Uses of Interface
org.forester.util.DescriptiveStatistics

Packages that use DescriptiveStatistics

Package	Description
org.forester.archaeopteryx.phylogeny.data
org.forester.msa
org.forester.pccx
org.forester.phylogeny
org.forester.surfacing
org.forester.util

Uses of DescriptiveStatistics in org.forester.archaeopteryx.phylogeny.data

Methods in org.forester.archaeopteryx.phylogeny.data with parameters of type DescriptiveStatistics

Modifier and Type	Method and Description
static RenderableVector	RenderableVector.createInstance(List<Double> values, DescriptiveStatistics stats, Configuration configuration)

Uses of DescriptiveStatistics in org.forester.msa

Methods in org.forester.msa that return DescriptiveStatistics

Modifier and Type	Method and Description
static DescriptiveStatistics	MsaMethods.calcBasicGapinessStatistics(Msa msa)
static DescriptiveStatistics	MsaMethods.calcNumberOfGapsStats(Msa msa)
static DescriptiveStatistics	MsaMethods.calculateEffectiveLengthStatistics(Msa msa)
static DescriptiveStatistics	MsaMethods.calculateIdentityRatio(int from, int to, Msa msa)

Uses of DescriptiveStatistics in org.forester.pccx

Constructors in org.forester.pccx with parameters of type DescriptiveStatistics

Constructor and Description
ExternalNodeBasedCoverage(DescriptiveStatistics stats, double average_raw_score, CoverageCalculationOptions options)

Uses of DescriptiveStatistics in org.forester.phylogeny

Methods in org.forester.phylogeny that return DescriptiveStatistics

Modifier and Type	Method and Description
static DescriptiveStatistics	PhylogenyMethods.calculateBranchLengthStatistics(Phylogeny phy)
static DescriptiveStatistics	PhylogenyMethods.calculateNumberOfDescendantsPerNodeStatistics(Phylogeny phy)

Methods in org.forester.phylogeny that return types with arguments of type DescriptiveStatistics

Modifier and Type	Method and Description
static List<DescriptiveStatistics>	PhylogenyMethods.calculateConfidenceStatistics(Phylogeny phy)

Uses of DescriptiveStatistics in org.forester.surfacing

Methods in org.forester.surfacing that return DescriptiveStatistics

Modifier and Type	Method and Description
static DescriptiveStatistics	SurfacingUtil.calculateDescriptiveStatisticsForMeanValues(Set<DomainSimilarity> similarities)
DescriptiveStatistics	DomainLengths.calculateMeanBasedStatistics() Returns descriptive statistics based on the arithmetic means for each species.
DescriptiveStatistics	DomainLengthsTable.calculateMeanBasedStatisticsForAllSpecies()
DescriptiveStatistics	DomainLengthsTable.calculateMeanBasedStatisticsForDomain(String domain_id)
DescriptiveStatistics	DomainLengthsTable.calculateMeanBasedStatisticsForSpecies(Species species)
DescriptiveStatistics	DomainLengths.getLengthStatistic(Species species)
DescriptiveStatistics	DomainLengthsTable.getLengthStatistic(String domain_id, Species species)
DescriptiveStatistics	GenomeWideCombinableDomains.getPerGenomeDomainPromiscuityStatistics() This should return a statistic for per domain promiscuity in a genome.
DescriptiveStatistics	BasicGenomeWideCombinableDomains.getPerGenomeDomainPromiscuityStatistics()

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

Modifier and Type	Method and Description
List<DescriptiveStatistics>	DomainLengths.getLengthStatisticsList()

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

Modifier and Type	Method and Description
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)

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

Modifier and Type	Method and Description
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)
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)
static void	SurfacingUtil.executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, String parameters_str, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> positive_filter, boolean output_binary_domain_combinations_for_graphs, List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, Map<String,DescriptiveStatistics> protein_length_stats_by_dc, Map<String,DescriptiveStatistics> domain_number_stats_by_dc, Map<String,DescriptiveStatistics> domain_length_stats_by_domain, Map<String,Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)
static void	SurfacingUtil.executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, String parameters_str, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> positive_filter, boolean output_binary_domain_combinations_for_graphs, List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, Map<String,DescriptiveStatistics> protein_length_stats_by_dc, Map<String,DescriptiveStatistics> domain_number_stats_by_dc, Map<String,DescriptiveStatistics> domain_length_stats_by_domain, Map<String,Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)
static void	SurfacingUtil.executeParsimonyAnalysis(long random_number_seed_for_fitch_parsimony, boolean radomize_fitch_parsimony, String outfile_name, DomainParsimonyCalculator domain_parsimony, Phylogeny phylogeny, Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, String parameters_str, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> positive_filter, boolean output_binary_domain_combinations_for_graphs, List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch, List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch, BinaryDomainCombination.DomainCombinationType dc_type, Map<String,DescriptiveStatistics> protein_length_stats_by_dc, Map<String,DescriptiveStatistics> domain_number_stats_by_dc, Map<String,DescriptiveStatistics> domain_length_stats_by_domain, Map<String,Integer> tax_code_to_id_map, boolean write_to_nexus, boolean use_last_in_fitch_parsimony, boolean perform_dc_fich)

Uses of DescriptiveStatistics in org.forester.util

Classes in org.forester.util that implement DescriptiveStatistics

Modifier and Type	Class and Description
class	BasicDescriptiveStatistics

Constructors in org.forester.util with parameters of type DescriptiveStatistics

Constructor and Description
AsciiHistogram(DescriptiveStatistics stats)
AsciiHistogram(DescriptiveStatistics stats, String title)