org.forester.surfacing

Class BasicCombinableDomains

java.lang.Object

org.forester.surfacing.BasicCombinableDomains

All Implemented Interfaces:

CombinableDomains

Direct Known Subclasses:

AdjactantDirectedCombinableDomains, DirectedCombinableDomains

public class BasicCombinableDomains
extends java.lang.Object
implements CombinableDomains

Constructor Summary

Constructors

Constructor and Description
BasicCombinableDomains(DomainId key_domain, Species species)

Method Summary

Methods

Modifier and Type	Method and Description
void	addCombinableDomain(DomainId protein_domain) To add a new combinable domain.
java.util.List<DomainId>	getAllDomains() This must return all domains in this set of combinable domains (i.e.
java.util.List<DomainId>	getCombinableDomains()
java.util.SortedMap<DomainId,java.lang.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
java.lang.StringBuilder	getCombiningDomainIdsAsStringBuilder()
protected java.util.TreeMap<DomainId,java.lang.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.
java.util.List<BinaryDomainCombination>	toBinaryDomainCombinations()
java.lang.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 java.util.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 java.util.List<DomainId> getCombinableDomains()

Specified by:

getCombinableDomains in interface CombinableDomains

getCombinableDomainsIds

public java.util.SortedMap<DomainId,java.lang.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 java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()

Specified by:

getCombiningDomainIdsAsStringBuilder in interface CombinableDomains

getCombiningDomains

protected java.util.TreeMap<DomainId,java.lang.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 java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()

Specified by:

toBinaryDomainCombinations in interface CombinableDomains

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object