Uses of Class
org.forester.protein.BinaryDomainCombination.DomainCombinationType

Packages that use BinaryDomainCombination.DomainCombinationType

Package	Description
org.forester.protein
org.forester.surfacing

Uses of BinaryDomainCombination.DomainCombinationType in org.forester.protein

Methods in org.forester.protein that return BinaryDomainCombination.DomainCombinationType

Modifier and Type	Method and Description
static BinaryDomainCombination.DomainCombinationType	BinaryDomainCombination.DomainCombinationType.valueOf(String name) Returns the enum constant of this type with the specified name.
static BinaryDomainCombination.DomainCombinationType[]	BinaryDomainCombination.DomainCombinationType.values() Returns an array containing the constants of this enum type, in the order they are declared.

Uses of BinaryDomainCombination.DomainCombinationType in org.forester.surfacing

Methods in org.forester.surfacing that return BinaryDomainCombination.DomainCombinationType

Modifier and Type	Method and Description
BinaryDomainCombination.DomainCombinationType	GenomeWideCombinableDomains.getDomainCombinationType()
BinaryDomainCombination.DomainCombinationType	BasicGenomeWideCombinableDomains.getDomainCombinationType()

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

Modifier and Type	Method and Description
static void	SurfacingUtil.collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
static BasicGenomeWideCombinableDomains	BasicGenomeWideCombinableDomains.createInstance(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type)
static BasicGenomeWideCombinableDomains	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)
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)