Uses of Class
org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField

Packages that use DomainSimilarity.DomainSimilaritySortField

Package	Description
org.forester.surfacing

Uses of DomainSimilarity.DomainSimilaritySortField in org.forester.surfacing

Methods in org.forester.surfacing that return DomainSimilarity.DomainSimilaritySortField

Modifier and Type	Method and Description
static DomainSimilarity.DomainSimilaritySortField	DomainSimilarity.DomainSimilaritySortField.valueOf(String name) Returns the enum constant of this type with the specified name.
static DomainSimilarity.DomainSimilaritySortField[]	DomainSimilarity.DomainSimilaritySortField.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.DomainSimilaritySortField

Modifier and Type

Method and Description

void

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)

Constructors in org.forester.surfacing with parameters of type DomainSimilarity.DomainSimilaritySortField

Constructor and Description
BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score)
BasicDomainSimilarityCalculator(DomainSimilarity.DomainSimilaritySortField sort, boolean sort_by_species_count_first, boolean treat_as_binary_comparison, boolean calc_similarity_score, boolean verbose)