/**
* To add a new combinable domain.
- *
+ *
* @param protein_domain
*/
public void addCombinableDomain( final String protein_domain );
* 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
- *
+ *
* @return combining domain identifiers sorted in alphabetical manner
*/
public SortedMap<String, Integer> getCombinableDomainsIds();
/**
* Returns the domain whose combinable domains are in stored in this
* combinable domains.
- *
+ *
* @return the domain identifier
*/
public String getKeyDomain();
/**
* Returns how many times the key domain is present in a given species
* genome.
- *
+ *
* @return key domain count in species
*/
public int getKeyDomainCount();
/**
* Returns how many proteins with the key domain are present in a given
* species genome.
- *
+ *
* @return key domain proteins count in species
*/
public int getKeyDomainProteinsCount();
/**
* Returns the species of this combinable domains.
- *
+ *
* @return the species
*/
public Species getSpecies();
void addKeyDomainProtein( String protein );
/**
- *
+ *
* 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).
- *
+ *
* @return all domains
*/
List<String> getAllDomains();
/**
* Sets how many times the key domain is present in a given species genome.
- *
+ *
* @param key_domain_count
* key domain count in species
*/