java.lang.Object
- org.forester.surfacing.BasicCombinableDomains

All Implemented Interfaces:

CombinableDomains

Direct Known Subclasses:

AdjactantDirectedCombinableDomains, DirectedCombinableDomains
```
public class BasicCombinableDomains
extends java.lang.Object
implements CombinableDomains
```

Constructor Summary

Constructors
Constructor Description

BasicCombinableDomains(java.lang.String key_domain, Species species)

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 combination
`java.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()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - BasicCombinableDomains
```
public BasicCombinableDomains(java.lang.String key_domain,
                              Species species)
```
- Method Detail
  - addCombinableDomain
```
public void addCombinableDomain(java.lang.String protein_domain)
```
    Description copied from interface: CombinableDomains
    
    To add a new combinable domain.
    
    Specified by:
    
    addCombinableDomain in interface CombinableDomains
  - addKeyDomainProtein
```
public void addKeyDomainProtein(java.lang.String protein)
```
    Specified by:
    
    addKeyDomainProtein in interface CombinableDomains
  - 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 interface CombinableDomains
    
    Returns:
    
    all domains
  - getCombinableDomains
```
public java.util.List<java.lang.String> getCombinableDomains()
```
    Specified by:
    
    getCombinableDomains in interface CombinableDomains
  - 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 interface CombinableDomains
    
    Returns:
    
    combining domain identifiers sorted in alphabetical manner
  - getCombiningDomainIdsAsStringBuilder
```
public java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()
```
    Specified by:
    
    getCombiningDomainIdsAsStringBuilder in interface CombinableDomains
  - 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 interface CombinableDomains
    
    Returns:
    
    the domain identifier
  - 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 interface CombinableDomains
    
    Returns:
    
    key domain count in species
  - getKeyDomainProteins
```
public java.util.Set<java.lang.String> getKeyDomainProteins()
```
    Specified by:
    
    getKeyDomainProteins in interface CombinableDomains
  - 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 interface CombinableDomains
    
    Returns:
    
    key domain proteins count in species
  - getNumberOfCombinableDomains
```
public int getNumberOfCombinableDomains()
```
    Specified by:
    
    getNumberOfCombinableDomains in interface CombinableDomains
  - getNumberOfProteinsExhibitingCombination
```
public int getNumberOfProteinsExhibitingCombination(java.lang.String protein_domain)
```
    Specified by:
    
    getNumberOfProteinsExhibitingCombination in interface CombinableDomains
  - getSpecies
```
public Species getSpecies()
```
    Description copied from interface: CombinableDomains
    
    Returns the species of this combinable domains.
    
    Specified by:
    
    getSpecies in interface CombinableDomains
    
    Returns:
    
    the species
  - isCombinable
```
public boolean isCombinable(java.lang.String protein_domain)
```
    Specified by:
    
    isCombinable in interface CombinableDomains
  - 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 interface CombinableDomains
    
    Parameters:
    
    key_domain_count - key domain count in species
  - toBinaryDomainCombinations
```
public java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()
```
    Specified by:
    
    toBinaryDomainCombinations in interface CombinableDomains
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getCombiningDomains
```
protected java.util.TreeMap<java.lang.String,java.lang.Integer> getCombiningDomains()
```

Class BasicCombinableDomains

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicCombinableDomains

Method Detail

addCombinableDomain

addKeyDomainProtein

getAllDomains

getCombinableDomains

getCombinableDomainsIds

getCombiningDomainIdsAsStringBuilder

getKeyDomain

getKeyDomainCount

getKeyDomainProteins

getKeyDomainProteinsCount

getNumberOfCombinableDomains

getNumberOfProteinsExhibitingCombination

getSpecies

isCombinable

setKeyDomainCount

toBinaryDomainCombinations

toString

getCombiningDomains