Uses of Class
org.forester.go.GoId
Packages that use GoId
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Uses of GoId in org.forester.go
Methods in org.forester.go that return GoIdModifier and TypeMethodDescriptionBasicGoRelationship.getGoId()BasicGoTerm.getGoId()GoRelationship.getGoId()GoTerm.getGoId()Mapping.getValue()PfamToGoMapping.getValue()Methods in org.forester.go that return types with arguments of type GoIdModifier and TypeMethodDescriptionstatic LinkedHashMap<GoId, Integer> GoUtils.countCategories(List<GoTerm> categories, List<GoTerm> experiment_set, Map<GoId, GoTerm> all_go_terms) This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.static LinkedHashMap<GoId, Integer> GoUtils.countCategoriesId(List<GoId> categories, List<GoId> experiment_set, Map<GoId, GoTerm> all_go_terms) GoUtils.createGoIdToGoTermMap(List<GoTerm> go_terms) GoUtils.getAllSuperGoIds(GoId go_id, Map<GoId, GoTerm> goid_to_term_map) BasicGoTerm.getAltIds()GoTerm.getAltIds()BasicGoTerm.getSuperGoIds()GoTerm.getSuperGoIds()GoUtils.parseGoIds(Object source, String start_of_comment_line, String start_of_label_line) Methods in org.forester.go with parameters of type GoIdModifier and TypeMethodDescriptionintGoUtils.getAllSuperGoIds(GoId go_id, Map<GoId, GoTerm> goid_to_term_map) GoUtils.getAllSuperGoTerms(GoId go_id, List<GoTerm> go_terms) GoUtils.getAllSuperGoTerms(GoId go_id, Map<GoId, GoTerm> goid_to_term_map) Method parameters in org.forester.go with type arguments of type GoIdModifier and TypeMethodDescriptionstatic LinkedHashMap<GoId, Integer> GoUtils.countCategories(List<GoTerm> categories, List<GoTerm> experiment_set, Map<GoId, GoTerm> all_go_terms) This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.static LinkedHashMap<GoId, Integer> GoUtils.countCategoriesId(List<GoId> categories, List<GoId> experiment_set, Map<GoId, GoTerm> all_go_terms) static LinkedHashMap<GoId, Integer> GoUtils.countCategoriesId(List<GoId> categories, List<GoId> experiment_set, Map<GoId, GoTerm> all_go_terms) GoUtils.getAllSuperGoIds(GoId go_id, Map<GoId, GoTerm> goid_to_term_map) GoUtils.getAllSuperGoTerms(GoId go_id, Map<GoId, GoTerm> goid_to_term_map) GoUtils.getAllSuperGoTerms(GoTerm go_term, Map<GoId, GoTerm> goid_to_term_map) static GoTermGoUtils.getPenultimateGoTerm(GoTerm go_term, Map<GoId, GoTerm> map) static GoTermGoUtils.getUltimateGoTerm(GoTerm go_term, Map<GoId, GoTerm> map) Constructors in org.forester.go with parameters of type GoIdModifierConstructorDescriptionBasicGoRelationship(GoRelationship.Type type, GoId go_id) BasicGoTerm(GoId id, String name, GoNameSpace namespace, boolean is_obsolete) PfamToGoMapping(String pfam_domain_id, GoId go_id) -
Uses of GoId in org.forester.go.etc
Methods in org.forester.go.etc that return GoId -
Uses of GoId in org.forester.surfacing
Methods in org.forester.surfacing that return types with arguments of type GoIdModifier and TypeMethodDescriptionSurfacingUtil.createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings) Method parameters in org.forester.surfacing with type arguments of type GoIdModifier and TypeMethodDescriptionstatic voidDomainCountsDifferenceUtil.calculateCopyNumberDifferences(List<GenomeWideCombinableDomains> genomes, SortedMap<Species, List<Protein>> protein_lists_per_species, List<String> high_copy_base_species, List<String> high_copy_target_species, List<String> low_copy_species, int min_diff, Double factor, File plain_output_dom, File html_output_dom, File html_output_dc, Map<String, List<GoId>> domain_id_to_go_ids_map, Map<GoId, GoTerm> go_id_to_term_map, File all_domains_go_ids_out_dom, File passing_domains_go_ids_out_dom, File proteins_file_base) 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 voidSurfacingUtil.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 voidSurfacingUtil.executePlusMinusAnalysis(File output_file, List<String> plus_minus_analysis_high_copy_base, List<String> plus_minus_analysis_high_copy_target, List<String> plus_minus_analysis_low_copy, List<GenomeWideCombinableDomains> gwcd_list, SortedMap<Species, List<Protein>> protein_lists_per_species, Map<String, List<GoId>> domain_id_to_go_ids_map, Map<GoId, GoTerm> go_id_to_term_map, List<Object> plus_minus_analysis_numbers) voidPairwiseGenomeComparator.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 voidSurfacingUtil.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)