Uses of Interface
org.forester.surfacing.PairwiseDomainSimilarityCalculator
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Packages that use PairwiseDomainSimilarityCalculator Package Description org.forester.surfacing -
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Uses of PairwiseDomainSimilarityCalculator in org.forester.surfacing
Classes in org.forester.surfacing that implement PairwiseDomainSimilarityCalculator Modifier and Type Class Description class
CombinationsBasedPairwiseDomainSimilarityCalculator
class
DomainCountsBasedPairwiseSimilarityCalculator
class
ProteinCountsBasedPairwiseDomainSimilarityCalculator
Methods in org.forester.surfacing with parameters of type PairwiseDomainSimilarityCalculator 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)
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)
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