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_ ignored

Methods 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