Uses of Class
org.forester.go.GoNameSpace
Packages that use GoNameSpace
-
Uses of GoNameSpace in org.forester.go
Methods in org.forester.go that return GoNameSpaceModifier and TypeMethodDescriptionstatic GoNameSpace
GoNameSpace.createBiologicalProcess()
static GoNameSpace
GoNameSpace.createCellularComponent()
static GoNameSpace
GoNameSpace.createMolecularFunction()
static GoNameSpace
GoNameSpace.createUnassigned()
BasicGoTerm.getGoNameSpace()
GoTerm.getGoNameSpace()
Constructors in org.forester.go with parameters of type GoNameSpaceModifierConstructorDescriptionBasicGoTerm
(GoId id, String name, GoNameSpace namespace, boolean is_obsolete) -
Uses of GoNameSpace in org.forester.surfacing
Methods in org.forester.surfacing with parameters of type GoNameSpaceModifier 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) void
PairwiseGenomeComparator.performPairwiseComparisons
(StringBuilder html_desc, boolean sort_by_species_count_first, DomainSimilarityCalculator.Detailedness detailedness, boolean ignore_domains_without_combs_in_all_spec, boolean ignore_domains_specific_to_one_species, DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field, DomainSimilarity.PRINT_OPTION domain_similarity_print_option, DomainSimilarity.DomainSimilarityScoring scoring, Map<String, List<GoId>> domain_id_to_go_ids_map, Map<GoId, GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, String automated_pairwise_comparison_suffix, boolean verbose, String automated_pairwise_comparison_prefix, String command_line_prg_name, File out_dir, boolean write_pairwise_comparisons, Map<String, Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy) static void
SurfacingUtil.writeBinaryStatesMatrixToList
(Map<String, List<GoId>> domain_id_to_go_ids_map, Map<GoId, GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, String title_for_html, String prefix_for_html, Map<String, Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> all_pfams_encountered, SortedSet<String> pfams_gained_or_lost, String suffix_for_per_node_events_file, Map<String, Integer> tax_code_to_id_map)