Uses of Interface
org.biojava.bio.program.homologene.Orthologue

Packages that use Orthologue

Package	Description
org.biojava.bio.program.homologene	Support classes for Homologene data.

Uses of Orthologue in org.biojava.bio.program.homologene

Classes in org.biojava.bio.program.homologene that implement Orthologue

Modifier and Type	Class	Description
class	SimpleOrthologue	this entry contains data about the orthologue.

Methods in org.biojava.bio.program.homologene that return Orthologue

Modifier and Type	Method	Description
Orthologue	HomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)	Create an orthologue.
Orthologue	HomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)	Create an orthologue.
Orthologue	SimpleHomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)
Orthologue	SimpleHomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
Orthologue	OrthoPair.getFirstOrthologue()	gets the first orthologue in the orthology relationship.
Orthologue	SimpleOrthoPair.getFirstOrthologue()
Orthologue	HomologeneDB.getOrthologue(String homologeneID)	Returns an orthologue of specified ID.
Orthologue	OrthologueSet.getOrthologue(String homologeneID)
Orthologue	SimpleHomologeneDB.getOrthologue(String homologeneID)
Orthologue	SimpleOrthologueSet.getOrthologue(String homologeneID)
Orthologue	OrthoPair.getSecondOrthologue()	gets the first orthologue in the orthology relationship.
Orthologue	SimpleOrthoPair.getSecondOrthologue()
Orthologue	OrthologueSet.Iterator.nextOrthologue()
Orthologue	SimpleOrthologueSet.Iterator.nextOrthologue()

Methods in org.biojava.bio.program.homologene with parameters of type Orthologue

Modifier and Type	Method	Description
boolean	OrthologueFilter.accept(Orthologue ortho)
boolean	OrthologueFilter.AcceptAll.accept(Orthologue ortho)
boolean	OrthologueFilter.And.accept(Orthologue ortho)
boolean	OrthologueFilter.ByAccession.accept(Orthologue ortho)
boolean	OrthologueFilter.ByHomologeneID.accept(Orthologue ortho)
boolean	OrthologueFilter.ByLocusID.accept(Orthologue ortho)
boolean	OrthologueFilter.ByTaxon.accept(Orthologue ortho)
boolean	OrthologueFilter.ByTaxonID.accept(Orthologue ortho)
boolean	OrthologueFilter.ByTitle.accept(Orthologue ortho)
boolean	OrthologueFilter.Not.accept(Orthologue ortho)
boolean	OrthologueFilter.Or.accept(Orthologue ortho)
boolean	OrthologueFilter.Xor.accept(Orthologue ortho)
void	OrthologueSet.addOrthologue(Orthologue ortho)	Add an orthologue to the set.
void	SimpleOrthologueSet.addOrthologue(Orthologue ortho)
OrthoPair	HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)	Create a curated orthology entry.
OrthoPair	HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)	Create a computed orthology entry.
OrthoPair	SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)
OrthoPair	SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
void	OrthologueSet.removeOrthologue(Orthologue ortho)	Remove an orthologue from the set.
void	SimpleOrthologueSet.removeOrthologue(Orthologue ortho)

Constructors in org.biojava.bio.program.homologene with parameters of type Orthologue

Constructor	Description
SimpleOrthoPair(Orthologue first, Orthologue second, String ref)	constructor for the curated form of an orthology relationship
SimpleOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)	constructor for the computed form of an orthology relationship.