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