public class DomainArchitectureBasedGenomeSimilarityCalculator
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static double |
MAX_SIMILARITY_SCORE |
static double |
MIN_SIMILARITY_SCORE |
Constructor and Description |
---|
DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0,
GenomeWideCombinableDomains combinable_domains_genome_1) |
Modifier and Type | Method and Description |
---|---|
void |
addDomainIdToIgnore(java.lang.String 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() |
java.util.Set<BinaryDomainCombination> |
getAllBinaryDomainCombinations()
Does not return binary combinations which contain one or two domains
to be ignored -- if ignoring is allowed.
|
java.util.Set<java.lang.String> |
getAllDomains()
Does not return domains which are to be
ignored -- if ignoring is allowed.
|
java.util.Set<BinaryDomainCombination> |
getBinaryDomainCombinationsSpecificToGenome0() |
java.util.Set<BinaryDomainCombination> |
getBinaryDomainCombinationsSpecificToGenome1() |
java.util.Set<java.lang.String> |
getDomainsSpecificToGenome0() |
java.util.Set<java.lang.String> |
getDomainsSpecificToGenome1() |
java.util.Set<BinaryDomainCombination> |
getSharedBinaryDomainCombinations() |
java.util.Set<java.lang.String> |
getSharedDomains() |
void |
setAllowDomainsToBeIgnored(boolean allow_domains_to_be_ignored) |
public static final double MAX_SIMILARITY_SCORE
public static final double MIN_SIMILARITY_SCORE
public DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)
public void addDomainIdToIgnore(java.lang.String domain_id_to_ignore)
public double calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore()
public double calculateSharedDomainsBasedGenomeSimilarityScore()
public void deleteAllDomainIdsToIgnore()
public java.util.Set<BinaryDomainCombination> getAllBinaryDomainCombinations()
public java.util.Set<java.lang.String> getAllDomains()
public java.util.Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome0()
public java.util.Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome1()
public java.util.Set<java.lang.String> getDomainsSpecificToGenome0()
public java.util.Set<java.lang.String> getDomainsSpecificToGenome1()
public java.util.Set<BinaryDomainCombination> getSharedBinaryDomainCombinations()
public java.util.Set<java.lang.String> getSharedDomains()
public void setAllowDomainsToBeIgnored(boolean allow_domains_to_be_ignored)