Uses of Class
org.forester.surfacing.DomainParsimonyCalculator
Packages that use DomainParsimonyCalculator
-
Uses of DomainParsimonyCalculator in org.forester.surfacing
Methods in org.forester.surfacing that return DomainParsimonyCalculatorModifier and TypeMethodDescriptionstatic DomainParsimonyCalculator
DomainParsimonyCalculator.createInstance
(Phylogeny phylogeny) static DomainParsimonyCalculator
DomainParsimonyCalculator.createInstance
(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list) static DomainParsimonyCalculator
DomainParsimonyCalculator.createInstance
(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<String, Set<String>> domain_id_to_secondary_features_map) Methods in org.forester.surfacing with parameters of type DomainParsimonyCalculatorModifier and TypeMethodDescriptionstatic 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.executeParsimonyAnalysisForSecondaryFeatures
(String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, String parameters_str, Map<Species, MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony) static void
SurfacingUtil.preparePhylogeny
(Phylogeny p, DomainParsimonyCalculator domain_parsimony, String date_time, String method, String name, String parameters_str)