Package org.forester.surfacing
Class DomainArchitectureBasedGenomeSimilarityCalculator
- java.lang.Object
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- org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator
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public class DomainArchitectureBasedGenomeSimilarityCalculator extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static double
MAX_SIMILARITY_SCORE
static double
MIN_SIMILARITY_SCORE
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Constructor Summary
Constructors Constructor Description DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Field Detail
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MAX_SIMILARITY_SCORE
public static final double MAX_SIMILARITY_SCORE
- See Also:
- Constant Field Values
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MIN_SIMILARITY_SCORE
public static final double MIN_SIMILARITY_SCORE
- See Also:
- Constant Field Values
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Constructor Detail
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DomainArchitectureBasedGenomeSimilarityCalculator
public DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)
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Method Detail
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addDomainIdToIgnore
public void addDomainIdToIgnore(java.lang.String domain_id_to_ignore)
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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
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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
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deleteAllDomainIdsToIgnore
public void deleteAllDomainIdsToIgnore()
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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
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getAllDomains
public java.util.Set<java.lang.String> getAllDomains()
Does not return domains which are to be ignored -- if ignoring is allowed.- Returns:
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getBinaryDomainCombinationsSpecificToGenome0
public java.util.Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome0()
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getBinaryDomainCombinationsSpecificToGenome1
public java.util.Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome1()
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getDomainsSpecificToGenome0
public java.util.Set<java.lang.String> getDomainsSpecificToGenome0()
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getDomainsSpecificToGenome1
public java.util.Set<java.lang.String> getDomainsSpecificToGenome1()
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getSharedBinaryDomainCombinations
public java.util.Set<BinaryDomainCombination> getSharedBinaryDomainCombinations()
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getSharedDomains
public java.util.Set<java.lang.String> getSharedDomains()
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setAllowDomainsToBeIgnored
public void setAllowDomainsToBeIgnored(boolean allow_domains_to_be_ignored)
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