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.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.application.surfacing;
  48 import org.forester.go.GoId;
  49 import org.forester.go.GoTerm;
  50 import org.forester.protein.BinaryDomainCombination;
  51 import org.forester.protein.Protein;
  52 import org.forester.species.Species;
  53 import org.forester.util.BasicDescriptiveStatistics;
  54 import org.forester.util.DescriptiveStatistics;
  55 import org.forester.util.ForesterUtil;
  56
  57 /*
  58  * Poorly designed static class which essential has one method:
  59  * calculateCopyNumberDifferences.
  60  */
  61 public final class DomainCountsDifferenceUtil {
  62
  63     private final static NumberFormat          FORMATTER                                   = new DecimalFormat( "0.0E0" );
  64     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES = COPY_CALCULATION_MODE.MIN;
  65     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES   = COPY_CALCULATION_MODE.MIN;
  66     private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_LOW_COPY_SPECIES         = COPY_CALCULATION_MODE.MAX;
  67     private static final String                PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX         = ".prot";
  68
  69     //FIXME really needs to be tested!
  70     private static void addCounts( final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
  71                                    final BinaryDomainCombination dc,
  72                                    final GenomeWideCombinableDomains genome,
  73                                    final Set<BinaryDomainCombination> bdc ) {
  74         if ( !copy_counts.containsKey( dc ) ) {
  75             copy_counts.put( dc, new ArrayList<Integer>() );
  76         }
  77         if ( bdc.contains( dc )
  78                 && ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
  79             final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains()
  80                     .get( dc.getId1() );
  81             copy_counts.get( dc ).add( count );
  82         }
  83         else {
  84             copy_counts.get( dc ).add( 0 );
  85         }
  86     }
  87
  88     private static void addCounts( final SortedMap<String, List<Integer>> copy_counts,
  89                                    final String domain,
  90                                    final GenomeWideCombinableDomains genome ) {
  91         if ( !copy_counts.containsKey( domain ) ) {
  92             copy_counts.put( domain, new ArrayList<Integer>() );
  93         }
  94         if ( genome.contains( domain ) ) {
  95             copy_counts.get( domain ).add( genome.get( domain ).getKeyDomainProteinsCount() );
  96         }
  97         else {
  98             copy_counts.get( domain ).add( 0 );
  99         }
 100     }
 101
 102     private static StringBuilder addGoInformation( final String d,
 103                                                    final Map<String, List<GoId>> domain_id_to_go_ids_map,
 104                                                    final Map<GoId, GoTerm> go_id_to_term_map ) {
 105         final StringBuilder sb = new StringBuilder();
 106         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty()
 107                 || !domain_id_to_go_ids_map.containsKey( d ) ) {
 108             return sb;
 109         }
 110         final List<GoId> go_ids = domain_id_to_go_ids_map.get( d );
 111         for( int i = 0; i < go_ids.size(); ++i ) {
 112             final GoId go_id = go_ids.get( i );
 113             if ( go_id_to_term_map.containsKey( go_id ) ) {
 114                 appendGoTerm( sb, go_id_to_term_map.get( go_id ) );
 115                 sb.append( "<br>" );
 116             }
 117             else {
 118                 sb.append( "go id \"" + go_id + "\" not found [" + d + "]" );
 119             }
 120         }
 121         return sb;
 122     }
 123
 124     private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) {
 125         final GoId go_id = go_term.getGoId();
 126         sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
 127                 + "</a>" );
 128         sb.append( ":" );
 129         sb.append( go_term.getName() );
 130         sb.append( " [" );
 131         sb.append( go_term.getGoNameSpace().toShortString() );
 132         sb.append( "]" );
 133     }
 134
 135     public static void calculateCopyNumberDifferences( final List<GenomeWideCombinableDomains> genomes,
 136                                                        final SortedMap<Species, List<Protein>> protein_lists_per_species,
 137                                                        final List<String> high_copy_base_species,
 138                                                        final List<String> high_copy_target_species,
 139                                                        final List<String> low_copy_species,
 140                                                        final int min_diff,
 141                                                        final Double factor,
 142                                                        final File plain_output_dom,
 143                                                        final File html_output_dom,
 144                                                        final File html_output_dc,
 145                                                        final Map<String, List<GoId>> domain_id_to_go_ids_map,
 146                                                        final Map<GoId, GoTerm> go_id_to_term_map,
 147                                                        final File all_domains_go_ids_out_dom,
 148                                                        final File passing_domains_go_ids_out_dom,
 149                                                        final File proteins_file_base ) throws IOException {
 150         if ( genomes.size() < 1 ) {
 151             throw new IllegalArgumentException( "attempt to use empty list of genomes for domain difference calculation" );
 152         }
 153         if ( ( high_copy_base_species.size() < 1 ) || ( low_copy_species.size() < 1 ) ) {
 154             throw new IllegalArgumentException( "attempt to use empty list of species for domain difference calculation" );
 155         }
 156         if ( high_copy_base_species.contains( high_copy_target_species )
 157                 || low_copy_species.contains( high_copy_target_species ) ) {
 158             throw new IllegalArgumentException( "species [" + high_copy_target_species
 159                     + "] appears in other list as well" );
 160         }
 161         if ( min_diff < 0 ) {
 162             throw new IllegalArgumentException( "attempt to use negative addition [" + min_diff + "]" );
 163         }
 164         if ( factor <= 0.0 ) {
 165             throw new IllegalArgumentException( "attempt to use factor equal or smaller than 0.0 [" + factor + "]" );
 166         }
 167         SurfacingUtil.checkForOutputFileWriteability( plain_output_dom );
 168         SurfacingUtil.checkForOutputFileWriteability( html_output_dom );
 169         SurfacingUtil.checkForOutputFileWriteability( html_output_dc );
 170         SurfacingUtil.checkForOutputFileWriteability( all_domains_go_ids_out_dom );
 171         SurfacingUtil.checkForOutputFileWriteability( passing_domains_go_ids_out_dom );
 172         final Writer plain_writer = new BufferedWriter( new FileWriter( plain_output_dom ) );
 173         final Writer html_writer = new BufferedWriter( new FileWriter( html_output_dom ) );
 174         final Writer html_writer_dc = new BufferedWriter( new FileWriter( html_output_dc ) );
 175         final Writer all_gos_writer = new BufferedWriter( new FileWriter( all_domains_go_ids_out_dom ) );
 176         final Writer passing_gos_writer = new BufferedWriter( new FileWriter( passing_domains_go_ids_out_dom ) );
 177         final SortedMap<String, Double> high_copy_base_values = new TreeMap<String, Double>();
 178         final SortedMap<String, Double> high_copy_target_values = new TreeMap<String, Double>();
 179         final SortedMap<String, Double> low_copy_values = new TreeMap<String, Double>();
 180         final SortedMap<String, List<Integer>> high_copy_base_copy_counts = new TreeMap<String, List<Integer>>();
 181         final SortedMap<String, List<Integer>> high_copy_target_copy_counts = new TreeMap<String, List<Integer>>();
 182         final SortedMap<String, List<Integer>> low_copy_copy_counts = new TreeMap<String, List<Integer>>();
 183         final SortedSet<String> all_domains = new TreeSet<String>();
 184         final SortedMap<BinaryDomainCombination, Double> high_copy_base_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 185         final SortedMap<BinaryDomainCombination, Double> high_copy_target_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 186         final SortedMap<BinaryDomainCombination, Double> low_copy_values_dc = new TreeMap<BinaryDomainCombination, Double>();
 187         final SortedMap<BinaryDomainCombination, List<Integer>> high_copy_base_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 188         final SortedMap<BinaryDomainCombination, List<Integer>> high_copy_target_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 189         final SortedMap<BinaryDomainCombination, List<Integer>> low_copy_copy_counts_dc = new TreeMap<BinaryDomainCombination, List<Integer>>();
 190         final SortedSet<BinaryDomainCombination> all_dcs = new TreeSet<BinaryDomainCombination>();
 191         final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome = new HashMap<String, Set<BinaryDomainCombination>>();
 192         final SortedSet<GoId> go_ids_of_passing_domains = new TreeSet<GoId>();
 193         final SortedSet<GoId> go_ids_all = new TreeSet<GoId>();
 194         for( final GenomeWideCombinableDomains genome : genomes ) {
 195             final SortedSet<String> domains = genome.getAllDomainIds();
 196             final SortedSet<BinaryDomainCombination> dcs = genome.toBinaryDomainCombinations();
 197             final String species = genome.getSpecies().getSpeciesId();
 198             bdcs_per_genome.put( species, genome.toBinaryDomainCombinations() );
 199             for( final String d : domains ) {
 200                 all_domains.add( d );
 201                 if ( domain_id_to_go_ids_map.containsKey( d ) ) {
 202                     go_ids_all.addAll( domain_id_to_go_ids_map.get( d ) );
 203                 }
 204             }
 205             for( final BinaryDomainCombination dc : dcs ) {
 206                 all_dcs.add( dc );
 207             }
 208         }
 209         for( final String domain : all_domains ) {
 210             for( final GenomeWideCombinableDomains genome : genomes ) {
 211                 final String species = genome.getSpecies().getSpeciesId();
 212                 if ( high_copy_base_species.contains( species ) ) {
 213                     DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts, domain, genome );
 214                 }
 215                 if ( high_copy_target_species.contains( species ) ) {
 216                     DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts, domain, genome );
 217                 }
 218                 if ( low_copy_species.contains( species ) ) {
 219                     DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts, domain, genome );
 220                 }
 221             }
 222         }
 223         for( final BinaryDomainCombination dc : all_dcs ) {
 224             for( final GenomeWideCombinableDomains genome : genomes ) {
 225                 final String species = genome.getSpecies().getSpeciesId();
 226                 if ( high_copy_base_species.contains( species ) ) {
 227                     DomainCountsDifferenceUtil.addCounts( high_copy_base_copy_counts_dc,
 228                                                           dc,
 229                                                           genome,
 230                                                           bdcs_per_genome.get( species ) );
 231                 }
 232                 if ( high_copy_target_species.contains( species ) ) {
 233                     DomainCountsDifferenceUtil.addCounts( high_copy_target_copy_counts_dc,
 234                                                           dc,
 235                                                           genome,
 236                                                           bdcs_per_genome.get( species ) );
 237                 }
 238                 if ( low_copy_species.contains( species ) ) {
 239                     DomainCountsDifferenceUtil.addCounts( low_copy_copy_counts_dc,
 240                                                           dc,
 241                                                           genome,
 242                                                           bdcs_per_genome.get( species ) );
 243                 }
 244             }
 245         }
 246         for( final String domain : all_domains ) {
 247             calculateDomainCountsBasedValue( high_copy_target_values,
 248                                              high_copy_target_copy_counts,
 249                                              domain,
 250                                              COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 251             calculateDomainCountsBasedValue( high_copy_base_values,
 252                                              high_copy_base_copy_counts,
 253                                              domain,
 254                                              COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 255             calculateDomainCountsBasedValue( low_copy_values,
 256                                              low_copy_copy_counts,
 257                                              domain,
 258                                              COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 259         }
 260         for( final BinaryDomainCombination dc : all_dcs ) {
 261             calculateDomainCountsBasedValue( high_copy_target_values_dc,
 262                                              high_copy_target_copy_counts_dc,
 263                                              dc,
 264                                              COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 265             calculateDomainCountsBasedValue( high_copy_base_values_dc,
 266                                              high_copy_base_copy_counts_dc,
 267                                              dc,
 268                                              COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 269             calculateDomainCountsBasedValue( low_copy_values_dc,
 270                                              low_copy_copy_counts_dc,
 271                                              dc,
 272                                              COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 273         }
 274         writeDomainValuesToFiles( genomes,
 275                                   high_copy_base_species,
 276                                   high_copy_target_species,
 277                                   low_copy_species,
 278                                   min_diff,
 279                                   factor,
 280                                   domain_id_to_go_ids_map,
 281                                   go_id_to_term_map,
 282                                   plain_writer,
 283                                   html_writer,
 284                                   proteins_file_base,
 285                                   high_copy_base_values,
 286                                   high_copy_target_values,
 287                                   low_copy_values,
 288                                   all_domains,
 289                                   go_ids_of_passing_domains,
 290                                   protein_lists_per_species );
 291         writeDomainCombinationValuesToFiles( genomes,
 292                                              high_copy_base_species,
 293                                              high_copy_target_species,
 294                                              low_copy_species,
 295                                              min_diff,
 296                                              factor,
 297                                              html_writer_dc,
 298                                              high_copy_base_values_dc,
 299                                              high_copy_target_values_dc,
 300                                              low_copy_values_dc,
 301                                              all_dcs,
 302                                              bdcs_per_genome );
 303         writeGoIdsToFile( all_gos_writer, go_ids_all );
 304         writeGoIdsToFile( passing_gos_writer, go_ids_of_passing_domains );
 305     }
 306
 307     private static void calculateDomainCountsBasedValue( final SortedMap<BinaryDomainCombination, Double> copy_values,
 308                                                          final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 309                                                          final BinaryDomainCombination bdc,
 310                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
 311         if ( copy_counts.containsKey( bdc ) ) {
 312             switch ( copy_calc_mode ) {
 313                 case MAX:
 314                     DomainCountsDifferenceUtil.calculateMaxCount( copy_values, copy_counts, bdc );
 315                     break;
 316                 case MIN:
 317                     DomainCountsDifferenceUtil.calculateMinCount( copy_values, copy_counts, bdc );
 318                     break;
 319                 case MEAN:
 320                     DomainCountsDifferenceUtil.calculateMeanCount( copy_values, copy_counts, bdc );
 321                     break;
 322                 case MEDIAN:
 323                     DomainCountsDifferenceUtil.calculateMedianCount( copy_values, copy_counts, bdc );
 324                     break;
 325                 default:
 326                     throw new IllegalArgumentException();
 327             }
 328         }
 329         else {
 330             copy_values.put( bdc, Double.valueOf( 0.0 ) );
 331         }
 332     }
 333
 334     private static void calculateDomainCountsBasedValue( final SortedMap<String, Double> copy_values,
 335                                                          final SortedMap<String, List<Integer>> copy_counts,
 336                                                          final String domain,
 337                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
 338         if ( copy_counts.containsKey( domain ) ) {
 339             switch ( copy_calc_mode ) {
 340                 case MAX:
 341                     DomainCountsDifferenceUtil.calculateMaxCount( copy_values, copy_counts, domain );
 342                     break;
 343                 case MIN:
 344                     DomainCountsDifferenceUtil.calculateMinCount( copy_values, copy_counts, domain );
 345                     break;
 346                 case MEAN:
 347                     DomainCountsDifferenceUtil.calculateMeanCount( copy_values, copy_counts, domain );
 348                     break;
 349                 case MEDIAN:
 350                     DomainCountsDifferenceUtil.calculateMedianCount( copy_values, copy_counts, domain );
 351                     break;
 352                 default:
 353                     throw new IllegalArgumentException();
 354             }
 355         }
 356         else {
 357             copy_values.put( domain, Double.valueOf( 0.0 ) );
 358         }
 359     }
 360
 361     private static void calculateMaxCount( final SortedMap<BinaryDomainCombination, Double> results,
 362                                            final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 363                                            final BinaryDomainCombination bdc ) {
 364         final List<Integer> counts = copy_counts.get( bdc );
 365         int max = 0;
 366         for( final Integer count : counts ) {
 367             if ( count > max ) {
 368                 max = count;
 369             }
 370         }
 371         results.put( bdc, ( double ) max );
 372     }
 373
 374     private static void calculateMaxCount( final SortedMap<String, Double> results,
 375                                            final SortedMap<String, List<Integer>> copy_counts,
 376                                            final String domain ) {
 377         final List<Integer> counts = copy_counts.get( domain );
 378         int max = 0;
 379         for( final Integer count : counts ) {
 380             if ( count > max ) {
 381                 max = count;
 382             }
 383         }
 384         results.put( domain, ( double ) max );
 385     }
 386
 387     private static void calculateMeanCount( final SortedMap<BinaryDomainCombination, Double> results,
 388                                             final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 389                                             final BinaryDomainCombination bdc ) {
 390         final List<Integer> counts = copy_counts.get( bdc );
 391         int sum = 0;
 392         for( final Integer count : counts ) {
 393             sum += count;
 394         }
 395         results.put( bdc, ( ( double ) sum ) / ( ( double ) counts.size() ) );
 396     }
 397
 398     private static void calculateMeanCount( final SortedMap<String, Double> results,
 399                                             final SortedMap<String, List<Integer>> copy_counts,
 400                                             final String domain ) {
 401         final List<Integer> counts = copy_counts.get( domain );
 402         int sum = 0;
 403         for( final Integer count : counts ) {
 404             sum += count;
 405         }
 406         results.put( domain, ( ( double ) sum ) / ( ( double ) counts.size() ) );
 407     }
 408
 409     private static void calculateMedianCount( final SortedMap<BinaryDomainCombination, Double> results,
 410                                               final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 411                                               final BinaryDomainCombination bdc ) {
 412         final List<Integer> counts = copy_counts.get( bdc );
 413         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 414         for( final Integer count : counts ) {
 415             stats.addValue( count );
 416         }
 417         results.put( bdc, stats.median() );
 418     }
 419
 420     private static void calculateMedianCount( final SortedMap<String, Double> results,
 421                                               final SortedMap<String, List<Integer>> copy_counts,
 422                                               final String domain ) {
 423         final List<Integer> counts = copy_counts.get( domain );
 424         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 425         for( final Integer count : counts ) {
 426             stats.addValue( count );
 427         }
 428         results.put( domain, stats.median() );
 429     }
 430
 431     private static void calculateMinCount( final SortedMap<BinaryDomainCombination, Double> results,
 432                                            final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
 433                                            final BinaryDomainCombination bdc ) {
 434         final List<Integer> counts = copy_counts.get( bdc );
 435         int min = Integer.MAX_VALUE;
 436         for( final Integer count : counts ) {
 437             if ( count < min ) {
 438                 min = count;
 439             }
 440         }
 441         results.put( bdc, ( double ) min );
 442     }
 443
 444     private static void calculateMinCount( final SortedMap<String, Double> results,
 445                                            final SortedMap<String, List<Integer>> copy_counts,
 446                                            final String domain ) {
 447         final List<Integer> counts = copy_counts.get( domain );
 448         int min = Integer.MAX_VALUE;
 449         for( final Integer count : counts ) {
 450             if ( count < min ) {
 451                 min = count;
 452             }
 453         }
 454         results.put( domain, ( double ) min );
 455     }
 456
 457     private static String combinableDomaindToString( final CombinableDomains cd ) {
 458         final StringBuilder sb = new StringBuilder();
 459         sb.append( cd.getKeyDomainProteinsCount() );
 460         sb.append( "\t[" );
 461         sb.append( FORMATTER.format( cd.getKeyDomainConfidenceDescriptiveStatistics().median() ) );
 462         sb.append( "]" );
 463         return sb.toString();
 464     }
 465
 466     private static String combinableDomaindToStringHtml( final CombinableDomains cd ) {
 467         final StringBuilder sb = new StringBuilder();
 468         sb.append( "[" );
 469         sb.append( cd.getKeyDomainCount() );
 470         sb.append( ", <b>" );
 471         sb.append( cd.getKeyDomainProteinsCount() );
 472         sb.append( "</b>, " );
 473         sb.append( cd.getNumberOfCombinableDomains() );
 474         sb.append( "]</td><td>[" );
 475         sb.append( FORMATTER.format( cd.getKeyDomainConfidenceDescriptiveStatistics().median() ) );
 476         sb.append( "]</td><td>" );
 477         sb.append( cd.getCombiningDomainIdsAsStringBuilder() );
 478         return sb.toString();
 479     }
 480
 481     private static void writeCopyNumberValues( final SortedMap<BinaryDomainCombination, Double> copy_means,
 482                                                final BinaryDomainCombination bdc,
 483                                                final GenomeWideCombinableDomains genome,
 484                                                final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome,
 485                                                final String species,
 486                                                final Writer html_writer,
 487                                                final String color ) throws IOException {
 488         html_writer.write( "<td> " );
 489         if ( !ForesterUtil.isEmpty( color ) ) {
 490             html_writer.write( "<font color=\"" + color + "\">" );
 491         }
 492         html_writer.write( "<b>" + species + ":</b> " );
 493         if ( !ForesterUtil.isEmpty( color ) ) {
 494             html_writer.write( "</font>" );
 495         }
 496         html_writer.write( "</td><td>" );
 497         if ( bdcs_per_genome.get( species ).contains( bdc ) && ( copy_means.get( bdc ) > 0 ) ) {
 498             final int count = ( ( BasicCombinableDomains ) genome.get( bdc.getId0() ) ).getCombiningDomains()
 499                     .get( bdc.getId1() );
 500             html_writer.write( count + "" );
 501         }
 502         else {
 503             html_writer.write( "0" );
 504         }
 505         html_writer.write( "</td>" );
 506     }
 507
 508     private static void writeCopyNumberValues( final SortedMap<String, Double> copy_means,
 509                                                final String domain,
 510                                                final GenomeWideCombinableDomains genome,
 511                                                final String species,
 512                                                final Writer plain_writer,
 513                                                final Writer html_writer,
 514                                                final String color ) throws IOException {
 515         plain_writer.write( "  " + species + "\t" );
 516         html_writer.write( "<td> " );
 517         if ( !ForesterUtil.isEmpty( color ) ) {
 518             html_writer.write( "<font color=\"" + color + "\">" );
 519         }
 520         html_writer.write( "<b>" + species + ":</b> " );
 521         if ( !ForesterUtil.isEmpty( color ) ) {
 522             html_writer.write( "</font>" );
 523         }
 524         html_writer.write( "</td><td>" );
 525         if ( genome.contains( domain ) && ( copy_means.get( domain ) > 0 ) ) {
 526             plain_writer.write( DomainCountsDifferenceUtil.combinableDomaindToString( genome.get( domain ) ) );
 527             html_writer.write( DomainCountsDifferenceUtil.combinableDomaindToStringHtml( genome.get( domain ) ) );
 528         }
 529         else {
 530             plain_writer.write( "0" );
 531             html_writer.write( "0" );
 532         }
 533         html_writer.write( "</td>" );
 534         plain_writer.write( SurfacingConstants.NL );
 535     }
 536
 537     private static void writeDomainCombinationValuesToFiles( final List<GenomeWideCombinableDomains> genomes,
 538                                                              final List<String> high_copy_base_species,
 539                                                              final List<String> high_copy_target_species,
 540                                                              final List<String> low_copy_species,
 541                                                              final int min_diff,
 542                                                              final Double factor,
 543                                                              final Writer html_writer,
 544                                                              final SortedMap<BinaryDomainCombination, Double> high_copy_base_values,
 545                                                              final SortedMap<BinaryDomainCombination, Double> high_copy_target_values,
 546                                                              final SortedMap<BinaryDomainCombination, Double> low_copy_values,
 547                                                              final SortedSet<BinaryDomainCombination> all_bdcs,
 548                                                              final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome )
 549             throws IOException {
 550         int counter = 0;
 551         int total_absense_counter = 0;
 552         int not_total_absense_counter = 0;
 553         SurfacingUtil.addHtmlHead( html_writer, "Binary Domain Combination Copy Differences" );
 554         html_writer.write( "<body><table>" );
 555         for( final BinaryDomainCombination bdc : all_bdcs ) {
 556             if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
 557                     && ( high_copy_base_values.get( bdc ) >= low_copy_values.get( bdc ) ) ) {
 558                 if ( high_copy_target_values.get( bdc ) >= ( min_diff + ( factor * low_copy_values.get( bdc ) ) ) ) {
 559                     if ( low_copy_values.get( bdc ) <= 0.0 ) {
 560                         ++total_absense_counter;
 561                     }
 562                     else {
 563                         ++not_total_absense_counter;
 564                     }
 565                     ++counter;
 566                     html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + bdc.getId0()
 567                             + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
 568                             + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
 569                     html_writer.write( "</td><td>" );
 570                     html_writer.write( "<table>" );
 571                     for( final GenomeWideCombinableDomains genome : genomes ) {
 572                         final String species = genome.getSpecies().getSpeciesId();
 573                         if ( high_copy_target_species.contains( species ) ) {
 574                             html_writer.write( "<tr>" );
 575                             writeCopyNumberValues( high_copy_target_values,
 576                                                    bdc,
 577                                                    genome,
 578                                                    bdcs_per_genome,
 579                                                    species,
 580                                                    html_writer,
 581                                                    "#0000FF" );
 582                             html_writer.write( "</tr>" );
 583                         }
 584                         else if ( low_copy_species.contains( species ) ) {
 585                             html_writer.write( "<tr>" );
 586                             writeCopyNumberValues( low_copy_values,
 587                                                    bdc,
 588                                                    genome,
 589                                                    bdcs_per_genome,
 590                                                    species,
 591                                                    html_writer,
 592                                                    "#A0A0A0" );
 593                             html_writer.write( "</tr>" );
 594                         }
 595                         else if ( high_copy_base_species.contains( species ) ) {
 596                             html_writer.write( "<tr>" );
 597                             writeCopyNumberValues( high_copy_base_values,
 598                                                    bdc,
 599                                                    genome,
 600                                                    bdcs_per_genome,
 601                                                    species,
 602                                                    html_writer,
 603                                                    "#404040" );
 604                             html_writer.write( "</tr>" );
 605                         }
 606                     }
 607                     html_writer.write( "</table>" );
 608                     html_writer.write( "</td></tr>" );
 609                     html_writer.write( SurfacingConstants.NL );
 610                 }
 611             }
 612         }
 613         html_writer.write( "</table>" );
 614         html_writer.write( SurfacingConstants.NL );
 615         html_writer.write( "<hr>" );
 616         html_writer.write( SurfacingConstants.NL );
 617         html_writer.write( "Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 618         html_writer.write( "<br>" );
 619         html_writer.write( SurfacingConstants.NL );
 620         html_writer.write( "Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 621         html_writer.write( "<br>" );
 622         html_writer.write( SurfacingConstants.NL );
 623         html_writer.write( "Calculation mode for high copy target : " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 624         html_writer.write( SurfacingConstants.NL );
 625         html_writer.write( "<br>" );
 626         html_writer.write( "Calculation mode for high copy base : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 627         html_writer.write( SurfacingConstants.NL );
 628         html_writer.write( "<br>" );
 629         html_writer.write( "Calculation mode for low copy : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 630         html_writer.write( SurfacingConstants.NL );
 631         html_writer.write( "<br>" );
 632         html_writer.write( "Minimal difference : " + min_diff );
 633         html_writer.write( SurfacingConstants.NL );
 634         html_writer.write( "<br>" );
 635         html_writer.write( "Factor : " + factor );
 636         html_writer.write( SurfacingConstants.NL );
 637         html_writer.write( "<br>" );
 638         html_writer.write( "Lower copy binary domain combinations : " + counter );
 639         html_writer.write( SurfacingConstants.NL );
 640         html_writer.write( "<br>" );
 641         html_writer.write( "Total absence : " + total_absense_counter );
 642         html_writer.write( SurfacingConstants.NL );
 643         html_writer.write( "<br>" );
 644         html_writer.write( "Not total absence : " + not_total_absense_counter );
 645         html_writer.write( SurfacingConstants.NL );
 646         html_writer.write( "<br>" );
 647         html_writer.write( "Total binary domain combinations : " + all_bdcs.size() );
 648         html_writer.write( SurfacingConstants.NL );
 649         html_writer.write( "<hr>" );
 650         html_writer.write( SurfacingConstants.NL );
 651         html_writer.write( "</body></html>" );
 652         html_writer.write( SurfacingConstants.NL );
 653         html_writer.close();
 654     }
 655
 656     private static void writeDomainValuesToFiles( final List<GenomeWideCombinableDomains> genomes,
 657                                                   final List<String> high_copy_base_species,
 658                                                   final List<String> high_copy_target_species,
 659                                                   final List<String> low_copy_species,
 660                                                   final int min_diff,
 661                                                   final Double factor,
 662                                                   final Map<String, List<GoId>> domain_id_to_go_ids_map,
 663                                                   final Map<GoId, GoTerm> go_id_to_term_map,
 664                                                   final Writer plain_writer,
 665                                                   final Writer html_writer,
 666                                                   final File proteins_file_base,
 667                                                   final SortedMap<String, Double> high_copy_base_values,
 668                                                   final SortedMap<String, Double> high_copy_target_values,
 669                                                   final SortedMap<String, Double> low_copy_values,
 670                                                   final SortedSet<String> all_domains,
 671                                                   final SortedSet<GoId> go_ids_of_passing_domains,
 672                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species )
 673             throws IOException {
 674         int counter = 0;
 675         int total_absense_counter = 0;
 676         int not_total_absense_counter = 0;
 677         SurfacingUtil.addHtmlHead( html_writer, "Domain Copy Differences" );
 678         html_writer.write( "<body><table>" );
 679         for( final String domain_id : all_domains ) {
 680             if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
 681                     && ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
 682                 if ( high_copy_target_values.get( domain_id ) >= ( min_diff + ( factor * low_copy_values
 683                         .get( domain_id ) ) ) ) {
 684                     if ( low_copy_values.get( domain_id ) <= 0.0 ) {
 685                         ++total_absense_counter;
 686                     }
 687                     else {
 688                         ++not_total_absense_counter;
 689                     }
 690                     ++counter;
 691                     writeProteinsToFile( proteins_file_base, protein_lists_per_species, domain_id );
 692                     if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
 693                         go_ids_of_passing_domains.addAll( domain_id_to_go_ids_map.get( domain_id ) );
 694                     }
 695                     plain_writer.write( domain_id );
 696                     plain_writer.write( SurfacingConstants.NL );
 697                     html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id
 698                             + "\">" + domain_id + "</a></td><td>" );
 699                     html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map )
 700                             .toString() );
 701                     html_writer.write( "</td><td>" );
 702                     html_writer.write( "<table>" );
 703                     for( final GenomeWideCombinableDomains genome : genomes ) {
 704                         final String species = genome.getSpecies().getSpeciesId();
 705                         if ( high_copy_target_species.contains( species ) ) {
 706                             html_writer.write( "<tr>" );
 707                             writeCopyNumberValues( high_copy_target_values,
 708                                                    domain_id,
 709                                                    genome,
 710                                                    species,
 711                                                    plain_writer,
 712                                                    html_writer,
 713                                                    "#0000FF" );
 714                             html_writer.write( "</tr>" );
 715                         }
 716                         else if ( low_copy_species.contains( species ) ) {
 717                             html_writer.write( "<tr>" );
 718                             writeCopyNumberValues( low_copy_values,
 719                                                    domain_id,
 720                                                    genome,
 721                                                    species,
 722                                                    plain_writer,
 723                                                    html_writer,
 724                                                    "#A0A0A0" );
 725                             html_writer.write( "</tr>" );
 726                         }
 727                         else if ( high_copy_base_species.contains( species ) ) {
 728                             html_writer.write( "<tr>" );
 729                             writeCopyNumberValues( high_copy_base_values,
 730                                                    domain_id,
 731                                                    genome,
 732                                                    species,
 733                                                    plain_writer,
 734                                                    html_writer,
 735                                                    "#404040" );
 736                             html_writer.write( "</tr>" );
 737                         }
 738                     }
 739                     html_writer.write( "</table>" );
 740                     html_writer.write( "</td></tr>" );
 741                     html_writer.write( SurfacingConstants.NL );
 742                     plain_writer.write( SurfacingConstants.NL );
 743                 }
 744             }
 745         }
 746         html_writer.write( "</table>" );
 747         html_writer.write( SurfacingConstants.NL );
 748         html_writer.write( "<hr>" );
 749         html_writer.write( SurfacingConstants.NL );
 750         html_writer.write( "Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 751         html_writer.write( "<br>" );
 752         html_writer.write( SurfacingConstants.NL );
 753         html_writer.write( "Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 754         html_writer.write( "<br>" );
 755         html_writer.write( SurfacingConstants.NL );
 756         html_writer.write( "Calculation mode for high copy target : " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 757         html_writer.write( SurfacingConstants.NL );
 758         html_writer.write( "<br>" );
 759         html_writer.write( "Calculation mode for high copy base : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 760         html_writer.write( SurfacingConstants.NL );
 761         html_writer.write( "<br>" );
 762         html_writer.write( "Calculation mode for low copy : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 763         html_writer.write( SurfacingConstants.NL );
 764         html_writer.write( "<br>" );
 765         html_writer.write( "Minimal difference : " + min_diff );
 766         html_writer.write( SurfacingConstants.NL );
 767         html_writer.write( "<br>" );
 768         html_writer.write( "Factor : " + factor );
 769         html_writer.write( SurfacingConstants.NL );
 770         html_writer.write( "<br>" );
 771         html_writer.write( "Lower copy domains : " + counter );
 772         html_writer.write( SurfacingConstants.NL );
 773         html_writer.write( "<br>" );
 774         html_writer.write( "Total absence : " + total_absense_counter );
 775         html_writer.write( SurfacingConstants.NL );
 776         html_writer.write( "<br>" );
 777         html_writer.write( "Not total absence : " + not_total_absense_counter );
 778         html_writer.write( SurfacingConstants.NL );
 779         html_writer.write( "<br>" );
 780         html_writer.write( "Total domains : " + all_domains.size() );
 781         html_writer.write( SurfacingConstants.NL );
 782         html_writer.write( "<hr>" );
 783         html_writer.write( SurfacingConstants.NL );
 784         html_writer.write( "</body></html>" );
 785         html_writer.write( SurfacingConstants.NL );
 786         html_writer.close();
 787         plain_writer.write( "# Rule 1: high-copy-base > 0 && high-copy-target > 0 && high-copy-base >= low-copy" );
 788         plain_writer.write( SurfacingConstants.NL );
 789         plain_writer.write( "# Rule 2: high-copy-target >= minimal-difference + ( factor * low-copy )" );
 790         plain_writer.write( SurfacingConstants.NL );
 791         plain_writer.write( "# Calculation mode for high copy target: " + COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES );
 792         plain_writer.write( SurfacingConstants.NL );
 793         plain_writer.write( "# Calculation mode for high copy base  : " + COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES );
 794         plain_writer.write( SurfacingConstants.NL );
 795         plain_writer.write( "# Calculation mode for low copy        : " + COPY_CALC_MODE_FOR_LOW_COPY_SPECIES );
 796         plain_writer.write( SurfacingConstants.NL );
 797         plain_writer.write( "# Minimal difference: " + min_diff );
 798         plain_writer.write( SurfacingConstants.NL );
 799         plain_writer.write( "# Factor            : " + factor );
 800         plain_writer.write( SurfacingConstants.NL );
 801         plain_writer.write( "# Lower copy domains: " + counter );
 802         plain_writer.write( SurfacingConstants.NL );
 803         plain_writer.write( "# Total absence     : " + total_absense_counter );
 804         plain_writer.write( SurfacingConstants.NL );
 805         plain_writer.write( "# Not total absence : " + not_total_absense_counter );
 806         plain_writer.write( SurfacingConstants.NL );
 807         plain_writer.write( "# Total domains     : " + all_domains.size() );
 808         plain_writer.write( SurfacingConstants.NL );
 809         plain_writer.close();
 810     }
 811
 812     private static void writeGoIdsToFile( final Writer writer, final SortedSet<GoId> gos ) throws IOException {
 813         for( final GoId go_id : gos ) {
 814             writer.write( go_id.toString() );
 815             writer.write( SurfacingConstants.NL );
 816         }
 817         writer.close();
 818     }
 819
 820     private static void writeProteinsToFile( final File proteins_file_base,
 821                                              final SortedMap<Species, List<Protein>> protein_lists_per_species,
 822                                              final String domain_id ) throws IOException {
 823         final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR
 824                 + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
 825         SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
 826         final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
 827         SurfacingUtil.extractProteinNames( protein_lists_per_species,
 828                                            domain_id,
 829                                            proteins_file_writer,
 830                                            "\t",
 831                                            surfacing.LIMIT_SPEC_FOR_PROT_EX,
 832                                            -1 );
 833         proteins_file_writer.close();
 834         System.out.println( "Wrote proteins list to \"" + my_proteins_file + "\"" );
 835     }
 836
 837     public static enum COPY_CALCULATION_MODE {
 838         MEAN, MEDIAN, MAX, MIN
 839     }
 840 }