org.forester.surfacing
public class BasicCombinableDomains extends java.lang.Object implements CombinableDomains
Constructor and Description |
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BasicCombinableDomains(DomainId key_domain,
Species species) |
Modifier and Type | Method and Description |
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void |
addCombinableDomain(DomainId protein_domain)
To add a new combinable domain.
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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
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java.lang.StringBuilder |
getCombiningDomainIdsAsStringBuilder() |
protected java.util.TreeMap<DomainId,java.lang.Integer> |
getCombiningDomains() |
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.
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int |
getNumberOfCombinableDomains() |
int |
getNumberOfProteinsExhibitingCombination(DomainId protein_domain) |
Species |
getSpecies()
Returns the species of this combinable domains.
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boolean |
isCombinable(DomainId protein_domain) |
void |
setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics key_domain_confidence_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.
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void |
setKeyDomainProteinsCount(int key_domain_proteins_count)
Sets how many proteins with the key domain are present in a given species
genome.
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java.util.List<BinaryDomainCombination> |
toBinaryDomainCombinations() |
java.lang.String |
toString() |
public void addCombinableDomain(DomainId protein_domain)
CombinableDomains
addCombinableDomain
in interface CombinableDomains
public java.util.List<DomainId> getAllDomains()
CombinableDomains
getAllDomains
in interface CombinableDomains
public java.util.List<DomainId> getCombinableDomains()
getCombinableDomains
in interface CombinableDomains
public java.util.SortedMap<DomainId,java.lang.Integer> getCombinableDomainsIds()
CombinableDomains
getCombinableDomainsIds
in interface CombinableDomains
public java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
getCombiningDomainIdsAsStringBuilder
in interface CombinableDomains
protected java.util.TreeMap<DomainId,java.lang.Integer> getCombiningDomains()
public DomainId getKeyDomain()
CombinableDomains
getKeyDomain
in interface CombinableDomains
public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics()
CombinableDomains
getKeyDomainConfidenceDescriptiveStatistics
in interface CombinableDomains
public int getKeyDomainCount()
CombinableDomains
getKeyDomainCount
in interface CombinableDomains
public int getKeyDomainProteinsCount()
CombinableDomains
getKeyDomainProteinsCount
in interface CombinableDomains
public int getNumberOfCombinableDomains()
getNumberOfCombinableDomains
in interface CombinableDomains
public int getNumberOfProteinsExhibitingCombination(DomainId protein_domain)
getNumberOfProteinsExhibitingCombination
in interface CombinableDomains
public Species getSpecies()
CombinableDomains
getSpecies
in interface CombinableDomains
public boolean isCombinable(DomainId protein_domain)
isCombinable
in interface CombinableDomains
public void setKeyDomainConfidenceDescriptiveStatistics(DescriptiveStatistics key_domain_confidence_statistics)
CombinableDomains
setKeyDomainConfidenceDescriptiveStatistics
in interface CombinableDomains
public void setKeyDomainCount(int key_domain_count)
CombinableDomains
setKeyDomainCount
in interface CombinableDomains
key_domain_count
- key domain count in speciespublic void setKeyDomainProteinsCount(int key_domain_proteins_count)
CombinableDomains
setKeyDomainProteinsCount
in interface CombinableDomains
key_domain_proteins_count
- key domain protein count in speciespublic java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()
toBinaryDomainCombinations
in interface CombinableDomains
public java.lang.String toString()
toString
in class java.lang.Object