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public interface CombinableDomains
Method Summary | |
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void |
addCombinableDomain(DomainId protein_domain)
To add a new combinable domain. |
List<DomainId> |
getAllDomains()
This must return all domains in this set of combinable domains (i.e. |
List<DomainId> |
getCombinableDomains()
|
SortedMap<DomainId,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()
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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()
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int |
getNumberOfProteinsExhibitingCombination(DomainId protein_domain)
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Species |
getSpecies()
Returns the species of this combinable domains. |
boolean |
isCombinable(DomainId protein_domain)
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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. |
List<BinaryDomainCombination> |
toBinaryDomainCombinations()
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Method Detail |
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void addCombinableDomain(DomainId protein_domain)
protein_domain
- List<DomainId> getAllDomains()
List<DomainId> getCombinableDomains()
SortedMap<DomainId,Integer> getCombinableDomainsIds()
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 speciesList<BinaryDomainCombination> toBinaryDomainCombinations()
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