Uses of Interface
org.forester.surfacing.PairwiseDomainSimilarityCalculator

Packages that use PairwiseDomainSimilarityCalculator

Package	Description
org.forester.surfacing

Uses of PairwiseDomainSimilarityCalculator in org.forester.surfacing

Classes in org.forester.surfacing that implement PairwiseDomainSimilarityCalculator

Modifier and Type	Class and Description
class	CombinationsBasedPairwiseDomainSimilarityCalculator
class	DomainCountsBasedPairwiseSimilarityCalculator
class	ProteinCountsBasedPairwiseDomainSimilarityCalculator

Methods in org.forester.surfacing with parameters of type PairwiseDomainSimilarityCalculator

Modifier and Type	Method and Description
SortedSet<DomainSimilarity>	BasicDomainSimilarityCalculator.calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome)
SortedSet<DomainSimilarity>	DomainSimilarityCalculator.calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome)
void	PairwiseGenomeComparator.performPairwiseComparisons(StringBuilder html_desc, boolean sort_by_species_count_first, DomainSimilarityCalculator.Detailedness detailedness, boolean ignore_domains_without_combs_in_all_spec, boolean ignore_domains_specific_to_one_species, DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field, DomainSimilarity.PRINT_OPTION domain_similarity_print_option, DomainSimilarity.DomainSimilarityScoring scoring, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, String automated_pairwise_comparison_suffix, boolean verbose, String automated_pairwise_comparison_prefix, String command_line_prg_name, File out_dir, boolean write_pairwise_comparisons, Map<String,Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)