Package org.forester.surfacing

Class DomainArchitectureBasedGenomeSimilarityCalculator

java.lang.Object
org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
public class DomainArchitectureBasedGenomeSimilarityCalculator extends Object

  • Field Details

  • Constructor Details

  • Method Details

    • addDomainIdToIgnore

      public void addDomainIdToIgnore(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 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 Set<String> getAllDomains()
      Does not return domains which are to be ignored -- if ignoring is allowed.
      Returns:

    • getBinaryDomainCombinationsSpecificToGenome0

      public Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome0()

    • getBinaryDomainCombinationsSpecificToGenome1

      public Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome1()

    • getDomainsSpecificToGenome0

      public Set<String> getDomainsSpecificToGenome0()

    • getDomainsSpecificToGenome1

      public Set<String> getDomainsSpecificToGenome1()

    • getSharedBinaryDomainCombinations

      public Set<BinaryDomainCombination> getSharedBinaryDomainCombinations()

    • getSharedDomains

      public Set<String> getSharedDomains()

    • setAllowDomainsToBeIgnored

      public void setAllowDomainsToBeIgnored(boolean allow_domains_to_be_ignored)