Uses of Interface
org.forester.protein.BinaryDomainCombination
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Packages that use BinaryDomainCombination Package Description org.forester.surfacing -
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Uses of BinaryDomainCombination in org.forester.surfacing
Classes in org.forester.surfacing that implement BinaryDomainCombination Modifier and Type Class Description class
AdjactantDirectedBinaryDomainCombination
class
BasicBinaryDomainCombination
class
DirectedBinaryDomainCombination
Methods in org.forester.surfacing that return BinaryDomainCombination Modifier and Type Method Description static BinaryDomainCombination
BasicBinaryDomainCombination. obtainInstance(java.lang.String ids)
static BinaryDomainCombination
DirectedBinaryDomainCombination. obtainInstance(java.lang.String ids)
Methods in org.forester.surfacing that return types with arguments of type BinaryDomainCombination Modifier and Type Method Description java.util.Set<BinaryDomainCombination>
DomainArchitectureBasedGenomeSimilarityCalculator. getAllBinaryDomainCombinations()
Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.java.util.Set<BinaryDomainCombination>
DomainArchitectureBasedGenomeSimilarityCalculator. getBinaryDomainCombinationsSpecificToGenome0()
java.util.Set<BinaryDomainCombination>
DomainArchitectureBasedGenomeSimilarityCalculator. getBinaryDomainCombinationsSpecificToGenome1()
java.util.Set<BinaryDomainCombination>
DomainArchitectureBasedGenomeSimilarityCalculator. getSharedBinaryDomainCombinations()
java.util.List<BinaryDomainCombination>
AdjactantDirectedCombinableDomains. toBinaryDomainCombinations()
java.util.List<BinaryDomainCombination>
BasicCombinableDomains. toBinaryDomainCombinations()
java.util.SortedSet<BinaryDomainCombination>
BasicGenomeWideCombinableDomains. toBinaryDomainCombinations()
java.util.List<BinaryDomainCombination>
CombinableDomains. toBinaryDomainCombinations()
java.util.List<BinaryDomainCombination>
DirectedCombinableDomains. toBinaryDomainCombinations()
java.util.SortedSet<BinaryDomainCombination>
GenomeWideCombinableDomains. toBinaryDomainCombinations()
This should return all binary domain combinations present in the genome.Methods in org.forester.surfacing with parameters of type BinaryDomainCombination Modifier and Type Method Description int
BasicBinaryDomainCombination. compareTo(BinaryDomainCombination binary_domain_combination)
Method parameters in org.forester.surfacing with type arguments of type BinaryDomainCombination Modifier and Type Method Description static void
SurfacingUtil. addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, java.util.SortedSet<BinaryDomainCombination> binary_domain_combinations)
static void
SurfacingUtil. collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
static void
SurfacingUtil. executeFitchGainsAnalysis(java.io.File output_file, java.util.List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, java.util.SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis)
Warning: This side-effects 'all_bin_domain_combinations_encountered'!static void
SurfacingUtil. executeFitchGainsAnalysis(java.io.File output_file, java.util.List<BinaryDomainCombination> all_bin_domain_combinations_changed, int sum_of_all_domains_encountered, java.util.SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered, boolean is_gains_analysis)
Warning: This side-effects 'all_bin_domain_combinations_encountered'!static void
SurfacingUtil. executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, java.lang.String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, 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, java.lang.String parameters_str, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> positive_filter, boolean output_binary_domain_combinations_for_graphs, java.util.List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, java.util.List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, java.util.Map<java.lang.String,DescriptiveStatistics> protein_length_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_number_stats_by_dc, java.util.Map<java.lang.String,DescriptiveStatistics> domain_length_stats_by_domain, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)
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