Uses of Class
org.forester.surfacing.DomainSimilarity
Packages that use DomainSimilarity
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Uses of DomainSimilarity in org.forester.surfacing
Methods in org.forester.surfacing that return types with arguments of type DomainSimilarityModifier and TypeMethodDescriptionBasicDomainSimilarityCalculator.calculateSimilarities
(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome) DomainSimilarityCalculator.calculateSimilarities
(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome) Methods in org.forester.surfacing with parameters of type DomainSimilarityModifier and TypeMethodDescriptionint
DomainSimilarity.compareTo
(DomainSimilarity domain_similarity) Method parameters in org.forester.surfacing with type arguments of type DomainSimilarityModifier and TypeMethodDescriptionstatic DescriptiveStatistics
SurfacingUtil.calculateDescriptiveStatisticsForMeanValues
(Set<DomainSimilarity> similarities) static void
SurfacingUtil.decoratePrintableDomainSimilarities
(SortedSet<DomainSimilarity> domain_similarities, DomainSimilarityCalculator.Detailedness detailedness) static void
SurfacingUtil.writeDomainSimilaritiesToFile
(StringBuilder html_desc, StringBuilder html_title, Writer simple_tab_writer, Writer single_writer, Map<Character, Writer> split_writers, SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, Map<String, Integer> tax_code_to_id_map, Phylogeny phy, Set<String> pos_filter_doms)