Package org.forester.surfacing

Interface CombinableDomains

All Known Implementing Classes:
AdjactantDirectedCombinableDomains, BasicCombinableDomains, DirectedCombinableDomains
public interface CombinableDomains

  • Method Details

    • 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