out.write( "</td>" );
1835                 out.write( "</tr>" );
1836                 out.write( SurfacingConstants.NL );
1837             }
1838             out.write( "</table>" );
1839             out.write( SurfacingConstants.NL );
1840             for( final String id : sorted_ids ) {
1841                 out.write( SurfacingConstants.NL );
1842                 out.write( "<h2>" );
1843                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1844                 writeTaxonomyLinks( out, id );
1845                 out.write( "</h2>" );
1846                 out.write( SurfacingConstants.NL );
1847                 out.write( "<table>" );
1848                 out.write( SurfacingConstants.NL );
1849                 out.write( "<tr>" );
1850                 out.write( "<td><b>" );
1851                 out.write( "Pfam domain(s)" );
1852                 out.write( "</b></td><td><b>" );
1853                 out.write( "GO term acc" );
1854                 out.write( "</b></td><td><b>" );
1855                 out.write( "GO term" );
1856                 out.write( "</b></td><td><b>" );
1857                 out.write( "Penultimate GO term" );
1858                 out.write( "</b></td><td><b>" );
1859                 out.write( "GO namespace" );
1860                 out.write( "</b></td>" );
1861                 out.write( "</tr>" );
1862                 out.write( SurfacingConstants.NL );
1863                 out.write( "</tr>" );
1864                 out.write( SurfacingConstants.NL );
1865                 per_node_counter = 0;
1866                 if ( matrix.getNumberOfCharacters() > 0 ) {
1867                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1868                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1869                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1870                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1871                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1872                 }
1873                 else {
1874                     per_node_go_mapped_domain_gain_loss_outfile = null;
1875                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1876                 }
1877                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1878                     // Not nice:
1879                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1880                     if ( ( matrix.getState( id, c ) == state )
1881                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1882                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1883                         final String character = matrix.getCharacter( c );
1884                         String domain_0 = "";
1885                         String domain_1 = "";
1886                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1887                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1888                             if ( s.length != 2 ) {
1889                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1890                                         + character + "]" );
1891                             }
1892                             domain_0 = s[ 0 ];
1893                             domain_1 = s[ 1 ];
1894                         }
1895                         else {
1896                             domain_0 = character;
1897                         }
1898                         writeDomainData( domain_id_to_go_ids_map,
1899                                          go_id_to_term_map,
1900                                          go_namespace_limit,
1901                                          out,
1902                                          domain_0,
1903                                          domain_1,
1904                                          prefix_for_html,
1905                                          character_separator,
1906                                          domain_id_to_secondary_features_maps,
1907                                          null );
1908                         all_pfams_encountered.add( domain_0 );
1909                         if ( pfams_gained_or_lost != null ) {
1910                             pfams_gained_or_lost.add( domain_0 );
1911                         }
1912                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1913                             all_pfams_encountered.add( domain_1 );
1914                             if ( pfams_gained_or_lost != null ) {
1915                                 pfams_gained_or_lost.add( domain_1 );
1916                             }
1917                         }
1918                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1919                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1920                                                                      domain_0,
1921                                                                      domain_1 );
1922                             per_node_counter++;
1923                         }
1924                     }
1925                 }
1926                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1927                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1928                     if ( per_node_counter < 1 ) {
1929                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1930                     }
1931                     per_node_counter = 0;
1932                 }
1933                 out.write( "</table>" );
1934                 out.write( SurfacingConstants.NL );
1935                 out.write( "<hr>" );
1936                 out.write( SurfacingConstants.NL );
1937             } // for( final String id : sorted_ids ) {
1938             out.write( "</body>" );
1939             out.write( SurfacingConstants.NL );
1940             out.write( "</html>" );
1941             out.write( SurfacingConstants.NL );
1942             out.flush();
1943             out.close();
1944         }
1945         catch ( final IOException e ) {
1946             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1947         }
1948         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1949     }
1950
1951     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1952                                                           final File output_dir,
1953                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1954                                                           final GenomeWideCombinableDomains gwcd,
1955                                                           final int i,
1956                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1957         File dc_outfile = new File( input_file_properties[ i ][ 0 ]
1958                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1959         if ( output_dir != null ) {
1960             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1961         }
1962         checkForOutputFileWriteability( dc_outfile );
1963         try {
1964             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1965             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1966             out.close();
1967         }
1968         catch ( final IOException e ) {
1969             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1970         }
1971         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1972         try {
1973             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
1974             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1975             if ( stats.getN() < 2 ) {
1976                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1977             }
1978             else {
1979                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1980                         .sampleStandardDeviation() ) + "\t" );
1981             }
1982             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1983             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1984             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1985             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1986             final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
1987             for( final DomainId mpd : mpds ) {
1988                 per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
1989             }
1990             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1991         }
1992         catch ( final IOException e ) {
1993             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1994         }
1995         if ( input_file_properties[ i ].length == 3 ) {
1996             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1997                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1998                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1999         }
2000         else {
2001             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2002                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
2003                     + dc_outfile + "\"" );
2004         }
2005     }
2006
2007     private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
2008                                          final Map<GoId, GoTerm> go_id_to_term_map,
2009                                          final GoNameSpace go_namespace_limit,
2010                                          final Writer out,
2011                                          final String domain_0,
2012                                          final String domain_1,
2013                                          final String prefix_for_html,
2014                                          final String character_separator_for_non_html_output,
2015                                          final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
2016                                          final Set<GoId> all_go_ids ) throws IOException {
2017         boolean any_go_annotation_present = false;
2018         boolean first_has_no_go = false;
2019         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2020         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2021             domain_count = 1;
2022         }
2023         // The following has a difficult to understand logic.
2024         for( int d = 0; d < domain_count; ++d ) {
2025             List<GoId> go_ids = null;
2026             boolean go_annotation_present = false;
2027             if ( d == 0 ) {
2028                 final DomainId domain_id = new DomainId( domain_0 );
2029                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2030                     go_annotation_present = true;
2031                     any_go_annotation_present = true;
2032                     go_ids = domain_id_to_go_ids_map.get( domain_id );
2033                 }
2034                 else {
2035                     first_has_no_go = true;
2036                 }
2037             }
2038             else {
2039                 final DomainId domain_id = new DomainId( domain_1 );
2040                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2041                     go_annotation_present = true;
2042                     any_go_annotation_present = true;
2043                     go_ids = domain_id_to_go_ids_map.get( domain_id );
2044                 }
2045             }
2046             if ( go_annotation_present ) {
2047                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2048                 for( final GoId go_id : go_ids ) {
2049                     out.write( "<tr>" );
2050                     if ( first ) {
2051                         first = false;
2052                         writeDomainIdsToHtml( out,
2053                                               domain_0,
2054                                               domain_1,
2055                                               prefix_for_html,
2056                                               domain_id_to_secondary_features_maps );
2057                     }
2058                     else {
2059                         out.write( "<td></td>" );
2060                     }
2061                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2062                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2063                     }
2064                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2065                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2066                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2067                         final String go_id_str = go_id.getId();
2068                         out.write( "<td>" );
2069                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2070                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2071                         out.write( "</td><td>" );
2072                         out.write( go_term.getName() );
2073                         if ( domain_count == 2 ) {
2074                             out.write( " (" + d + ")" );
2075                         }
2076                         out.write( "</td><td>" );
2077                         // out.write( top );
2078                         // out.write( "</td><td>" );
2079                         out.write( "[" );
2080                         out.write( go_term.getGoNameSpace().toShortString() );
2081                         out.write( "]" );
2082                         out.write( "</td>" );
2083                         if ( all_go_ids != null ) {
2084                             all_go_ids.add( go_id );
2085                         }
2086                     }
2087                     else {
2088                         out.write( "<td>" );
2089                         out.write( "</td><td>" );
2090                         out.write( "</td><td>" );
2091                         out.write( "</td><td>" );
2092                         out.write( "</td>" );
2093                     }
2094                     out.write( "</tr>" );
2095                     out.write( SurfacingConstants.NL );
2096                 }
2097             }
2098         } //  for( int d = 0; d < domain_count; ++d )
2099         if ( !any_go_annotation_present ) {
2100             out.write( "<tr>" );
2101             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2102             out.write( "<td>" );
2103             out.write( "</td><td>" );
2104             out.write( "</td><td>" );
2105             out.write( "</td><td>" );
2106             out.write( "</td>" );
2107             out.write( "</tr>" );
2108             out.write( SurfacingConstants.NL );
2109         }
2110     }
2111
2112     private static void writeDomainIdsToHtml( final Writer out,
2113                                               final String domain_0,
2114                                               final String domain_1,
2115                                               final String prefix_for_detailed_html,
2116                                               final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
2117             throws IOException {
2118         out.write( "<td>" );
2119         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2120             out.write( prefix_for_detailed_html );
2121             out.write( " " );
2122         }
2123         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2124         out.write( "</td>" );
2125     }
2126
2127     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2128                                                                        final StringBuilder html_title,
2129                                                                        final Writer single_writer,
2130                                                                        Map<Character, Writer> split_writers,
2131                                                                        final SortedSet<DomainSimilarity> similarities,
2132                                                                        final boolean treat_as_binary,
2133                                                                        final List<Species> species_order,
2134                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
2135                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
2136                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
2137                                                                        final boolean verbose ) throws IOException {
2138         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2139         String histogram_title = null;
2140         switch ( sort_field ) {
2141             case ABS_MAX_COUNTS_DIFFERENCE:
2142                 if ( treat_as_binary ) {
2143                     histogram_title = "absolute counts difference:";
2144                 }
2145                 else {
2146                     histogram_title = "absolute (maximal) counts difference:";
2147                 }
2148                 break;
2149             case MAX_COUNTS_DIFFERENCE:
2150                 if ( treat_as_binary ) {
2151                     histogram_title = "counts difference:";
2152                 }
2153                 else {
2154                     histogram_title = "(maximal) counts difference:";
2155                 }
2156                 break;
2157             case DOMAIN_ID:
2158                 histogram_title = "score mean:";
2159                 break;
2160             case MIN:
2161                 histogram_title = "score minimum:";
2162                 break;
2163             case MAX:
2164                 histogram_title = "score maximum:";
2165                 break;
2166             case MAX_DIFFERENCE:
2167                 if ( treat_as_binary ) {
2168                     histogram_title = "difference:";
2169                 }
2170                 else {
2171                     histogram_title = "(maximal) difference:";
2172                 }
2173                 break;
2174             case MEAN:
2175                 histogram_title = "score mean:";
2176                 break;
2177             case SD:
2178                 histogram_title = "score standard deviation:";
2179                 break;
2180             case SPECIES_COUNT:
2181                 histogram_title = "species number:";
2182                 break;
2183             default:
2184                 throw new AssertionError( "Unknown sort field: " + sort_field );
2185         }
2186         for( final DomainSimilarity similarity : similarities ) {
2187             switch ( sort_field ) {
2188                 case ABS_MAX_COUNTS_DIFFERENCE:
2189                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
2190                     break;
2191                 case MAX_COUNTS_DIFFERENCE:
2192                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
2193                     break;
2194                 case DOMAIN_ID:
2195                     stats.addValue( similarity.getMeanSimilarityScore() );
2196                     break;
2197                 case MIN:
2198                     stats.addValue( similarity.getMinimalSimilarityScore() );
2199                     break;
2200                 case MAX:
2201                     stats.addValue( similarity.getMaximalSimilarityScore() );
2202                     break;
2203                 case MAX_DIFFERENCE:
2204                     stats.addValue( similarity.getMaximalDifference() );
2205                     break;
2206                 case MEAN:
2207                     stats.addValue( similarity.getMeanSimilarityScore() );
2208                     break;
2209                 case SD:
2210                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
2211                     break;
2212                 case SPECIES_COUNT:
2213                     stats.addValue( similarity.getSpecies().size() );
2214                     break;
2215                 default:
2216                     throw new AssertionError( "Unknown sort field: " + sort_field );
2217             }
2218         }
2219         //
2220         // final HistogramData[] hists = new HistogramData[ 1 ];
2221         //
2222         //
2223         // List<HistogramDataItem> data_items = new
2224         // ArrayList<HistogramDataItem>();
2225         // double[] values = stats.getDataAsDoubleArray();
2226         // for( int i = 0; i < values.length; i++ ) {
2227         // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
2228         // i ] );
2229         // data_items.add( data_item );
2230         // }
2231         //
2232         //
2233         // HistogramData hd0 = new HistogramData( "name",
2234         // data_items,
2235         // null, 20,
2236         // 40 );
2237         //
2238         //
2239         //
2240         //
2241         // hists[ 0 ] = hd0;
2242         //
2243         // final HistogramsFrame hf = new HistogramsFrame( hists );
2244         // hf.setVisible( true );
2245         //
2246         AsciiHistogram histo = null;
2247         if ( stats.getMin() < stats.getMin() ) {
2248             histo = new AsciiHistogram( stats, histogram_title );
2249         }
2250         if ( verbose ) {
2251             if ( histo != null ) {
2252                 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
2253             }
2254             System.out.println();
2255             System.out.println( "N                   : " + stats.getN() );
2256             System.out.println( "Min                 : " + stats.getMin() );
2257             System.out.println( "Max                 : " + stats.getMax() );
2258             System.out.println( "Mean                : " + stats.arithmeticMean() );
2259             if ( stats.getN() > 1 ) {
2260                 System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
2261             }
2262             else {
2263                 System.out.println( "SD                  : n/a" );
2264             }
2265             System.out.println( "Median              : " + stats.median() );
2266             if ( stats.getN() > 1 ) {
2267                 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
2268             }
2269             else {
2270                 System.out.println( "Pearsonian skewness : n/a" );
2271             }
2272         }
2273         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2274             split_writers = new HashMap<Character, Writer>();
2275             split_writers.put( '_', single_writer );
2276         }
2277         switch ( print_option ) {
2278             case SIMPLE_TAB_DELIMITED:
2279                 break;
2280             case HTML:
2281                 for( final Character key : split_writers.keySet() ) {
2282                     final Writer w = split_writers.get( key );
2283                     w.write( "<html>" );
2284                     w.write( SurfacingConstants.NL );
2285                     if ( key != '_' ) {
2286                         addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
2287                     }
2288                     else {
2289                         addHtmlHead( w, "DCs (" + html_title + ")" );
2290                     }
2291                     w.write( SurfacingConstants.NL );
2292                     w.write( "<body>" );
2293                     w.write( SurfacingConstants.NL );
2294                     w.write( html_desc.toString() );
2295                     w.write( SurfacingConstants.NL );
2296                     w.write( "<hr>" );
2297                     w.write( "<br>" );
2298                     w.write( SurfacingConstants.NL );
2299                     w.write( "<tt><pre>" );
2300                     w.write( SurfacingConstants.NL );
2301                     if ( histo != null ) {
2302                         w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2303                         w.write( SurfacingConstants.NL );
2304                     }
2305                     w.write( "</pre></tt>" );
2306                     w.write( SurfacingConstants.NL );
2307                     w.write( "<table>" );
2308                     w.write( SurfacingConstants.NL );
2309                     w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2310                     w.write( SurfacingConstants.NL );
2311                     w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2312                     w.write( SurfacingConstants.NL );
2313                     w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2314                     w.write( SurfacingConstants.NL );
2315                     w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2316                     w.write( SurfacingConstants.NL );
2317                     if ( stats.getN() > 1 ) {
2318                         w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2319                     }
2320                     else {
2321                         w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2322                     }
2323                     w.write( SurfacingConstants.NL );
2324                     w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
2325                     w.write( SurfacingConstants.NL );
2326                     if ( stats.getN() > 1 ) {
2327                         w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
2328                     }
2329                     else {
2330                         w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
2331                     }
2332                     w.write( SurfacingConstants.NL );
2333                     w.write( "</table>" );
2334                     w.write( SurfacingConstants.NL );
2335                     w.write( "<br>" );
2336                     w.write( SurfacingConstants.NL );
2337                     w.write( "<hr>" );
2338                     w.write( SurfacingConstants.NL );
2339                     w.write( "<br>" );
2340                     w.write( SurfacingConstants.NL );
2341                     w.write( "<table>" );
2342                     w.write( SurfacingConstants.NL );
2343                 }
2344                 break;
2345         }
2346         for( final Writer w : split_writers.values() ) {
2347             w.write( SurfacingConstants.NL );
2348         }
2349         for( final DomainSimilarity similarity : similarities ) {
2350             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2351                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2352             }
2353             if ( single_writer != null ) {
2354                 single_writer.write( similarity.toStringBuffer( print_option ).toString() );
2355             }
2356             else {
2357                 Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
2358                         .toLowerCase().charAt( 0 ) );
2359                 if ( local_writer == null ) {
2360                     local_writer = split_writers.get( '0' );
2361                 }
2362                 local_writer.write( similarity.toStringBuffer( print_option ).toString() );
2363             }
2364             for( final Writer w : split_writers.values() ) {
2365                 w.write( SurfacingConstants.NL );
2366             }
2367         }
2368         switch ( print_option ) {
2369             case HTML:
2370                 for( final Writer w : split_writers.values() ) {
2371                     w.write( SurfacingConstants.NL );
2372                     w.write( "</table>" );
2373                     w.write( SurfacingConstants.NL );
2374                     w.write( "</font>" );
2375                     w.write( SurfacingConstants.NL );
2376                     w.write( "</body>" );
2377                     w.write( SurfacingConstants.NL );
2378                     w.write( "</html>" );
2379                     w.write( SurfacingConstants.NL );
2380                 }
2381                 break;
2382         }
2383         for( final Writer w : split_writers.values() ) {
2384             w.close();
2385         }
2386         return stats;
2387     }
2388
2389     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2390                                                                  final String domain_0,
2391                                                                  final String domain_1 ) throws IOException {
2392         individual_files_writer.write( domain_0 );
2393         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2394         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2395             individual_files_writer.write( domain_1 );
2396             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2397         }
2398     }
2399
2400     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2401                                           final String filename,
2402                                           final Format format ) {
2403         final File outfile = new File( filename );
2404         checkForOutputFileWriteability( outfile );
2405         try {
2406             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2407             matrix.toWriter( out, format );
2408             out.flush();
2409             out.close();
2410         }
2411         catch ( final IOException e ) {
2412             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2413         }
2414         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2415     }
2416
2417     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2418         checkForOutputFileWriteability( matrix_outfile );
2419         try {
2420             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2421             for( final DistanceMatrix distance_matrix : matrices ) {
2422                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2423                 out.write( ForesterUtil.LINE_SEPARATOR );
2424                 out.flush();
2425             }
2426             out.close();
2427         }
2428         catch ( final IOException e ) {
2429             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2430         }
2431         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2432     }
2433
2434     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2435         try {
2436             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2437             for( final String pfam : pfams ) {
2438                 writer.write( pfam );
2439                 writer.write( ForesterUtil.LINE_SEPARATOR );
2440             }
2441             writer.close();
2442             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2443                     + "]" );
2444         }
2445         catch ( final IOException e ) {
2446             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2447         }
2448     }
2449
2450     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2451         final PhylogenyWriter writer = new PhylogenyWriter();
2452         try {
2453             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2454         }
2455         catch ( final IOException e ) {
2456             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2457                     + e );
2458         }
2459         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2460     }
2461
2462     public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
2463         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2464             final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2465             writer.write( " [" );
2466             if ( matcher.matches() ) {
2467                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2468                         + "\" target=\"taxonomy_window\">uniprot</a>" );
2469             }
2470             else {
2471                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2472                         + "\" target=\"taxonomy_window\">eol</a>" );
2473                 writer.write( "|" );
2474                 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2475                         + "\" target=\"taxonomy_window\">tol</a>" );
2476             }
2477             writer.write( "]" );
2478         }
2479     }
2480
2481     private static void writeToNexus( final String outfile_name,
2482                                       final CharacterStateMatrix<BinaryStates> matrix,
2483                                       final Phylogeny phylogeny ) {
2484         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2485             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2486                     + "] to nexus" );
2487         }
2488         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2489         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2490         phylogenies.add( phylogeny );
2491         try {
2492             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2493             w.write( NexusConstants.NEXUS );
2494             w.write( ForesterUtil.LINE_SEPARATOR );
2495             my_matrix.writeNexusTaxaBlock( w );
2496             my_matrix.writeNexusBinaryChractersBlock( w );
2497             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2498             w.flush();
2499             w.close();
2500             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2501         }
2502         catch ( final IOException e ) {
2503             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2504         }
2505     }
2506
2507     private static void writeToNexus( final String outfile_name,
2508                                       final DomainParsimonyCalculator domain_parsimony,
2509                                       final Phylogeny phylogeny ) {
2510         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2511                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2512                       phylogeny );
2513         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2514                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2515                       phylogeny );
2516     }
2517
2518     public static void domainsPerProteinsStatistics( final String genome,
2519                                                      final List<Protein> protein_list,
2520                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
2521                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2522                                                      final SortedSet<String> domains_which_are_always_single,
2523                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
2524                                                      final SortedSet<String> domains_which_never_single,
2525                                                      final Writer writer ) {
2526         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2527         for( final Protein protein : protein_list ) {
2528             final int domains = protein.getNumberOfProteinDomains();
2529             //System.out.println( domains );
2530             stats.addValue( domains );
2531             all_genomes_domains_per_potein_stats.addValue( domains );
2532             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
2533                 all_genomes_domains_per_potein_histo.put( domains, 1 );
2534             }
2535             else {
2536                 all_genomes_domains_per_potein_histo.put( domains,
2537                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
2538             }
2539             if ( domains == 1 ) {
2540                 final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
2541                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2542                     if ( domains_which_never_single.contains( domain ) ) {
2543                         domains_which_never_single.remove( domain );
2544                         domains_which_are_sometimes_single_sometimes_not.add( domain );
2545                     }
2546                     else {
2547                         domains_which_are_always_single.add( domain );
2548                     }
2549                 }
2550             }
2551             else if ( domains > 1 ) {
2552                 for( final Domain d : protein.getProteinDomains() ) {
2553                     final String domain = d.getDomainId().getId();
2554                     // System.out.println( domain );
2555                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2556                         if ( domains_which_are_always_single.contains( domain ) ) {
2557                             domains_which_are_always_single.remove( domain );
2558                             domains_which_are_sometimes_single_sometimes_not.add( domain );
2559                         }
2560                         else {
2561                             domains_which_never_single.add( domain );
2562                         }
2563                     }
2564                 }
2565             }
2566         }
2567         try {
2568             writer.write( genome );
2569             writer.write( "\t" );
2570             if ( stats.getN() >= 1 ) {
2571                 writer.write( stats.arithmeticMean() + "" );
2572                 writer.write( "\t" );
2573                 if ( stats.getN() >= 2 ) {
2574                     writer.write( stats.sampleStandardDeviation() + "" );
2575                 }
2576                 else {
2577                     writer.write( "" );
2578                 }
2579                 writer.write( "\t" );
2580                 writer.write( stats.median() + "" );
2581                 writer.write( "\t" );
2582                 writer.write( stats.getN() + "" );
2583                 writer.write( "\t" );
2584                 writer.write( stats.getMin() + "" );
2585                 writer.write( "\t" );
2586                 writer.write( stats.getMax() + "" );
2587             }
2588             else {
2589                 writer.write( "\t" );
2590                 writer.write( "\t" );
2591                 writer.write( "\t" );
2592                 writer.write( "0" );
2593                 writer.write( "\t" );
2594                 writer.write( "\t" );
2595             }
2596             writer.write( "\n" );
2597         }
2598         catch ( final IOException e ) {
2599             e.printStackTrace();
2600         }
2601     }
2602 }