Uses of Interface
org.forester.surfacing.GenomeWideCombinableDomains
Packages that use GenomeWideCombinableDomains
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Uses of GenomeWideCombinableDomains in org.forester.surfacing
Classes in org.forester.surfacing that implement GenomeWideCombinableDomainsMethods in org.forester.surfacing with parameters of type GenomeWideCombinableDomainsModifier and TypeMethodDescriptionstatic void
SurfacingUtil.addAllBinaryDomainCombinationToSet
(GenomeWideCombinableDomains genome, SortedSet<BinaryDomainCombination> binary_domain_combinations) static void
SurfacingUtil.addAllDomainIdsToSet
(GenomeWideCombinableDomains genome, SortedSet<String> domain_ids) static void
SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis
(String[][] input_file_properties, File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order) static void
SurfacingUtil.writeDomainCombinationsCountsFile
(String[][] input_file_properties, File output_dir, Writer per_genome_domain_promiscuity_statistics_writer, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order) Method parameters in org.forester.surfacing with type arguments of type GenomeWideCombinableDomainsModifier and TypeMethodDescriptionstatic void
DomainCountsDifferenceUtil.calculateCopyNumberDifferences
(List<GenomeWideCombinableDomains> genomes, SortedMap<Species, List<Protein>> protein_lists_per_species, List<String> high_copy_base_species, List<String> high_copy_target_species, List<String> low_copy_species, int min_diff, Double factor, File plain_output_dom, File html_output_dom, File html_output_dc, Map<String, List<GoId>> domain_id_to_go_ids_map, Map<GoId, GoTerm> go_id_to_term_map, File all_domains_go_ids_out_dom, File passing_domains_go_ids_out_dom, File proteins_file_base) BasicDomainSimilarityCalculator.calculateSimilarities
(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome) DomainSimilarityCalculator.calculateSimilarities
(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome) static DomainParsimonyCalculator
DomainParsimonyCalculator.createInstance
(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list) static DomainParsimonyCalculator
DomainParsimonyCalculator.createInstance
(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<String, Set<String>> domain_id_to_secondary_features_map) DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence
(List<GenomeWideCombinableDomains> gwcd_list) DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence
(List<GenomeWideCombinableDomains> gwcd_list, SortedSet<String> positive_filter) DomainParsimonyCalculator.createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence
(List<GenomeWideCombinableDomains> gwcd_list, Map<String, String> domain_id_to_second_features_map) SurfacingUtil.getAllDomainIds
(List<GenomeWideCombinableDomains> gwcd_list) 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) void
PairwiseGenomeComparator.performPairwiseComparisonsJacknifed
(Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, boolean verbose, int number_of_resamplings, double jacknife_ratio, long random_seed) static void
SurfacingUtil.writePresentToNexus
(File output_file, File positive_filter_file, SortedSet<String> filter, List<GenomeWideCombinableDomains> gwcd_list) static void
SurfacingUtil.writeProteinListsForAllSpecies
(File output_dir, SortedMap<Species, List<Protein>> protein_lists_per_species, List<GenomeWideCombinableDomains> gwcd_list, double domain_e_cutoff, Set<String> pos_filter_doms) Constructors in org.forester.surfacing with parameters of type GenomeWideCombinableDomainsModifierConstructorDescriptionDomainArchitectureBasedGenomeSimilarityCalculator
(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)