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.phylogeny.Phylogeny;
  47 import org.forester.species.Species;
  48 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  49 import org.forester.util.DescriptiveStatistics;
  50 import org.forester.util.ForesterUtil;
  51
  52 public class PairwiseGenomeComparator {
  53
  54     private List<DistanceMatrix> _domain_distance_scores_means;
  55     private List<DistanceMatrix> _shared_binary_combinations_based_distances;
  56     private List<DistanceMatrix> _shared_domains_based_distances;
  57
  58     public PairwiseGenomeComparator() {
  59         init();
  60     }
  61
  62     public List<DistanceMatrix> getDomainDistanceScoresMeans() {
  63         return _domain_distance_scores_means;
  64     }
  65
  66     public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
  67         return _shared_binary_combinations_based_distances;
  68     }
  69
  70     public List<DistanceMatrix> getSharedDomainsBasedDistances() {
  71         return _shared_domains_based_distances;
  72     }
  73
  74     public void performPairwiseComparisons( final StringBuilder html_desc,
  75                                             final boolean sort_by_species_count_first,
  76                                             final Detailedness detailedness,
  77                                             final boolean ignore_domains_without_combs_in_all_spec,
  78                                             final boolean ignore_domains_specific_to_one_species,
  79                                             final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
  80                                             final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
  81                                             final DomainSimilarity.DomainSimilarityScoring scoring,
  82                                             final Map<String, List<GoId>> domain_id_to_go_ids_map,
  83                                             final Map<GoId, GoTerm> go_id_to_term_map,
  84                                             final GoNameSpace go_namespace_limit,
  85                                             final Species[] species,
  86                                             final int number_of_genomes,
  87                                             final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
  88                                             final PairwiseDomainSimilarityCalculator pw_calc,
  89                                             final String automated_pairwise_comparison_suffix,
  90                                             final boolean verbose,
  91                                             final String automated_pairwise_comparison_prefix,
  92                                             final String command_line_prg_name,
  93                                             final File out_dir,
  94                                             final boolean write_pairwise_comparisons,
  95                                             final Map<String, Integer> tax_code_to_id_map,
  96                                             final boolean calc_similarity_scores,
  97                                             final Phylogeny phy ) {
  98         init();
  99         final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 100         final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 101         final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 102         if ( verbose ) {
 103             System.out.println();
 104             System.out.println( "Pairwise genome distances:" );
 105             System.out.print( "[species-i - species-j:" );
 106             System.out.print( " mean-score-based" );
 107             System.out.print( " (sd)" );
 108             System.out.print( " [N]" );
 109             System.out.print( " | shared-domains-based" );
 110             System.out.println( " | shared-binary-combinations-based]" );
 111             System.out.println();
 112         }
 113         for( int i = 0; i < number_of_genomes; ++i ) {
 114             final String species_i = species[ i ].getSpeciesId();
 115             domain_distance_scores_means.setIdentifier( i, species_i );
 116             shared_domains_based_distances.setIdentifier( i, species_i );
 117             shared_binary_combinations_based_distances.setIdentifier( i, species_i );
 118             if ( verbose ) {
 119                 System.out.println( ( i + 1 ) + "/" + number_of_genomes );
 120             }
 121             for( int j = 0; j < i; ++j ) {
 122                 if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
 123                         || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
 124                     domain_distance_scores_means
 125                             .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
 126                     shared_domains_based_distances
 127                             .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
 128                     shared_binary_combinations_based_distances
 129                             .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
 130                     continue;
 131                 }
 132                 final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
 133                 genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
 134                 genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
 135                 DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
 136                 if ( domain_id_to_go_ids_map != null ) {
 137                     go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
 138                 }
 139                 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
 140                                                                                              sort_by_species_count_first,
 141                                                                                              true,
 142                                                                                              calc_similarity_scores );
 143                 final SortedSet<DomainSimilarity> similarities = calc
 144                         .calculateSimilarities( pw_calc,
 145                                                 genome_pair,
 146                                                 ignore_domains_without_combs_in_all_spec,
 147                                                 ignore_domains_specific_to_one_species );
 148                 SurfacingUtil.decoratePrintableDomainSimilarities( similarities, detailedness );
 149                 final DescriptiveStatistics stats = SurfacingUtil
 150                         .calculateDescriptiveStatisticsForMeanValues( similarities );
 151                 final String species_j = species[ j ].getSpeciesId();
 152                 final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
 153                                                                                                                                                                       .get( i ),
 154                                                                                                                                                               list_of_genome_wide_combinable_domains
 155                                                                                                                                                                       .get( j ) );
 156                 genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
 157                 double dissimilarity_score_mean;
 158                 if ( stats.getN() < 1 ) {
 159                     // No domains in common
 160                     dissimilarity_score_mean = 1.0;
 161                 }
 162                 else {
 163                     dissimilarity_score_mean = 1.0 - stats.arithmeticMean();
 164                 }
 165                 final double shared_domains_based_genome_distance = 1.0 - genome_similarity_calculator
 166                         .calculateSharedDomainsBasedGenomeSimilarityScore();
 167                 final double shared_binary_combinations_based_genome_distance = 1.0 - genome_similarity_calculator
 168                         .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore();
 169                 domain_distance_scores_means.setValue( i, j, dissimilarity_score_mean );
 170                 shared_domains_based_distances.setValue( i, j, shared_domains_based_genome_distance );
 171                 shared_binary_combinations_based_distances.setValue( i,
 172                                                                      j,
 173                                                                      shared_binary_combinations_based_genome_distance );
 174                 if ( verbose ) {
 175                     System.out.print( species_i + "-" );
 176                     System.out.print( species_j + ": " );
 177                     System.out.print( ForesterUtil.round( dissimilarity_score_mean, 2 ) );
 178                     if ( stats.getN() > 1 ) {
 179                         System.out.print( " (" + ForesterUtil.round( stats.sampleStandardDeviation(), 2 ) + ")" );
 180                     }
 181                     else {
 182                         System.out.print( " (n/a)" );
 183                     }
 184                     System.out.print( " [" + stats.getN() + "]" );
 185                     System.out.print( " | " );
 186                     System.out.print( ForesterUtil.round( shared_domains_based_genome_distance, 2 ) );
 187                     System.out.print( " | " );
 188                     System.out.println( ForesterUtil.round( shared_binary_combinations_based_genome_distance, 2 ) );
 189                 }
 190                 String pairwise_similarities_output_file_str = automated_pairwise_comparison_prefix + species_i + "_"
 191                         + species_j + automated_pairwise_comparison_suffix;
 192                 switch ( domain_similarity_print_option ) {
 193                     case HTML:
 194                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 195                             pairwise_similarities_output_file_str += ".html";
 196                         }
 197                         break;
 198                 }
 199                 if ( write_pairwise_comparisons ) {
 200                     try {
 201                         final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
 202                                 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 203                         SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
 204                                                                      new StringBuilder( species_i + "-" + species_j ),
 205                                                                      null,
 206                                                                      writer,
 207                                                                      null,
 208                                                                      similarities,
 209                                                                      true,
 210                                                                      null,
 211                                                                      domain_similarity_print_option,
 212                                                                      scoring,
 213                                                                      false,
 214                                                                      tax_code_to_id_map,
 215                                                                      phy,
 216                                                                      null );
 217                     }
 218                     catch ( final IOException e ) {
 219                         ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
 220                                 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
 221                     }
 222                 }
 223             }
 224         }
 225         getDomainDistanceScoresMeans().add( domain_distance_scores_means );
 226         getSharedDomainsBasedDistances().add( shared_domains_based_distances );
 227         getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
 228         if ( verbose ) {
 229             System.out.println();
 230         }
 231     }
 232
 233     public void performPairwiseComparisonsJacknifed( final Species[] species,
 234                                                      final int number_of_genomes,
 235                                                      final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains,
 236                                                      final boolean verbose,
 237                                                      final int number_of_resamplings,
 238                                                      final double jacknife_ratio,
 239                                                      final long random_seed ) {
 240         init();
 241         if ( number_of_resamplings < 2 ) {
 242             throw new IllegalArgumentException( "attempt to perform jacknife resampling with less than 2 resamplings" );
 243         }
 244         if ( jacknife_ratio <= 0.0 ) {
 245             throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio of 0.0 or less" );
 246         }
 247         else if ( jacknife_ratio >= 1.0 ) {
 248             throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
 249         }
 250         final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
 251         if ( verbose ) {
 252             System.out.println();
 253             System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
 254         }
 255         if ( verbose ) {
 256             System.out.print( "resampling " );
 257         }
 258         final Random generator = new Random( random_seed );
 259         for( int r = 0; r < number_of_resamplings; ++r ) {
 260             if ( verbose ) {
 261                 System.out.print( " " + r );
 262             }
 263             final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
 264                                                                                   jacknife_ratio,
 265                                                                                   generator );
 266             final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 267             final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
 268             for( int i = 0; i < number_of_genomes; ++i ) {
 269                 final String species_i = species[ i ].getSpeciesId();
 270                 shared_domains_based_distances.setIdentifier( i, species_i );
 271                 shared_binary_combinations_based_distances.setIdentifier( i, species_i );
 272                 for( int j = 0; j < i; ++j ) {
 273                     final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
 274                     genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
 275                     genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
 276                     final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
 277                                                                                                                                                                          .get( i ),
 278                                                                                                                                                                  list_of_genome_wide_combinable_domains
 279                                                                                                                                                                          .get( j ) );
 280                     genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
 281                     genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
 282                     shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
 283                             .calculateSharedDomainsBasedGenomeSimilarityScore() );
 284                     shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
 285                             .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
 286                 }
 287             }
 288             getSharedDomainsBasedDistances().add( shared_domains_based_distances );
 289             getSharedBinaryCombinationsBasedDistances().add( shared_binary_combinations_based_distances );
 290         }
 291         if ( verbose ) {
 292             System.out.println();
 293         }
 294     }
 295
 296     private void init() {
 297         _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
 298         _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
 299         _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
 300     }
 301
 302     static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
 303         String[] all_domain_ids_array;
 304         final SortedSet<String> all_domain_ids = new TreeSet<String>();
 305         for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
 306             final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
 307             for( final String domain : all_domains ) {
 308                 all_domain_ids.add( domain );
 309             }
 310         }
 311         all_domain_ids_array = new String[ all_domain_ids.size() ];
 312         int n = 0;
 313         for( final String domain_id : all_domain_ids ) {
 314             all_domain_ids_array[ n++ ] = domain_id;
 315         }
 316         return all_domain_ids_array;
 317     }
 318
 319     static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
 320                                                             final double jacknife_ratio,
 321                                                             final Random generator ) {
 322         final int size = all_domain_ids_array.length;
 323         final SortedSet<String> random_domain_ids = new TreeSet<String>();
 324         final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
 325         while ( random_domain_ids.size() < number_of_ids_pick ) {
 326             final int r = generator.nextInt( size );
 327             random_domain_ids.add( all_domain_ids_array[ r ] );
 328         }
 329         return random_domain_ids;
 330     }
 331 }