Uses of Class
org.forester.go.GoId

Packages that use GoId

Package	Description
org.forester.go
org.forester.go.etc
org.forester.surfacing

Uses of GoId in org.forester.go

Methods in org.forester.go that return GoId

Modifier and Type	Method and Description
GoId	BasicGoTerm.getGoId()
GoId	GoRelationship.getGoId()
GoId	GoTerm.getGoId()
GoId	BasicGoRelationship.getGoId()
GoId	Mapping.getValue()
GoId	PfamToGoMapping.getValue()

Methods in org.forester.go that return types with arguments of type GoId

Modifier and Type	Method and Description
static 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 Map<GoId,GoTerm>	GoUtils.createGoIdToGoTermMap(List<GoTerm> go_terms)
static SortedSet<GoId>	GoUtils.getAllSuperGoIds(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)
List<GoId>	BasicGoTerm.getAltIds()
List<GoId>	GoTerm.getAltIds()
List<GoId>	BasicGoTerm.getSuperGoIds()
List<GoId>	GoTerm.getSuperGoIds()
static SortedMap<String,List<GoId>>	GoUtils.parseGoIds(Object source, String start_of_comment_line, String start_of_label_line)

Methods in org.forester.go with parameters of type GoId

Modifier and Type	Method and Description
int	GoId.compareTo(GoId id)
static SortedSet<GoId>	GoUtils.getAllSuperGoIds(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)
static SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, List<GoTerm> go_terms)
static SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)

Method parameters in org.forester.go with type arguments of type GoId

Modifier and Type	Method and Description
static 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)
static LinkedHashMap<GoId,Integer>	GoUtils.countCategoriesId(List<GoId> categories, List<GoId> experiment_set, Map<GoId,GoTerm> all_go_terms)
static SortedSet<GoId>	GoUtils.getAllSuperGoIds(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)
static SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)
static SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoTerm go_term, Map<GoId,GoTerm> goid_to_term_map)
static GoTerm	GoUtils.getPenultimateGoTerm(GoTerm go_term, Map<GoId,GoTerm> map)
static GoTerm	GoUtils.getUltimateGoTerm(GoTerm go_term, Map<GoId,GoTerm> map)

Constructors in org.forester.go with parameters of type GoId

Constructor and Description
BasicGoRelationship(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

Modifier and Type	Method and Description
GoId	OntologizerResult.getGoId()

Uses of GoId in org.forester.surfacing

Methods in org.forester.surfacing that return types with arguments of type GoId

Modifier and Type	Method and Description
static Map<String,List<GoId>>	SurfacingUtil.createDomainIdToGoIdMap(List<PfamToGoMapping> pfam_to_go_mappings)

Method parameters in org.forester.surfacing with type arguments of type GoId

Modifier and Type	Method and Description
static void	DomainCountsDifferenceUtil.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)
static void	DomainCountsDifferenceUtil.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)
static BasicGenomeWideCombinableDomains	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 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.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.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)
static void	SurfacingUtil.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)
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)
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)
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)