forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.surfacing;
  28
  29 import java.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.util.ArrayList;
  35 import java.util.List;
  36 import java.util.Map;
  37 import java.util.Random;
  38 import java.util.SortedSet;
  39 import java.util.TreeSet;
  40
  41 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  42 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  43 import org.forester.go.GoId;
  44 import org.forester.go.GoNameSpace;
  45 import org.forester.go.GoTerm;
  46 import org.forester.species.Species;
  47 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  48 import org.forester.util.DescriptiveStatistics;
  49 import org.forester.util.ForesterUtil;
  50
  51 public class PairwiseGenomeComparator {
  52
  53     private List<DistanceMatrix> _domain_distance_scores_means;
  54     private List<DistanceMatrix> _shared_domains_based_distances;
  55     private List<DistanceMatrix> _shared_binary_combinations_based_distances;
  56
  57     public PairwiseGenomeComparator() {
  58         init();
  59     }
  60
  61     public List<DistanceMatrix> getDomainDistanceScoresMeans() {
  62         return _domain_distance_scores_means;
  63     }
  64
  65     public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
  66         return _shared_binary_combinations_based_distances;
  67     }
  68
  69     public List<DistanceMatrix> getSharedDomainsBasedDistances() {
  70         return _shared_domains_based_distances;
  71     }
  72
  73     private void init() {
  74         _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
  75         _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
  76         _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
  77     }
  78
  79     public void performPairwiseComparisons( final StringBuilder html_desc,
  80                                             final boolean sort_by_species_count_first,
  81                                             final Detailedness detailedness,
  82                                             final boolean ignore_domains_without_combs_in_all_spec,
  83                                             final boolean ignore_domains_specific_to_one_species,
  84                                             final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
  85                                             final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
  86                                             final DomainSimilarity.DomainSimilarityScoring scoring,
  87                                             final Map<String, List<GoId>> domain_id_to_go_ids_map,
  88                                             final Map<GoId, GoTerm> go_id_to_term_map,
  89                                             final GoNameSpace go_namespace_limit,
  90                                             final Species[] species,
  91                                             final int number_of_genomes,
  92                                             final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
  93                                             final PairwiseDomainSimilarityCalculator pw_calc,
  94                                             final String automated_pairwise_comparison_suffix,
  95                                             final boolean verbose,
  96                                             final String automated_pairwise_comparison_prefix,
  97                                             final String command_line_prg_name,
  98                                             final File out_dir,
  99                                             final boolean write_pairwise_comparisons,
 100                                             final Map<String, Integer> tax_code_to_id_map,
 101                                             final boolean calc_similarity_scores ) {
 102         init();
 103         final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 104         final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 105         final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 106         if ( verbose ) {
 107             System.out.println();
 108             System.out.println( "Pairwise genome distances:" );
 109             System.out.print( "[species-i - species-j:" );
 110             System.out.print( " mean-score-based" );
 111             System.out.print( " (sd)" );
 112             System.out.print( " [N]" );
 113             System.out.print( " | shared-domains-based" );
 114             System.out.println( " | shared-binary-combinations-based]" );
 115             System.out.println();
 116         }
 117         for( int i = 0; i < number_of_genomes; ++i ) {
 118             final String species_i = species[ i ].getSpeciesId();
 119             domain_distance_scores_means.setIdentifier( i, species_i );
 120             shared_domains_based_distances.setIdentifier( i, species_i );
 121             shared_binary_combinations_based_distances.setIdentifier( i, species_i );
 122             if ( verbose ) {
 123                 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
 124             }
 125             for( int j = 0; j < i; ++j ) {
 126                 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
 127                         || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
 128                     domain_distance_scores_means
 129                             .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
 130                     shared_domains_based_distances
 131                             .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
 132                     shared_binary_combinations_based_distances
 133                             .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
 134                     continue;
 135                 }
 136                 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
 137                 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
 138                 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
 139                 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
 140                 if ( domain_id_to_go_ids_map != null ) {
 141                     go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
 142                 }
 143                 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
 144                                                                                              sort_by_species_count_first,
 145                                                                                              true,
 146                                                                                              calc_similarity_scores );
 147                 final SortedSet<DomainSimilarity> similarities = calc
 148                         .calculateSimilarities( pw_calc,
 149                                                 genome_pair,
 150                                                 ignore_domains_without_combs_in_all_spec,
 151                                                 ignore_domains_specific_to_one_species );
 152                 SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
 153                 final DescriptiveStatistics stats = SurfacingUtil
 154                         .calculateDescriptiveStatisticsForMeanValues( similarities );
 155                 final String species_j = species[ j ].getSpeciesId();
 156                 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
 157                                                                                                                                                                       .get( i ),
 158                                                                                                                                                               list_of_genome_wide_combinable_domains
 159                                                                                                                                                                       .get( j ) );
 160                 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
 161                 double dissimilarity_score_mean;
 162                 if ( stats.getN() < 1 ) {
 163                     // No domains in common
 164                     dissimilarity_score_mean = 1.0;
 165                 }
 166                 else {
 167                     dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
 168                 }
 169                 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
 170                         .calculateSharedDomainsBasedGenomeSimilarityScore();
 171                 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
 172                         .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
 173                 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
 174                 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
 175                 shared_binary_combinations_based_distances.setValue( i,
 176                                                                      j,
 177                                                                      shared_binary_combinations_based_genome_distance );
 178                 if ( verbose ) {
 179                     System.out.print( species_i + "-" );
 180                     System.out.print( species_j + ": " );
 181                     System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
 182                     if ( stats.getN() > 1 ) {
 183                         System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
 184                     }
 185                     else {
 186                         System.out.print( " (n/a)" );
 187                     }
 188                     System.out.print( " [" + stats.getN() + "]" );
 189                     System.out.print( " | " );
 190                     System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
 191                     System.out.print( " | " );
 192                     System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
 193                 }
 194                 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
 195                         + species_j + automated_pairwise_comparison_suffix;
 196                 switch ( domain_similarity_print_option ) {
 197                     case HTML:
 198                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 199                             pairwise_similarities_output_file_str += ".html";
 200                         }
 201                         break;
 202                 }
 203                 if ( write_pairwise_comparisons ) {
 204                     try {
 205                         final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
 206                                 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 207                         SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
 208                                                                      new StringBuilder( species_i + "-" + species_j ),
 209                                                                      null,
 210                                                                      writer,
 211                                                                      null,
 212                                                                      similarities,
 213                                                                      true,
 214                                                                      null,
 215                                                                      domain_similarity_print_option,
 216                                                                      scoring,
 217                                                                      false,
 218                                                                      tax_code_to_id_map );
 219                     }
 220                     catch ( final IOException e ) {
 221                         ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
 222                                 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
 223                     }
 224                 }
 225             }
 226         }
 227         getDomainDistanceScoresMeans().add( domain_distance_scores_means );
 228         getSharedDomainsBasedDistances().add( shared_domains_based_distances );
 229         getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
 230         if ( verbose ) {
 231             System.out.println();
 232         }
 233     }
 234
 235     public void performPairwiseComparisonsJacknifed( final Species[] species,
 236                                                      final int number_of_genomes,
 237                                                      final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
 238                                                      final boolean verbose,
 239                                                      final int number_of_resamplings,
 240                                                      final double jacknife_ratio,
 241                                                      final long random_seed ) {
 242         init();
 243         if ( number_of_resamplings < 2 ) {
 244             throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
 245         }
 246         if ( jacknife_ratio <= 0.0 ) {
 247             throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
 248         }
 249         else if ( jacknife_ratio >= 1.0 ) {
 250             throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
 251         }
 252         final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
 253         if ( verbose ) {
 254             System.out.println();
 255             System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
 256         }
 257         if ( verbose ) {
 258             System.out.print( "resampling " );
 259         }
 260         final Random generator = new Random( random_seed );
 261         for( int r = 0; r < number_of_resamplings; ++r ) {
 262             if ( verbose ) {
 263                 System.out.print( " " + r );
 264             }
 265             final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
 266                                                                                   jacknife_ratio,
 267                                                                                   generator );
 268             final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 269             final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 270             for( int i = 0; i < number_of_genomes; ++i ) {
 271                 final String species_i = species[ i ].getSpeciesId();
 272                 shared_domains_based_distances.setIdentifier( i, species_i );
 273                 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
 274                 for( int j = 0; j < i; ++j ) {
 275                     final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
 276                     genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
 277                     genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
 278                     final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
 279                                                                                                                                                                          .get( i ),
 280                                                                                                                                                                  list_of_genome_wide_combinable_domains
 281                                                                                                                                                                          .get( j ) );
 282                     genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
 283                     genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
 284                     shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
 285                             .calculateSharedDomainsBasedGenomeSimilarityScore() );
 286                     shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
 287                             .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
 288                 }
 289             }
 290             getSharedDomainsBasedDistances().add( shared_domains_based_distances );
 291             getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
 292         }
 293         if ( verbose ) {
 294             System.out.println();
 295         }
 296     }
 297
 298     static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
 299         String[] all_domain_ids_array;
 300         final SortedSet<String> all_domain_ids = new TreeSet<String>();
 301         for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
 302             final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
 303             for( final String domain : all_domains ) {
 304                 all_domain_ids.add( domain );
 305             }
 306         }
 307         all_domain_ids_array = new String[ all_domain_ids.size() ];
 308         int n = 0;
 309         for( final String domain_id : all_domain_ids ) {
 310             all_domain_ids_array[ n++ ] = domain_id;
 311         }
 312         return all_domain_ids_array;
 313     }
 314
 315     static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
 316                                                             final double jacknife_ratio,
 317                                                             final Random generator ) {
 318         final int size = all_domain_ids_array.length;
 319         final SortedSet<String> random_domain_ids = new TreeSet<String>();
 320         final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
 321         while ( random_domain_ids.size() < number_of_ids_pick ) {
 322             final int r = generator.nextInt( size );
 323             random_domain_ids.add( all_domain_ids_array[ r ] );
 324         }
 325         return random_domain_ids;
 326     }
 327 }