Uses of Interface
org.forester.surfacing.CombinableDomains

Packages that use CombinableDomains

Package	Description
org.forester.surfacing

Uses of CombinableDomains in org.forester.surfacing

Classes in org.forester.surfacing that implement CombinableDomains

Modifier and Type	Class and Description
class	AdjactantDirectedCombinableDomains
class	BasicCombinableDomains
class	DirectedCombinableDomains

Methods in org.forester.surfacing that return CombinableDomains

Modifier and Type	Method and Description
CombinableDomains	GenomeWideCombinableDomains.get(String key_id)
CombinableDomains	BasicGenomeWideCombinableDomains.get(String key_id)

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

Modifier and Type	Method and Description
SortedMap<String,CombinableDomains>	GenomeWideCombinableDomains.getAllCombinableDomainsIds()
SortedMap<String,CombinableDomains>	BasicGenomeWideCombinableDomains.getAllCombinableDomainsIds()

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

Modifier and Type	Method and Description
PairwiseDomainSimilarity	PairwiseDomainSimilarityCalculator.calculateSimilarity(CombinableDomains domains_1, CombinableDomains domains_2)
PairwiseDomainSimilarity	DomainCountsBasedPairwiseSimilarityCalculator.calculateSimilarity(CombinableDomains domains_1, CombinableDomains domains_2)
PairwiseDomainSimilarity	CombinationsBasedPairwiseDomainSimilarityCalculator.calculateSimilarity(CombinableDomains domains_1, CombinableDomains domains_2)
PairwiseDomainSimilarity	ProteinCountsBasedPairwiseDomainSimilarityCalculator.calculateSimilarity(CombinableDomains domains_1, CombinableDomains domains_2)

Constructors in org.forester.surfacing with parameters of type CombinableDomains

Constructor and Description
DomainSimilarity(CombinableDomains combinable_domains, double min, double max, double mean, double median, double sd, int n, int max_difference_in_counts, int max_difference, SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)
DomainSimilarity(CombinableDomains combinable_domains, int max_difference_in_counts, int max_difference, SortedMap<Species,org.forester.surfacing.SpeciesSpecificDcData> species_data, boolean sort_by_species_count_first, boolean treat_as_binary_comparison)