org.forester.surfacing
Class DomainArchitectureBasedGenomeSimilarityCalculator

java.lang.Object
  extended by org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

public class DomainArchitectureBasedGenomeSimilarityCalculator
extends Object


Field Summary
static double MAX_SIMILARITY_SCORE
           
static double MIN_SIMILARITY_SCORE
           
 
Constructor Summary
DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)
           
 
Method Summary
 void addDomainIdToIgnore(DomainId domain_id_to_ignore)
           
 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 )
 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 )
 void deleteAllDomainIdsToIgnore()
           
 Set<BinaryDomainCombination> getAllBinaryDomainCombinations()
          Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.
 Set<DomainId> getAllDomains()
          Does not return domains which are to be ignored -- if ignoring is allowed.
 Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome0()
           
 Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome1()
           
 Set<DomainId> getDomainsSpecificToGenome0()
           
 Set<DomainId> getDomainsSpecificToGenome1()
           
 Set<BinaryDomainCombination> getSharedBinaryDomainCombinations()
           
 Set<DomainId> getSharedDomains()
           
 void setAllowDomainsToBeIgnored(boolean allow_domains_to_be_ignored)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

MAX_SIMILARITY_SCORE

public static final double MAX_SIMILARITY_SCORE
See Also:
Constant Field Values

MIN_SIMILARITY_SCORE

public static final double MIN_SIMILARITY_SCORE
See Also:
Constant Field Values
Constructor Detail

DomainArchitectureBasedGenomeSimilarityCalculator

public DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0,
                                                         GenomeWideCombinableDomains combinable_domains_genome_1)
Method Detail

addDomainIdToIgnore

public void addDomainIdToIgnore(DomainId 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<DomainId> 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<DomainId> getDomainsSpecificToGenome0()

getDomainsSpecificToGenome1

public Set<DomainId> getDomainsSpecificToGenome1()

getSharedBinaryDomainCombinations

public Set<BinaryDomainCombination> getSharedBinaryDomainCombinations()

getSharedDomains

public Set<DomainId> getSharedDomains()

setAllowDomainsToBeIgnored

public void setAllowDomainsToBeIgnored(boolean allow_domains_to_be_ignored)