Uses of Interface
org.forester.protein.Protein
Packages that use Protein
Package
Description
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Uses of Protein in org.forester.io.parsers
Methods in org.forester.io.parsers that return types with arguments of type Protein -
Uses of Protein in org.forester.protein
Classes in org.forester.protein that implement Protein -
Uses of Protein in org.forester.surfacing
Methods in org.forester.surfacing with parameters of type ProteinModifier and TypeMethodDescriptionstatic StringBuffer
SurfacingUtil.proteinToDomainCombinations
(Protein protein, String protein_id, String separator) SurfacingUtil.sortDomainsWithAscendingConfidenceValues
(Protein protein) Method parameters in org.forester.surfacing with type arguments of type ProteinModifier and TypeMethodDescriptionvoid
DomainLengthsTable.addLengths
(List<Protein> protein_list) 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) 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) static void
SurfacingUtil.doit
(List<Protein> proteins, List<String> query_domain_ids_nc_order, Writer out, String separator, String limit_to_species, Map<String, List<Integer>> average_protein_lengths_by_dc) static void
SurfacingUtil.domainsPerProteinsStatistics
(String genome, List<Protein> protein_list, DescriptiveStatistics all_genomes_domains_per_potein_stats, SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo, SortedSet<String> domains_which_are_always_single, SortedSet<String> domains_which_are_sometimes_single_sometimes_not, SortedSet<String> domains_which_never_single, Writer writer) 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
(List<Protein> proteins, List<String> query_domain_ids_nc_order, Writer out, String separator, String limit_to_species) 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) SurfacingUtil.getDomainCounts
(List<Protein> protein_domain_collections) static int
SurfacingUtil.storeDomainArchitectures
(String genome, SortedMap<String, Set<String>> domain_architecutures, List<Protein> protein_list, Map<String, Integer> distinct_domain_architecuture_counts) 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) -
Uses of Protein in org.forester.util
Methods in org.forester.util that return ProteinModifier and TypeMethodDescriptionstatic Protein
ForesterUtil.removeOverlappingDomains
(int max_allowed_overlap, boolean remove_engulfed_domains, Protein protein) Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ ignoredMethods in org.forester.util with parameters of type ProteinModifier and TypeMethodDescriptionstatic Protein
ForesterUtil.removeOverlappingDomains
(int max_allowed_overlap, boolean remove_engulfed_domains, Protein protein) Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ ignored