Package org.forester.surfacing
Interface CombinableDomains
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- All Known Implementing Classes:
AdjactantDirectedCombinableDomains
,BasicCombinableDomains
,DirectedCombinableDomains
public interface CombinableDomains
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Method Summary
All Methods Instance Methods Abstract Methods 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 combinationjava.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()
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Method Detail
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addCombinableDomain
void addCombinableDomain(java.lang.String protein_domain)
To add a new combinable domain.- Parameters:
protein_domain
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getCombinableDomainsIds
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- Returns:
- combining domain identifiers sorted in alphabetical manner
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getCombiningDomainIdsAsStringBuilder
java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
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getKeyDomain
java.lang.String getKeyDomain()
Returns the domain whose combinable domains are in stored in this combinable domains.- Returns:
- the domain identifier
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getKeyDomainCount
int getKeyDomainCount()
Returns how many times the key domain is present in a given species genome.- Returns:
- key domain count in species
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getKeyDomainProteins
java.util.Set<java.lang.String> getKeyDomainProteins()
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getKeyDomainProteinsCount
int getKeyDomainProteinsCount()
Returns how many proteins with the key domain are present in a given species genome.- Returns:
- key domain proteins count in species
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getNumberOfCombinableDomains
int getNumberOfCombinableDomains()
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getNumberOfProteinsExhibitingCombination
int getNumberOfProteinsExhibitingCombination(java.lang.String protein_domain)
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getSpecies
Species getSpecies()
Returns the species of this combinable domains.- Returns:
- the species
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isCombinable
boolean isCombinable(java.lang.String protein_domain)
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toBinaryDomainCombinations
java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()
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addKeyDomainProtein
void addKeyDomainProtein(java.lang.String protein)
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getAllDomains
java.util.List<java.lang.String> getAllDomains()
This must return all domains in this set of combinable domains (i.e. the key domain and all domains which can combine with the key domain).- Returns:
- all domains
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getCombinableDomains
java.util.List<java.lang.String> getCombinableDomains()
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setKeyDomainCount
void setKeyDomainCount(int key_domain_count)
Sets how many times the key domain is present in a given species genome.- Parameters:
key_domain_count
- key domain count in species
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