CombinableDomains
AdjactantDirectedCombinableDomains
, DirectedCombinableDomains
public class BasicCombinableDomains extends java.lang.Object implements CombinableDomains
Constructor | Description |
---|---|
BasicCombinableDomains(java.lang.String key_domain,
Species species) |
Modifier and Type | Method | Description |
---|---|---|
void |
addCombinableDomain(java.lang.String protein_domain) |
To add a new combinable domain.
|
void |
addKeyDomainProtein(java.lang.String protein) |
|
java.util.List<java.lang.String> |
getAllDomains() |
This must return all domains in this set of combinable domains (i.e.
|
java.util.List<java.lang.String> |
getCombinableDomains() |
|
java.util.SortedMap<java.lang.String,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<java.lang.String,java.lang.Integer> |
getCombiningDomains() |
|
java.lang.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.
|
java.util.Set<java.lang.String> |
getKeyDomainProteins() |
|
int |
getKeyDomainProteinsCount() |
Returns how many proteins with the key domain are present in a given
species genome.
|
int |
getNumberOfCombinableDomains() |
|
int |
getNumberOfProteinsExhibitingCombination(java.lang.String protein_domain) |
|
Species |
getSpecies() |
Returns the species of this combinable domains.
|
boolean |
isCombinable(java.lang.String protein_domain) |
|
void |
setKeyDomainCount(int key_domain_count) |
Sets how many times the key domain is present in a given species genome.
|
java.util.List<BinaryDomainCombination> |
toBinaryDomainCombinations() |
|
java.lang.String |
toString() |
public BasicCombinableDomains(java.lang.String key_domain, Species species)
public void addCombinableDomain(java.lang.String protein_domain)
CombinableDomains
addCombinableDomain
in interface CombinableDomains
public void addKeyDomainProtein(java.lang.String protein)
addKeyDomainProtein
in interface CombinableDomains
public java.util.List<java.lang.String> getAllDomains()
CombinableDomains
getAllDomains
in interface CombinableDomains
public java.util.List<java.lang.String> getCombinableDomains()
getCombinableDomains
in interface CombinableDomains
public java.util.SortedMap<java.lang.String,java.lang.Integer> getCombinableDomainsIds()
CombinableDomains
getCombinableDomainsIds
in interface CombinableDomains
public java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
getCombiningDomainIdsAsStringBuilder
in interface CombinableDomains
public java.lang.String getKeyDomain()
CombinableDomains
getKeyDomain
in interface CombinableDomains
public int getKeyDomainCount()
CombinableDomains
getKeyDomainCount
in interface CombinableDomains
public java.util.Set<java.lang.String> getKeyDomainProteins()
getKeyDomainProteins
in interface CombinableDomains
public int getKeyDomainProteinsCount()
CombinableDomains
getKeyDomainProteinsCount
in interface CombinableDomains
public int getNumberOfCombinableDomains()
getNumberOfCombinableDomains
in interface CombinableDomains
public int getNumberOfProteinsExhibitingCombination(java.lang.String protein_domain)
getNumberOfProteinsExhibitingCombination
in interface CombinableDomains
public Species getSpecies()
CombinableDomains
getSpecies
in interface CombinableDomains
public boolean isCombinable(java.lang.String protein_domain)
isCombinable
in interface CombinableDomains
public void setKeyDomainCount(int key_domain_count)
CombinableDomains
setKeyDomainCount
in interface CombinableDomains
key_domain_count
- key domain count in speciespublic java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()
toBinaryDomainCombinations
in interface CombinableDomains
public java.lang.String toString()
toString
in class java.lang.Object
protected java.util.TreeMap<java.lang.String,java.lang.Integer> getCombiningDomains()