Uses of Interface
org.forester.species.Species
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Packages that use Species Package Description org.forester.protein org.forester.species org.forester.surfacing -
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Uses of Species in org.forester.protein
Methods in org.forester.protein that return Species Modifier and Type Method Description Species
BasicProtein. getSpecies()
Species
Protein. getSpecies()
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Uses of Species in org.forester.species
Classes in org.forester.species that implement Species Modifier and Type Class Description class
BasicSpecies
Methods in org.forester.species with parameters of type Species Modifier and Type Method Description int
BasicSpecies. compareTo(Species species)
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Uses of Species in org.forester.surfacing
Methods in org.forester.surfacing that return Species Modifier and Type Method Description Species
BasicCombinableDomains. getSpecies()
Species
BasicGenomeWideCombinableDomains. getSpecies()
Species
CombinableDomains. getSpecies()
Returns the species of this combinable domains.Species
GenomeWideCombinableDomains. getSpecies()
Methods in org.forester.surfacing that return types with arguments of type Species Modifier and Type Method Description java.util.List<Species>
DomainLengths. getMeanBasedOutlierSpecies(double z_score_limit)
java.util.List<Species>
DomainLengthsTable. getSpecies()
java.util.SortedSet<Species>
DomainSimilarity. getSpecies()
java.util.List<Species>
DomainSimilarity. getSpeciesCustomOrder()
java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData>
DomainSimilarity. getSpeciesData()
This should return a map, which maps species names to SpeciesSpecificDomainSimilariyDatajava.util.List<Species>
DomainLengths. getSpeciesList()
Methods in org.forester.surfacing with parameters of type Species Modifier and Type Method Description void
DomainLengths. addLength(Species species, int domain_length)
DescriptiveStatistics
DomainLengthsTable. calculateMeanBasedStatisticsForSpecies(Species species)
double
DomainLengths. calculateZScoreForSpecies(Species species)
Note.static BasicGenomeWideCombinableDomains
BasicGenomeWideCombinableDomains. createInstance(java.util.List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species)
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 BasicGenomeWideCombinableDomains
BasicGenomeWideCombinableDomains. createInstance(java.util.List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type)
java.util.SortedSet<java.lang.String>
DomainSimilarity. getCombinableDomainIds(Species species_of_combinable_domain)
DescriptiveStatistics
DomainLengths. getLengthStatistic(Species species)
DescriptiveStatistics
DomainLengthsTable. getLengthStatistic(java.lang.String domain_id, Species species)
boolean
DomainLengths. isHasLengthStatistic(Species species)
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)
void
PairwiseGenomeComparator. performPairwiseComparisonsJacknifed(Species[] species, int number_of_genomes, java.util.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 Species 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)
void
DomainParsimonyCalculator. executeDolloParsimonyOnSecondaryFeatures(java.util.Map<Species,MappingResults> mapping_results_map)
static void
SurfacingUtil. executeParsimonyAnalysisForSecondaryFeatures(java.lang.String outfile_name, DomainParsimonyCalculator secondary_features_parsimony, Phylogeny phylogeny, java.lang.String parameters_str, java.util.Map<Species,MappingResults> mapping_results_map, boolean use_last_in_fitch_parsimony)
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)
static void
SurfacingUtil. extractProteinNames(java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.lang.String domain_id, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species, double domain_e_cutoff)
void
DomainSimilarity. setSpeciesOrder(java.util.List<Species> species_order)
static void
SurfacingUtil. writeDomainSimilaritiesToFile(java.lang.StringBuilder html_desc, java.lang.StringBuilder html_title, java.io.Writer simple_tab_writer, java.io.Writer single_writer, java.util.Map<java.lang.Character,java.io.Writer> split_writers, java.util.SortedSet<DomainSimilarity> similarities, boolean treat_as_binary, java.util.List<Species> species_order, DomainSimilarity.PRINT_OPTION print_option, DomainSimilarity.DomainSimilarityScoring scoring, boolean verbose, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map, Phylogeny phy, java.util.Set<java.lang.String> pos_filter_doms)
static void
SurfacingUtil. writeProteinListsForAllSpecies(java.io.File output_dir, java.util.SortedMap<Species,java.util.List<Protein>> protein_lists_per_species, java.util.List<GenomeWideCombinableDomains> gwcd_list, double domain_e_cutoff, java.util.Set<java.lang.String> pos_filter_doms)
Constructors in org.forester.surfacing with parameters of type Species Constructor Description AdjactantDirectedCombinableDomains(java.lang.String n_terminal_key_domain, Species species)
BasicCombinableDomains(java.lang.String key_domain, Species species)
DirectedCombinableDomains(java.lang.String n_terminal_key_domain, Species species)
Constructor parameters in org.forester.surfacing with type arguments of type Species Constructor Description DomainSimilarity(CombinableDomains combinable_domains, double min, double max, double mean, double median, double sd, int n, int max_difference_in_counts, int max_difference, java.util.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, java.util.SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)
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