org.forester.surfacing

Class DomainArchitectureBasedGenomeSimilarityCalculator

java.lang.Object

org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator

public class DomainArchitectureBasedGenomeSimilarityCalculator
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static double	MAX_SIMILARITY_SCORE
static double	MIN_SIMILARITY_SCORE

Constructor Summary

Constructors

Constructor and Description
DomainArchitectureBasedGenomeSimilarityCalculator(GenomeWideCombinableDomains combinable_domains_genome_0, GenomeWideCombinableDomains combinable_domains_genome_1)

Method Summary

Modifier and Type	Method and Description
void	addDomainIdToIgnore(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()
Set<BinaryDomainCombination>	getAllBinaryDomainCombinations() Does not return binary combinations which contain one or two domains to be ignored -- if ignoring is allowed.
Set<String>	getAllDomains() Does not return domains which are to be ignored -- if ignoring is allowed.
Set<BinaryDomainCombination>	getBinaryDomainCombinationsSpecificToGenome0()
Set<BinaryDomainCombination>	getBinaryDomainCombinationsSpecificToGenome1()
Set<String>	getDomainsSpecificToGenome0()
Set<String>	getDomainsSpecificToGenome1()
Set<BinaryDomainCombination>	getSharedBinaryDomainCombinations()
Set<String>	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(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)