Uses of Interface
org.forester.species.Species
Packages that use Species
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Uses of Species in org.forester.protein
Methods in org.forester.protein that return Species -
Uses of Species in org.forester.species
Classes in org.forester.species that implement SpeciesMethods in org.forester.species with parameters of type Species -
Uses of Species in org.forester.surfacing
Methods in org.forester.surfacing that return SpeciesModifier and TypeMethodDescriptionBasicCombinableDomains.getSpecies()
BasicGenomeWideCombinableDomains.getSpecies()
CombinableDomains.getSpecies()
Returns the species of this combinable domains.GenomeWideCombinableDomains.getSpecies()
Methods in org.forester.surfacing that return types with arguments of type SpeciesModifier and TypeMethodDescriptionDomainLengths.getMeanBasedOutlierSpecies
(double z_score_limit) DomainLengthsTable.getSpecies()
DomainSimilarity.getSpecies()
DomainSimilarity.getSpeciesCustomOrder()
DomainSimilarity.getSpeciesData()
This should return a map, which maps species names to SpeciesSpecificDomainSimilariyDataDomainLengths.getSpeciesList()
Methods in org.forester.surfacing with parameters of type SpeciesModifier and TypeMethodDescriptionvoid
DomainLengthsTable.calculateMeanBasedStatisticsForSpecies
(Species species) double
DomainLengths.calculateZScoreForSpecies
(Species species) Note.BasicGenomeWideCombinableDomains.createInstance
(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species) 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) BasicGenomeWideCombinableDomains.createInstance
(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type) DomainSimilarity.getCombinableDomainIds
(Species species_of_combinable_domain) DomainLengths.getLengthStatistic
(Species species) DomainLengthsTable.getLengthStatistic
(String domain_id, Species species) boolean
DomainLengths.isHasLengthStatistic
(Species species) 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.performPairwiseComparisonsJacknifed
(Species[] species, int number_of_genomes, List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains, boolean verbose, int number_of_resamplings, double jacknife_ratio, long random_seed) Method parameters in org.forester.surfacing with type arguments of type SpeciesModifier and TypeMethodDescriptionstatic 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) void
DomainParsimonyCalculator.executeDolloParsimonyOnSecondaryFeatures
(Map<Species, MappingResults> mapping_results_map) 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.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.extractProteinNames
(SortedMap<Species, List<Protein>> protein_lists_per_species, String domain_id, Writer out, String separator, String limit_to_species, double domain_e_cutoff) void
DomainSimilarity.setSpeciesOrder
(List<Species> species_order) static void
SurfacingUtil.writeDomainSimilaritiesToFile
(StringBuilder html_desc, StringBuilder html_title, Writer simple_tab_writer, Writer single_writer, Map<Character, Writer> split_writers, SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, Map<String, Integer> tax_code_to_id_map, Phylogeny phy, Set<String> pos_filter_doms) static void
SurfacingUtil.writeProteinListsForAllSpecies
(File output_dir, SortedMap<Species, List<Protein>> protein_lists_per_species, List<GenomeWideCombinableDomains> gwcd_list, double domain_e_cutoff, Set<String> pos_filter_doms) Constructors in org.forester.surfacing with parameters of type SpeciesModifierConstructorDescriptionAdjactantDirectedCombinableDomains
(String n_terminal_key_domain, Species species) BasicCombinableDomains
(String key_domain, Species species) DirectedCombinableDomains
(String n_terminal_key_domain, Species species) Constructor parameters in org.forester.surfacing with type arguments of type SpeciesModifierConstructorDescriptionDomainSimilarity
(CombinableDomains combinable_domains, double min, double max, double mean, double median, double sd, int n, int max_difference_in_counts, int max_difference, SortedMap<Species, org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison) DomainSimilarity
(CombinableDomains combinable_domains, int max_difference_in_counts, int max_difference, SortedMap<Species, org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)