Class SimpleOrthoPair
java.lang.Object
org.biojava.bio.program.homologene.SimpleOrthoPair
- All Implemented Interfaces:
OrthoPair
A no-frills implementation of the OrthoPair interface
- Author:
- David Huen
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Constructor Summary
ConstructorsConstructorDescriptionSimpleOrthoPair
(Orthologue first, Orthologue second, String ref) constructor for the curated form of an orthology relationshipSimpleOrthoPair
(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) constructor for the computed form of an orthology relationship. -
Method Summary
Modifier and TypeMethodDescriptionboolean
gets the first orthologue in the orthology relationship.double
get percentage identity.getRef()
get reference to evidence for orthology.gets the first orthologue in the orthology relationship.gets the second orthologue in the orthology relationship.
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Constructor Details
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SimpleOrthoPair
public SimpleOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) constructor for the computed form of an orthology relationship. -
SimpleOrthoPair
constructor for the curated form of an orthology relationship
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Method Details
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getFirstOrthologue
Description copied from interface:OrthoPair
gets the first orthologue in the orthology relationship.I agree that this access route is somewhat sucky for a symmetric relationship but I'd hate returning a Set of orthologues more and all the fiddling would require.
- Specified by:
getFirstOrthologue
in interfaceOrthoPair
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getSecondOrthologue
Description copied from interface:OrthoPair
gets the first orthologue in the orthology relationship. This will be the one with the lower TaxonID.- Specified by:
getSecondOrthologue
in interfaceOrthoPair
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getSimilarity
Description copied from interface:OrthoPair
gets the second orthologue in the orthology relationship. This will be the one with the higher TaxonID.- Specified by:
getSimilarity
in interfaceOrthoPair
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getPercentIdentity
Description copied from interface:OrthoPair
get percentage identity.- Specified by:
getPercentIdentity
in interfaceOrthoPair
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getRef
Description copied from interface:OrthoPair
get reference to evidence for orthology. -
equals
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