CombinableDomains (Forester 1.038 API)

All Known Implementing Classes:

AdjactantDirectedCombinableDomains, BasicCombinableDomains, DirectedCombinableDomains
```
public interface CombinableDomains
```

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`addCombinableDomain(String protein_domain)` To add a new combinable domain.
`void`	`addKeyDomainProtein(String protein)`
`List<String>`	`getAllDomains()` This must return all domains in this set of combinable domains (i.e.
`List<String>`	`getCombinableDomains()`
`SortedMap<String,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()`
`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.
`Set<String>`	`getKeyDomainProteins()`
`int`	`getKeyDomainProteinsCount()` Returns how many proteins with the key domain are present in a given species genome.
`int`	`getNumberOfCombinableDomains()`
`int`	`getNumberOfProteinsExhibitingCombination(String protein_domain)`
`Species`	`getSpecies()` Returns the species of this combinable domains.
`boolean`	`isCombinable(String protein_domain)`
`void`	`setKeyDomainCount(int key_domain_count)` Sets how many times the key domain is present in a given species genome.
`List<BinaryDomainCombination>`	`toBinaryDomainCombinations()`

- Method Detail
  - addCombinableDomain
```
void addCombinableDomain(String protein_domain)
```
    To add a new combinable domain.
    
    Parameters:
    
    protein_domain -
  - getCombinableDomainsIds
```
SortedMap<String,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
  - getCombiningDomainIdsAsStringBuilder
```
StringBuilder getCombiningDomainIdsAsStringBuilder()
```
  - getKeyDomain
```
String getKeyDomain()
```
    Returns the domain whose combinable domains are in stored in this combinable domains.
    
    Returns:
    
    the domain identifier
  - getKeyDomainCount
```
int getKeyDomainCount()
```
    Returns how many times the key domain is present in a given species genome.
    
    Returns:
    
    key domain count in species
  - getKeyDomainProteins
```
Set<String> getKeyDomainProteins()
```
  - 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
  - getNumberOfCombinableDomains
```
int getNumberOfCombinableDomains()
```
  - getNumberOfProteinsExhibitingCombination
```
int getNumberOfProteinsExhibitingCombination(String protein_domain)
```
  - getSpecies
```
Species getSpecies()
```
    Returns the species of this combinable domains.
    
    Returns:
    
    the species
  - isCombinable
```
boolean isCombinable(String protein_domain)
```
  - toBinaryDomainCombinations
```
List<BinaryDomainCombination> toBinaryDomainCombinations()
```
  - addKeyDomainProtein
```
void addKeyDomainProtein(String protein)
```
  - getAllDomains
```
List<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
  - getCombinableDomains
```
List<String> getCombinableDomains()
```
  - 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

Interface CombinableDomains

Method Summary

Method Detail

addCombinableDomain

getCombinableDomainsIds

getCombiningDomainIdsAsStringBuilder

getKeyDomain

getKeyDomainCount

getKeyDomainProteins

getKeyDomainProteinsCount

getNumberOfCombinableDomains

getNumberOfProteinsExhibitingCombination

getSpecies

isCombinable

toBinaryDomainCombinations

addKeyDomainProtein

getAllDomains

getCombinableDomains

setKeyDomainCount