Uses of Interface
org.forester.protein.Protein
-
Packages that use Protein Package Description org.forester.io.parsers org.forester.protein org.forester.surfacing org.forester.util -
-
Uses of Protein in org.forester.io.parsers
Methods in org.forester.io.parsers that return types with arguments of type Protein Modifier and Type Method Description java.util.List<Protein>
HmmPfamOutputParser. parse()
java.util.List<Protein>
HmmscanPerDomainTableParser. parse()
-
Uses of Protein in org.forester.protein
Classes in org.forester.protein that implement Protein Modifier and Type Class Description class
BasicProtein
-
Uses of Protein in org.forester.surfacing
Methods in org.forester.surfacing with parameters of type Protein Modifier and Type Method Description static java.lang.StringBuffer
SurfacingUtil. proteinToDomainCombinations(Protein protein, java.lang.String protein_id, java.lang.String separator)
static java.util.List<Domain>
SurfacingUtil. sortDomainsWithAscendingConfidenceValues(Protein protein)
Method parameters in org.forester.surfacing with type arguments of type Protein Modifier and Type Method Description void
DomainLengthsTable. addLengths(java.util.List<Protein> protein_list)
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)
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)
static void
SurfacingUtil. doit(java.util.List<Protein> proteins, java.util.List<java.lang.String> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species, java.util.Map<java.lang.String,java.util.List<java.lang.Integer>> average_protein_lengths_by_dc)
static void
SurfacingUtil. domainsPerProteinsStatistics(java.lang.String genome, java.util.List<Protein> protein_list, DescriptiveStatistics all_genomes_domains_per_potein_stats, java.util.SortedMap<java.lang.Integer,java.lang.Integer> all_genomes_domains_per_potein_histo, java.util.SortedSet<java.lang.String> domains_which_are_always_single, java.util.SortedSet<java.lang.String> domains_which_are_sometimes_single_sometimes_not, java.util.SortedSet<java.lang.String> domains_which_never_single, java.io.Writer writer)
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.List<Protein> proteins, java.util.List<java.lang.String> query_domain_ids_nc_order, java.io.Writer out, java.lang.String separator, java.lang.String limit_to_species)
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)
static java.util.SortedMap<java.lang.String,java.lang.Integer>
SurfacingUtil. getDomainCounts(java.util.List<Protein> protein_domain_collections)
static int
SurfacingUtil. storeDomainArchitectures(java.lang.String genome, java.util.SortedMap<java.lang.String,java.util.Set<java.lang.String>> domain_architecutures, java.util.List<Protein> protein_list, java.util.Map<java.lang.String,java.lang.Integer> distinct_domain_architecuture_counts)
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)
-
Uses of Protein in org.forester.util
Methods in org.forester.util that return Protein Modifier and Type Method Description static 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 Protein Modifier and Type Method Description static 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
-