org.forester.surfacing
Interface GenomeWideCombinableDomains

All Known Implementing Classes:
BasicGenomeWideCombinableDomains

public interface GenomeWideCombinableDomains


Nested Class Summary
static class GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
           
 
Method Summary
 boolean contains(DomainId key_id)
           
 CombinableDomains get(DomainId key_id)
           
 SortedMap<DomainId,CombinableDomains> getAllCombinableDomainsIds()
           
 SortedSet<DomainId> getAllDomainIds()
          This should return all domains ids present in the genome.
 BinaryDomainCombination.DomainCombinationType getDomainCombinationType()
           
 SortedSet<DomainId> getMostPromiscuosDomain()
           
 DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics()
          This should return a statistic for per domain promiscuity in a genome.
 int getSize()
           
 Species getSpecies()
           
 SortedSet<BinaryDomainCombination> toBinaryDomainCombinations()
          This should return all binary domain combinations present in the genome.
 StringBuilder toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder order)
           
 

Method Detail

contains

boolean contains(DomainId key_id)

get

CombinableDomains get(DomainId key_id)

getAllCombinableDomainsIds

SortedMap<DomainId,CombinableDomains> getAllCombinableDomainsIds()

getAllDomainIds

SortedSet<DomainId> getAllDomainIds()
This should return all domains ids present in the genome.

Returns:
a sorted set of domains ids

getDomainCombinationType

BinaryDomainCombination.DomainCombinationType getDomainCombinationType()

getMostPromiscuosDomain

SortedSet<DomainId> getMostPromiscuosDomain()

getPerGenomeDomainPromiscuityStatistics

DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics()
This should return a statistic for per domain promiscuity in a genome.

Returns:
descriptive statistics for per domain promiscuity in a genome

getSize

int getSize()

getSpecies

Species getSpecies()

toBinaryDomainCombinations

SortedSet<BinaryDomainCombination> toBinaryDomainCombinations()
This should return all binary domain combinations present in the genome.

Returns:
a sorted set of binary domain combinations

toStringBuilder

StringBuilder toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder order)