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.BasicDomain;
  76 import org.forester.protein.BasicProtein;
  77 import org.forester.protein.BinaryDomainCombination;
  78 import org.forester.protein.Domain;
  79 import org.forester.protein.DomainId;
  80 import org.forester.protein.Protein;
  81 import org.forester.species.Species;
  82 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  83 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  84 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  85 import org.forester.util.AsciiHistogram;
  86 import org.forester.util.BasicDescriptiveStatistics;
  87 import org.forester.util.BasicTable;
  88 import org.forester.util.BasicTableParser;
  89 import org.forester.util.DescriptiveStatistics;
  90 import org.forester.util.ForesterUtil;
  91
  92 public final class SurfacingUtil {
  93
  94     private final static NumberFormat       FORMATTER                        = new DecimalFormat( "0.0E0" );
  95     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  96     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  97
  98                                                                                  @Override
  99                                                                                  public int compare( final Domain d1,
 100                                                                                                      final Domain d2 ) {
 101                                                                                      if ( d1.getPerSequenceEvalue() < d2
 102                                                                                              .getPerSequenceEvalue() ) {
 103                                                                                          return -1;
 104                                                                                      }
 105                                                                                      else if ( d1
 106                                                                                              .getPerSequenceEvalue() > d2
 107                                                                                              .getPerSequenceEvalue() ) {
 108                                                                                          return 1;
 109                                                                                      }
 110                                                                                      else {
 111                                                                                          return d1.compareTo( d2 );
 112                                                                                      }
 113                                                                                  }
 114                                                                              };
 115     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 116     private static final boolean            USE_LAST                         = true;
 117
 118     private SurfacingUtil() {
 119         // Hidden constructor.
 120     }
 121
 122     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 123                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 124         final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 125         for( final DomainId domain_id : all_cd.keySet() ) {
 126             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 127         }
 128     }
 129
 130     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 131                                              final SortedSet<DomainId> domain_ids ) {
 132         final SortedSet<DomainId> domains = genome.getAllDomainIds();
 133         for( final DomainId domain : domains ) {
 134             domain_ids.add( domain );
 135         }
 136     }
 137
 138     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 139         w.write( SurfacingConstants.NL );
 140         w.write( "<head>" );
 141         w.write( "<title>" );
 142         w.write( title );
 143         w.write( "</title>" );
 144         w.write( SurfacingConstants.NL );
 145         w.write( "<style>" );
 146         w.write( SurfacingConstants.NL );
 147         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 148         w.write( SurfacingConstants.NL );
 149         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 150         w.write( SurfacingConstants.NL );
 151         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 152         w.write( SurfacingConstants.NL );
 153         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 154         w.write( SurfacingConstants.NL );
 155         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 156         w.write( SurfacingConstants.NL );
 157         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 158         w.write( SurfacingConstants.NL );
 159         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 160         w.write( SurfacingConstants.NL );
 161         w.write( "</style>" );
 162         w.write( SurfacingConstants.NL );
 163         w.write( "</head>" );
 164         w.write( SurfacingConstants.NL );
 165     }
 166
 167     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 168         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 169         for( final DomainSimilarity similarity : similarities ) {
 170             stats.addValue( similarity.getMeanSimilarityScore() );
 171         }
 172         return stats;
 173     }
 174
 175     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
 176                                                                     final String outfilename_for_counts,
 177                                                                     final String outfilename_for_dc,
 178                                                                     final String outfilename_for_dc_for_go_mapping,
 179                                                                     final String outfilename_for_dc_for_go_mapping_unique,
 180                                                                     final String outfilename_for_rank_counts,
 181                                                                     final String outfilename_for_ancestor_species_counts,
 182                                                                     final String outfilename_for_protein_stats,
 183                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 184                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 185                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
 186         try {
 187             //
 188             //            if ( protein_length_stats_by_dc != null ) {
 189             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
 190             //                    System.out.print( entry.getKey().toString() );
 191             //                    System.out.print( ": " );
 192             //                    double[] a = entry.getValue().getDataAsDoubleArray();
 193             //                    for( int i = 0; i < a.length; i++ ) {
 194             //                        System.out.print( a[ i ] + " " );
 195             //                    }
 196             //                    System.out.println();
 197             //                }
 198             //            }
 199             //            if ( domain_number_stats_by_dc != null ) {
 200             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
 201             //                    System.out.print( entry.getKey().toString() );
 202             //                    System.out.print( ": " );
 203             //                    double[] a = entry.getValue().getDataAsDoubleArray();
 204             //                    for( int i = 0; i < a.length; i++ ) {
 205             //                        System.out.print( a[ i ] + " " );
 206             //                    }
 207             //                    System.out.println();
 208             //                }
 209             //            }
 210             //
 211             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
 212             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
 213             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
 214             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
 215             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
 216             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
 217                 final PhylogenyNode n = it.next();
 218                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
 219                 for( final String dc : gained_dc ) {
 220                     if ( dc_gain_counts.containsKey( dc ) ) {
 221                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
 222                     }
 223                     else {
 224                         dc_gain_counts.put( dc, 1 );
 225                     }
 226                 }
 227             }
 228             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
 229             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
 230             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
 231             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
 232             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
 233             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
 234             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
 235             final Set<String> dcs = dc_gain_counts.keySet();
 236             final SortedSet<String> more_than_once = new TreeSet<String>();
 237             final DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
 238             final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
 239             final DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
 240             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
 241             final DescriptiveStatistics gained_multiple_times_domain_length_stats = new BasicDescriptiveStatistics();
 242             final DescriptiveStatistics gained_once_domain_length_stats = new BasicDescriptiveStatistics();
 243             for( final String dc : dcs ) {
 244                 final int count = dc_gain_counts.get( dc );
 245                 if ( histogram.containsKey( count ) ) {
 246                     histogram.put( count, histogram.get( count ) + 1 );
 247                     domain_lists.get( count ).append( ", " + dc );
 248                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
 249                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
 250                 }
 251                 else {
 252                     histogram.put( count, 1 );
 253                     domain_lists.put( count, new StringBuilder( dc ) );
 254                     final PriorityQueue<String> q = new PriorityQueue<String>();
 255                     q.addAll( splitDomainCombination( dc ) );
 256                     domain_lists_go.put( count, q );
 257                     final SortedSet<String> set = new TreeSet<String>();
 258                     set.addAll( splitDomainCombination( dc ) );
 259                     domain_lists_go_unique.put( count, set );
 260                 }
 261                 if ( protein_length_stats_by_dc != null ) {
 262                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
 263                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
 264                     }
 265                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
 266                             .arithmeticMean() );
 267                 }
 268                 if ( domain_number_stats_by_dc != null ) {
 269                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
 270                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
 271                     }
 272                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
 273                             .arithmeticMean() );
 274                 }
 275                 if ( domain_length_stats_by_domain != null ) {
 276                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
 277                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
 278                     }
 279                     final String[] ds = dc.split( "=" );
 280                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
 281                             .get( ds[ 0 ] ).arithmeticMean() );
 282                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
 283                             .get( ds[ 1 ] ).arithmeticMean() );
 284                 }
 285                 if ( count > 1 ) {
 286                     more_than_once.add( dc );
 287                     if ( protein_length_stats_by_dc != null ) {
 288                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
 289                         final double[] a = s.getDataAsDoubleArray();
 290                         for( final double element : a ) {
 291                             gained_multiple_times_lengths_stats.addValue( element );
 292                         }
 293                     }
 294                     if ( domain_number_stats_by_dc != null ) {
 295                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
 296                         final double[] a = s.getDataAsDoubleArray();
 297                         for( final double element : a ) {
 298                             gained_multiple_times_domain_count_stats.addValue( element );
 299                         }
 300                     }
 301                     if ( domain_length_stats_by_domain != null ) {
 302                         final String[] ds = dc.split( "=" );
 303                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
 304                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
 305                         final double[] a0 = s0.getDataAsDoubleArray();
 306                         final double[] a1 = s1.getDataAsDoubleArray();
 307                         for( final double element : a0 ) {
 308                             gained_multiple_times_domain_length_stats.addValue( element );
 309                         }
 310                         for( final double element : a1 ) {
 311                             gained_multiple_times_domain_length_stats.addValue( element );
 312                         }
 313                     }
 314                 }
 315                 else {
 316                     if ( protein_length_stats_by_dc != null ) {
 317                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
 318                         final double[] a = s.getDataAsDoubleArray();
 319                         for( final double element : a ) {
 320                             gained_once_lengths_stats.addValue( element );
 321                         }
 322                     }
 323                     if ( domain_number_stats_by_dc != null ) {
 324                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
 325                         final double[] a = s.getDataAsDoubleArray();
 326                         for( final double element : a ) {
 327                             gained_once_domain_count_stats.addValue( element );
 328                         }
 329                     }
 330                     if ( domain_length_stats_by_domain != null ) {
 331                         final String[] ds = dc.split( "=" );
 332                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
 333                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
 334                         final double[] a0 = s0.getDataAsDoubleArray();
 335                         final double[] a1 = s1.getDataAsDoubleArray();
 336                         for( final double element : a0 ) {
 337                             gained_once_domain_length_stats.addValue( element );
 338                         }
 339                         for( final double element : a1 ) {
 340                             gained_once_domain_length_stats.addValue( element );
 341                         }
 342                     }
 343                 }
 344             }
 345             final Set<Integer> histogram_keys = histogram.keySet();
 346             for( final Integer histogram_key : histogram_keys ) {
 347                 final int count = histogram.get( histogram_key );
 348                 final StringBuilder dc = domain_lists.get( histogram_key );
 349                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 350                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
 351                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 352                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
 353                 Arrays.sort( sorted );
 354                 for( final Object domain : sorted ) {
 355                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
 356                 }
 357                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 358                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
 359                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
 360                 }
 361             }
 362             out_counts.close();
 363             out_dc.close();
 364             out_dc_for_go_mapping.close();
 365             out_dc_for_go_mapping_unique.close();
 366             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
 367             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
 368             for( final String dc : more_than_once ) {
 369                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
 370                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
 371                     final PhylogenyNode n = it.next();
 372                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
 373                         nodes.add( n );
 374                     }
 375                 }
 376                 for( int i = 0; i < nodes.size() - 1; ++i ) {
 377                     for( int j = i + 1; j < nodes.size(); ++j ) {
 378                         final PhylogenyNode lca = PhylogenyMethods.getInstance().obtainLCA( nodes.get( i ),
 379                                                                                             nodes.get( j ) );
 380                         String rank = "unknown";
 381                         if ( lca.getNodeData().isHasTaxonomy()
 382                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
 383                             rank = lca.getNodeData().getTaxonomy().getRank();
 384                         }
 385                         addToCountMap( lca_rank_counts, rank );
 386                         String lca_species;
 387                         if ( lca.getNodeData().isHasTaxonomy()
 388                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
 389                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
 390                         }
 391                         else if ( lca.getNodeData().isHasTaxonomy()
 392                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
 393                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
 394                         }
 395                         else {
 396                             lca_species = lca.getName();
 397                         }
 398                         addToCountMap( lca_ancestor_species_counts, lca_species );
 399                     }
 400                 }
 401             }
 402             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
 403             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
 404             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
 405             ForesterUtil.map2writer( out_for_ancestor_species_counts,
 406                                      lca_ancestor_species_counts,
 407                                      "\t",
 408                                      ForesterUtil.LINE_SEPARATOR );
 409             out_for_rank_counts.close();
 410             out_for_ancestor_species_counts.close();
 411             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
 412                     && ( ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
 413                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
 414                 w.write( "Domain Lengths: " );
 415                 w.write( "\n" );
 416                 if ( domain_length_stats_by_domain != null ) {
 417                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
 418                             .entrySet() ) {
 419                         w.write( entry.getKey().toString() );
 420                         w.write( "\t" + entry.getValue().arithmeticMean() );
 421                         w.write( "\t" + entry.getValue().median() );
 422                         w.write( "\n" );
 423                     }
 424                 }
 425                 w.flush();
 426                 w.write( "\n" );
 427                 w.write( "\n" );
 428                 w.write( "Protein Lengths: " );
 429                 w.write( "\n" );
 430                 if ( protein_length_stats_by_dc != null ) {
 431                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
 432                             .entrySet() ) {
 433                         w.write( entry.getKey().toString() );
 434                         w.write( "\t" + entry.getValue().arithmeticMean() );
 435                         w.write( "\t" + entry.getValue().median() );
 436                         w.write( "\n" );
 437                     }
 438                 }
 439                 w.flush();
 440                 w.write( "\n" );
 441                 w.write( "\n" );
 442                 w.write( "Number of domains: " );
 443                 w.write( "\n" );
 444                 if ( domain_number_stats_by_dc != null ) {
 445                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
 446                             .entrySet() ) {
 447                         w.write( entry.getKey().toString() );
 448                         w.write( "\t" + entry.getValue().arithmeticMean() );
 449                         w.write( "\t" + entry.getValue().median() );
 450                         w.write( "\n" );
 451                     }
 452                 }
 453                 w.flush();
 454                 w.write( "\n" );
 455                 w.write( "\n" );
 456                 w.write( "Gained once, domain lengths:" );
 457                 w.write( "\n" );
 458                 w.write( gained_once_domain_length_stats.toString() );
 459                 w.write( "\n" );
 460                 w.write( "\n" );
 461                 w.write( "Gained multiple times, domain lengths:" );
 462                 w.write( "\n" );
 463                 w.write( gained_multiple_times_domain_length_stats.toString() );
 464                 w.write( "\n" );
 465                 w.write( "\n" );
 466                 w.write( "\n" );
 467                 w.write( "\n" );
 468                 w.write( "Gained once, protein lengths:" );
 469                 w.write( "\n" );
 470                 w.write( gained_once_lengths_stats.toString() );
 471                 w.write( "\n" );
 472                 w.write( "\n" );
 473                 w.write( "Gained once, domain counts:" );
 474                 w.write( "\n" );
 475                 w.write( gained_once_domain_count_stats.toString() );
 476                 w.write( "\n" );
 477                 w.write( "\n" );
 478                 w.write( "Gained multiple times, protein lengths:" );
 479                 w.write( "\n" );
 480                 w.write( gained_multiple_times_lengths_stats.toString() );
 481                 w.write( "\n" );
 482                 w.write( "\n" );
 483                 w.write( "Gained multiple times, domain counts:" );
 484                 w.write( "\n" );
 485                 w.write( gained_multiple_times_domain_count_stats.toString() );
 486                 w.flush();
 487                 w.close();
 488             }
 489         }
 490         catch ( final IOException e ) {
 491             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
 492         }
 493         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
 494                 + outfilename_for_counts + "]" );
 495         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
 496                 + outfilename_for_dc + "]" );
 497         ForesterUtil.programMessage( surfacing.PRG_NAME,
 498                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
 499                                              + outfilename_for_dc_for_go_mapping + "]" );
 500         ForesterUtil.programMessage( surfacing.PRG_NAME,
 501                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
 502                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
 503     }
 504
 505     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
 506         if ( map.containsKey( s ) ) {
 507             map.put( s, map.get( s ) + 1 );
 508         }
 509         else {
 510             map.put( s, 1 );
 511         }
 512     }
 513
 514     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 515         int overlap_count = 0;
 516         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 517             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 518                 ++overlap_count;
 519             }
 520         }
 521         return overlap_count;
 522     }
 523
 524     public static void checkForOutputFileWriteability( final File outfile ) {
 525         final String error = ForesterUtil.isWritableFile( outfile );
 526         if ( !ForesterUtil.isEmpty( error ) ) {
 527             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 528         }
 529     }
 530
 531     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
 532                                                                         final boolean get_gains ) {
 533         final SortedSet<String> domains = new TreeSet<String>();
 534         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
 535             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
 536             if ( get_gains ) {
 537                 domains.addAll( chars.getGainedCharacters() );
 538             }
 539             else {
 540                 domains.addAll( chars.getLostCharacters() );
 541             }
 542         }
 543         return domains;
 544     }
 545
 546     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 547                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 548                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 549                                                                                            final boolean get_gains ) {
 550         final SortedSet<String> sorted_ids = new TreeSet<String>();
 551         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 552             sorted_ids.add( matrix.getIdentifier( i ) );
 553         }
 554         for( final String id : sorted_ids ) {
 555             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 556                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 557                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 558                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 559                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 560                                 .createInstance( matrix.getCharacter( c ) ) );
 561                     }
 562                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 563                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 564                                 .createInstance( matrix.getCharacter( c ) ) );
 565                     }
 566                     else {
 567                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 568                                 .getCharacter( c ) ) );
 569                     }
 570                 }
 571             }
 572         }
 573     }
 574
 575     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
 576                                                             final boolean domain_combinations,
 577                                                             final CharacterStateMatrix.GainLossStates state,
 578                                                             final String outfile ) {
 579         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
 580                 + ForesterUtil.FILE_SEPARATOR + base_dir );
 581         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 582             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 583         }
 584         if ( domain_combinations ) {
 585             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 586                     + ForesterUtil.FILE_SEPARATOR + "DC" );
 587         }
 588         else {
 589             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 590                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
 591         }
 592         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 593             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 594         }
 595         if ( state == GainLossStates.GAIN ) {
 596             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 597                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
 598         }
 599         else if ( state == GainLossStates.LOSS ) {
 600             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 601                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
 602         }
 603         else {
 604             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 605                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
 606         }
 607         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 608             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 609         }
 610         return per_node_go_mapped_domain_gain_loss_files_base_dir;
 611     }
 612
 613     public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 614         final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
 615                 .size() );
 616         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 617             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 618                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 619             }
 620             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 621         }
 622         return domain_id_to_go_ids_map;
 623     }
 624
 625     public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 626             throws IOException {
 627         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
 628         final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
 629         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 630             final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
 631             if ( !map.containsKey( domain_id ) ) {
 632                 map.put( domain_id, new HashSet<String>() );
 633             }
 634             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 635         }
 636         return map;
 637     }
 638
 639     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 640         checkForOutputFileWriteability( nj_tree_outfile );
 641         final NeighborJoining nj = NeighborJoining.createInstance();
 642         final Phylogeny phylogeny = nj.execute( distance );
 643         phylogeny.setName( nj_tree_outfile.getName() );
 644         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 645         return phylogeny;
 646     }
 647
 648     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
 649         final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
 650         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
 651         for( final DomainId domain_id : cds.keySet() ) {
 652             final CombinableDomains cd = cds.get( domain_id );
 653             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
 654         }
 655         return binary_combinations;
 656     }
 657
 658     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 659                                                             final Detailedness detailedness,
 660                                                             final GoAnnotationOutput go_annotation_output,
 661                                                             final Map<GoId, GoTerm> go_id_to_term_map,
 662                                                             final GoNameSpace go_namespace_limit ) {
 663         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
 664             throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
 665         }
 666         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 667             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 668                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 669                 printable_domain_similarity.setDetailedness( detailedness );
 670                 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
 671                 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
 672                 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
 673             }
 674         }
 675     }
 676
 677     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 678                                                     final int number_of_genomes,
 679                                                     final DomainLengthsTable domain_lengths_table,
 680                                                     final File outfile ) throws IOException {
 681         final DecimalFormat df = new DecimalFormat( "#.00" );
 682         checkForOutputFileWriteability( outfile );
 683         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 684         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 685         out.write( ForesterUtil.LINE_SEPARATOR );
 686         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 687         out.write( ForesterUtil.LINE_SEPARATOR );
 688         out.write( ForesterUtil.LINE_SEPARATOR );
 689         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 690         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 691         out.write( ForesterUtil.LINE_SEPARATOR );
 692         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 693             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 694             if ( species_list.size() > 0 ) {
 695                 out.write( domain_lengths.getDomainId() + "\t" );
 696                 for( final Species species : species_list ) {
 697                     out.write( species + "\t" );
 698                 }
 699                 out.write( ForesterUtil.LINE_SEPARATOR );
 700                 // DescriptiveStatistics stats_for_domain = domain_lengths
 701                 //         .calculateMeanBasedStatistics();
 702                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 703                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 704             }
 705         }
 706         out.write( ForesterUtil.LINE_SEPARATOR );
 707         out.write( ForesterUtil.LINE_SEPARATOR );
 708         out.write( "OUTLIER SPECIES (Z 1.0)" );
 709         out.write( ForesterUtil.LINE_SEPARATOR );
 710         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 711                 .calculateMeanBasedStatisticsForAllSpecies();
 712         out.write( stats_for_all_species.asSummary() );
 713         out.write( ForesterUtil.LINE_SEPARATOR );
 714         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 715         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 716         out.write( ForesterUtil.LINE_SEPARATOR );
 717         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 718         final double population_mean = stats_for_all_species.arithmeticMean();
 719         for( final Species species : domain_lengths_table.getSpecies() ) {
 720             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 721             final double z = ( x - population_mean ) / population_sd;
 722             out.write( species + "\t" + z );
 723             out.write( ForesterUtil.LINE_SEPARATOR );
 724         }
 725         out.write( ForesterUtil.LINE_SEPARATOR );
 726         for( final Species species : domain_lengths_table.getSpecies() ) {
 727             final DescriptiveStatistics stats_for_species = domain_lengths_table
 728                     .calculateMeanBasedStatisticsForSpecies( species );
 729             final double x = stats_for_species.arithmeticMean();
 730             final double z = ( x - population_mean ) / population_sd;
 731             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 732                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 733                 out.write( ForesterUtil.LINE_SEPARATOR );
 734             }
 735         }
 736         out.close();
 737         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 738         //        for( int i = 0; i < number_of_genomes; ++i ) {
 739         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 740         //            histogram_datas
 741         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 742         //                            .calculateMeanBasedStatisticsForSpecies( species )
 743         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 744         //        }
 745         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 746         //        hf.setVisible( true );
 747         System.gc();
 748     }
 749
 750     /**
 751      *
 752      * @param all_binary_domains_combination_lost_fitch
 753      * @param consider_directedness_and_adjacency_for_bin_combinations
 754      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 755      * which were gained under unweighted (Fitch) parsimony.
 756      */
 757     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 758                                                  final boolean radomize_fitch_parsimony,
 759                                                  final String outfile_name,
 760                                                  final DomainParsimonyCalculator domain_parsimony,
 761                                                  final Phylogeny phylogeny,
 762                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 763                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 764                                                  final GoNameSpace go_namespace_limit,
 765                                                  final String parameters_str,
 766                                                  final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
 767                                                  final SortedSet<DomainId> positive_filter,
 768                                                  final boolean output_binary_domain_combinations_for_graphs,
 769                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 770                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 771                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 772                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 773                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 774                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
 775         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 776         final String date_time = ForesterUtil.getCurrentDateTime();
 777         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 778         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 779         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 780         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 781         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 782         writeToNexus( outfile_name, domain_parsimony, phylogeny );
 783         // DOLLO DOMAINS
 784         // -------------
 785         Phylogeny local_phylogeny_l = phylogeny.copy();
 786         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 787             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 788         }
 789         else {
 790             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 791         }
 792         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 793                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 794         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 795                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 796         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 797                                                            CharacterStateMatrix.GainLossStates.GAIN,
 798                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 799                                                            sep,
 800                                                            ForesterUtil.LINE_SEPARATOR,
 801                                                            null );
 802         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 803                                                            CharacterStateMatrix.GainLossStates.LOSS,
 804                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 805                                                            sep,
 806                                                            ForesterUtil.LINE_SEPARATOR,
 807                                                            null );
 808         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 809                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 810         //HTML:
 811         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 812                                        go_id_to_term_map,
 813                                        go_namespace_limit,
 814                                        false,
 815                                        domain_parsimony.getGainLossMatrix(),
 816                                        CharacterStateMatrix.GainLossStates.GAIN,
 817                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 818                                        sep,
 819                                        ForesterUtil.LINE_SEPARATOR,
 820                                        "Dollo Parsimony | Gains | Domains",
 821                                        "+",
 822                                        domain_id_to_secondary_features_maps,
 823                                        all_pfams_encountered,
 824                                        all_pfams_gained_as_domains,
 825                                        "_dollo_gains_d" );
 826         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 827                                        go_id_to_term_map,
 828                                        go_namespace_limit,
 829                                        false,
 830                                        domain_parsimony.getGainLossMatrix(),
 831                                        CharacterStateMatrix.GainLossStates.LOSS,
 832                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 833                                        sep,
 834                                        ForesterUtil.LINE_SEPARATOR,
 835                                        "Dollo Parsimony | Losses | Domains",
 836                                        "-",
 837                                        domain_id_to_secondary_features_maps,
 838                                        all_pfams_encountered,
 839                                        all_pfams_lost_as_domains,
 840                                        "_dollo_losses_d" );
 841         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 842                                        go_id_to_term_map,
 843                                        go_namespace_limit,
 844                                        false,
 845                                        domain_parsimony.getGainLossMatrix(),
 846                                        null,
 847                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 848                                        sep,
 849                                        ForesterUtil.LINE_SEPARATOR,
 850                                        "Dollo Parsimony | Present | Domains",
 851                                        "",
 852                                        domain_id_to_secondary_features_maps,
 853                                        all_pfams_encountered,
 854                                        null,
 855                                        "_dollo_present_d" );
 856         preparePhylogeny( local_phylogeny_l,
 857                           domain_parsimony,
 858                           date_time,
 859                           "Dollo parsimony on domain presence/absence",
 860                           "dollo_on_domains_" + outfile_name,
 861                           parameters_str );
 862         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 863                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 864         try {
 865             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 866             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 867         }
 868         catch ( final IOException e ) {
 869             e.printStackTrace();
 870             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 871         }
 872         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 873             // FITCH DOMAIN COMBINATIONS
 874             // -------------------------
 875             local_phylogeny_l = phylogeny.copy();
 876             String randomization = "no";
 877             if ( radomize_fitch_parsimony ) {
 878                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 879                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 880             }
 881             else {
 882                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
 883             }
 884             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 885                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 886             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 887                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 888             SurfacingUtil
 889                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 890                                                           CharacterStateMatrix.GainLossStates.GAIN,
 891                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 892                                                           sep,
 893                                                           ForesterUtil.LINE_SEPARATOR,
 894                                                           null );
 895             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 896                                                                CharacterStateMatrix.GainLossStates.LOSS,
 897                                                                outfile_name
 898                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 899                                                                sep,
 900                                                                ForesterUtil.LINE_SEPARATOR,
 901                                                                null );
 902             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 903                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 904             if ( all_binary_domains_combination_gained_fitch != null ) {
 905                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 906                                                                                     dc_type,
 907                                                                                     all_binary_domains_combination_gained_fitch,
 908                                                                                     true );
 909             }
 910             if ( all_binary_domains_combination_lost_fitch != null ) {
 911                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 912                                                                                     dc_type,
 913                                                                                     all_binary_domains_combination_lost_fitch,
 914                                                                                     false );
 915             }
 916             if ( output_binary_domain_combinations_for_graphs ) {
 917                 SurfacingUtil
 918                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 919                                                                                                            .getGainLossMatrix(),
 920                                                                                                    null,
 921                                                                                                    outfile_name
 922                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 923                                                                                                    sep,
 924                                                                                                    ForesterUtil.LINE_SEPARATOR,
 925                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 926             }
 927             // HTML:
 928             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 929                                            go_id_to_term_map,
 930                                            go_namespace_limit,
 931                                            true,
 932                                            domain_parsimony.getGainLossMatrix(),
 933                                            CharacterStateMatrix.GainLossStates.GAIN,
 934                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 935                                            sep,
 936                                            ForesterUtil.LINE_SEPARATOR,
 937                                            "Fitch Parsimony | Gains | Domain Combinations",
 938                                            "+",
 939                                            null,
 940                                            all_pfams_encountered,
 941                                            all_pfams_gained_as_dom_combinations,
 942                                            "_fitch_gains_dc" );
 943             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 944                                            go_id_to_term_map,
 945                                            go_namespace_limit,
 946                                            true,
 947                                            domain_parsimony.getGainLossMatrix(),
 948                                            CharacterStateMatrix.GainLossStates.LOSS,
 949                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 950                                            sep,
 951                                            ForesterUtil.LINE_SEPARATOR,
 952                                            "Fitch Parsimony | Losses | Domain Combinations",
 953                                            "-",
 954                                            null,
 955                                            all_pfams_encountered,
 956                                            all_pfams_lost_as_dom_combinations,
 957                                            "_fitch_losses_dc" );
 958             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 959                                            go_id_to_term_map,
 960                                            go_namespace_limit,
 961                                            true,
 962                                            domain_parsimony.getGainLossMatrix(),
 963                                            null,
 964                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 965                                            sep,
 966                                            ForesterUtil.LINE_SEPARATOR,
 967                                            "Fitch Parsimony | Present | Domain Combinations",
 968                                            "",
 969                                            null,
 970                                            all_pfams_encountered,
 971                                            null,
 972                                            "_fitch_present_dc" );
 973             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 974                                             go_id_to_term_map,
 975                                             outfile_name,
 976                                             all_pfams_encountered );
 977             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 978             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 979             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 980                               all_pfams_gained_as_dom_combinations );
 981             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 982             preparePhylogeny( local_phylogeny_l,
 983                               domain_parsimony,
 984                               date_time,
 985                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 986                                       + randomization,
 987                               "fitch_on_binary_domain_combinations_" + outfile_name,
 988                               parameters_str );
 989             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 990                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 991             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 992                                                         outfile_name
 993                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 994                                                         outfile_name
 995                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 996                                                         outfile_name
 997                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 998                                                         outfile_name
 999                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
1000                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
1001                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
1002                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
1003                                                         protein_length_stats_by_dc,
1004                                                         domain_number_stats_by_dc,
1005                                                         domain_length_stats_by_domain );
1006         }
1007     }
1008
1009     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
1010                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
1011                                                                      final Phylogeny phylogeny,
1012                                                                      final String parameters_str,
1013                                                                      final Map<Species, MappingResults> mapping_results_map ) {
1014         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
1015         final String date_time = ForesterUtil.getCurrentDateTime();
1016         System.out.println();
1017         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
1018                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
1019                       phylogeny );
1020         Phylogeny local_phylogeny_copy = phylogeny.copy();
1021         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
1022         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
1023                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
1024         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
1025                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
1026         SurfacingUtil
1027                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1028                                                       CharacterStateMatrix.GainLossStates.GAIN,
1029                                                       outfile_name
1030                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
1031                                                       sep,
1032                                                       ForesterUtil.LINE_SEPARATOR,
1033                                                       null );
1034         SurfacingUtil
1035                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1036                                                       CharacterStateMatrix.GainLossStates.LOSS,
1037                                                       outfile_name
1038                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
1039                                                       sep,
1040                                                       ForesterUtil.LINE_SEPARATOR,
1041                                                       null );
1042         SurfacingUtil
1043                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1044                                                       null,
1045                                                       outfile_name
1046                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
1047                                                       sep,
1048                                                       ForesterUtil.LINE_SEPARATOR,
1049                                                       null );
1050         preparePhylogeny( local_phylogeny_copy,
1051                           secondary_features_parsimony,
1052                           date_time,
1053                           "Dollo parsimony on secondary feature presence/absence",
1054                           "dollo_on_secondary_features_" + outfile_name,
1055                           parameters_str );
1056         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1057                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
1058         // FITCH DOMAIN COMBINATIONS
1059         // -------------------------
1060         local_phylogeny_copy = phylogeny.copy();
1061         final String randomization = "no";
1062         secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
1063         preparePhylogeny( local_phylogeny_copy,
1064                           secondary_features_parsimony,
1065                           date_time,
1066                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
1067                                   + randomization,
1068                           "fitch_on_binary_domain_combinations_" + outfile_name,
1069                           parameters_str );
1070         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1071                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
1072         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
1073                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
1074                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
1075                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
1076                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
1077                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
1078                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
1079     }
1080
1081     public static void doit( final List<Protein> proteins,
1082                              final List<DomainId> query_domain_ids_nc_order,
1083                              final Writer out,
1084                              final String separator,
1085                              final String limit_to_species,
1086                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
1087         for( final Protein protein : proteins ) {
1088             if ( ForesterUtil.isEmpty( limit_to_species )
1089                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1090                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1091                     out.write( protein.getSpecies().getSpeciesId() );
1092                     out.write( separator );
1093                     out.write( protein.getProteinId().getId() );
1094                     out.write( separator );
1095                     out.write( "[" );
1096                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
1097                     boolean first = true;
1098                     for( final Domain domain : protein.getProteinDomains() ) {
1099                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1100                             visited_domain_ids.add( domain.getDomainId() );
1101                             if ( first ) {
1102                                 first = false;
1103                             }
1104                             else {
1105                                 out.write( " " );
1106                             }
1107                             out.write( domain.getDomainId().getId() );
1108                             out.write( " {" );
1109                             out.write( "" + domain.getTotalCount() );
1110                             out.write( "}" );
1111                         }
1112                     }
1113                     out.write( "]" );
1114                     out.write( separator );
1115                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1116                             .equals( SurfacingConstants.NONE ) ) ) {
1117                         out.write( protein.getDescription() );
1118                     }
1119                     out.write( separator );
1120                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1121                             .equals( SurfacingConstants.NONE ) ) ) {
1122                         out.write( protein.getAccession() );
1123                     }
1124                     out.write( SurfacingConstants.NL );
1125                 }
1126             }
1127         }
1128         out.flush();
1129     }
1130
1131     public static void extractProteinNames( final List<Protein> proteins,
1132                                             final List<DomainId> query_domain_ids_nc_order,
1133                                             final Writer out,
1134                                             final String separator,
1135                                             final String limit_to_species ) throws IOException {
1136         for( final Protein protein : proteins ) {
1137             if ( ForesterUtil.isEmpty( limit_to_species )
1138                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1139                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1140                     out.write( protein.getSpecies().getSpeciesId() );
1141                     out.write( separator );
1142                     out.write( protein.getProteinId().getId() );
1143                     out.write( separator );
1144                     out.write( "[" );
1145                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
1146                     boolean first = true;
1147                     for( final Domain domain : protein.getProteinDomains() ) {
1148                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1149                             visited_domain_ids.add( domain.getDomainId() );
1150                             if ( first ) {
1151                                 first = false;
1152                             }
1153                             else {
1154                                 out.write( " " );
1155                             }
1156                             out.write( domain.getDomainId().getId() );
1157                             out.write( " {" );
1158                             out.write( "" + domain.getTotalCount() );
1159                             out.write( "}" );
1160                         }
1161                     }
1162                     out.write( "]" );
1163                     out.write( separator );
1164                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1165                             .equals( SurfacingConstants.NONE ) ) ) {
1166                         out.write( protein.getDescription() );
1167                     }
1168                     out.write( separator );
1169                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1170                             .equals( SurfacingConstants.NONE ) ) ) {
1171                         out.write( protein.getAccession() );
1172                     }
1173                     out.write( SurfacingConstants.NL );
1174                 }
1175             }
1176         }
1177         out.flush();
1178     }
1179
1180     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
1181                                             final DomainId domain_id,
1182                                             final Writer out,
1183                                             final String separator,
1184                                             final String limit_to_species ) throws IOException {
1185         for( final Species species : protein_lists_per_species.keySet() ) {
1186             for( final Protein protein : protein_lists_per_species.get( species ) ) {
1187                 if ( ForesterUtil.isEmpty( limit_to_species )
1188                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1189                     final List<Domain> domains = protein.getProteinDomains( domain_id );
1190                     if ( domains.size() > 0 ) {
1191                         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
1192                         for( final Domain domain : domains ) {
1193                             stats.addValue( domain.getPerSequenceEvalue() );
1194                         }
1195                         out.write( protein.getSpecies().getSpeciesId() );
1196                         out.write( separator );
1197                         out.write( protein.getProteinId().getId() );
1198                         out.write( separator );
1199                         out.write( "[" + FORMATTER.format( stats.median() ) + "]" );
1200                         out.write( separator );
1201                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1202                                 .equals( SurfacingConstants.NONE ) ) ) {
1203                             out.write( protein.getDescription() );
1204                         }
1205                         out.write( separator );
1206                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1207                                 .equals( SurfacingConstants.NONE ) ) ) {
1208                             out.write( protein.getAccession() );
1209                         }
1210                         out.write( SurfacingConstants.NL );
1211                     }
1212                 }
1213             }
1214         }
1215         out.flush();
1216     }
1217
1218     public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
1219         final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
1220         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1221             final Set<DomainId> all_domains = gwcd.getAllDomainIds();
1222             //    for( final Domain domain : all_domains ) {
1223             all_domains_ids.addAll( all_domains );
1224             //    }
1225         }
1226         return all_domains_ids;
1227     }
1228
1229     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
1230         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
1231         for( final Protein protein_domain_collection : protein_domain_collections ) {
1232             for( final Object name : protein_domain_collection.getProteinDomains() ) {
1233                 final BasicDomain protein_domain = ( BasicDomain ) name;
1234                 final String id = protein_domain.getDomainId().getId();
1235                 if ( map.containsKey( id ) ) {
1236                     map.put( id, map.get( id ) + 1 );
1237                 }
1238                 else {
1239                     map.put( id, 1 );
1240                 }
1241             }
1242         }
1243         return map;
1244     }
1245
1246     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1247         final PhylogenyNodeIterator it = p.iteratorPostorder();
1248         int c = 0;
1249         while ( it.hasNext() ) {
1250             final PhylogenyNode n = it.next();
1251             if ( ForesterUtil.isEmpty( n.getName() )
1252                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1253                             .getScientificName() ) )
1254                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1255                             .getCommonName() ) ) ) {
1256                 if ( n.getParent() != null ) {
1257                     names.append( " " );
1258                     names.append( n.getParent().getName() );
1259                 }
1260                 final List l = n.getAllExternalDescendants();
1261                 for( final Object object : l ) {
1262                     System.out.println( l.toString() );
1263                 }
1264                 ++c;
1265             }
1266         }
1267         return c;
1268     }
1269
1270     /**
1271      * Returns true is Domain domain falls in an uninterrupted stretch of
1272      * covered positions.
1273      *
1274      * @param domain
1275      * @param covered_positions
1276      * @return
1277      */
1278     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1279         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1280             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1281                 return false;
1282             }
1283         }
1284         return true;
1285     }
1286
1287     public static void preparePhylogeny( final Phylogeny p,
1288                                          final DomainParsimonyCalculator domain_parsimony,
1289                                          final String date_time,
1290                                          final String method,
1291                                          final String name,
1292                                          final String parameters_str ) {
1293         domain_parsimony.decoratePhylogenyWithDomains( p );
1294         final StringBuilder desc = new StringBuilder();
1295         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1296         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1297         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1298         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1299         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1300         desc.append( "[Parameters: " + parameters_str + "]" );
1301         p.setName( name );
1302         p.setDescription( desc.toString() );
1303         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1304         p.setRerootable( false );
1305         p.setRooted( true );
1306     }
1307
1308     /*
1309      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1310      *
1311      *
1312      */
1313     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1314                                                             final String protein_id,
1315                                                             final String separator ) {
1316         final StringBuffer sb = new StringBuffer();
1317         if ( protein.getSpecies() == null ) {
1318             throw new IllegalArgumentException( "species must not be null" );
1319         }
1320         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1321             throw new IllegalArgumentException( "species id must not be empty" );
1322         }
1323         final List<Domain> domains = protein.getProteinDomains();
1324         if ( domains.size() > 1 ) {
1325             final Map<String, Integer> counts = new HashMap<String, Integer>();
1326             for( final Domain domain : domains ) {
1327                 final String id = domain.getDomainId().getId();
1328                 if ( counts.containsKey( id ) ) {
1329                     counts.put( id, counts.get( id ) + 1 );
1330                 }
1331                 else {
1332                     counts.put( id, 1 );
1333                 }
1334             }
1335             final Set<String> dcs = new HashSet<String>();
1336             for( int i = 1; i < domains.size(); ++i ) {
1337                 for( int j = 0; j < i; ++j ) {
1338                     Domain domain_n = domains.get( i );
1339                     Domain domain_c = domains.get( j );
1340                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1341                         domain_n = domains.get( j );
1342                         domain_c = domains.get( i );
1343                     }
1344                     final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
1345                     if ( !dcs.contains( dc ) ) {
1346                         dcs.add( dc );
1347                         sb.append( protein.getSpecies() );
1348                         sb.append( separator );
1349                         sb.append( protein_id );
1350                         sb.append( separator );
1351                         sb.append( domain_n.getDomainId().getId() );
1352                         sb.append( separator );
1353                         sb.append( domain_c.getDomainId().getId() );
1354                         sb.append( separator );
1355                         sb.append( domain_n.getPerDomainEvalue() );
1356                         sb.append( separator );
1357                         sb.append( domain_c.getPerDomainEvalue() );
1358                         sb.append( separator );
1359                         sb.append( counts.get( domain_n.getDomainId().getId() ) );
1360                         sb.append( separator );
1361                         sb.append( counts.get( domain_c.getDomainId().getId() ) );
1362                         sb.append( ForesterUtil.LINE_SEPARATOR );
1363                     }
1364                 }
1365             }
1366         }
1367         else if ( domains.size() == 1 ) {
1368             sb.append( protein.getSpecies() );
1369             sb.append( separator );
1370             sb.append( protein_id );
1371             sb.append( separator );
1372             sb.append( domains.get( 0 ).getDomainId().getId() );
1373             sb.append( separator );
1374             sb.append( separator );
1375             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1376             sb.append( separator );
1377             sb.append( separator );
1378             sb.append( 1 );
1379             sb.append( separator );
1380             sb.append( ForesterUtil.LINE_SEPARATOR );
1381         }
1382         else {
1383             sb.append( protein.getSpecies() );
1384             sb.append( separator );
1385             sb.append( protein_id );
1386             sb.append( separator );
1387             sb.append( separator );
1388             sb.append( separator );
1389             sb.append( separator );
1390             sb.append( separator );
1391             sb.append( separator );
1392             sb.append( ForesterUtil.LINE_SEPARATOR );
1393         }
1394         return sb;
1395     }
1396
1397     /**
1398      *
1399      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1400      * domain with 0.3 is ignored
1401      *
1402      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1403      *
1404      *
1405      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1406      * ignored
1407      *
1408      * @param max_allowed_overlap
1409      *            maximal allowed overlap (inclusive) to be still considered not
1410      *            overlapping (zero or negative value to allow any overlap)
1411      * @param remove_engulfed_domains
1412      *            to remove domains which are completely engulfed by coverage of
1413      *            domains with better support
1414      * @param protein
1415      * @return
1416      */
1417     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1418                                                     final boolean remove_engulfed_domains,
1419                                                     final Protein protein ) {
1420         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1421                 .getSpeciesId(), protein.getLength() );
1422         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1423         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1424         for( final Domain domain : sorted ) {
1425             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1426                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1427                 final int covered_positions_size = covered_positions.size();
1428                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1429                     covered_positions.add( false );
1430                 }
1431                 final int new_covered_positions_size = covered_positions.size();
1432                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1433                     if ( i < new_covered_positions_size ) {
1434                         covered_positions.set( i, true );
1435                     }
1436                     else {
1437                         covered_positions.add( true );
1438                     }
1439                 }
1440                 pruned_protein.addProteinDomain( domain );
1441             }
1442         }
1443         return pruned_protein;
1444     }
1445
1446     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1447         final List<Domain> domains = new ArrayList<Domain>();
1448         for( final Domain d : protein.getProteinDomains() ) {
1449             domains.add( d );
1450         }
1451         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1452         return domains;
1453     }
1454
1455     private static List<String> splitDomainCombination( final String dc ) {
1456         final String[] s = dc.split( "=" );
1457         if ( s.length != 2 ) {
1458             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
1459                     + dc );
1460             System.exit( -1 );
1461         }
1462         final List<String> l = new ArrayList<String>( 2 );
1463         l.add( s[ 0 ] );
1464         l.add( s[ 1 ] );
1465         return l;
1466     }
1467
1468     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1469                                                             final boolean get_gains,
1470                                                             final String outdir,
1471                                                             final String suffix_for_filename ) throws IOException {
1472         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1473         if ( !get_gains ) {
1474             state = CharacterStateMatrix.GainLossStates.LOSS;
1475         }
1476         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1477                                                                   false,
1478                                                                   state,
1479                                                                   outdir );
1480         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1481             final PhylogenyNode node = it.next();
1482             if ( !node.isExternal() ) {
1483                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1484                 if ( domains.size() > 0 ) {
1485                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1486                             + node.getName() + suffix_for_filename );
1487                     for( final String domain : domains ) {
1488                         writer.write( domain );
1489                         writer.write( ForesterUtil.LINE_SEPARATOR );
1490                     }
1491                     writer.close();
1492                 }
1493             }
1494         }
1495     }
1496
1497     private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1498                                                         final Map<GoId, GoTerm> go_id_to_term_map,
1499                                                         final String outfile_name,
1500                                                         final SortedSet<String> all_pfams_encountered ) {
1501         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
1502         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
1503                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
1504         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
1505         int biological_process_counter = 0;
1506         int cellular_component_counter = 0;
1507         int molecular_function_counter = 0;
1508         int pfams_with_mappings_counter = 0;
1509         int pfams_without_mappings_counter = 0;
1510         int pfams_without_mappings_to_bp_or_mf_counter = 0;
1511         int pfams_with_mappings_to_bp_or_mf_counter = 0;
1512         try {
1513             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
1514             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
1515             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
1516             summary_writer.write( "# Pfam to GO mapping summary" );
1517             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1518             summary_writer.write( "# Actual summary is at the end of this file." );
1519             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1520             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
1521             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1522             for( final String pfam : all_pfams_encountered ) {
1523                 all_pfams_encountered_writer.write( pfam );
1524                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
1525                 final DomainId domain_id = new DomainId( pfam );
1526                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1527                     ++pfams_with_mappings_counter;
1528                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
1529                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
1530                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
1531                     boolean maps_to_bp = false;
1532                     boolean maps_to_cc = false;
1533                     boolean maps_to_mf = false;
1534                     for( final GoId go_id : go_ids ) {
1535                         final GoTerm go_term = go_id_to_term_map.get( go_id );
1536                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
1537                             maps_to_bp = true;
1538                         }
1539                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
1540                             maps_to_cc = true;
1541                         }
1542                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
1543                             maps_to_mf = true;
1544                         }
1545                     }
1546                     if ( maps_to_bp ) {
1547                         ++biological_process_counter;
1548                     }
1549                     if ( maps_to_cc ) {
1550                         ++cellular_component_counter;
1551                     }
1552                     if ( maps_to_mf ) {
1553                         ++molecular_function_counter;
1554                     }
1555                     if ( maps_to_bp || maps_to_mf ) {
1556                         ++pfams_with_mappings_to_bp_or_mf_counter;
1557                     }
1558                     else {
1559                         ++pfams_without_mappings_to_bp_or_mf_counter;
1560                     }
1561                 }
1562                 else {
1563                     ++pfams_without_mappings_to_bp_or_mf_counter;
1564                     ++pfams_without_mappings_counter;
1565                     summary_writer.write( pfam );
1566                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1567                 }
1568             }
1569             all_pfams_encountered_writer.close();
1570             all_pfams_encountered_with_go_annotation_writer.close();
1571             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
1572                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
1573             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
1574                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
1575                     + "\"" );
1576             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
1577                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
1578                     + encountered_pfams_summary_file + "\"" );
1579             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
1580                     + all_pfams_encountered.size() );
1581             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
1582                     + pfams_without_mappings_counter + " ["
1583                     + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1584             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
1585                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1586                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1587             ForesterUtil.programMessage( surfacing.PRG_NAME,
1588                                          "Pfams with a mapping                    : " + pfams_with_mappings_counter
1589                                                  + " ["
1590                                                  + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
1591                                                  + "%]" );
1592             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
1593                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1594                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1595             ForesterUtil.programMessage( surfacing.PRG_NAME,
1596                                          "Pfams with mapping to biological process: " + biological_process_counter
1597                                                  + " ["
1598                                                  + ( 100 * biological_process_counter / all_pfams_encountered.size() )
1599                                                  + "%]" );
1600             ForesterUtil.programMessage( surfacing.PRG_NAME,
1601                                          "Pfams with mapping to molecular function: " + molecular_function_counter
1602                                                  + " ["
1603                                                  + ( 100 * molecular_function_counter / all_pfams_encountered.size() )
1604                                                  + "%]" );
1605             ForesterUtil.programMessage( surfacing.PRG_NAME,
1606                                          "Pfams with mapping to cellular component: " + cellular_component_counter
1607                                                  + " ["
1608                                                  + ( 100 * cellular_component_counter / all_pfams_encountered.size() )
1609                                                  + "%]" );
1610             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1611             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
1612             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1613             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
1614                     + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1615             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1616             summary_writer.write( "# Pfams without mapping to proc. or func. : "
1617                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1618                     + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1619             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1620             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
1621                     + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
1622             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1623             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
1624                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1625                     + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
1626             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1627             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
1628                     + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
1629             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1630             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
1631                     + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
1632             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1633             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
1634                     + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
1635             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1636             summary_writer.close();
1637         }
1638         catch ( final IOException e ) {
1639             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
1640         }
1641     }
1642
1643     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1644                                                                           final File output_dir,
1645                                                                           final GenomeWideCombinableDomains gwcd,
1646                                                                           final int i,
1647                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1648         File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
1649                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1650         if ( output_dir != null ) {
1651             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1652         }
1653         checkForOutputFileWriteability( dc_outfile_dot );
1654         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1655         try {
1656             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1657             for( final BinaryDomainCombination bdc : binary_combinations ) {
1658                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1659                         .toString() );
1660                 out_dot.write( SurfacingConstants.NL );
1661             }
1662             out_dot.close();
1663         }
1664         catch ( final IOException e ) {
1665             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1666         }
1667         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1668                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1669                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1670     }
1671
1672     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1673                                                             final CharacterStateMatrix.GainLossStates state,
1674                                                             final String filename,
1675                                                             final String indentifier_characters_separator,
1676                                                             final String character_separator,
1677                                                             final Map<String, String> descriptions ) {
1678         final File outfile = new File( filename );
1679         checkForOutputFileWriteability( outfile );
1680         final SortedSet<String> sorted_ids = new TreeSet<String>();
1681         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1682             sorted_ids.add( matrix.getIdentifier( i ) );
1683         }
1684         try {
1685             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1686             for( final String id : sorted_ids ) {
1687                 out.write( indentifier_characters_separator );
1688                 out.write( "#" + id );
1689                 out.write( indentifier_characters_separator );
1690                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1691                     // Not nice:
1692                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1693                     if ( ( matrix.getState( id, c ) == state )
1694                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1695                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1696                         out.write( matrix.getCharacter( c ) );
1697                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1698                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1699                             out.write( "\t" );
1700                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1701                         }
1702                         out.write( character_separator );
1703                     }
1704                 }
1705             }
1706             out.flush();
1707             out.close();
1708         }
1709         catch ( final IOException e ) {
1710             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1711         }
1712         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1713     }
1714
1715     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1716                                                                                                  final CharacterStateMatrix.GainLossStates state,
1717                                                                                                  final String filename,
1718                                                                                                  final String indentifier_characters_separator,
1719                                                                                                  final String character_separator,
1720                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1721         final File outfile = new File( filename );
1722         checkForOutputFileWriteability( outfile );
1723         final SortedSet<String> sorted_ids = new TreeSet<String>();
1724         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1725             sorted_ids.add( matrix.getIdentifier( i ) );
1726         }
1727         try {
1728             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1729             for( final String id : sorted_ids ) {
1730                 out.write( indentifier_characters_separator );
1731                 out.write( "#" + id );
1732                 out.write( indentifier_characters_separator );
1733                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1734                     // Not nice:
1735                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1736                     if ( ( matrix.getState( id, c ) == state )
1737                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1738                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1739                         BinaryDomainCombination bdc = null;
1740                         try {
1741                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1742                         }
1743                         catch ( final Exception e ) {
1744                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1745                         }
1746                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1747                         out.write( character_separator );
1748                     }
1749                 }
1750             }
1751             out.flush();
1752             out.close();
1753         }
1754         catch ( final IOException e ) {
1755             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1756         }
1757         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1758     }
1759
1760     public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1761                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1762                                                       final GoNameSpace go_namespace_limit,
1763                                                       final boolean domain_combinations,
1764                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1765                                                       final CharacterStateMatrix.GainLossStates state,
1766                                                       final String filename,
1767                                                       final String indentifier_characters_separator,
1768                                                       final String character_separator,
1769                                                       final String title_for_html,
1770                                                       final String prefix_for_html,
1771                                                       final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1772                                                       final SortedSet<String> all_pfams_encountered,
1773                                                       final SortedSet<String> pfams_gained_or_lost,
1774                                                       final String suffix_for_per_node_events_file ) {
1775         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1776             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1777         }
1778         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1779             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1780         }
1781         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1782             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1783         }
1784         final File outfile = new File( filename );
1785         checkForOutputFileWriteability( outfile );
1786         final SortedSet<String> sorted_ids = new TreeSet<String>();
1787         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1788             sorted_ids.add( matrix.getIdentifier( i ) );
1789         }
1790         try {
1791             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1792             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1793                                                                                                                 domain_combinations,
1794                                                                                                                 state,
1795                                                                                                                 filename );
1796             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1797             File per_node_go_mapped_domain_gain_loss_outfile = null;
1798             int per_node_counter = 0;
1799             out.write( "<html>" );
1800             out.write( SurfacingConstants.NL );
1801             addHtmlHead( out, title_for_html );
1802             out.write( SurfacingConstants.NL );
1803             out.write( "<body>" );
1804             out.write( SurfacingConstants.NL );
1805             out.write( "<h1>" );
1806             out.write( SurfacingConstants.NL );
1807             out.write( title_for_html );
1808             out.write( SurfacingConstants.NL );
1809             out.write( "</h1>" );
1810             out.write( SurfacingConstants.NL );
1811             out.write( "<table>" );
1812             out.write( SurfacingConstants.NL );
1813             for( final String id : sorted_ids ) {
1814                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1815                 if ( matcher.matches() ) {
1816                     continue;
1817                 }
1818                 out.write( "<tr>" );
1819                 out.write( "<td>" );
1820                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1821                 out.write( "</td>" );
1822                 out.write( "</tr>" );
1823                 out.write( SurfacingConstants.NL );
1824             }
1825             out.write( "</table>" );
1826             out.write( SurfacingConstants.NL );
1827             for( final String id : sorted_ids ) {
1828                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1829                 if ( matcher.matches() ) {
1830                     continue;
1831                 }
1832                 out.write( SurfacingConstants.NL );
1833                 out.write( "<h2>" );
1834                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1835                 writeTaxonomyLinks( out, id );
1836                 out.write( "</h2>" );
1837                 out.write( SurfacingConstants.NL );
1838                 out.write( "<table>" );
1839                 out.write( SurfacingConstants.NL );
1840                 out.write( "<tr>" );
1841                 out.write( "<td><b>" );
1842                 out.write( "Pfam domain(s)" );
1843                 out.write( "</b></td><td><b>" );
1844                 out.write( "GO term acc" );
1845                 out.write( "</b></td><td><b>" );
1846                 out.write( "GO term" );
1847                 out.write( "</b></td><td><b>" );
1848                 out.write( "GO namespace" );
1849                 out.write( "</b></td>" );
1850                 out.write( "</tr>" );
1851                 out.write( SurfacingConstants.NL );
1852                 out.write( "</tr>" );
1853                 out.write( SurfacingConstants.NL );
1854                 per_node_counter = 0;
1855                 if ( matrix.getNumberOfCharacters() > 0 ) {
1856                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1857                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1858                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1859                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1860                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1861                 }
1862                 else {
1863                     per_node_go_mapped_domain_gain_loss_outfile = null;
1864                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1865                 }
1866                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1867                     // Not nice:
1868                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1869                     if ( ( matrix.getState( id, c ) == state )
1870                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1871                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1872                         final String character = matrix.getCharacter( c );
1873                         String domain_0 = "";
1874                         String domain_1 = "";
1875                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1876                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1877                             if ( s.length != 2 ) {
1878                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1879                                         + character + "]" );
1880                             }
1881                             domain_0 = s[ 0 ];
1882                             domain_1 = s[ 1 ];
1883                         }
1884                         else {
1885                             domain_0 = character;
1886                         }
1887                         writeDomainData( domain_id_to_go_ids_map,
1888                                          go_id_to_term_map,
1889                                          go_namespace_limit,
1890                                          out,
1891                                          domain_0,
1892                                          domain_1,
1893                                          prefix_for_html,
1894                                          character_separator,
1895                                          domain_id_to_secondary_features_maps,
1896                                          null );
1897                         all_pfams_encountered.add( domain_0 );
1898                         if ( pfams_gained_or_lost != null ) {
1899                             pfams_gained_or_lost.add( domain_0 );
1900                         }
1901                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
1902                             all_pfams_encountered.add( domain_1 );
1903                             if ( pfams_gained_or_lost != null ) {
1904                                 pfams_gained_or_lost.add( domain_1 );
1905                             }
1906                         }
1907                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1908                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
1909                                                                      domain_0,
1910                                                                      domain_1 );
1911                             per_node_counter++;
1912                         }
1913                     }
1914                 }
1915                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
1916                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
1917                     if ( per_node_counter < 1 ) {
1918                         per_node_go_mapped_domain_gain_loss_outfile.delete();
1919                     }
1920                     per_node_counter = 0;
1921                 }
1922                 out.write( "</table>" );
1923                 out.write( SurfacingConstants.NL );
1924                 out.write( "<hr>" );
1925                 out.write( SurfacingConstants.NL );
1926             } // for( final String id : sorted_ids ) {
1927             out.write( "</body>" );
1928             out.write( SurfacingConstants.NL );
1929             out.write( "</html>" );
1930             out.write( SurfacingConstants.NL );
1931             out.flush();
1932             out.close();
1933         }
1934         catch ( final IOException e ) {
1935             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1936         }
1937         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
1938     }
1939
1940     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
1941                                                           final File output_dir,
1942                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
1943                                                           final GenomeWideCombinableDomains gwcd,
1944                                                           final int i,
1945                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1946         File dc_outfile = new File( input_file_properties[ i ][ 0 ]
1947                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
1948         if ( output_dir != null ) {
1949             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
1950         }
1951         checkForOutputFileWriteability( dc_outfile );
1952         try {
1953             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
1954             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
1955             out.close();
1956         }
1957         catch ( final IOException e ) {
1958             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1959         }
1960         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
1961         try {
1962             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
1963             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
1964             if ( stats.getN() < 2 ) {
1965                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
1966             }
1967             else {
1968                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
1969                         .sampleStandardDeviation() ) + "\t" );
1970             }
1971             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
1972             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
1973             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
1974             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
1975             final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
1976             for( final DomainId mpd : mpds ) {
1977                 per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
1978             }
1979             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
1980         }
1981         catch ( final IOException e ) {
1982             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1983         }
1984         if ( input_file_properties[ i ].length == 3 ) {
1985             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1986                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1987                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
1988         }
1989         else {
1990             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
1991                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
1992                     + dc_outfile + "\"" );
1993         }
1994     }
1995
1996     private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1997                                          final Map<GoId, GoTerm> go_id_to_term_map,
1998                                          final GoNameSpace go_namespace_limit,
1999                                          final Writer out,
2000                                          final String domain_0,
2001                                          final String domain_1,
2002                                          final String prefix_for_html,
2003                                          final String character_separator_for_non_html_output,
2004                                          final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
2005                                          final Set<GoId> all_go_ids ) throws IOException {
2006         boolean any_go_annotation_present = false;
2007         boolean first_has_no_go = false;
2008         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2009         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2010             domain_count = 1;
2011         }
2012         // The following has a difficult to understand logic.
2013         for( int d = 0; d < domain_count; ++d ) {
2014             List<GoId> go_ids = null;
2015             boolean go_annotation_present = false;
2016             if ( d == 0 ) {
2017                 final DomainId domain_id = new DomainId( domain_0 );
2018                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2019                     go_annotation_present = true;
2020                     any_go_annotation_present = true;
2021                     go_ids = domain_id_to_go_ids_map.get( domain_id );
2022                 }
2023                 else {
2024                     first_has_no_go = true;
2025                 }
2026             }
2027             else {
2028                 final DomainId domain_id = new DomainId( domain_1 );
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             }
2035             if ( go_annotation_present ) {
2036                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2037                 for( final GoId go_id : go_ids ) {
2038                     out.write( "<tr>" );
2039                     if ( first ) {
2040                         first = false;
2041                         writeDomainIdsToHtml( out,
2042                                               domain_0,
2043                                               domain_1,
2044                                               prefix_for_html,
2045                                               domain_id_to_secondary_features_maps );
2046                     }
2047                     else {
2048                         out.write( "<td></td>" );
2049                     }
2050                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2051                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2052                     }
2053                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2054                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2055                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2056                         final String go_id_str = go_id.getId();
2057                         out.write( "<td>" );
2058                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2059                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2060                         out.write( "</td><td>" );
2061                         out.write( go_term.getName() );
2062                         if ( domain_count == 2 ) {
2063                             out.write( " (" + d + ")" );
2064                         }
2065                         out.write( "</td><td>" );
2066                         // out.write( top );
2067                         // out.write( "</td><td>" );
2068                         out.write( "[" );
2069                         out.write( go_term.getGoNameSpace().toShortString() );
2070                         out.write( "]" );
2071                         out.write( "</td>" );
2072                         if ( all_go_ids != null ) {
2073                             all_go_ids.add( go_id );
2074                         }
2075                     }
2076                     else {
2077                         out.write( "<td>" );
2078                         out.write( "</td><td>" );
2079                         out.write( "</td><td>" );
2080                         out.write( "</td><td>" );
2081                         out.write( "</td>" );
2082                     }
2083                     out.write( "</tr>" );
2084                     out.write( SurfacingConstants.NL );
2085                 }
2086             }
2087         } //  for( int d = 0; d < domain_count; ++d )
2088         if ( !any_go_annotation_present ) {
2089             out.write( "<tr>" );
2090             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2091             out.write( "<td>" );
2092             out.write( "</td><td>" );
2093             out.write( "</td><td>" );
2094             out.write( "</td><td>" );
2095             out.write( "</td>" );
2096             out.write( "</tr>" );
2097             out.write( SurfacingConstants.NL );
2098         }
2099     }
2100
2101     private static void writeDomainIdsToHtml( final Writer out,
2102                                               final String domain_0,
2103                                               final String domain_1,
2104                                               final String prefix_for_detailed_html,
2105                                               final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
2106             throws IOException {
2107         out.write( "<td>" );
2108         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2109             out.write( prefix_for_detailed_html );
2110             out.write( " " );
2111         }
2112         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2113         out.write( "</td>" );
2114     }
2115
2116     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2117                                                                        final StringBuilder html_title,
2118                                                                        final Writer single_writer,
2119                                                                        Map<Character, Writer> split_writers,
2120                                                                        final SortedSet<DomainSimilarity> similarities,
2121                                                                        final boolean treat_as_binary,
2122                                                                        final List<Species> species_order,
2123                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
2124                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
2125                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
2126                                                                        final boolean verbose ) throws IOException {
2127         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2128         String histogram_title = null;
2129         switch ( sort_field ) {
2130             case ABS_MAX_COUNTS_DIFFERENCE:
2131                 if ( treat_as_binary ) {
2132                     histogram_title = "absolute counts difference:";
2133                 }
2134                 else {
2135                     histogram_title = "absolute (maximal) counts difference:";
2136                 }
2137                 break;
2138             case MAX_COUNTS_DIFFERENCE:
2139                 if ( treat_as_binary ) {
2140                     histogram_title = "counts difference:";
2141                 }
2142                 else {
2143                     histogram_title = "(maximal) counts difference:";
2144                 }
2145                 break;
2146             case DOMAIN_ID:
2147                 histogram_title = "score mean:";
2148                 break;
2149             case MIN:
2150                 histogram_title = "score minimum:";
2151                 break;
2152             case MAX:
2153                 histogram_title = "score maximum:";
2154                 break;
2155             case MAX_DIFFERENCE:
2156                 if ( treat_as_binary ) {
2157                     histogram_title = "difference:";
2158                 }
2159                 else {
2160                     histogram_title = "(maximal) difference:";
2161                 }
2162                 break;
2163             case MEAN:
2164                 histogram_title = "score mean:";
2165                 break;
2166             case SD:
2167                 histogram_title = "score standard deviation:";
2168                 break;
2169             case SPECIES_COUNT:
2170                 histogram_title = "species number:";
2171                 break;
2172             default:
2173                 throw new AssertionError( "Unknown sort field: " + sort_field );
2174         }
2175         for( final DomainSimilarity similarity : similarities ) {
2176             switch ( sort_field ) {
2177                 case ABS_MAX_COUNTS_DIFFERENCE:
2178                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
2179                     break;
2180                 case MAX_COUNTS_DIFFERENCE:
2181                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
2182                     break;
2183                 case DOMAIN_ID:
2184                     stats.addValue( similarity.getMeanSimilarityScore() );
2185                     break;
2186                 case MIN:
2187                     stats.addValue( similarity.getMinimalSimilarityScore() );
2188                     break;
2189                 case MAX:
2190                     stats.addValue( similarity.getMaximalSimilarityScore() );
2191                     break;
2192                 case MAX_DIFFERENCE:
2193                     stats.addValue( similarity.getMaximalDifference() );
2194                     break;
2195                 case MEAN:
2196                     stats.addValue( similarity.getMeanSimilarityScore() );
2197                     break;
2198                 case SD:
2199                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
2200                     break;
2201                 case SPECIES_COUNT:
2202                     stats.addValue( similarity.getSpecies().size() );
2203                     break;
2204                 default:
2205                     throw new AssertionError( "Unknown sort field: " + sort_field );
2206             }
2207         }
2208         //
2209         // final HistogramData[] hists = new HistogramData[ 1 ];
2210         //
2211         //
2212         // List<HistogramDataItem> data_items = new
2213         // ArrayList<HistogramDataItem>();
2214         // double[] values = stats.getDataAsDoubleArray();
2215         // for( int i = 0; i < values.length; i++ ) {
2216         // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
2217         // i ] );
2218         // data_items.add( data_item );
2219         // }
2220         //
2221         //
2222         // HistogramData hd0 = new HistogramData( "name",
2223         // data_items,
2224         // null, 20,
2225         // 40 );
2226         //
2227         //
2228         //
2229         //
2230         // hists[ 0 ] = hd0;
2231         //
2232         // final HistogramsFrame hf = new HistogramsFrame( hists );
2233         // hf.setVisible( true );
2234         //
2235         AsciiHistogram histo = null;
2236         if ( stats.getMin() < stats.getMin() ) {
2237             histo = new AsciiHistogram( stats, histogram_title );
2238         }
2239         if ( verbose ) {
2240             if ( histo != null ) {
2241                 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
2242             }
2243             System.out.println();
2244             System.out.println( "N                   : " + stats.getN() );
2245             System.out.println( "Min                 : " + stats.getMin() );
2246             System.out.println( "Max                 : " + stats.getMax() );
2247             System.out.println( "Mean                : " + stats.arithmeticMean() );
2248             if ( stats.getN() > 1 ) {
2249                 System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
2250             }
2251             else {
2252                 System.out.println( "SD                  : n/a" );
2253             }
2254             System.out.println( "Median              : " + stats.median() );
2255             if ( stats.getN() > 1 ) {
2256                 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
2257             }
2258             else {
2259                 System.out.println( "Pearsonian skewness : n/a" );
2260             }
2261         }
2262         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2263             split_writers = new HashMap<Character, Writer>();
2264             split_writers.put( '_', single_writer );
2265         }
2266         switch ( print_option ) {
2267             case SIMPLE_TAB_DELIMITED:
2268                 break;
2269             case HTML:
2270                 for( final Character key : split_writers.keySet() ) {
2271                     final Writer w = split_writers.get( key );
2272                     w.write( "<html>" );
2273                     w.write( SurfacingConstants.NL );
2274                     if ( key != '_' ) {
2275                         addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
2276                     }
2277                     else {
2278                         addHtmlHead( w, "DCs (" + html_title + ")" );
2279                     }
2280                     w.write( SurfacingConstants.NL );
2281                     w.write( "<body>" );
2282                     w.write( SurfacingConstants.NL );
2283                     w.write( html_desc.toString() );
2284                     w.write( SurfacingConstants.NL );
2285                     w.write( "<hr>" );
2286                     w.write( "<br>" );
2287                     w.write( SurfacingConstants.NL );
2288                     w.write( "<tt><pre>" );
2289                     w.write( SurfacingConstants.NL );
2290                     if ( histo != null ) {
2291                         w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2292                         w.write( SurfacingConstants.NL );
2293                     }
2294                     w.write( "</pre></tt>" );
2295                     w.write( SurfacingConstants.NL );
2296                     w.write( "<table>" );
2297                     w.write( SurfacingConstants.NL );
2298                     w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2299                     w.write( SurfacingConstants.NL );
2300                     w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2301                     w.write( SurfacingConstants.NL );
2302                     w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2303                     w.write( SurfacingConstants.NL );
2304                     w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2305                     w.write( SurfacingConstants.NL );
2306                     if ( stats.getN() > 1 ) {
2307                         w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2308                     }
2309                     else {
2310                         w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2311                     }
2312                     w.write( SurfacingConstants.NL );
2313                     w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
2314                     w.write( SurfacingConstants.NL );
2315                     if ( stats.getN() > 1 ) {
2316                         w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
2317                     }
2318                     else {
2319                         w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
2320                     }
2321                     w.write( SurfacingConstants.NL );
2322                     w.write( "</table>" );
2323                     w.write( SurfacingConstants.NL );
2324                     w.write( "<br>" );
2325                     w.write( SurfacingConstants.NL );
2326                     w.write( "<hr>" );
2327                     w.write( SurfacingConstants.NL );
2328                     w.write( "<br>" );
2329                     w.write( SurfacingConstants.NL );
2330                     w.write( "<table>" );
2331                     w.write( SurfacingConstants.NL );
2332                 }
2333                 break;
2334         }
2335         for( final Writer w : split_writers.values() ) {
2336             w.write( SurfacingConstants.NL );
2337         }
2338         for( final DomainSimilarity similarity : similarities ) {
2339             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2340                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2341             }
2342             if ( single_writer != null ) {
2343                 single_writer.write( similarity.toStringBuffer( print_option ).toString() );
2344             }
2345             else {
2346                 Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
2347                         .toLowerCase().charAt( 0 ) );
2348                 if ( local_writer == null ) {
2349                     local_writer = split_writers.get( '0' );
2350                 }
2351                 local_writer.write( similarity.toStringBuffer( print_option ).toString() );
2352             }
2353             for( final Writer w : split_writers.values() ) {
2354                 w.write( SurfacingConstants.NL );
2355             }
2356         }
2357         switch ( print_option ) {
2358             case HTML:
2359                 for( final Writer w : split_writers.values() ) {
2360                     w.write( SurfacingConstants.NL );
2361                     w.write( "</table>" );
2362                     w.write( SurfacingConstants.NL );
2363                     w.write( "</font>" );
2364                     w.write( SurfacingConstants.NL );
2365                     w.write( "</body>" );
2366                     w.write( SurfacingConstants.NL );
2367                     w.write( "</html>" );
2368                     w.write( SurfacingConstants.NL );
2369                 }
2370                 break;
2371         }
2372         for( final Writer w : split_writers.values() ) {
2373             w.close();
2374         }
2375         return stats;
2376     }
2377
2378     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2379                                                                  final String domain_0,
2380                                                                  final String domain_1 ) throws IOException {
2381         individual_files_writer.write( domain_0 );
2382         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2383         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2384             individual_files_writer.write( domain_1 );
2385             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2386         }
2387     }
2388
2389     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2390                                           final String filename,
2391                                           final Format format ) {
2392         final File outfile = new File( filename );
2393         checkForOutputFileWriteability( outfile );
2394         try {
2395             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2396             matrix.toWriter( out, format );
2397             out.flush();
2398             out.close();
2399         }
2400         catch ( final IOException e ) {
2401             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2402         }
2403         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2404     }
2405
2406     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2407         checkForOutputFileWriteability( matrix_outfile );
2408         try {
2409             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2410             for( final DistanceMatrix distance_matrix : matrices ) {
2411                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2412                 out.write( ForesterUtil.LINE_SEPARATOR );
2413                 out.flush();
2414             }
2415             out.close();
2416         }
2417         catch ( final IOException e ) {
2418             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2419         }
2420         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2421     }
2422
2423     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2424         try {
2425             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2426             for( final String pfam : pfams ) {
2427                 writer.write( pfam );
2428                 writer.write( ForesterUtil.LINE_SEPARATOR );
2429             }
2430             writer.close();
2431             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2432                     + "]" );
2433         }
2434         catch ( final IOException e ) {
2435             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2436         }
2437     }
2438
2439     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2440         final PhylogenyWriter writer = new PhylogenyWriter();
2441         try {
2442             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2443         }
2444         catch ( final IOException e ) {
2445             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2446                     + e );
2447         }
2448         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2449     }
2450
2451     public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
2452         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2453             final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2454             writer.write( " [" );
2455             if ( matcher.matches() ) {
2456                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2457                         + "\" target=\"taxonomy_window\">uniprot</a>" );
2458             }
2459             else {
2460                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2461                         + "\" target=\"taxonomy_window\">eol</a>" );
2462                 writer.write( "|" );
2463                 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2464                         + "\" target=\"taxonomy_window\">tol</a>" );
2465             }
2466             writer.write( "]" );
2467         }
2468     }
2469
2470     private static void writeToNexus( final String outfile_name,
2471                                       final CharacterStateMatrix<BinaryStates> matrix,
2472                                       final Phylogeny phylogeny ) {
2473         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2474             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2475                     + "] to nexus" );
2476         }
2477         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2478         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2479         phylogenies.add( phylogeny );
2480         try {
2481             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2482             w.write( NexusConstants.NEXUS );
2483             w.write( ForesterUtil.LINE_SEPARATOR );
2484             my_matrix.writeNexusTaxaBlock( w );
2485             my_matrix.writeNexusBinaryChractersBlock( w );
2486             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2487             w.flush();
2488             w.close();
2489             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2490         }
2491         catch ( final IOException e ) {
2492             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2493         }
2494     }
2495
2496     private static void writeToNexus( final String outfile_name,
2497                                       final DomainParsimonyCalculator domain_parsimony,
2498                                       final Phylogeny phylogeny ) {
2499         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2500                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2501                       phylogeny );
2502         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2503                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2504                       phylogeny );
2505     }
2506
2507     public static void domainsPerProteinsStatistics( final String genome,
2508                                                      final List<Protein> protein_list,
2509                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
2510                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2511                                                      final SortedSet<String> domains_which_are_always_single,
2512                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
2513                                                      final SortedSet<String> domains_which_never_single,
2514                                                      final Writer writer ) {
2515         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2516         for( final Protein protein : protein_list ) {
2517             final int domains = protein.getNumberOfProteinDomains();
2518             //System.out.println( domains );
2519             stats.addValue( domains );
2520             all_genomes_domains_per_potein_stats.addValue( domains );
2521             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
2522                 all_genomes_domains_per_potein_histo.put( domains, 1 );
2523             }
2524             else {
2525                 all_genomes_domains_per_potein_histo.put( domains,
2526                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
2527             }
2528             if ( domains == 1 ) {
2529                 final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
2530                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2531                     if ( domains_which_never_single.contains( domain ) ) {
2532                         domains_which_never_single.remove( domain );
2533                         domains_which_are_sometimes_single_sometimes_not.add( domain );
2534                     }
2535                     else {
2536                         domains_which_are_always_single.add( domain );
2537                     }
2538                 }
2539             }
2540             else if ( domains > 1 ) {
2541                 for( final Domain d : protein.getProteinDomains() ) {
2542                     final String domain = d.getDomainId().getId();
2543                     // System.out.println( domain );
2544                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2545                         if ( domains_which_are_always_single.contains( domain ) ) {
2546                             domains_which_are_always_single.remove( domain );
2547                             domains_which_are_sometimes_single_sometimes_not.add( domain );
2548                         }
2549                         else {
2550                             domains_which_never_single.add( domain );
2551                         }
2552                     }
2553                 }
2554             }
2555         }
2556         try {
2557             writer.write( genome );
2558             writer.write( "\t" );
2559             if ( stats.getN() >= 1 ) {
2560                 writer.write( stats.arithmeticMean() + "" );
2561                 writer.write( "\t" );
2562                 if ( stats.getN() >= 2 ) {
2563                     writer.write( stats.sampleStandardDeviation() + "" );
2564                 }
2565                 else {
2566                     writer.write( "" );
2567                 }
2568                 writer.write( "\t" );
2569                 writer.write( stats.median() + "" );
2570                 writer.write( "\t" );
2571                 writer.write( stats.getN() + "" );
2572                 writer.write( "\t" );
2573                 writer.write( stats.getMin() + "" );
2574                 writer.write( "\t" );
2575                 writer.write( stats.getMax() + "" );
2576             }
2577             else {
2578                 writer.write( "\t" );
2579                 writer.write( "\t" );
2580                 writer.write( "\t" );
2581                 writer.write( "0" );
2582                 writer.write( "\t" );
2583                 writer.write( "\t" );
2584             }
2585             writer.write( "\n" );
2586         }
2587         catch ( final IOException e ) {
2588             e.printStackTrace();
2589         }
2590     }
2591 }