Uses of Interface
org.forester.surfacing.GenomeWideCombinableDomains

Packages that use GenomeWideCombinableDomains

Package	Description
org.forester.surfacing

Uses of GenomeWideCombinableDomains in org.forester.surfacing

Classes in org.forester.surfacing that implement GenomeWideCombinableDomains

Modifier and Type	Class and Description
class	BasicGenomeWideCombinableDomains

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

Modifier and Type	Method and Description
static void	SurfacingUtil.addAllBinaryDomainCombinationToSet(GenomeWideCombinableDomains genome, SortedSet<BinaryDomainCombination> binary_domain_combinations)
static void	SurfacingUtil.addAllDomainIdsToSet(GenomeWideCombinableDomains genome, SortedSet<String> domain_ids)
static void	SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis(String[][] input_file_properties, File output_dir, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)
static void	SurfacingUtil.writeDomainCombinationsCountsFile(String[][] input_file_properties, File output_dir, Writer per_genome_domain_promiscuity_statistics_writer, GenomeWideCombinableDomains gwcd, int i, GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order)

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

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)
SortedSet<DomainSimilarity>	BasicDomainSimilarityCalculator.calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome)
SortedSet<DomainSimilarity>	DomainSimilarityCalculator.calculateSimilarities(PairwiseDomainSimilarityCalculator pairwise_calculator, List<GenomeWideCombinableDomains> cdc_list, boolean ignore_domains_without_combinations_in_any_genome, boolean ignore_domains_specific_to_one_genome)
static DomainParsimonyCalculator	DomainParsimonyCalculator.createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list)
static DomainParsimonyCalculator	DomainParsimonyCalculator.createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<String,Set<String>> domain_id_to_secondary_features_map)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, SortedSet<String> positive_filter)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, Map<String,String> domain_id_to_second_features_map)
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 SortedSet<String>	SurfacingUtil.getAllDomainIds(List<GenomeWideCombinableDomains> gwcd_list)
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)
static void	SurfacingUtil.writePresentToNexus(File output_file, File positive_filter_file, SortedSet<String> filter, List<GenomeWideCombinableDomains> gwcd_list)
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 GenomeWideCombinableDomains

Constructor and Description
DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)