public class BasicGenomeWideCombinableDomains extends java.lang.Object implements GenomeWideCombinableDomains
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
Modifier and Type | Method and Description |
---|---|
boolean |
contains(DomainId key_id) |
static BasicGenomeWideCombinableDomains |
createInstance(java.util.List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species) |
static BasicGenomeWideCombinableDomains |
createInstance(java.util.List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species,
BinaryDomainCombination.DomainCombinationType dc_type) |
static BasicGenomeWideCombinableDomains |
createInstance(java.util.List<Protein> protein_list,
boolean ignore_combination_with_same_domain,
Species species,
java.util.Map<DomainId,java.util.List<GoId>> domain_id_to_go_ids_map,
BinaryDomainCombination.DomainCombinationType dc_type) |
CombinableDomains |
get(DomainId key_id) |
java.util.SortedMap<DomainId,CombinableDomains> |
getAllCombinableDomainsIds() |
java.util.SortedSet<DomainId> |
getAllDomainIds()
This should return all domains ids present in the genome.
|
BinaryDomainCombination.DomainCombinationType |
getDomainCombinationType() |
java.util.SortedSet<DomainId> |
getMostPromiscuosDomain() |
DescriptiveStatistics |
getPerGenomeDomainPromiscuityStatistics()
This should return a statistic for per domain
promiscuity in a genome.
|
int |
getSize() |
Species |
getSpecies() |
java.util.SortedSet<BinaryDomainCombination> |
toBinaryDomainCombinations()
This should return all binary domain combinations present in the genome.
|
java.lang.String |
toString() |
java.lang.StringBuilder |
toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order) |
public boolean contains(DomainId key_id)
contains
in interface GenomeWideCombinableDomains
public CombinableDomains get(DomainId key_id)
get
in interface GenomeWideCombinableDomains
public java.util.SortedMap<DomainId,CombinableDomains> getAllCombinableDomainsIds()
getAllCombinableDomainsIds
in interface GenomeWideCombinableDomains
public java.util.SortedSet<DomainId> getAllDomainIds()
GenomeWideCombinableDomains
getAllDomainIds
in interface GenomeWideCombinableDomains
public BinaryDomainCombination.DomainCombinationType getDomainCombinationType()
getDomainCombinationType
in interface GenomeWideCombinableDomains
public java.util.SortedSet<DomainId> getMostPromiscuosDomain()
getMostPromiscuosDomain
in interface GenomeWideCombinableDomains
public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics()
GenomeWideCombinableDomains
getPerGenomeDomainPromiscuityStatistics
in interface GenomeWideCombinableDomains
public int getSize()
getSize
in interface GenomeWideCombinableDomains
public Species getSpecies()
getSpecies
in interface GenomeWideCombinableDomains
public java.util.SortedSet<BinaryDomainCombination> toBinaryDomainCombinations()
GenomeWideCombinableDomains
toBinaryDomainCombinations
in interface GenomeWideCombinableDomains
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.StringBuilder toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order)
toStringBuilder
in interface GenomeWideCombinableDomains
public static BasicGenomeWideCombinableDomains createInstance(java.util.List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species)
public static BasicGenomeWideCombinableDomains createInstance(java.util.List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type)
public static BasicGenomeWideCombinableDomains createInstance(java.util.List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, java.util.Map<DomainId,java.util.List<GoId>> domain_id_to_go_ids_map, BinaryDomainCombination.DomainCombinationType dc_type)