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 Object
implements CombinableDomains

Constructor Summary

Constructors

Constructor and Description
BasicCombinableDomains(String key_domain, Species species)

Method Summary

Modifier and Type	Method and Description
void	addCombinableDomain(String protein_domain) To add a new combinable domain.
void	addKeyDomainProtein(String protein)
List<String>	getAllDomains() This must return all domains in this set of combinable domains (i.e.
List<String>	getCombinableDomains()
SortedMap<String,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<String,Integer>	getCombiningDomains()
String	getKeyDomain() Returns the domain whose combinable domains are in stored in this combinable domains.
int	getKeyDomainCount() Returns how many times the key domain is present in a given species genome.
Set<String>	getKeyDomainProteins()
int	getKeyDomainProteinsCount() Returns how many proteins with the key domain are present in a given species genome.
int	getNumberOfCombinableDomains()
int	getNumberOfProteinsExhibitingCombination(String protein_domain)
Species	getSpecies() Returns the species of this combinable domains.
boolean	isCombinable(String protein_domain)
void	setKeyDomainCount(int key_domain_count) Sets how many times the key domain is 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(String key_domain,
                              Species species)

Method Detail

addCombinableDomain

public void addCombinableDomain(String protein_domain)

Description copied from interface: CombinableDomains

To add a new combinable domain.

Specified by:

addCombinableDomain in interface CombinableDomains

addKeyDomainProtein

public void addKeyDomainProtein(String protein)

Specified by:

addKeyDomainProtein in interface CombinableDomains

getAllDomains

public List<String> 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<String> getCombinableDomains()

Specified by:

getCombinableDomains in interface CombinableDomains

getCombinableDomainsIds

public SortedMap<String,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

getKeyDomain

public String 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

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

getKeyDomainProteins

public Set<String> getKeyDomainProteins()

Specified by:

getKeyDomainProteins in interface CombinableDomains

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(String 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(String protein_domain)

Specified by:

isCombinable 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

toBinaryDomainCombinations

public List<BinaryDomainCombination> toBinaryDomainCombinations()

Specified by:

toBinaryDomainCombinations in interface CombinableDomains

toString

public String toString()

Overrides:

toString in class Object

getCombiningDomains

protected TreeMap<String,Integer> getCombiningDomains()