Uses of Interface
org.forester.protein.BinaryDomainCombination

Packages that use BinaryDomainCombination

Package	Description
org.forester.surfacing

Uses of BinaryDomainCombination in org.forester.surfacing

Classes in org.forester.surfacing that implement BinaryDomainCombination

Modifier and Type	Class and Description
class	AdjactantDirectedBinaryDomainCombination
class	BasicBinaryDomainCombination
class	DirectedBinaryDomainCombination

Methods in org.forester.surfacing that return BinaryDomainCombination

Modifier and Type	Method and Description
static BinaryDomainCombination	DirectedBinaryDomainCombination.obtainInstance(String ids)
static BinaryDomainCombination	BasicBinaryDomainCombination.obtainInstance(String ids)

Methods in org.forester.surfacing that return types with arguments of type BinaryDomainCombination

Modifier and Type	Method and Description
Set<BinaryDomainCombination>	DomainArchitectureBasedGenomeSimilarityCalculator.getAllBinaryDomainCombinations() Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.
Set<BinaryDomainCombination>	DomainArchitectureBasedGenomeSimilarityCalculator.getBinaryDomainCombinationsSpecificToGenome0()
Set<BinaryDomainCombination>	DomainArchitectureBasedGenomeSimilarityCalculator.getBinaryDomainCombinationsSpecificToGenome1()
Set<BinaryDomainCombination>	DomainArchitectureBasedGenomeSimilarityCalculator.getSharedBinaryDomainCombinations()
SortedSet<BinaryDomainCombination>	GenomeWideCombinableDomains.toBinaryDomainCombinations() This should return all binary domain combinations present in the genome.
List<BinaryDomainCombination>	DirectedCombinableDomains.toBinaryDomainCombinations()
List<BinaryDomainCombination>	BasicCombinableDomains.toBinaryDomainCombinations()
List<BinaryDomainCombination>	CombinableDomains.toBinaryDomainCombinations()
SortedSet<BinaryDomainCombination>	BasicGenomeWideCombinableDomains.toBinaryDomainCombinations()
List<BinaryDomainCombination>	AdjactantDirectedCombinableDomains.toBinaryDomainCombinations()

Methods in org.forester.surfacing with parameters of type BinaryDomainCombination

Modifier and Type	Method and Description
int	BasicBinaryDomainCombination.compareTo(BinaryDomainCombination binary_domain_combination)

Method parameters in org.forester.surfacing with type arguments of type BinaryDomainCombination

Modifier and Type	Method and Description
static void	SurfacingUtil.addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, SortedSet<BinaryDomainCombination> binary_domain_combinations)
static void	SurfacingUtil.collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
static void	SurfacingUtil.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 void	SurfacingUtil.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 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)
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)