org.forester.surfacing
public interface CombinableDomains
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() |
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 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() |
void addCombinableDomain(DomainId protein_domain)
protein_domain
- java.util.List<DomainId> getAllDomains()
java.util.List<DomainId> getCombinableDomains()
java.util.SortedMap<DomainId,java.lang.Integer> getCombinableDomainsIds()
java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
DomainId getKeyDomain()
DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics()
int getKeyDomainCount()
int getKeyDomainProteinsCount()
int getNumberOfCombinableDomains()
int getNumberOfProteinsExhibitingCombination(DomainId protein_domain)
Species getSpecies()
boolean isCombinable(DomainId protein_domain)
void setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics statistics)
statistics
- void setKeyDomainCount(int key_domain_count)
key_domain_count
- key domain count in speciesvoid setKeyDomainProteinsCount(int key_domain_proteins_count)
key_domain_proteins_count
- key domain protein count in speciesjava.util.List<BinaryDomainCombination> toBinaryDomainCombinations()