org.forester.surfacing
Interface CombinableDomains

All Known Implementing Classes:
AdjactantDirectedCombinableDomains, BasicCombinableDomains, DirectedCombinableDomains

public interface CombinableDomains


Method Summary
 void addCombinableDomain(DomainId protein_domain)
          To add a new combinable domain.
 List<DomainId> getAllDomains()
          This must return all domains in this set of combinable domains (i.e.
 List<DomainId> getCombinableDomains()
           
 SortedMap<DomainId,Integer> getCombinableDomainsIds()
          Returns the combinable domain identifiers sorted in alphabetical manner: - keys are the combinable domain identifiers - values are the counts of proteins exhibiting a particular combination
 StringBuilder getCombiningDomainIdsAsStringBuilder()
           
 DomainId getKeyDomain()
          Returns the domain whose combinable domains are in stored in this combinable domains.
 DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics()
          Gets descriptive statistics for the confidence (i.e.
 int getKeyDomainCount()
          Returns how many times the key domain is present in a given species genome.
 int getKeyDomainProteinsCount()
          Returns how many proteins with the key domain are present in a given species genome.
 int getNumberOfCombinableDomains()
           
 int getNumberOfProteinsExhibitingCombination(DomainId protein_domain)
           
 Species getSpecies()
          Returns the species of this combinable domains.
 boolean isCombinable(DomainId protein_domain)
           
 void setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics statistics)
          This is to set descriptive statistics for the confidence (i.e.
 void setKeyDomainCount(int key_domain_count)
          Sets how many times the key domain is present in a given species genome.
 void setKeyDomainProteinsCount(int key_domain_proteins_count)
          Sets how many proteins with the key domain are present in a given species genome.
 List<BinaryDomainCombination> toBinaryDomainCombinations()
           
 

Method Detail

addCombinableDomain

void addCombinableDomain(DomainId protein_domain)
To add a new combinable domain.

Parameters:
protein_domain -

getAllDomains

List<DomainId> getAllDomains()
This must return all domains in this set of combinable domains (i.e. the key domain and all domains which can combine with the key domain).

Returns:
all domains

getCombinableDomains

List<DomainId> getCombinableDomains()

getCombinableDomainsIds

SortedMap<DomainId,Integer> getCombinableDomainsIds()
Returns the combinable domain identifiers sorted in alphabetical manner: - keys are the combinable domain identifiers - values are the counts of proteins exhibiting a particular combination

Returns:
combining domain identifiers sorted in alphabetical manner

getCombiningDomainIdsAsStringBuilder

StringBuilder getCombiningDomainIdsAsStringBuilder()

getKeyDomain

DomainId getKeyDomain()
Returns the domain whose combinable domains are in stored in this combinable domains.

Returns:
the domain identifier

getKeyDomainConfidenceDescriptiveStatistics

DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics()
Gets descriptive statistics for the confidence (i.e. E-values) of the key domain.

Returns:
descriptive statistics for the confidence of the key domain

getKeyDomainCount

int getKeyDomainCount()
Returns how many times the key domain is present in a given species genome.

Returns:
key domain count in species

getKeyDomainProteinsCount

int getKeyDomainProteinsCount()
Returns how many proteins with the key domain are present in a given species genome.

Returns:
key domain proteins count in species

getNumberOfCombinableDomains

int getNumberOfCombinableDomains()

getNumberOfProteinsExhibitingCombination

int getNumberOfProteinsExhibitingCombination(DomainId protein_domain)

getSpecies

Species getSpecies()
Returns the species of this combinable domains.

Returns:
the species

isCombinable

boolean isCombinable(DomainId protein_domain)

setKeyDomainConfidenceDescriptiveStatistics

void setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics statistics)
This is to set descriptive statistics for the confidence (i.e. E-values) of the key domain.

Parameters:
statistics -

setKeyDomainCount

void setKeyDomainCount(int key_domain_count)
Sets how many times the key domain is present in a given species genome.

Parameters:
key_domain_count - key domain count in species

setKeyDomainProteinsCount

void setKeyDomainProteinsCount(int key_domain_proteins_count)
Sets how many proteins with the key domain are present in a given species genome.

Parameters:
key_domain_proteins_count - key domain protein count in species

toBinaryDomainCombinations

List<BinaryDomainCombination> toBinaryDomainCombinations()