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: https://sites.google.com/site/cmzmasek/home/software/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.util.ArrayList;
  36 import java.util.HashMap;
  37 import java.util.List;
  38 import java.util.Map;
  39 import java.util.Set;
  40 import java.util.SortedMap;
  41 import java.util.SortedSet;
  42 import java.util.TreeMap;
  43 import java.util.TreeSet;
  44
  45 import org.forester.application.surfacing;
  46 import org.forester.go.GoId;
  47 import org.forester.go.GoTerm;
  48 import org.forester.protein.BinaryDomainCombination;
  49 import org.forester.protein.Protein;
  50 import org.forester.species.Species;
  51 import org.forester.util.BasicDescriptiveStatistics;
  52 import org.forester.util.DescriptiveStatistics;
  53 import org.forester.util.ForesterUtil;
  54
  55 /*
  56  * Poorly designed static class which essential has one method:
  57  * calculateCopyNumberDifferences.
  58  */
  59 public final class DomainCountsDifferenceUtil {
  60
  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_HIGH_COPY_TARGET_SPECIES = COPY_CALCULATION_MODE.MIN;
  63     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_LOW_COPY_SPECIES         = COPY_CALCULATION_MODE.MAX;
  64     private static final String                PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX         = ".prot";
  65
  66     public static void calculateCopyNumberDifferences( final List<GenomeWideCombinableDomains> genomes,
  67                                                        final SortedMap<Species, List<Protein>> protein_lists_per_species,
  68                                                        final List<String> high_copy_base_species,
  69                                                        final List<String> high_copy_target_species,
  70                                                        final List<String> low_copy_species,
  71                                                        final int min_diff,
  72                                                        final Double factor,
  73                                                        final File plain_output_dom,
  74                                                        final File html_output_dom,
  75                                                        final File html_output_dc,
  76                                                        final Map<String, List<GoId>> domain_id_to_go_ids_map,
  77                                                        final Map<GoId, GoTerm> go_id_to_term_map,
  78                                                        final File all_domains_go_ids_out_dom,
  79                                                        final File passing_domains_go_ids_out_dom,
  80                                                        final File proteins_file_base ) throws IOException {
  81         if ( genomes.size() < 1 ) {
  82             throw new IllegalArgumentException( "attempt to use empty list of genomes for domain difference calculation" );
  83         }
  84         if ( ( high_copy_base_species.size() < 1 ) || ( low_copy_species.size() < 1 ) ) {
  85             throw new IllegalArgumentException( "attempt to use empty list of species for domain difference calculation" );
  86         }
  87         if ( high_copy_base_species.contains( high_copy_target_species )
  88                 || low_copy_species.contains( high_copy_target_species ) ) {
  89             throw new IllegalArgumentException( "species [" + high_copy_target_species
  90                     + "] appears in other list as well" );
  91         }
  92         if ( min_diff < 0 ) {
  93             throw new IllegalArgumentException( "attempt to use negative addition [" + min_diff + "]" );
  94         }
  95         if ( factor <= 0.0 ) {
  96             throw new IllegalArgumentException( "attempt to use factor equal or smaller than 0.0 [" + factor + "]" );
  97         }
  98         SurfacingUtil.checkForOutputFileWriteability( plain_output_dom );
  99         SurfacingUtil.checkForOutputFileWriteability( html_output_dom );
 100         SurfacingUtil.checkForOutputFileWriteability( html_output_dc );
 101         SurfacingUtil.checkForOutputFileWriteability( all_domains_go_ids_out_dom );
 102         SurfacingUtil.checkForOutputFileWriteability( passing_domains_go_ids_out_dom );
 103         final Writer plain_writer = new BufferedWriter( new FileWriter( plain_output_dom ) );
 104         final Writer html_writer = new BufferedWriter( new FileWriter( html_output_dom ) );
 105         final Writer html_writer_dc = new BufferedWriter( new FileWriter( html_output_dc ) );
 106         final Writer all_gos_writer = new BufferedWriter( new FileWriter( all_domains_go_ids_out_dom ) );
 107         final Writer passing_gos_writer = new BufferedWriter( new FileWriter( passing_domains_go_ids_out_dom ) );
 108         final SortedMap<String, Double> high_copy_base_values = new TreeMap<String, Double>();
 109         final SortedMap<String, Double> high_copy_target_values = new TreeMap<String, Double>();
 110         final SortedMap<String, Double> low_copy_values = new TreeMap<String, Double>();
 111         final SortedMap<String, List<Integer>> high_copy_base_copy_counts = new TreeMap<String, List<Integer>>();
 112         final SortedMap<String, List<Integer>> high_copy_target_copy_counts = new TreeMap<String, List<Integer>>();
 113         final SortedMap<String, List<Integer>> low_copy_copy_counts = new TreeMap<String, List<Integer>>();
 114         final SortedSet<String> all_domains = new TreeSet<String>();
 115         final SortedMap<BinaryDomainCombination, Double> high_copy_base_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 116         final SortedMap<BinaryDomainCombination, Double> high_copy_target_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 117         final SortedMap<BinaryDomainCombination, Double> low_copy_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 118         final SortedMap<BinaryDomainCombination, List<Integer>> high_copy_base_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 119         final SortedMap<BinaryDomainCombination, List<Integer>> high_copy_target_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 120         final SortedMap<BinaryDomainCombination, List<Integer>> low_copy_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 121         final SortedSet<BinaryDomainCombination> all_dcs = new TreeSet<BinaryDomainCombination>();
 122         final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome = new HashMap<String, Set<BinaryDomainCombination>>();
 123         final SortedSet<GoId> go_ids_of_passing_domains = new TreeSet<GoId>();
 124         final SortedSet<GoId> go_ids_all = new TreeSet<GoId>();
 125         for( final GenomeWideCombinableDomains genome : genomes ) {
 126             final SortedSet<String> domains = genome.getAllDomainIds();
 127             final SortedSet<BinaryDomainCombination> dcs = genome.toBinaryDomainCombinations();
 128             final String species = genome.getSpecies().getSpeciesId();
 129             bdcs_per_genome.put( species, genome.toBinaryDomainCombinations() );
 130             for( final String d : domains ) {
 131                 all_domains.add( d );
 132                 if ( domain_id_to_go_ids_map.containsKey( d ) ) {
 133                     go_ids_all.addAll( domain_id_to_go_ids_map.get( d ) );
 134                 }
 135             }
 136             for( final BinaryDomainCombination dc : dcs ) {
 137                 all_dcs.add( dc );
 138             }
 139         }
 140         for( final String domain : all_domains ) {
 141             for( final GenomeWideCombinableDomains genome : genomes ) {
 142                 final String species = genome.getSpecies().getSpeciesId();
 143                 if ( high_copy_base_species.contains( species ) ) {
 144                     DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts, domain, genome );
 145                 }
 146                 if ( high_copy_target_species.contains( species ) ) {
 147                     DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts, domain, genome );
 148                 }
 149                 if ( low_copy_species.contains( species ) ) {
 150                     DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts, domain, genome );
 151                 }
 152             }
 153         }
 154         for( final BinaryDomainCombination dc : all_dcs ) {
 155             for( final GenomeWideCombinableDomains genome : genomes ) {
 156                 final String species = genome.getSpecies().getSpeciesId();
 157                 if ( high_copy_base_species.contains( species ) ) {
 158                     DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc,
 159                                                           dc,
 160                                                           genome,
 161                                                           bdcs_per_genome.get( species ) );
 162                 }
 163                 if ( high_copy_target_species.contains( species ) ) {
 164                     DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc,
 165                                                           dc,
 166                                                           genome,
 167                                                           bdcs_per_genome.get( species ) );
 168                 }
 169                 if ( low_copy_species.contains( species ) ) {
 170                     DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc,
 171                                                           dc,
 172                                                           genome,
 173                                                           bdcs_per_genome.get( species ) );
 174                 }
 175             }
 176         }
 177         for( final String domain : all_domains ) {
 178             calculateDomainCountsBasedValue( high_copy_target_values,
 179                                              high_copy_target_copy_counts,
 180                                              domain,
 181                                              COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 182             calculateDomainCountsBasedValue( high_copy_base_values,
 183                                              high_copy_base_copy_counts,
 184                                              domain,
 185                                              COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 186             calculateDomainCountsBasedValue( low_copy_values,
 187                                              low_copy_copy_counts,
 188                                              domain,
 189                                              COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 190         }
 191         for( final BinaryDomainCombination dc : all_dcs ) {
 192             calculateDomainCountsBasedValue( high_copy_target_values_dc,
 193                                              high_copy_target_copy_counts_dc,
 194                                              dc,
 195                                              COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 196             calculateDomainCountsBasedValue( high_copy_base_values_dc,
 197                                              high_copy_base_copy_counts_dc,
 198                                              dc,
 199                                              COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 200             calculateDomainCountsBasedValue( low_copy_values_dc,
 201                                              low_copy_copy_counts_dc,
 202                                              dc,
 203                                              COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 204         }
 205         writeDomainValuesToFiles( genomes,
 206                                   high_copy_base_species,
 207                                   high_copy_target_species,
 208                                   low_copy_species,
 209                                   min_diff,
 210                                   factor,
 211                                   domain_id_to_go_ids_map,
 212                                   go_id_to_term_map,
 213                                   plain_writer,
 214                                   html_writer,
 215                                   proteins_file_base,
 216                                   high_copy_base_values,
 217                                   high_copy_target_values,
 218                                   low_copy_values,
 219                                   all_domains,
 220                                   go_ids_of_passing_domains,
 221                                   protein_lists_per_species );
 222         writeDomainCombinationValuesToFiles( genomes,
 223                                              high_copy_base_species,
 224                                              high_copy_target_species,
 225                                              low_copy_species,
 226                                              min_diff,
 227                                              factor,
 228                                              html_writer_dc,
 229                                              high_copy_base_values_dc,
 230                                              high_copy_target_values_dc,
 231                                              low_copy_values_dc,
 232                                              all_dcs,
 233                                              bdcs_per_genome );
 234         writeGoIdsToFile( all_gos_writer, go_ids_all );
 235         writeGoIdsToFile( passing_gos_writer, go_ids_of_passing_domains );
 236     }
 237
 238     //FIXME really needs to be tested!
 239     private static void addCounts( final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 240                                    final BinaryDomainCombination dc,
 241                                    final GenomeWideCombinableDomains genome,
 242                                    final Set<BinaryDomainCombination> bdc ) {
 243         if ( !copy_counts.containsKey( dc ) ) {
 244             copy_counts.put( dc, new ArrayList<Integer>() );
 245         }
 246         if ( bdc.contains( dc )
 247                 && ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
 248             final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains()
 249                     .get( dc.getId1() );
 250             copy_counts.get( dc ).add( count );
 251         }
 252         else {
 253             copy_counts.get( dc ).add( 0 );
 254         }
 255     }
 256
 257     private static void addCounts( final SortedMap<String, List<Integer>> copy_counts,
 258                                    final String domain,
 259                                    final GenomeWideCombinableDomains genome ) {
 260         if ( !copy_counts.containsKey( domain ) ) {
 261             copy_counts.put( domain, new ArrayList<Integer>() );
 262         }
 263         if ( genome.contains( domain ) ) {
 264             copy_counts.get( domain ).add( genome.get( domain ).getKeyDomainProteinsCount() );
 265         }
 266         else {
 267             copy_counts.get( domain ).add( 0 );
 268         }
 269     }
 270
 271     private static StringBuilder addGoInformation( final String d,
 272                                                    final Map<String, List<GoId>> domain_id_to_go_ids_map,
 273                                                    final Map<GoId, GoTerm> go_id_to_term_map ) {
 274         final StringBuilder sb = new StringBuilder();
 275         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty()
 276                 || !domain_id_to_go_ids_map.containsKey( d ) ) {
 277             return sb;
 278         }
 279         final List<GoId> go_ids = domain_id_to_go_ids_map.get( d );
 280         for( int i = 0; i < go_ids.size(); ++i ) {
 281             final GoId go_id = go_ids.get( i );
 282             if ( go_id_to_term_map.containsKey( go_id ) ) {
 283                 appendGoTerm( sb, go_id_to_term_map.get( go_id ) );
 284                 sb.append( "<br>" );
 285             }
 286             else {
 287                 sb.append( "go id \"" + go_id + "\" not found [" + d + "]" );
 288             }
 289         }
 290         return sb;
 291     }
 292
 293     private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) {
 294         final GoId go_id = go_term.getGoId();
 295         sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
 296                 + "</a>" );
 297         sb.append( ":" );
 298         sb.append( go_term.getName() );
 299         sb.append( " [" );
 300         sb.append( go_term.getGoNameSpace().toShortString() );
 301         sb.append( "]" );
 302     }
 303
 304     private static void calculateDomainCountsBasedValue( final SortedMap<BinaryDomainCombination, Double> copy_values,
 305                                                          final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 306                                                          final BinaryDomainCombination bdc,
 307                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
 308         if ( copy_counts.containsKey( bdc ) ) {
 309             switch ( copy_calc_mode ) {
 310                 case MAX:
 311                     DomainCountsDifferenceUtil.calculateMaxCount( copy_values, copy_counts, bdc );
 312                     break;
 313                 case MIN:
 314                     DomainCountsDifferenceUtil.calculateMinCount( copy_values, copy_counts, bdc );
 315                     break;
 316                 case MEAN:
 317                     DomainCountsDifferenceUtil.calculateMeanCount( copy_values, copy_counts, bdc );
 318                     break;
 319                 case MEDIAN:
 320                     DomainCountsDifferenceUtil.calculateMedianCount( copy_values, copy_counts, bdc );
 321                     break;
 322                 default:
 323                     throw new IllegalArgumentException();
 324             }
 325         }
 326         else {
 327             copy_values.put( bdc, Double.valueOf( 0.0 ) );
 328         }
 329     }
 330
 331     private static void calculateDomainCountsBasedValue( final SortedMap<String, Double> copy_values,
 332                                                          final SortedMap<String, List<Integer>> copy_counts,
 333                                                          final String domain,
 334                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
 335         if ( copy_counts.containsKey( domain ) ) {
 336             switch ( copy_calc_mode ) {
 337                 case MAX:
 338                     DomainCountsDifferenceUtil.calculateMaxCount( copy_values, copy_counts, domain );
 339                     break;
 340                 case MIN:
 341                     DomainCountsDifferenceUtil.calculateMinCount( copy_values, copy_counts, domain );
 342                     break;
 343                 case MEAN:
 344                     DomainCountsDifferenceUtil.calculateMeanCount( copy_values, copy_counts, domain );
 345                     break;
 346                 case MEDIAN:
 347                     DomainCountsDifferenceUtil.calculateMedianCount( copy_values, copy_counts, domain );
 348                     break;
 349                 default:
 350                     throw new IllegalArgumentException();
 351             }
 352         }
 353         else {
 354             copy_values.put( domain, Double.valueOf( 0.0 ) );
 355         }
 356     }
 357
 358     private static void calculateMaxCount( final SortedMap<BinaryDomainCombination, Double> results,
 359                                            final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 360                                            final BinaryDomainCombination bdc ) {
 361         final List<Integer> counts = copy_counts.get( bdc );
 362         int max = 0;
 363         for( final Integer count : counts ) {
 364             if ( count > max ) {
 365                 max = count;
 366             }
 367         }
 368         results.put( bdc, ( double ) max );
 369     }
 370
 371     private static void calculateMaxCount( final SortedMap<String, Double> results,
 372                                            final SortedMap<String, List<Integer>> copy_counts,
 373                                            final String domain ) {
 374         final List<Integer> counts = copy_counts.get( domain );
 375         int max = 0;
 376         for( final Integer count : counts ) {
 377             if ( count > max ) {
 378                 max = count;
 379             }
 380         }
 381         results.put( domain, ( double ) max );
 382     }
 383
 384     private static void calculateMeanCount( final SortedMap<BinaryDomainCombination, Double> results,
 385                                             final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 386                                             final BinaryDomainCombination bdc ) {
 387         final List<Integer> counts = copy_counts.get( bdc );
 388         int sum = 0;
 389         for( final Integer count : counts ) {
 390             sum += count;
 391         }
 392         results.put( bdc, ( ( double ) sum ) / ( ( double ) counts.size() ) );
 393     }
 394
 395     private static void calculateMeanCount( final SortedMap<String, Double> results,
 396                                             final SortedMap<String, List<Integer>> copy_counts,
 397                                             final String domain ) {
 398         final List<Integer> counts = copy_counts.get( domain );
 399         int sum = 0;
 400         for( final Integer count : counts ) {
 401             sum += count;
 402         }
 403         results.put( domain, ( ( double ) sum ) / ( ( double ) counts.size() ) );
 404     }
 405
 406     private static void calculateMedianCount( final SortedMap<BinaryDomainCombination, Double> results,
 407                                               final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 408                                               final BinaryDomainCombination bdc ) {
 409         final List<Integer> counts = copy_counts.get( bdc );
 410         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 411         for( final Integer count : counts ) {
 412             stats.addValue( count );
 413         }
 414         results.put( bdc, stats.median() );
 415     }
 416
 417     private static void calculateMedianCount( final SortedMap<String, Double> results,
 418                                               final SortedMap<String, List<Integer>> copy_counts,
 419                                               final String domain ) {
 420         final List<Integer> counts = copy_counts.get( domain );
 421         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 422         for( final Integer count : counts ) {
 423             stats.addValue( count );
 424         }
 425         results.put( domain, stats.median() );
 426     }
 427
 428     private static void calculateMinCount( final SortedMap<BinaryDomainCombination, Double> results,
 429                                            final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 430                                            final BinaryDomainCombination bdc ) {
 431         final List<Integer> counts = copy_counts.get( bdc );
 432         int min = Integer.MAX_VALUE;
 433         for( final Integer count : counts ) {
 434             if ( count < min ) {
 435                 min = count;
 436             }
 437         }
 438         results.put( bdc, ( double ) min );
 439     }
 440
 441     private static void calculateMinCount( final SortedMap<String, Double> results,
 442                                            final SortedMap<String, List<Integer>> copy_counts,
 443                                            final String domain ) {
 444         final List<Integer> counts = copy_counts.get( domain );
 445         int min = Integer.MAX_VALUE;
 446         for( final Integer count : counts ) {
 447             if ( count < min ) {
 448                 min = count;
 449             }
 450         }
 451         results.put( domain, ( double ) min );
 452     }
 453
 454     private static String combinableDomaindToString( final CombinableDomains cd ) {
 455         final StringBuilder sb = new StringBuilder();
 456         sb.append( cd.getKeyDomainProteinsCount() );
 457         return sb.toString();
 458     }
 459
 460     private static String combinableDomaindToStringHtml( final CombinableDomains cd ) {
 461         final StringBuilder sb = new StringBuilder();
 462         sb.append( "[" );
 463         sb.append( cd.getKeyDomainCount() );
 464         sb.append( ", <b>" );
 465         sb.append( cd.getKeyDomainProteinsCount() );
 466         sb.append( "</b>, " );
 467         sb.append( cd.getNumberOfCombinableDomains() );
 468         sb.append( "]</td><td>" );
 469         sb.append( cd.getCombiningDomainIdsAsStringBuilder() );
 470         return sb.toString();
 471     }
 472
 473     private static void writeCopyNumberValues( final SortedMap<BinaryDomainCombination, Double> copy_means,
 474                                                final BinaryDomainCombination bdc,
 475                                                final GenomeWideCombinableDomains genome,
 476                                                final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome,
 477                                                final String species,
 478                                                final Writer html_writer,
 479                                                final String color ) throws IOException {
 480         html_writer.write( "<td> " );
 481         if ( !ForesterUtil.isEmpty( color ) ) {
 482             html_writer.write( "<font color=\"" + color + "\">" );
 483         }
 484         html_writer.write( "<b>" + species + ":</b> " );
 485         if ( !ForesterUtil.isEmpty( color ) ) {
 486             html_writer.write( "</font>" );
 487         }
 488         html_writer.write( "</td><td>" );
 489         if ( bdcs_per_genome.get( species ).contains( bdc ) && ( copy_means.get( bdc ) > 0 ) ) {
 490             final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains()
 491                     .get( bdc.getId1() );
 492             html_writer.write( count + "" );
 493         }
 494         else {
 495             html_writer.write( "0" );
 496         }
 497         html_writer.write( "</td>" );
 498     }
 499
 500     private static void writeCopyNumberValues( final SortedMap<String, Double> copy_means,
 501                                                final String domain,
 502                                                final GenomeWideCombinableDomains genome,
 503                                                final String species,
 504                                                final Writer plain_writer,
 505                                                final Writer html_writer,
 506                                                final String color ) throws IOException {
 507         plain_writer.write( "  " + species + "\t" );
 508         html_writer.write( "<td> " );
 509         if ( !ForesterUtil.isEmpty( color ) ) {
 510             html_writer.write( "<font color=\"" + color + "\">" );
 511         }
 512         html_writer.write( "<b>" + species + ":</b> " );
 513         if ( !ForesterUtil.isEmpty( color ) ) {
 514             html_writer.write( "</font>" );
 515         }
 516         html_writer.write( "</td><td>" );
 517         if ( genome.contains( domain ) && ( copy_means.get( domain ) > 0 ) ) {
 518             plain_writer.write( DomainCountsDifferenceUtil.combinableDomaindToString( genome.get( domain ) ) );
 519             html_writer.write( DomainCountsDifferenceUtil.combinableDomaindToStringHtml( genome.get( domain ) ) );
 520         }
 521         else {
 522             plain_writer.write( "0" );
 523             html_writer.write( "0" );
 524         }
 525         html_writer.write( "</td>" );
 526         plain_writer.write( SurfacingConstants.NL );
 527     }
 528
 529     private static void writeDomainCombinationValuesToFiles( final List<GenomeWideCombinableDomains> genomes,
 530                                                              final List<String> high_copy_base_species,
 531                                                              final List<String> high_copy_target_species,
 532                                                              final List<String> low_copy_species,
 533                                                              final int min_diff,
 534                                                              final Double factor,
 535                                                              final Writer html_writer,
 536                                                              final SortedMap<BinaryDomainCombination, Double> high_copy_base_values,
 537                                                              final SortedMap<BinaryDomainCombination, Double> high_copy_target_values,
 538                                                              final SortedMap<BinaryDomainCombination, Double> low_copy_values,
 539                                                              final SortedSet<BinaryDomainCombination> all_bdcs,
 540                                                              final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome )
 541             throws IOException {
 542         int counter = 0;
 543         int total_absense_counter = 0;
 544         int not_total_absense_counter = 0;
 545         SurfacingUtil.writeHtmlHead( html_writer, "Binary Domain Combination Copy Differences" );
 546         html_writer.write( "<body><table>" );
 547         for( final BinaryDomainCombination bdc : all_bdcs ) {
 548             if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
 549                     && ( high_copy_base_values.get( bdc ) >= low_copy_values.get( bdc ) ) ) {
 550                 if ( high_copy_target_values.get( bdc ) >= ( min_diff + ( factor * low_copy_values.get( bdc ) ) ) ) {
 551                     if ( low_copy_values.get( bdc ) <= 0.0 ) {
 552                         ++total_absense_counter;
 553                     }
 554                     else {
 555                         ++not_total_absense_counter;
 556                     }
 557                     ++counter;
 558                     html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + bdc.getId0()
 559                             + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
 560                             + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
 561                     html_writer.write( "</td><td>" );
 562                     html_writer.write( "<table>" );
 563                     for( final GenomeWideCombinableDomains genome : genomes ) {
 564                         final String species = genome.getSpecies().getSpeciesId();
 565                         if ( high_copy_target_species.contains( species ) ) {
 566                             html_writer.write( "<tr>" );
 567                             writeCopyNumberValues( high_copy_target_values,
 568                                                    bdc,
 569                                                    genome,
 570                                                    bdcs_per_genome,
 571                                                    species,
 572                                                    html_writer,
 573                                                    "#0000FF" );
 574                             html_writer.write( "</tr>" );
 575                         }
 576                         else if ( low_copy_species.contains( species ) ) {
 577                             html_writer.write( "<tr>" );
 578                             writeCopyNumberValues( low_copy_values,
 579                                                    bdc,
 580                                                    genome,
 581                                                    bdcs_per_genome,
 582                                                    species,
 583                                                    html_writer,
 584                                                    "#A0A0A0" );
 585                             html_writer.write( "</tr>" );
 586                         }
 587                         else if ( high_copy_base_species.contains( species ) ) {
 588                             html_writer.write( "<tr>" );
 589                             writeCopyNumberValues( high_copy_base_values,
 590                                                    bdc,
 591                                                    genome,
 592                                                    bdcs_per_genome,
 593                                                    species,
 594                                                    html_writer,
 595                                                    "#404040" );
 596                             html_writer.write( "</tr>" );
 597                         }
 598                     }
 599                     html_writer.write( "</table>" );
 600                     html_writer.write( "</td></tr>" );
 601                     html_writer.write( SurfacingConstants.NL );
 602                 }
 603             }
 604         }
 605         html_writer.write( "</table>" );
 606         html_writer.write( SurfacingConstants.NL );
 607         html_writer.write( "<hr>" );
 608         html_writer.write( SurfacingConstants.NL );
 609         html_writer.write( "Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 610         html_writer.write( "<br>" );
 611         html_writer.write( SurfacingConstants.NL );
 612         html_writer.write( "Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 613         html_writer.write( "<br>" );
 614         html_writer.write( SurfacingConstants.NL );
 615         html_writer.write( "Calculation mode for high copy target : " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 616         html_writer.write( SurfacingConstants.NL );
 617         html_writer.write( "<br>" );
 618         html_writer.write( "Calculation mode for high copy base : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 619         html_writer.write( SurfacingConstants.NL );
 620         html_writer.write( "<br>" );
 621         html_writer.write( "Calculation mode for low copy : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 622         html_writer.write( SurfacingConstants.NL );
 623         html_writer.write( "<br>" );
 624         html_writer.write( "Minimal difference : " + min_diff );
 625         html_writer.write( SurfacingConstants.NL );
 626         html_writer.write( "<br>" );
 627         html_writer.write( "Factor : " + factor );
 628         html_writer.write( SurfacingConstants.NL );
 629         html_writer.write( "<br>" );
 630         html_writer.write( "Lower copy binary domain combinations : " + counter );
 631         html_writer.write( SurfacingConstants.NL );
 632         html_writer.write( "<br>" );
 633         html_writer.write( "Total absence : " + total_absense_counter );
 634         html_writer.write( SurfacingConstants.NL );
 635         html_writer.write( "<br>" );
 636         html_writer.write( "Not total absence : " + not_total_absense_counter );
 637         html_writer.write( SurfacingConstants.NL );
 638         html_writer.write( "<br>" );
 639         html_writer.write( "Total binary domain combinations : " + all_bdcs.size() );
 640         html_writer.write( SurfacingConstants.NL );
 641         html_writer.write( "<hr>" );
 642         html_writer.write( SurfacingConstants.NL );
 643         html_writer.write( "</body></html>" );
 644         html_writer.write( SurfacingConstants.NL );
 645         html_writer.close();
 646     }
 647
 648     private static void writeDomainValuesToFiles( final List<GenomeWideCombinableDomains> genomes,
 649                                                   final List<String> high_copy_base_species,
 650                                                   final List<String> high_copy_target_species,
 651                                                   final List<String> low_copy_species,
 652                                                   final int min_diff,
 653                                                   final Double factor,
 654                                                   final Map<String, List<GoId>> domain_id_to_go_ids_map,
 655                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 656                                                   final Writer plain_writer,
 657                                                   final Writer html_writer,
 658                                                   final File proteins_file_base,
 659                                                   final SortedMap<String, Double> high_copy_base_values,
 660                                                   final SortedMap<String, Double> high_copy_target_values,
 661                                                   final SortedMap<String, Double> low_copy_values,
 662                                                   final SortedSet<String> all_domains,
 663                                                   final SortedSet<GoId> go_ids_of_passing_domains,
 664                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species )
 665             throws IOException {
 666         int counter = 0;
 667         int total_absense_counter = 0;
 668         int not_total_absense_counter = 0;
 669         SurfacingUtil.writeHtmlHead( html_writer, "Domain Copy Differences" );
 670         html_writer.write( "<body><table>" );
 671         for( final String domain_id : all_domains ) {
 672             if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
 673                     && ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
 674                 if ( high_copy_target_values.get( domain_id ) >= ( min_diff + ( factor * low_copy_values
 675                         .get( domain_id ) ) ) ) {
 676                     if ( low_copy_values.get( domain_id ) <= 0.0 ) {
 677                         ++total_absense_counter;
 678                     }
 679                     else {
 680                         ++not_total_absense_counter;
 681                     }
 682                     ++counter;
 683                     writeProteinsToFile( proteins_file_base, protein_lists_per_species, domain_id );
 684                     if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
 685                         go_ids_of_passing_domains.addAll( domain_id_to_go_ids_map.get( domain_id ) );
 686                     }
 687                     plain_writer.write( domain_id );
 688                     plain_writer.write( SurfacingConstants.NL );
 689                     html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id
 690                             + "\">" + domain_id + "</a></td><td>" );
 691                     html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map )
 692                             .toString() );
 693                     html_writer.write( "</td><td>" );
 694                     html_writer.write( "<table>" );
 695                     for( final GenomeWideCombinableDomains genome : genomes ) {
 696                         final String species = genome.getSpecies().getSpeciesId();
 697                         if ( high_copy_target_species.contains( species ) ) {
 698                             html_writer.write( "<tr>" );
 699                             writeCopyNumberValues( high_copy_target_values,
 700                                                    domain_id,
 701                                                    genome,
 702                                                    species,
 703                                                    plain_writer,
 704                                                    html_writer,
 705                                                    "#0000FF" );
 706                             html_writer.write( "</tr>" );
 707                         }
 708                         else if ( low_copy_species.contains( species ) ) {
 709                             html_writer.write( "<tr>" );
 710                             writeCopyNumberValues( low_copy_values,
 711                                                    domain_id,
 712                                                    genome,
 713                                                    species,
 714                                                    plain_writer,
 715                                                    html_writer,
 716                                                    "#A0A0A0" );
 717                             html_writer.write( "</tr>" );
 718                         }
 719                         else if ( high_copy_base_species.contains( species ) ) {
 720                             html_writer.write( "<tr>" );
 721                             writeCopyNumberValues( high_copy_base_values,
 722                                                    domain_id,
 723                                                    genome,
 724                                                    species,
 725                                                    plain_writer,
 726                                                    html_writer,
 727                                                    "#404040" );
 728                             html_writer.write( "</tr>" );
 729                         }
 730                     }
 731                     html_writer.write( "</table>" );
 732                     html_writer.write( "</td></tr>" );
 733                     html_writer.write( SurfacingConstants.NL );
 734                     plain_writer.write( SurfacingConstants.NL );
 735                 }
 736             }
 737         }
 738         html_writer.write( "</table>" );
 739         html_writer.write( SurfacingConstants.NL );
 740         html_writer.write( "<hr>" );
 741         html_writer.write( SurfacingConstants.NL );
 742         html_writer.write( "Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 743         html_writer.write( "<br>" );
 744         html_writer.write( SurfacingConstants.NL );
 745         html_writer.write( "Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 746         html_writer.write( "<br>" );
 747         html_writer.write( SurfacingConstants.NL );
 748         html_writer.write( "Calculation mode for high copy target : " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 749         html_writer.write( SurfacingConstants.NL );
 750         html_writer.write( "<br>" );
 751         html_writer.write( "Calculation mode for high copy base : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 752         html_writer.write( SurfacingConstants.NL );
 753         html_writer.write( "<br>" );
 754         html_writer.write( "Calculation mode for low copy : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 755         html_writer.write( SurfacingConstants.NL );
 756         html_writer.write( "<br>" );
 757         html_writer.write( "Minimal difference : " + min_diff );
 758         html_writer.write( SurfacingConstants.NL );
 759         html_writer.write( "<br>" );
 760         html_writer.write( "Factor : " + factor );
 761         html_writer.write( SurfacingConstants.NL );
 762         html_writer.write( "<br>" );
 763         html_writer.write( "Lower copy domains : " + counter );
 764         html_writer.write( SurfacingConstants.NL );
 765         html_writer.write( "<br>" );
 766         html_writer.write( "Total absence : " + total_absense_counter );
 767         html_writer.write( SurfacingConstants.NL );
 768         html_writer.write( "<br>" );
 769         html_writer.write( "Not total absence : " + not_total_absense_counter );
 770         html_writer.write( SurfacingConstants.NL );
 771         html_writer.write( "<br>" );
 772         html_writer.write( "Total domains : " + all_domains.size() );
 773         html_writer.write( SurfacingConstants.NL );
 774         html_writer.write( "<hr>" );
 775         html_writer.write( SurfacingConstants.NL );
 776         html_writer.write( "</body></html>" );
 777         html_writer.write( SurfacingConstants.NL );
 778         html_writer.close();
 779         plain_writer.write( "# Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 780         plain_writer.write( SurfacingConstants.NL );
 781         plain_writer.write( "# Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 782         plain_writer.write( SurfacingConstants.NL );
 783         plain_writer.write( "# Calculation mode for high copy target: " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 784         plain_writer.write( SurfacingConstants.NL );
 785         plain_writer.write( "# Calculation mode for high copy base  : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 786         plain_writer.write( SurfacingConstants.NL );
 787         plain_writer.write( "# Calculation mode for low copy        : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 788         plain_writer.write( SurfacingConstants.NL );
 789         plain_writer.write( "# Minimal difference: " + min_diff );
 790         plain_writer.write( SurfacingConstants.NL );
 791         plain_writer.write( "# Factor            : " + factor );
 792         plain_writer.write( SurfacingConstants.NL );
 793         plain_writer.write( "# Lower copy domains: " + counter );
 794         plain_writer.write( SurfacingConstants.NL );
 795         plain_writer.write( "# Total absence     : " + total_absense_counter );
 796         plain_writer.write( SurfacingConstants.NL );
 797         plain_writer.write( "# Not total absence : " + not_total_absense_counter );
 798         plain_writer.write( SurfacingConstants.NL );
 799         plain_writer.write( "# Total domains     : " + all_domains.size() );
 800         plain_writer.write( SurfacingConstants.NL );
 801         plain_writer.close();
 802     }
 803
 804     private static void writeGoIdsToFile( final Writer writer, final SortedSet<GoId> gos ) throws IOException {
 805         for( final GoId go_id : gos ) {
 806             writer.write( go_id.toString() );
 807             writer.write( SurfacingConstants.NL );
 808         }
 809         writer.close();
 810     }
 811
 812     private static void writeProteinsToFile( final File proteins_file_base,
 813                                              final SortedMap<Species, List<Protein>> protein_lists_per_species,
 814                                              final String domain_id ) throws IOException {
 815         final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR
 816                 + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
 817         SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
 818         final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
 819         SurfacingUtil.extractProteinNames( protein_lists_per_species,
 820                                            domain_id,
 821                                            proteins_file_writer,
 822                                            "\t",
 823                                            surfacing.LIMIT_SPEC_FOR_PROT_EX,
 824                                            -1 );
 825         proteins_file_writer.close();
 826         System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
 827     }
 828
 829     public static enum COPY_CALCULATION_MODE {
 830         MAX, MEAN, MEDIAN, MIN
 831     }
 832 }