Method Detail

• addCombinableDomain

  void addCombinableDomain​(java.lang.String protein_domain)

  To add a new combinable domain.

  Parameters:

  protein_domain -

• getCombinableDomainsIds

  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

  Returns:

  combining domain identifiers sorted in alphabetical manner

• getCombiningDomainIdsAsStringBuilder

  java.lang.StringBuilder getCombiningDomainIdsAsStringBuilder()

• getKeyDomain

  java.lang.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

  java.util.Set<java.lang.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​(java.lang.String protein_domain)

• getSpecies

  Species getSpecies()

  Returns the species of this combinable domains.

  Returns:

  the species

• isCombinable

  boolean isCombinable​(java.lang.String protein_domain)

• toBinaryDomainCombinations

  java.util.List<BinaryDomainCombination> toBinaryDomainCombinations()

• addKeyDomainProtein

  void addKeyDomainProtein​(java.lang.String protein)

• getAllDomains

  java.util.List<java.lang.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

  java.util.List<java.lang.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