Uses of Class
org.forester.go.GoId
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Packages that use GoId Package Description org.forester.go org.forester.go.etc org.forester.surfacing -
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Uses of GoId in org.forester.go
Methods in org.forester.go that return GoId Modifier and Type Method Description GoId
BasicGoRelationship. getGoId()
GoId
BasicGoTerm. getGoId()
GoId
GoRelationship. getGoId()
GoId
GoTerm. getGoId()
GoId
Mapping. getValue()
GoId
PfamToGoMapping. getValue()
Methods in org.forester.go that return types with arguments of type GoId Modifier and Type Method Description static java.util.LinkedHashMap<GoId,java.lang.Integer>
GoUtils. countCategories(java.util.List<GoTerm> categories, java.util.List<GoTerm> experiment_set, java.util.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 java.util.LinkedHashMap<GoId,java.lang.Integer>
GoUtils. countCategoriesId(java.util.List<GoId> categories, java.util.List<GoId> experiment_set, java.util.Map<GoId,GoTerm> all_go_terms)
static java.util.Map<GoId,GoTerm>
GoUtils. createGoIdToGoTermMap(java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoId>
GoUtils. getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
java.util.List<GoId>
BasicGoTerm. getAltIds()
java.util.List<GoId>
GoTerm. getAltIds()
java.util.List<GoId>
BasicGoTerm. getSuperGoIds()
java.util.List<GoId>
GoTerm. getSuperGoIds()
static java.util.SortedMap<java.lang.String,java.util.List<GoId>>
GoUtils. parseGoIds(java.lang.Object source, java.lang.String start_of_comment_line, java.lang.String start_of_label_line)
Methods in org.forester.go with parameters of type GoId Modifier and Type Method Description int
GoId. compareTo(GoId id)
static java.util.SortedSet<GoId>
GoUtils. getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>
GoUtils. getAllSuperGoTerms(GoId go_id, java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoTerm>
GoUtils. getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
Method parameters in org.forester.go with type arguments of type GoId Modifier and Type Method Description static java.util.LinkedHashMap<GoId,java.lang.Integer>
GoUtils. countCategories(java.util.List<GoTerm> categories, java.util.List<GoTerm> experiment_set, java.util.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 java.util.LinkedHashMap<GoId,java.lang.Integer>
GoUtils. countCategoriesId(java.util.List<GoId> categories, java.util.List<GoId> experiment_set, java.util.Map<GoId,GoTerm> all_go_terms)
static java.util.LinkedHashMap<GoId,java.lang.Integer>
GoUtils. countCategoriesId(java.util.List<GoId> categories, java.util.List<GoId> experiment_set, java.util.Map<GoId,GoTerm> all_go_terms)
static java.util.SortedSet<GoId>
GoUtils. getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>
GoUtils. getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>
GoUtils. getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
static GoTerm
GoUtils. getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
static GoTerm
GoUtils. getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
Constructors in org.forester.go with parameters of type GoId Constructor Description BasicGoRelationship(GoRelationship.Type type, GoId go_id)
BasicGoTerm(GoId id, java.lang.String name, GoNameSpace namespace, boolean is_obsolete)
PfamToGoMapping(java.lang.String pfam_domain_id, GoId go_id)
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Uses of GoId in org.forester.go.etc
Methods in org.forester.go.etc that return GoId Modifier and Type Method Description GoId
OntologizerResult. getGoId()
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Uses of GoId in org.forester.surfacing
Methods in org.forester.surfacing that return types with arguments of type GoId Modifier and Type Method Description static java.util.Map<java.lang.String,java.util.List<GoId>>
SurfacingUtil. createDomainIdToGoIdMap(java.util.List<PfamToGoMapping> pfam_to_go_mappings)
Method parameters in org.forester.surfacing with type arguments of type GoId Modifier and Type Method Description static void
DomainCountsDifferenceUtil. calculateCopyNumberDifferences(java.util.List<GenomeWideCombinableDomains> genomes, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.List<java.lang.String> high_copy_base_species, java.util.List<java.lang.String> high_copy_target_species, java.util.List<java.lang.String> low_copy_species, int min_diff, java.lang.Double factor, java.io.File plain_output_dom, java.io.File html_output_dom, java.io.File html_output_dc, 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, java.io.File all_domains_go_ids_out_dom, java.io.File passing_domains_go_ids_out_dom, java.io.File proteins_file_base)
static BasicGenomeWideCombinableDomains
BasicGenomeWideCombinableDomains. createInstance(java.util.List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, 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)
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. executePlusMinusAnalysis(java.io.File output_file, java.util.List<java.lang.String> plus_minus_analysis_high_copy_base, java.util.List<java.lang.String> plus_minus_analysis_high_copy_target, java.util.List<java.lang.String> plus_minus_analysis_low_copy, java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, 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, java.util.List<java.lang.Object> plus_minus_analysis_numbers)
void
PairwiseGenomeComparator. performPairwiseComparisons(java.lang.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, 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, Species[] species, int number_of_genomes, java.util.List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, PairwiseDomainSimilarityCalculator pw_calc, java.lang.String automated_pairwise_comparison_suffix, boolean verbose, java.lang.String automated_pairwise_comparison_prefix, java.lang.String command_line_prg_name, java.io.File out_dir, boolean write_pairwise_comparisons, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, boolean calc_similarity_scores, Phylogeny phy)
static void
SurfacingUtil. writeBinaryStatesMatrixToList(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, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.lang.String title_for_html, java.lang.String prefix_for_html, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> all_pfams_encountered, java.util.SortedSet<java.lang.String> pfams_gained_or_lost, java.lang.String suffix_for_per_node_events_file, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map)
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