Uses of Class
org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
-
Packages that use DomainSimilarity.DomainSimilarityScoring Package Description org.forester.surfacing -
-
Uses of DomainSimilarity.DomainSimilarityScoring in org.forester.surfacing
Methods in org.forester.surfacing that return DomainSimilarity.DomainSimilarityScoring Modifier and Type Method Description static DomainSimilarity.DomainSimilarityScoring
DomainSimilarity.DomainSimilarityScoring. valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static DomainSimilarity.DomainSimilarityScoring[]
DomainSimilarity.DomainSimilarityScoring. values()
Returns an array containing the constants of this enum type, in the order they are declared.Methods in org.forester.surfacing with parameters of type DomainSimilarity.DomainSimilarityScoring Modifier and Type Method Description void
PairwiseGenomeComparator. performPairwiseComparisons(java.lang.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, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, java.util.List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, java.lang.String automated_pairwise_comparison_suffix, boolean verbose, java.lang.String automated_pairwise_comparison_prefix, java.lang.String command_line_prg_name, java.io.File out_dir, boolean write_pairwise_comparisons, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)
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)
-