org.forester.surfacing
Class DomainArchitectureBasedGenomeSimilarityCalculator
java.lang.Object
org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
public class DomainArchitectureBasedGenomeSimilarityCalculator
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
DomainArchitectureBasedGenomeSimilarityCalculator
public DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0,
GenomeWideCombinableDomains combinable_domains_genome_1)
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)