Uses of Enum Class
org.forester.protein.BinaryDomainCombination.DomainCombinationType
Packages that use BinaryDomainCombination.DomainCombinationType
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Uses of BinaryDomainCombination.DomainCombinationType in org.forester.protein
Methods in org.forester.protein that return BinaryDomainCombination.DomainCombinationTypeModifier and TypeMethodDescriptionReturns the enum constant of this class with the specified name.BinaryDomainCombination.DomainCombinationType.values()
Returns an array containing the constants of this enum class, in the order they are declared. -
Uses of BinaryDomainCombination.DomainCombinationType in org.forester.surfacing
Methods in org.forester.surfacing that return BinaryDomainCombination.DomainCombinationTypeModifier and TypeMethodDescriptionBasicGenomeWideCombinableDomains.getDomainCombinationType()
GenomeWideCombinableDomains.getDomainCombinationType()
Methods in org.forester.surfacing with parameters of type BinaryDomainCombination.DomainCombinationTypeModifier and TypeMethodDescriptionstatic void
SurfacingUtil.collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile
(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains) BasicGenomeWideCombinableDomains.createInstance
(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, Map<String, List<GoId>> domain_id_to_go_ids_map, BinaryDomainCombination.DomainCombinationType dc_type, Map<String, DescriptiveStatistics> protein_length_stats_by_dc, Map<String, DescriptiveStatistics> domain_number_stats_by_dc) BasicGenomeWideCombinableDomains.createInstance
(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type) static StringBuilder
SurfacingUtil.createParametersAsString
(boolean ignore_dufs, double ie_value_max, double fs_e_value_max, int max_allowed_overlap, boolean no_engulfing_overlaps, File cutoff_scores_file, BinaryDomainCombination.DomainCombinationType dc_type) static void
SurfacingUtil.executeParsimonyAnalysis
(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, Map<String, List<GoId>> domain_id_to_go_ids_map, Map<GoId, GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, String parameters_str, Map<String, Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> positive_filter, boolean output_binary_domain_combinations_for_graphs, List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, Map<String, DescriptiveStatistics> protein_length_stats_by_dc, Map<String, DescriptiveStatistics> domain_number_stats_by_dc, Map<String, DescriptiveStatistics> domain_length_stats_by_domain, Map<String, Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)