org.forester.surfacing
Class BasicCombinableDomains

java.lang.Object
  extended by org.forester.surfacing.BasicCombinableDomains
All Implemented Interfaces:
CombinableDomains
Direct Known Subclasses:
AdjactantDirectedCombinableDomains, DirectedCombinableDomains

public class BasicCombinableDomains
extends Object
implements CombinableDomains


Constructor Summary
BasicCombinableDomains(DomainId key_domain, Species species)
           
 
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()
           
protected  TreeMap<DomainId,Integer> getCombiningDomains()
           
 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 key_domain_confidence_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()
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

BasicCombinableDomains

public BasicCombinableDomains(DomainId key_domain,
                              Species species)
Method Detail

addCombinableDomain

public void addCombinableDomain(DomainId protein_domain)
Description copied from interface: CombinableDomains
To add a new combinable domain.

Specified by:
addCombinableDomain in interface CombinableDomains

getAllDomains

public List<DomainId> getAllDomains()
Description copied from interface: CombinableDomains
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).

Specified by:
getAllDomains in interface CombinableDomains
Returns:
all domains

getCombinableDomains

public List<DomainId> getCombinableDomains()
Specified by:
getCombinableDomains in interface CombinableDomains

getCombinableDomainsIds

public SortedMap<DomainId,Integer> getCombinableDomainsIds()
Description copied from interface: CombinableDomains
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

Specified by:
getCombinableDomainsIds in interface CombinableDomains
Returns:
combining domain identifiers sorted in alphabetical manner

getCombiningDomainIdsAsStringBuilder

public StringBuilder getCombiningDomainIdsAsStringBuilder()
Specified by:
getCombiningDomainIdsAsStringBuilder in interface CombinableDomains

getCombiningDomains

protected TreeMap<DomainId,Integer> getCombiningDomains()

getKeyDomain

public DomainId getKeyDomain()
Description copied from interface: CombinableDomains
Returns the domain whose combinable domains are in stored in this combinable domains.

Specified by:
getKeyDomain in interface CombinableDomains
Returns:
the domain identifier

getKeyDomainConfidenceDescriptiveStatistics

public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics()
Description copied from interface: CombinableDomains
Gets descriptive statistics for the confidence (i.e. E-values) of the key domain.

Specified by:
getKeyDomainConfidenceDescriptiveStatistics in interface CombinableDomains
Returns:
descriptive statistics for the confidence of the key domain

getKeyDomainCount

public int getKeyDomainCount()
Description copied from interface: CombinableDomains
Returns how many times the key domain is present in a given species genome.

Specified by:
getKeyDomainCount in interface CombinableDomains
Returns:
key domain count in species

getKeyDomainProteinsCount

public int getKeyDomainProteinsCount()
Description copied from interface: CombinableDomains
Returns how many proteins with the key domain are present in a given species genome.

Specified by:
getKeyDomainProteinsCount in interface CombinableDomains
Returns:
key domain proteins count in species

getNumberOfCombinableDomains

public int getNumberOfCombinableDomains()
Specified by:
getNumberOfCombinableDomains in interface CombinableDomains

getNumberOfProteinsExhibitingCombination

public int getNumberOfProteinsExhibitingCombination(DomainId protein_domain)
Specified by:
getNumberOfProteinsExhibitingCombination in interface CombinableDomains

getSpecies

public Species getSpecies()
Description copied from interface: CombinableDomains
Returns the species of this combinable domains.

Specified by:
getSpecies in interface CombinableDomains
Returns:
the species

isCombinable

public boolean isCombinable(DomainId protein_domain)
Specified by:
isCombinable in interface CombinableDomains

setKeyDomainConfidenceDescriptiveStatistics

public void setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics key_domain_confidence_statistics)
Description copied from interface: CombinableDomains
This is to set descriptive statistics for the confidence (i.e. E-values) of the key domain.

Specified by:
setKeyDomainConfidenceDescriptiveStatistics in interface CombinableDomains

setKeyDomainCount

public void setKeyDomainCount(int key_domain_count)
Description copied from interface: CombinableDomains
Sets how many times the key domain is present in a given species genome.

Specified by:
setKeyDomainCount in interface CombinableDomains
Parameters:
key_domain_count - key domain count in species

setKeyDomainProteinsCount

public void setKeyDomainProteinsCount(int key_domain_proteins_count)
Description copied from interface: CombinableDomains
Sets how many proteins with the key domain are present in a given species genome.

Specified by:
setKeyDomainProteinsCount in interface CombinableDomains
Parameters:
key_domain_proteins_count - key domain protein count in species

toBinaryDomainCombinations

public List<BinaryDomainCombination> toBinaryDomainCombinations()
Specified by:
toBinaryDomainCombinations in interface CombinableDomains

toString

public String toString()
Overrides:
toString in class Object