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

Modifier and Type	Method and Description
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

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

Orthologue getSecondOrthologue()

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

getSimilarity

SimilarityType getSimilarity()

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

getPercentIdentity

double getPercentIdentity()

get percentage identity.

getRef

String getRef()

get reference to evidence for orthology.