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