Uses of Interface
org.forester.protein.BinaryDomainCombination
Packages that use BinaryDomainCombination
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Uses of BinaryDomainCombination in org.forester.surfacing
Classes in org.forester.surfacing that implement BinaryDomainCombinationModifier and TypeClassDescriptionclassclassclassMethods in org.forester.surfacing that return BinaryDomainCombinationModifier and TypeMethodDescriptionstatic BinaryDomainCombinationBasicBinaryDomainCombination.obtainInstance(String ids) static final BinaryDomainCombinationDirectedBinaryDomainCombination.obtainInstance(String ids) Methods in org.forester.surfacing that return types with arguments of type BinaryDomainCombinationModifier and TypeMethodDescriptionDomainArchitectureBasedGenomeSimilarityCalculator.getAllBinaryDomainCombinations()Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.DomainArchitectureBasedGenomeSimilarityCalculator.getBinaryDomainCombinationsSpecificToGenome0()DomainArchitectureBasedGenomeSimilarityCalculator.getBinaryDomainCombinationsSpecificToGenome1()DomainArchitectureBasedGenomeSimilarityCalculator.getSharedBinaryDomainCombinations()AdjactantDirectedCombinableDomains.toBinaryDomainCombinations()BasicCombinableDomains.toBinaryDomainCombinations()BasicGenomeWideCombinableDomains.toBinaryDomainCombinations()CombinableDomains.toBinaryDomainCombinations()DirectedCombinableDomains.toBinaryDomainCombinations()GenomeWideCombinableDomains.toBinaryDomainCombinations()This should return all binary domain combinations present in the genome.Methods in org.forester.surfacing with parameters of type BinaryDomainCombinationModifier and TypeMethodDescriptionfinal intBasicBinaryDomainCombination.compareTo(BinaryDomainCombination binary_domain_combination) Method parameters in org.forester.surfacing with type arguments of type BinaryDomainCombinationModifier and TypeMethodDescriptionstatic voidSurfacingUtil.addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, SortedSet<BinaryDomainCombination> binary_domain_combinations) static voidSurfacingUtil.collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains) static voidSurfacingUtil.executeFitchGainsAnalysis(File output_file, List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis) Warning: This side-effects 'all_bin_domain_combinations_encountered'!static voidSurfacingUtil.executeFitchGainsAnalysis(File output_file, List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis) Warning: This side-effects 'all_bin_domain_combinations_encountered'!static voidSurfacingUtil.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)