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