Uses of Class
org.forester.surfacing.DomainSimilarity

Packages that use DomainSimilarity

Package	Description
org.forester.surfacing

Uses of DomainSimilarity in org.forester.surfacing

Methods in org.forester.surfacing that return types with arguments of type DomainSimilarity

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)

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

Modifier and Type	Method and Description
int	DomainSimilarity.compareTo(DomainSimilarity domain_similarity)

Method parameters in org.forester.surfacing with type arguments of type DomainSimilarity

Modifier and Type	Method and Description
static 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)