Uses of Interface
org.forester.species.Species

Packages that use Species

Package	Description
org.forester.protein
org.forester.species
org.forester.surfacing

Uses of Species in org.forester.protein

Methods in org.forester.protein that return Species

Modifier and Type	Method and Description
Species	Protein.getSpecies()
Species	BasicProtein.getSpecies()

Uses of Species in org.forester.species

Classes in org.forester.species that implement Species

Modifier and Type	Class and Description
class	BasicSpecies

Methods in org.forester.species with parameters of type Species

Modifier and Type	Method and Description
int	BasicSpecies.compareTo(Species species)

Uses of Species in org.forester.surfacing

Methods in org.forester.surfacing that return Species

Modifier and Type	Method and Description
Species	GenomeWideCombinableDomains.getSpecies()
Species	BasicCombinableDomains.getSpecies()
Species	CombinableDomains.getSpecies() Returns the species of this combinable domains.
Species	BasicGenomeWideCombinableDomains.getSpecies()

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

Modifier and Type	Method and Description
List<Species>	DomainLengths.getMeanBasedOutlierSpecies(double z_score_limit)
List<Species>	DomainLengthsTable.getSpecies()
SortedSet<Species>	DomainSimilarity.getSpecies()
List<Species>	DomainSimilarity.getSpeciesCustomOrder()
SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData>	DomainSimilarity.getSpeciesData() This should return a map, which maps species names to SpeciesSpecificDomainSimilariyData
List<Species>	DomainLengths.getSpeciesList()

Methods in org.forester.surfacing with parameters of type Species

Modifier and Type	Method and Description
void	DomainLengths.addLength(Species species, int domain_length)
DescriptiveStatistics	DomainLengthsTable.calculateMeanBasedStatisticsForSpecies(Species species)
double	DomainLengths.calculateZScoreForSpecies(Species species) Note.
static BasicGenomeWideCombinableDomains	BasicGenomeWideCombinableDomains.createInstance(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species)
static BasicGenomeWideCombinableDomains	BasicGenomeWideCombinableDomains.createInstance(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type)
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)
SortedSet<String>	DomainSimilarity.getCombinableDomainIds(Species species_of_combinable_domain)
DescriptiveStatistics	DomainLengths.getLengthStatistic(Species species)
DescriptiveStatistics	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 Species

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)
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 Species

Constructor and Description
AdjactantDirectedCombinableDomains(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 Species

Constructor and 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, 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)