Class BasicCombinableDomains

    • Constructor Detail

      • BasicCombinableDomains

        public BasicCombinableDomains​(java.lang.String key_domain,
                                      Species species)
    • Method Detail

      • getAllDomains

        public java.util.List<java.lang.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
      • getCombinableDomainsIds

        public java.util.SortedMap<java.lang.String,​java.lang.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
      • getKeyDomain

        public java.lang.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
      • 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
      • 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
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • getCombiningDomains

        protected java.util.TreeMap<java.lang.String,​java.lang.Integer> getCombiningDomains()