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 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,