forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java

   1 // $Id:
   2 // $
   3 //
   4 // FORESTER -- software libraries and applications
   5 // for evolutionary biology research and applications.
   6 //
   7 // Copyright (C) 2008-2009 Christian M. Zmasek
   8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   9 // All rights reserved
  10 //
  11 // This library is free software; you can redistribute it and/or
  12 // modify it under the terms of the GNU Lesser General Public
  13 // License as published by the Free Software Foundation; either
  14 // version 2.1 of the License, or (at your option) any later version.
  15 //
  16 // This library is distributed in the hope that it will be useful,
  17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  19 // Lesser General Public License for more details.
  20 //
  21 // You should have received a copy of the GNU Lesser General Public
  22 // License along with this library; if not, write to the Free Software
  23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: www.phylosoft.org/forester
  27
  28 package org.forester.surfacing;
  29
  30 import java.io.BufferedWriter;
  31 import java.io.File;
  32 import java.io.FileWriter;
  33 import java.io.IOException;
  34 import java.io.Writer;
  35 import java.text.DecimalFormat;
  36 import java.text.NumberFormat;
  37 import java.util.ArrayList;
  38 import java.util.HashMap;
  39 import java.util.List;
  40 import java.util.Map;
  41 import java.util.Set;
  42 import java.util.SortedMap;
  43 import java.util.SortedSet;
  44 import java.util.TreeMap;
  45 import java.util.TreeSet;
  46
  47 import org.forester.go.GoId;
  48 import org.forester.go.GoTerm;
  49 import org.forester.util.BasicDescriptiveStatistics;
  50 import org.forester.util.DescriptiveStatistics;
  51 import org.forester.util.ForesterUtil;
  52
  53 /*
  54  * Poorly designed static class which essential has one method:
  55  * calculateCopyNumberDifferences.
  56  */
  57 public final class DomainCountsDifferenceUtil {
  58
  59     private final static NumberFormat          FORMATTER                                   = new DecimalFormat( "0.0E0" );
  60     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES = COPY_CALCULATION_MODE.MIN;
  61     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES   = COPY_CALCULATION_MODE.MIN;
  62     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_LOW_COPY_SPECIES         = COPY_CALCULATION_MODE.MAX;
  63     private static final String                PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX         = ".prot";
  64
  65     //FIXME really needs to be tested!
  66     private static void addCounts( final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
  67                                    final BinaryDomainCombination dc,
  68                                    final GenomeWideCombinableDomains genome,
  69                                    final Set<BinaryDomainCombination> bdc ) {
  70         if ( !copy_counts.containsKey( dc ) ) {
  71             copy_counts.put( dc, new ArrayList<Integer>() );
  72         }
  73         if ( bdc.contains( dc )
  74                 && ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
  75             final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc
  76                     .getId1() );
  77             copy_counts.get( dc ).add( count );
  78         }
  79         else {
  80             copy_counts.get( dc ).add( 0 );
  81         }
  82     }
  83
  84     private static void addCounts( final SortedMap<DomainId, List<Integer>> copy_counts,
  85                                    final DomainId domain,
  86                                    final GenomeWideCombinableDomains genome ) {
  87         if ( !copy_counts.containsKey( domain ) ) {
  88             copy_counts.put( domain, new ArrayList<Integer>() );
  89         }
  90         if ( genome.contains( domain ) ) {
  91             copy_counts.get( domain ).add( genome.get( domain ).getKeyDomainProteinsCount() );
  92         }
  93         else {
  94             copy_counts.get( domain ).add( 0 );
  95         }
  96     }
  97
  98     private static StringBuilder addGoInformation( final DomainId d,
  99                                                    final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 100                                                    final Map<GoId, GoTerm> go_id_to_term_map ) {
 101         final StringBuilder sb = new StringBuilder();
 102         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty()
 103                 || !domain_id_to_go_ids_map.containsKey( d ) ) {
 104             return sb;
 105         }
 106         final List<GoId> go_ids = domain_id_to_go_ids_map.get( d );
 107         for( int i = 0; i < go_ids.size(); ++i ) {
 108             final GoId go_id = go_ids.get( i );
 109             if ( go_id_to_term_map.containsKey( go_id ) ) {
 110                 appendGoTerm( sb, go_id_to_term_map.get( go_id ) );
 111                 sb.append( "<br>" );
 112             }
 113             else {
 114                 sb.append( "go id \"" + go_id + "\" not found [" + d.getId() + "]" );
 115             }
 116         }
 117         return sb;
 118     }
 119
 120     private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) {
 121         final GoId go_id = go_term.getGoId();
 122         sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
 123                 + "</a>" );
 124         sb.append( ":" );
 125         sb.append( go_term.getName() );
 126         sb.append( " [" );
 127         sb.append( go_term.getGoNameSpace().toShortString() );
 128         sb.append( "]" );
 129     }
 130
 131     public static void calculateCopyNumberDifferences( final List<GenomeWideCombinableDomains> genomes,
 132                                                        final SortedMap<Species, List<Protein>> protein_lists_per_species,
 133                                                        final List<String> high_copy_base_species,
 134                                                        final List<String> high_copy_target_species,
 135                                                        final List<String> low_copy_species,
 136                                                        final int min_diff,
 137                                                        final Double factor,
 138                                                        final File plain_output_dom,
 139                                                        final File html_output_dom,
 140                                                        final File html_output_dc,
 141                                                        final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 142                                                        final Map<GoId, GoTerm> go_id_to_term_map,
 143                                                        final File all_domains_go_ids_out_dom,
 144                                                        final File passing_domains_go_ids_out_dom,
 145                                                        final File proteins_file_base ) throws IOException {
 146         if ( genomes.size() < 1 ) {
 147             throw new IllegalArgumentException( "attempt to use empty list of genomes for domain difference calculation" );
 148         }
 149         if ( ( high_copy_base_species.size() < 1 ) || ( low_copy_species.size() < 1 ) ) {
 150             throw new IllegalArgumentException( "attempt to use empty list of species for domain difference calculation" );
 151         }
 152         if ( high_copy_base_species.contains( high_copy_target_species )
 153                 || low_copy_species.contains( high_copy_target_species ) ) {
 154             throw new IllegalArgumentException( "species [" + high_copy_target_species
 155                     + "] appears in other list as well" );
 156         }
 157         if ( min_diff < 0 ) {
 158             throw new IllegalArgumentException( "attempt to use negative addition [" + min_diff + "]" );
 159         }
 160         if ( factor <= 0.0 ) {
 161             throw new IllegalArgumentException( "attempt to use factor equal or smaller than 0.0 [" + factor + "]" );
 162         }
 163         SurfacingUtil.checkForOutputFileWriteability( plain_output_dom );
 164         SurfacingUtil.checkForOutputFileWriteability( html_output_dom );
 165         SurfacingUtil.checkForOutputFileWriteability( html_output_dc );
 166         SurfacingUtil.checkForOutputFileWriteability( all_domains_go_ids_out_dom );
 167         SurfacingUtil.checkForOutputFileWriteability( passing_domains_go_ids_out_dom );
 168         final Writer plain_writer = new BufferedWriter( new FileWriter( plain_output_dom ) );
 169         final Writer html_writer = new BufferedWriter( new FileWriter( html_output_dom ) );
 170         final Writer html_writer_dc = new BufferedWriter( new FileWriter( html_output_dc ) );
 171         final Writer all_gos_writer = new BufferedWriter( new FileWriter( all_domains_go_ids_out_dom ) );
 172         final Writer passing_gos_writer = new BufferedWriter( new FileWriter( passing_domains_go_ids_out_dom ) );
 173         final SortedMap<DomainId, Double> high_copy_base_values = new TreeMap<DomainId, Double>();
 174         final SortedMap<DomainId, Double> high_copy_target_values = new TreeMap<DomainId, Double>();
 175         final SortedMap<DomainId, Double> low_copy_values = new TreeMap<DomainId, Double>();
 176         final SortedMap<DomainId, List<Integer>> high_copy_base_copy_counts = new TreeMap<DomainId, List<Integer>>();
 177         final SortedMap<DomainId, List<Integer>> high_copy_target_copy_counts = new TreeMap<DomainId, List<Integer>>();
 178         final SortedMap<DomainId, List<Integer>> low_copy_copy_counts = new TreeMap<DomainId, List<Integer>>();
 179         final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
 180         final SortedMap<BinaryDomainCombination, Double> high_copy_base_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 181         final SortedMap<BinaryDomainCombination, Double> high_copy_target_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 182         final SortedMap<BinaryDomainCombination, Double> low_copy_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 183         final SortedMap<BinaryDomainCombination, List<Integer>> high_copy_base_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 184         final SortedMap<BinaryDomainCombination, List<Integer>> high_copy_target_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 185         final SortedMap<BinaryDomainCombination, List<Integer>> low_copy_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 186         final SortedSet<BinaryDomainCombination> all_dcs = new TreeSet<BinaryDomainCombination>();
 187         final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome = new HashMap<String, Set<BinaryDomainCombination>>();
 188         final SortedSet<GoId> go_ids_of_passing_domains = new TreeSet<GoId>();
 189         final SortedSet<GoId> go_ids_all = new TreeSet<GoId>();
 190         for( final GenomeWideCombinableDomains genome : genomes ) {
 191             final SortedSet<DomainId> domains = genome.getAllDomainIds();
 192             final SortedSet<BinaryDomainCombination> dcs = genome.toBinaryDomainCombinations();
 193             final String species = genome.getSpecies().getSpeciesId();
 194             bdcs_per_genome.put( species, genome.toBinaryDomainCombinations() );
 195             for( final DomainId d : domains ) {
 196                 all_domains.add( d );
 197                 if ( domain_id_to_go_ids_map.containsKey( d ) ) {
 198                     go_ids_all.addAll( domain_id_to_go_ids_map.get( d ) );
 199                 }
 200             }
 201             for( final BinaryDomainCombination dc : dcs ) {
 202                 all_dcs.add( dc );
 203             }
 204         }
 205         for( final DomainId domain : all_domains ) {
 206             for( final GenomeWideCombinableDomains genome : genomes ) {
 207                 final String species = genome.getSpecies().getSpeciesId();
 208                 if ( high_copy_base_species.contains( species ) ) {
 209                     DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts, domain, genome );
 210                 }
 211                 if ( high_copy_target_species.contains( species ) ) {
 212                     DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts, domain, genome );
 213                 }
 214                 if ( low_copy_species.contains( species ) ) {
 215                     DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts, domain, genome );
 216                 }
 217             }
 218         }
 219         for( final BinaryDomainCombination dc : all_dcs ) {
 220             for( final GenomeWideCombinableDomains genome : genomes ) {
 221                 final String species = genome.getSpecies().getSpeciesId();
 222                 if ( high_copy_base_species.contains( species ) ) {
 223                     DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc, dc, genome, bdcs_per_genome
 224                             .get( species ) );
 225                 }
 226                 if ( high_copy_target_species.contains( species ) ) {
 227                     DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc, dc, genome, bdcs_per_genome
 228                             .get( species ) );
 229                 }
 230                 if ( low_copy_species.contains( species ) ) {
 231                     DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc, dc, genome, bdcs_per_genome
 232                             .get( species ) );
 233                 }
 234             }
 235         }
 236         for( final DomainId domain : all_domains ) {
 237             calculateDomainCountsBasedValue( high_copy_target_values,
 238                                              high_copy_target_copy_counts,
 239                                              domain,
 240                                              COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 241             calculateDomainCountsBasedValue( high_copy_base_values,
 242                                              high_copy_base_copy_counts,
 243                                              domain,
 244                                              COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 245             calculateDomainCountsBasedValue( low_copy_values,
 246                                              low_copy_copy_counts,
 247                                              domain,
 248                                              COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 249         }
 250         for( final BinaryDomainCombination dc : all_dcs ) {
 251             calculateDomainCountsBasedValue( high_copy_target_values_dc,
 252                                              high_copy_target_copy_counts_dc,
 253                                              dc,
 254                                              COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 255             calculateDomainCountsBasedValue( high_copy_base_values_dc,
 256                                              high_copy_base_copy_counts_dc,
 257                                              dc,
 258                                              COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 259             calculateDomainCountsBasedValue( low_copy_values_dc,
 260                                              low_copy_copy_counts_dc,
 261                                              dc,
 262                                              COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 263         }
 264         writeDomainValuesToFiles( genomes,
 265                                   high_copy_base_species,
 266                                   high_copy_target_species,
 267                                   low_copy_species,
 268                                   min_diff,
 269                                   factor,
 270                                   domain_id_to_go_ids_map,
 271                                   go_id_to_term_map,
 272                                   plain_writer,
 273                                   html_writer,
 274                                   proteins_file_base,
 275                                   high_copy_base_values,
 276                                   high_copy_target_values,
 277                                   low_copy_values,
 278                                   all_domains,
 279                                   go_ids_of_passing_domains,
 280                                   protein_lists_per_species );
 281         writeDomainCombinationValuesToFiles( genomes,
 282                                              high_copy_base_species,
 283                                              high_copy_target_species,
 284                                              low_copy_species,
 285                                              min_diff,
 286                                              factor,
 287                                              html_writer_dc,
 288                                              high_copy_base_values_dc,
 289                                              high_copy_target_values_dc,
 290                                              low_copy_values_dc,
 291                                              all_dcs,
 292                                              bdcs_per_genome );
 293         writeGoIdsToFile( all_gos_writer, go_ids_all );
 294         writeGoIdsToFile( passing_gos_writer, go_ids_of_passing_domains );
 295     }
 296
 297     private static void calculateDomainCountsBasedValue( final SortedMap<BinaryDomainCombination, Double> copy_values,
 298                                                          final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 299                                                          final BinaryDomainCombination bdc,
 300                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
 301         if ( copy_counts.containsKey( bdc ) ) {
 302             switch ( copy_calc_mode ) {
 303                 case MAX:
 304                     DomainCountsDifferenceUtil.calculateMaxCount( copy_values, copy_counts, bdc );
 305                     break;
 306                 case MIN:
 307                     DomainCountsDifferenceUtil.calculateMinCount( copy_values, copy_counts, bdc );
 308                     break;
 309                 case MEAN:
 310                     DomainCountsDifferenceUtil.calculateMeanCount( copy_values, copy_counts, bdc );
 311                     break;
 312                 case MEDIAN:
 313                     DomainCountsDifferenceUtil.calculateMedianCount( copy_values, copy_counts, bdc );
 314                     break;
 315                 default:
 316                     throw new IllegalArgumentException();
 317             }
 318         }
 319         else {
 320             copy_values.put( bdc, Double.valueOf( 0.0 ) );
 321         }
 322     }
 323
 324     private static void calculateDomainCountsBasedValue( final SortedMap<DomainId, Double> copy_values,
 325                                                          final SortedMap<DomainId, List<Integer>> copy_counts,
 326                                                          final DomainId domain,
 327                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
 328         if ( copy_counts.containsKey( domain ) ) {
 329             switch ( copy_calc_mode ) {
 330                 case MAX:
 331                     DomainCountsDifferenceUtil.calculateMaxCount( copy_values, copy_counts, domain );
 332                     break;
 333                 case MIN:
 334                     DomainCountsDifferenceUtil.calculateMinCount( copy_values, copy_counts, domain );
 335                     break;
 336                 case MEAN:
 337                     DomainCountsDifferenceUtil.calculateMeanCount( copy_values, copy_counts, domain );
 338                     break;
 339                 case MEDIAN:
 340                     DomainCountsDifferenceUtil.calculateMedianCount( copy_values, copy_counts, domain );
 341                     break;
 342                 default:
 343                     throw new IllegalArgumentException();
 344             }
 345         }
 346         else {
 347             copy_values.put( domain, Double.valueOf( 0.0 ) );
 348         }
 349     }
 350
 351     private static void calculateMaxCount( final SortedMap<BinaryDomainCombination, Double> results,
 352                                            final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 353                                            final BinaryDomainCombination bdc ) {
 354         final List<Integer> counts = copy_counts.get( bdc );
 355         int max = 0;
 356         for( final Integer count : counts ) {
 357             if ( count > max ) {
 358                 max = count;
 359             }
 360         }
 361         results.put( bdc, ( double ) max );
 362     }
 363
 364     private static void calculateMaxCount( final SortedMap<DomainId, Double> results,
 365                                            final SortedMap<DomainId, List<Integer>> copy_counts,
 366                                            final DomainId domain ) {
 367         final List<Integer> counts = copy_counts.get( domain );
 368         int max = 0;
 369         for( final Integer count : counts ) {
 370             if ( count > max ) {
 371                 max = count;
 372             }
 373         }
 374         results.put( domain, ( double ) max );
 375     }
 376
 377     private static void calculateMeanCount( final SortedMap<BinaryDomainCombination, Double> results,
 378                                             final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 379                                             final BinaryDomainCombination bdc ) {
 380         final List<Integer> counts = copy_counts.get( bdc );
 381         int sum = 0;
 382         for( final Integer count : counts ) {
 383             sum += count;
 384         }
 385         results.put( bdc, ( ( double ) sum ) / ( ( double ) counts.size() ) );
 386     }
 387
 388     private static void calculateMeanCount( final SortedMap<DomainId, Double> results,
 389                                             final SortedMap<DomainId, List<Integer>> copy_counts,
 390                                             final DomainId domain ) {
 391         final List<Integer> counts = copy_counts.get( domain );
 392         int sum = 0;
 393         for( final Integer count : counts ) {
 394             sum += count;
 395         }
 396         results.put( domain, ( ( double ) sum ) / ( ( double ) counts.size() ) );
 397     }
 398
 399     private static void calculateMedianCount( final SortedMap<BinaryDomainCombination, Double> results,
 400                                               final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 401                                               final BinaryDomainCombination bdc ) {
 402         final List<Integer> counts = copy_counts.get( bdc );
 403         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 404         for( final Integer count : counts ) {
 405             stats.addValue( count );
 406         }
 407         results.put( bdc, stats.median() );
 408     }
 409
 410     private static void calculateMedianCount( final SortedMap<DomainId, Double> results,
 411                                               final SortedMap<DomainId, List<Integer>> copy_counts,
 412                                               final DomainId domain ) {
 413         final List<Integer> counts = copy_counts.get( domain );
 414         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 415         for( final Integer count : counts ) {
 416             stats.addValue( count );
 417         }
 418         results.put( domain, stats.median() );
 419     }
 420
 421     private static void calculateMinCount( final SortedMap<BinaryDomainCombination, Double> results,
 422                                            final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 423                                            final BinaryDomainCombination bdc ) {
 424         final List<Integer> counts = copy_counts.get( bdc );
 425         int min = Integer.MAX_VALUE;
 426         for( final Integer count : counts ) {
 427             if ( count < min ) {
 428                 min = count;
 429             }
 430         }
 431         results.put( bdc, ( double ) min );
 432     }
 433
 434     private static void calculateMinCount( final SortedMap<DomainId, Double> results,
 435                                            final SortedMap<DomainId, List<Integer>> copy_counts,
 436                                            final DomainId domain ) {
 437         final List<Integer> counts = copy_counts.get( domain );
 438         int min = Integer.MAX_VALUE;
 439         for( final Integer count : counts ) {
 440             if ( count < min ) {
 441                 min = count;
 442             }
 443         }
 444         results.put( domain, ( double ) min );
 445     }
 446
 447     private static String combinableDomaindToString( final CombinableDomains cd ) {
 448         final StringBuilder sb = new StringBuilder();
 449         sb.append( cd.getKeyDomainProteinsCount() );
 450         sb.append( "\t[" );
 451         sb.append( FORMATTER.format( cd.getKeyDomainConfidenceDescriptiveStatistics().median() ) );
 452         sb.append( "]" );
 453         return sb.toString();
 454     }
 455
 456     private static String combinableDomaindToStringHtml( final CombinableDomains cd ) {
 457         final StringBuilder sb = new StringBuilder();
 458         sb.append( "[" );
 459         sb.append( cd.getKeyDomainCount() );
 460         sb.append( ", <b>" );
 461         sb.append( cd.getKeyDomainProteinsCount() );
 462         sb.append( "</b>, " );
 463         sb.append( cd.getNumberOfCombinableDomains() );
 464         sb.append( "]</td><td>[" );
 465         sb.append( FORMATTER.format( cd.getKeyDomainConfidenceDescriptiveStatistics().median() ) );
 466         sb.append( "]</td><td>" );
 467         sb.append( cd.getCombiningDomainIdsAsStringBuilder() );
 468         return sb.toString();
 469     }
 470
 471     private static void writeCopyNumberValues( final SortedMap<BinaryDomainCombination, Double> copy_means,
 472                                                final BinaryDomainCombination bdc,
 473                                                final GenomeWideCombinableDomains genome,
 474                                                final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome,
 475                                                final String species,
 476                                                final Writer html_writer,
 477                                                final String color ) throws IOException {
 478         html_writer.write( "<td> " );
 479         if ( !ForesterUtil.isEmpty( color ) ) {
 480             html_writer.write( "<font color=\"" + color + "\">" );
 481         }
 482         html_writer.write( "<b>" + species + ":</b> " );
 483         if ( !ForesterUtil.isEmpty( color ) ) {
 484             html_writer.write( "</font>" );
 485         }
 486         html_writer.write( "</td><td>" );
 487         if ( bdcs_per_genome.get( species ).contains( bdc ) && ( copy_means.get( bdc ) > 0 ) ) {
 488             final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains().get( bdc
 489                     .getId1() );
 490             html_writer.write( count + "" );
 491         }
 492         else {
 493             html_writer.write( "0" );
 494         }
 495         html_writer.write( "</td>" );
 496     }
 497
 498     private static void writeCopyNumberValues( final SortedMap<DomainId, Double> copy_means,
 499                                                final DomainId domain,
 500                                                final GenomeWideCombinableDomains genome,
 501                                                final String species,
 502                                                final Writer plain_writer,
 503                                                final Writer html_writer,
 504                                                final String color ) throws IOException {
 505         plain_writer.write( "  " + species + "\t" );
 506         html_writer.write( "<td> " );
 507         if ( !ForesterUtil.isEmpty( color ) ) {
 508             html_writer.write( "<font color=\"" + color + "\">" );
 509         }
 510         html_writer.write( "<b>" + species + ":</b> " );
 511         if ( !ForesterUtil.isEmpty( color ) ) {
 512             html_writer.write( "</font>" );
 513         }
 514         html_writer.write( "</td><td>" );
 515         if ( genome.contains( domain ) && ( copy_means.get( domain ) > 0 ) ) {
 516             plain_writer.write( DomainCountsDifferenceUtil.combinableDomaindToString( genome.get( domain ) ) );
 517             html_writer.write( DomainCountsDifferenceUtil.combinableDomaindToStringHtml( genome.get( domain ) ) );
 518         }
 519         else {
 520             plain_writer.write( "0" );
 521             html_writer.write( "0" );
 522         }
 523         html_writer.write( "</td>" );
 524         plain_writer.write( SurfacingConstants.NL );
 525     }
 526
 527     private static void writeDomainCombinationValuesToFiles( final List<GenomeWideCombinableDomains> genomes,
 528                                                              final List<String> high_copy_base_species,
 529                                                              final List<String> high_copy_target_species,
 530                                                              final List<String> low_copy_species,
 531                                                              final int min_diff,
 532                                                              final Double factor,
 533                                                              final Writer html_writer,
 534                                                              final SortedMap<BinaryDomainCombination, Double> high_copy_base_values,
 535                                                              final SortedMap<BinaryDomainCombination, Double> high_copy_target_values,
 536                                                              final SortedMap<BinaryDomainCombination, Double> low_copy_values,
 537                                                              final SortedSet<BinaryDomainCombination> all_bdcs,
 538                                                              final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome )
 539             throws IOException {
 540         int counter = 0;
 541         int total_absense_counter = 0;
 542         int not_total_absense_counter = 0;
 543         SurfacingUtil.addHtmlHead( html_writer, "Binary Domain Combination Copy Differences" );
 544         html_writer.write( "<body><table>" );
 545         for( final BinaryDomainCombination bdc : all_bdcs ) {
 546             if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
 547                     && ( high_copy_base_values.get( bdc ) >= low_copy_values.get( bdc ) ) ) {
 548                 if ( high_copy_target_values.get( bdc ) >= min_diff + ( factor * low_copy_values.get( bdc ) ) ) {
 549                     if ( low_copy_values.get( bdc ) <= 0.0 ) {
 550                         ++total_absense_counter;
 551                     }
 552                     else {
 553                         ++not_total_absense_counter;
 554                     }
 555                     ++counter;
 556                     html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + bdc.getId0()
 557                             + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
 558                             + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
 559                     html_writer.write( "</td><td>" );
 560                     html_writer.write( "<table>" );
 561                     for( final GenomeWideCombinableDomains genome : genomes ) {
 562                         final String species = genome.getSpecies().getSpeciesId();
 563                         if ( high_copy_target_species.contains( species ) ) {
 564                             html_writer.write( "<tr>" );
 565                             writeCopyNumberValues( high_copy_target_values,
 566                                                    bdc,
 567                                                    genome,
 568                                                    bdcs_per_genome,
 569                                                    species,
 570                                                    html_writer,
 571                                                    "#0000FF" );
 572                             html_writer.write( "</tr>" );
 573                         }
 574                         else if ( low_copy_species.contains( species ) ) {
 575                             html_writer.write( "<tr>" );
 576                             writeCopyNumberValues( low_copy_values,
 577                                                    bdc,
 578                                                    genome,
 579                                                    bdcs_per_genome,
 580                                                    species,
 581                                                    html_writer,
 582                                                    "#A0A0A0" );
 583                             html_writer.write( "</tr>" );
 584                         }
 585                         else if ( high_copy_base_species.contains( species ) ) {
 586                             html_writer.write( "<tr>" );
 587                             writeCopyNumberValues( high_copy_base_values,
 588                                                    bdc,
 589                                                    genome,
 590                                                    bdcs_per_genome,
 591                                                    species,
 592                                                    html_writer,
 593                                                    "#404040" );
 594                             html_writer.write( "</tr>" );
 595                         }
 596                     }
 597                     html_writer.write( "</table>" );
 598                     html_writer.write( "</td></tr>" );
 599                     html_writer.write( SurfacingConstants.NL );
 600                 }
 601             }
 602         }
 603         html_writer.write( "</table>" );
 604         html_writer.write( SurfacingConstants.NL );
 605         html_writer.write( "<hr>" );
 606         html_writer.write( SurfacingConstants.NL );
 607         html_writer.write( "Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 608         html_writer.write( "<br>" );
 609         html_writer.write( SurfacingConstants.NL );
 610         html_writer.write( "Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 611         html_writer.write( "<br>" );
 612         html_writer.write( SurfacingConstants.NL );
 613         html_writer.write( "Calculation mode for high copy target : " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 614         html_writer.write( SurfacingConstants.NL );
 615         html_writer.write( "<br>" );
 616         html_writer.write( "Calculation mode for high copy base : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 617         html_writer.write( SurfacingConstants.NL );
 618         html_writer.write( "<br>" );
 619         html_writer.write( "Calculation mode for low copy : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 620         html_writer.write( SurfacingConstants.NL );
 621         html_writer.write( "<br>" );
 622         html_writer.write( "Minimal difference : " + min_diff );
 623         html_writer.write( SurfacingConstants.NL );
 624         html_writer.write( "<br>" );
 625         html_writer.write( "Factor : " + factor );
 626         html_writer.write( SurfacingConstants.NL );
 627         html_writer.write( "<br>" );
 628         html_writer.write( "Lower copy binary domain combinations : " + counter );
 629         html_writer.write( SurfacingConstants.NL );
 630         html_writer.write( "<br>" );
 631         html_writer.write( "Total absence : " + total_absense_counter );
 632         html_writer.write( SurfacingConstants.NL );
 633         html_writer.write( "<br>" );
 634         html_writer.write( "Not total absence : " + not_total_absense_counter );
 635         html_writer.write( SurfacingConstants.NL );
 636         html_writer.write( "<br>" );
 637         html_writer.write( "Total binary domain combinations : " + all_bdcs.size() );
 638         html_writer.write( SurfacingConstants.NL );
 639         html_writer.write( "<hr>" );
 640         html_writer.write( SurfacingConstants.NL );
 641         html_writer.write( "</body></html>" );
 642         html_writer.write( SurfacingConstants.NL );
 643         html_writer.close();
 644     }
 645
 646     private static void writeDomainValuesToFiles( final List<GenomeWideCombinableDomains> genomes,
 647                                                   final List<String> high_copy_base_species,
 648                                                   final List<String> high_copy_target_species,
 649                                                   final List<String> low_copy_species,
 650                                                   final int min_diff,
 651                                                   final Double factor,
 652                                                   final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 653                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 654                                                   final Writer plain_writer,
 655                                                   final Writer html_writer,
 656                                                   final File proteins_file_base,
 657                                                   final SortedMap<DomainId, Double> high_copy_base_values,
 658                                                   final SortedMap<DomainId, Double> high_copy_target_values,
 659                                                   final SortedMap<DomainId, Double> low_copy_values,
 660                                                   final SortedSet<DomainId> all_domains,
 661                                                   final SortedSet<GoId> go_ids_of_passing_domains,
 662                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species )
 663             throws IOException {
 664         int counter = 0;
 665         int total_absense_counter = 0;
 666         int not_total_absense_counter = 0;
 667         SurfacingUtil.addHtmlHead( html_writer, "Domain Copy Differences" );
 668         html_writer.write( "<body><table>" );
 669         for( final DomainId domain_id : all_domains ) {
 670             if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
 671                     && ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
 672                 if ( high_copy_target_values.get( domain_id ) >= min_diff
 673                         + ( factor * low_copy_values.get( domain_id ) ) ) {
 674                     if ( low_copy_values.get( domain_id ) <= 0.0 ) {
 675                         ++total_absense_counter;
 676                     }
 677                     else {
 678                         ++not_total_absense_counter;
 679                     }
 680                     ++counter;
 681                     writeProteinsToFile( proteins_file_base, protein_lists_per_species, domain_id );
 682                     if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
 683                         go_ids_of_passing_domains.addAll( domain_id_to_go_ids_map.get( domain_id ) );
 684                     }
 685                     plain_writer.write( domain_id.getId() );
 686                     plain_writer.write( SurfacingConstants.NL );
 687                     html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
 688                             + domain_id.getId() + "\">" + domain_id.getId() + "</a></td><td>" );
 689                     html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map )
 690                             .toString() );
 691                     html_writer.write( "</td><td>" );
 692                     html_writer.write( "<table>" );
 693                     for( final GenomeWideCombinableDomains genome : genomes ) {
 694                         final String species = genome.getSpecies().getSpeciesId();
 695                         if ( high_copy_target_species.contains( species ) ) {
 696                             html_writer.write( "<tr>" );
 697                             writeCopyNumberValues( high_copy_target_values,
 698                                                    domain_id,
 699                                                    genome,
 700                                                    species,
 701                                                    plain_writer,
 702                                                    html_writer,
 703                                                    "#0000FF" );
 704                             html_writer.write( "</tr>" );
 705                         }
 706                         else if ( low_copy_species.contains( species ) ) {
 707                             html_writer.write( "<tr>" );
 708                             writeCopyNumberValues( low_copy_values,
 709                                                    domain_id,
 710                                                    genome,
 711                                                    species,
 712                                                    plain_writer,
 713                                                    html_writer,
 714                                                    "#A0A0A0" );
 715                             html_writer.write( "</tr>" );
 716                         }
 717                         else if ( high_copy_base_species.contains( species ) ) {
 718                             html_writer.write( "<tr>" );
 719                             writeCopyNumberValues( high_copy_base_values,
 720                                                    domain_id,
 721                                                    genome,
 722                                                    species,
 723                                                    plain_writer,
 724                                                    html_writer,
 725                                                    "#404040" );
 726                             html_writer.write( "</tr>" );
 727                         }
 728                     }
 729                     html_writer.write( "</table>" );
 730                     html_writer.write( "</td></tr>" );
 731                     html_writer.write( SurfacingConstants.NL );
 732                     plain_writer.write( SurfacingConstants.NL );
 733                 }
 734             }
 735         }
 736         html_writer.write( "</table>" );
 737         html_writer.write( SurfacingConstants.NL );
 738         html_writer.write( "<hr>" );
 739         html_writer.write( SurfacingConstants.NL );
 740         html_writer.write( "Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 741         html_writer.write( "<br>" );
 742         html_writer.write( SurfacingConstants.NL );
 743         html_writer.write( "Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 744         html_writer.write( "<br>" );
 745         html_writer.write( SurfacingConstants.NL );
 746         html_writer.write( "Calculation mode for high copy target : " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 747         html_writer.write( SurfacingConstants.NL );
 748         html_writer.write( "<br>" );
 749         html_writer.write( "Calculation mode for high copy base : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 750         html_writer.write( SurfacingConstants.NL );
 751         html_writer.write( "<br>" );
 752         html_writer.write( "Calculation mode for low copy : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 753         html_writer.write( SurfacingConstants.NL );
 754         html_writer.write( "<br>" );
 755         html_writer.write( "Minimal difference : " + min_diff );
 756         html_writer.write( SurfacingConstants.NL );
 757         html_writer.write( "<br>" );
 758         html_writer.write( "Factor : " + factor );
 759         html_writer.write( SurfacingConstants.NL );
 760         html_writer.write( "<br>" );
 761         html_writer.write( "Lower copy domains : " + counter );
 762         html_writer.write( SurfacingConstants.NL );
 763         html_writer.write( "<br>" );
 764         html_writer.write( "Total absence : " + total_absense_counter );
 765         html_writer.write( SurfacingConstants.NL );
 766         html_writer.write( "<br>" );
 767         html_writer.write( "Not total absence : " + not_total_absense_counter );
 768         html_writer.write( SurfacingConstants.NL );
 769         html_writer.write( "<br>" );
 770         html_writer.write( "Total domains : " + all_domains.size() );
 771         html_writer.write( SurfacingConstants.NL );
 772         html_writer.write( "<hr>" );
 773         html_writer.write( SurfacingConstants.NL );
 774         html_writer.write( "</body></html>" );
 775         html_writer.write( SurfacingConstants.NL );
 776         html_writer.close();
 777         plain_writer.write( "# Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 778         plain_writer.write( SurfacingConstants.NL );
 779         plain_writer.write( "# Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 780         plain_writer.write( SurfacingConstants.NL );
 781         plain_writer.write( "# Calculation mode for high copy target: " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 782         plain_writer.write( SurfacingConstants.NL );
 783         plain_writer.write( "# Calculation mode for high copy base  : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 784         plain_writer.write( SurfacingConstants.NL );
 785         plain_writer.write( "# Calculation mode for low copy        : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 786         plain_writer.write( SurfacingConstants.NL );
 787         plain_writer.write( "# Minimal difference: " + min_diff );
 788         plain_writer.write( SurfacingConstants.NL );
 789         plain_writer.write( "# Factor            : " + factor );
 790         plain_writer.write( SurfacingConstants.NL );
 791         plain_writer.write( "# Lower copy domains: " + counter );
 792         plain_writer.write( SurfacingConstants.NL );
 793         plain_writer.write( "# Total absence     : " + total_absense_counter );
 794         plain_writer.write( SurfacingConstants.NL );
 795         plain_writer.write( "# Not total absence : " + not_total_absense_counter );
 796         plain_writer.write( SurfacingConstants.NL );
 797         plain_writer.write( "# Total domains     : " + all_domains.size() );
 798         plain_writer.write( SurfacingConstants.NL );
 799         plain_writer.close();
 800     }
 801
 802     private static void writeGoIdsToFile( final Writer writer, final SortedSet<GoId> gos ) throws IOException {
 803         for( final GoId go_id : gos ) {
 804             writer.write( go_id.toString() );
 805             writer.write( SurfacingConstants.NL );
 806         }
 807         writer.close();
 808     }
 809
 810     private static void writeProteinsToFile( final File proteins_file_base,
 811                                              final SortedMap<Species, List<Protein>> protein_lists_per_species,
 812                                              final DomainId domain_id ) throws IOException {
 813         final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR
 814                 + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
 815         SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
 816         final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
 817         SurfacingUtil.extractProteinNames( protein_lists_per_species, domain_id, proteins_file_writer, "\t" );
 818         proteins_file_writer.close();
 819         System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
 820     }
 821
 822     public static enum COPY_CALCULATION_MODE {
 823         MEAN, MEDIAN, MAX, MIN
 824     }
 825 }