Class DomainArchitectureBasedGenomeSimilarityCalculator


  • public class DomainArchitectureBasedGenomeSimilarityCalculator
    extends java.lang.Object
    • Method Detail

      • addDomainIdToIgnore

        public void addDomainIdToIgnore​(java.lang.String domain_id_to_ignore)
      • calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore

        public double calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore()
        This returns a score between 0.0 (no binary domain combination in common) and 1.0 (all binary domain combinations in common) measuring the similarity between two genomes based on the number of shared binary domain combinations: t: sum of (distinct) binary domain combinations s: sum of shared (distinct) binary domain combinations 1 - ( ( t - s ) / t )
        Returns:
        shared binary domain combinations based similarity score
      • calculateSharedDomainsBasedGenomeSimilarityScore

        public double calculateSharedDomainsBasedGenomeSimilarityScore()
        This returns a score between 0.0 (no domains in common) and 1.0 (all domains in common) measuring the similarity between two genomes based on the number of shared domains: t: sum of (distinct) domains s: sum of shared (distinct) domains 1 - ( ( t - s ) / t )
        Returns:
        shared domains based similarity score
      • deleteAllDomainIdsToIgnore

        public void deleteAllDomainIdsToIgnore()
      • getAllBinaryDomainCombinations

        public java.util.Set<BinaryDomainCombination> getAllBinaryDomainCombinations()
        Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.
        Returns:
        SortedSet
      • getAllDomains

        public java.util.Set<java.lang.String> getAllDomains()
        Does not return domains which are to be ignored -- if ignoring is allowed.
        Returns:
      • getBinaryDomainCombinationsSpecificToGenome0

        public java.util.Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome0()
      • getBinaryDomainCombinationsSpecificToGenome1

        public java.util.Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome1()
      • getDomainsSpecificToGenome0

        public java.util.Set<java.lang.String> getDomainsSpecificToGenome0()
      • getDomainsSpecificToGenome1

        public java.util.Set<java.lang.String> getDomainsSpecificToGenome1()
      • getSharedBinaryDomainCombinations

        public java.util.Set<BinaryDomainCombination> getSharedBinaryDomainCombinations()
      • getSharedDomains

        public java.util.Set<java.lang.String> getSharedDomains()
      • setAllowDomainsToBeIgnored

        public void setAllowDomainsToBeIgnored​(boolean allow_domains_to_be_ignored)