org.biojava.bio.program.homologene
Interface OrthoPair

All Known Implementing Classes:

SimpleOrthoPair

public interface OrthoPair

Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.

Method Summary

Orthologue	getFirstOrthologue() gets the first orthologue in the orthology relationship.
double	getPercentIdentity() get percentage identity.
String	getRef() get reference to evidence for orthology.
Orthologue	getSecondOrthologue() gets the first orthologue in the orthology relationship.
SimilarityType	getSimilarity() gets the second orthologue in the orthology relationship.

Method Detail

getFirstOrthologue

public Orthologue getFirstOrthologue()

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.

getSecondOrthologue

public Orthologue getSecondOrthologue()

gets the first orthologue in the orthology relationship. This will be the one with the lower TaxonID.

getSimilarity

public SimilarityType getSimilarity()

gets the second orthologue in the orthology relationship. This will be the one with the higher TaxonID.

getPercentIdentity

public double getPercentIdentity()

get percentage identity.

getRef

public String getRef()

get reference to evidence for orthology.