Uses of Enum Class
org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring
Packages that use DomainSimilarity.DomainSimilarityScoring
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Uses of DomainSimilarity.DomainSimilarityScoring in org.forester.surfacing
Methods in org.forester.surfacing that return DomainSimilarity.DomainSimilarityScoringModifier and TypeMethodDescriptionReturns the enum constant of this class with the specified name.DomainSimilarity.DomainSimilarityScoring.values()
Returns an array containing the constants of this enum class, in the order they are declared.Methods in org.forester.surfacing with parameters of type DomainSimilarity.DomainSimilarityScoringModifier and TypeMethodDescriptionvoid
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) 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)