Package org.forester.surfacing
Class BasicCombinableDomains
- java.lang.Object
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- org.forester.surfacing.BasicCombinableDomains
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- All Implemented Interfaces:
CombinableDomains
- Direct Known Subclasses:
AdjactantDirectedCombinableDomains
,DirectedCombinableDomains
public class BasicCombinableDomains extends java.lang.Object implements CombinableDomains
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Constructor Summary
Constructors Constructor Description BasicCombinableDomains(java.lang.String key_domain, Species species)
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Method Summary
All Methods Instance Methods Concrete 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()
protected java.util.TreeMap<java.lang.String,java.lang.Integer>
getCombiningDomains()
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()
java.lang.String
toString()
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Constructor Detail
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BasicCombinableDomains
public BasicCombinableDomains(java.lang.String key_domain, Species species)
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Method Detail
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addCombinableDomain
public void addCombinableDomain(java.lang.String protein_domain)
Description copied from interface:CombinableDomains
To add a new combinable domain.- Specified by:
addCombinableDomain
in interfaceCombinableDomains
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addKeyDomainProtein
public void addKeyDomainProtein(java.lang.String protein)
- Specified by:
addKeyDomainProtein
in interfaceCombinableDomains
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getAllDomains
public java.util.List<java.lang.String> getAllDomains()
Description copied from interface:CombinableDomains
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).- Specified by:
getAllDomains
in interfaceCombinableDomains
- Returns:
- all domains
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getCombinableDomains
public java.util.List<java.lang.String> getCombinableDomains()
- Specified by:
getCombinableDomains
in interfaceCombinableDomains
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getCombinableDomainsIds
public java.util.SortedMap<java.lang.String,java.lang.Integer> getCombinableDomainsIds()
Description copied from interface:CombinableDomains
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- Specified by:
getCombinableDomainsIds
in interfaceCombinableDomains
- Returns:
- combining domain identifiers sorted in alphabetical manner
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getCombiningDomainIdsAsStringBuilder
public java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
- Specified by:
getCombiningDomainIdsAsStringBuilder
in interfaceCombinableDomains
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getKeyDomain
public java.lang.String getKeyDomain()
Description copied from interface:CombinableDomains
Returns the domain whose combinable domains are in stored in this combinable domains.- Specified by:
getKeyDomain
in interfaceCombinableDomains
- Returns:
- the domain identifier
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getKeyDomainCount
public int getKeyDomainCount()
Description copied from interface:CombinableDomains
Returns how many times the key domain is present in a given species genome.- Specified by:
getKeyDomainCount
in interfaceCombinableDomains
- Returns:
- key domain count in species
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getKeyDomainProteins
public java.util.Set<java.lang.String> getKeyDomainProteins()
- Specified by:
getKeyDomainProteins
in interfaceCombinableDomains
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getKeyDomainProteinsCount
public int getKeyDomainProteinsCount()
Description copied from interface:CombinableDomains
Returns how many proteins with the key domain are present in a given species genome.- Specified by:
getKeyDomainProteinsCount
in interfaceCombinableDomains
- Returns:
- key domain proteins count in species
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getNumberOfCombinableDomains
public int getNumberOfCombinableDomains()
- Specified by:
getNumberOfCombinableDomains
in interfaceCombinableDomains
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getNumberOfProteinsExhibitingCombination
public int getNumberOfProteinsExhibitingCombination(java.lang.String protein_domain)
- Specified by:
getNumberOfProteinsExhibitingCombination
in interfaceCombinableDomains
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getSpecies
public Species getSpecies()
Description copied from interface:CombinableDomains
Returns the species of this combinable domains.- Specified by:
getSpecies
in interfaceCombinableDomains
- Returns:
- the species
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isCombinable
public boolean isCombinable(java.lang.String protein_domain)
- Specified by:
isCombinable
in interfaceCombinableDomains
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setKeyDomainCount
public void setKeyDomainCount(int key_domain_count)
Description copied from interface:CombinableDomains
Sets how many times the key domain is present in a given species genome.- Specified by:
setKeyDomainCount
in interfaceCombinableDomains
- Parameters:
key_domain_count
- key domain count in species
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toBinaryDomainCombinations
public java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()
- Specified by:
toBinaryDomainCombinations
in interfaceCombinableDomains
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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getCombiningDomains
protected java.util.TreeMap<java.lang.String,java.lang.Integer> getCombiningDomains()
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