Uses of Class
org.forester.surfacing.DomainParsimonyCalculator

Packages that use DomainParsimonyCalculator

Package	Description
org.forester.surfacing

Uses of DomainParsimonyCalculator in org.forester.surfacing

Methods in org.forester.surfacing that return DomainParsimonyCalculator

Modifier and Type	Method and Description
static 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 DomainParsimonyCalculator

Modifier and Type	Method and Description
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.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)