Class BasicCombinableDomains

Method Details

• addCombinableDomain

  public void addCombinableDomain(String protein_domain)

  Description copied from interface: CombinableDomains

  To add a new combinable domain.

  Specified by:

  addCombinableDomain in interface CombinableDomains

• addKeyDomainProtein

  public void addKeyDomainProtein(String protein)

  Specified by:

  addKeyDomainProtein in interface CombinableDomains

• getAllDomains

  public List<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 List<String> getCombinableDomains()

  Specified by:

  getCombinableDomains in interface CombinableDomains

• getCombinableDomainsIds

  public SortedMap<String,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 StringBuilder getCombiningDomainIdsAsStringBuilder()

  Specified by:

  getCombiningDomainIdsAsStringBuilder in interface CombinableDomains

• getKeyDomain

  public 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 Set<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(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(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 List<BinaryDomainCombination> toBinaryDomainCombinations()

  Specified by:

  toBinaryDomainCombinations in interface CombinableDomains

• toString

  public String toString()

  Overrides:

  toString in class Object

• getCombiningDomains

  protected TreeMap<String,Integer> getCombiningDomains()