/**
* To add a new combinable domain.
- *
+ *
* @param protein_domain
*/
public void addCombinableDomain( final String protein_domain );
/**
- *
- * 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();
-
- List<String> getCombinableDomains();
-
- /**
* 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();
+ public Set<String> getKeyDomainProteins();
+
/**
* 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();
- public Set<String> getKeyDomainProteins();
-
public int getNumberOfCombinableDomains();
public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
/**
* Returns the species of this combinable domains.
- *
+ *
* @return the species
*/
public Species getSpecies();
public boolean isCombinable( final String protein_domain );
+ public List<BinaryDomainCombination> toBinaryDomainCombinations();
+
+ 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();
+
+ List<String> getCombinableDomains();
+
/**
* Sets how many times the key domain is present in a given species genome.
- *
+ *
* @param key_domain_count
* key domain count in species
*/
void setKeyDomainCount( final int key_domain_count );
-
- public List<BinaryDomainCombination> toBinaryDomainCombinations();
-
- void addKeyDomainProtein( String protein );
}
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