Interface CombinableDomains

    • 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)
      • 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