public interface CombinableDomains
Modifier and Type | Method and 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() |
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() |
void addCombinableDomain(java.lang.String protein_domain)
protein_domain
- java.util.SortedMap<java.lang.String,java.lang.Integer> getCombinableDomainsIds()
java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
java.lang.String getKeyDomain()
int getKeyDomainCount()
java.util.Set<java.lang.String> getKeyDomainProteins()
int getKeyDomainProteinsCount()
int getNumberOfCombinableDomains()
int getNumberOfProteinsExhibitingCombination(java.lang.String protein_domain)
Species getSpecies()
boolean isCombinable(java.lang.String protein_domain)
java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()
void addKeyDomainProtein(java.lang.String protein)
java.util.List<java.lang.String> getAllDomains()
java.util.List<java.lang.String> getCombinableDomains()
void setKeyDomainCount(int key_domain_count)
key_domain_count
- key domain count in species