final Detailedness detailedness,
final boolean ignore_domains_without_combs_in_all_spec,
final boolean ignore_domains_specific_to_one_species,
- final PrintableDomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
- final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
- final PrintableDomainSimilarity.DomainSimilarityScoring scoring,
+ final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
+ final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final DomainSimilarity.DomainSimilarityScoring scoring,
final Map<String, List<GoId>> domain_id_to_go_ids_map,
final Map<GoId, GoTerm> go_id_to_term_map,
final GoNameSpace go_namespace_limit,
final boolean calc_similarity_scores,
final Phylogeny phy ) {
init();
- final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
- final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
- final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
if ( verbose ) {
System.out.println();
System.out.println( "Pairwise genome distances:" );
if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 )
|| ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) {
domain_distance_scores_means
- .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
+ .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
shared_domains_based_distances
- .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
+ .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
shared_binary_combinations_based_distances
- .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
+ .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE );
continue;
}
final List<GenomeWideCombinableDomains> genome_pair = new ArrayList<GenomeWideCombinableDomains>( 2 );
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
sort_by_species_count_first,
true,
- calc_similarity_scores );
- final SortedSet<PrintableDomainSimilarity> similarities = calc
+ calc_similarity_scores,
+ true );
+ final SortedSet<DomainSimilarity> similarities = calc
.calculateSimilarities( pw_calc,
genome_pair,
ignore_domains_without_combs_in_all_spec,
.calculateDescriptiveStatisticsForMeanValues( similarities );
final String species_j = species[ j ].getSpeciesId();
final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
- .get( i ),
+ .get( i ),
list_of_genome_wide_combinable_domains
- .get( j ) );
+ .get( j ) );
genome_similarity_calculator.setAllowDomainsToBeIgnored( false );
double dissimilarity_score_mean;
if ( stats.getN() < 1 ) {
final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
jacknife_ratio,
generator );
- final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
- final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+ final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
for( int i = 0; i < number_of_genomes; ++i ) {
final String species_i = species[ i ].getSpeciesId();
shared_domains_based_distances.setIdentifier( i, species_i );
genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) );
genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) );
final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains
- .get( i ),
+ .get( i ),
list_of_genome_wide_combinable_domains
- .get( j ) );
+ .get( j ) );
genome_simiarity_calculator.setAllowDomainsToBeIgnored( true );
genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore );
shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
- .calculateSharedDomainsBasedGenomeSimilarityScore() );
+ .calculateSharedDomainsBasedGenomeSimilarityScore() );
shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator
- .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
+ .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() );
}
}
getSharedDomainsBasedDistances().add( shared_domains_based_distances );