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

Packages that use Orthologue
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
`class` `SimpleOrthologue` this entry contains data about the orthologue.

Methods in org.biojava.bio.program.homologene that return Orthologue
`Orthologue` `SimpleHomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)`
`Orthologue` `HomologeneDB.createOrthologue(int taxonID, String locusID, String homologeneID, String accession)` Create an orthologue.
`Orthologue` `SimpleHomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)`
`Orthologue` `HomologeneDB.createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)` Create an orthologue.
`Orthologue` `SimpleOrthoPair.getFirstOrthologue()`
`Orthologue` `OrthoPair.getFirstOrthologue()` gets the first orthologue in the orthology relationship.
`Orthologue` `SimpleOrthologueSet.getOrthologue(String homologeneID)`
`Orthologue` `SimpleHomologeneDB.getOrthologue(String homologeneID)`
`Orthologue` `OrthologueSet.getOrthologue(String homologeneID)`
`Orthologue` `HomologeneDB.getOrthologue(String homologeneID)` Returns an orthologue of specified ID.
`Orthologue` `SimpleOrthoPair.getSecondOrthologue()`
`Orthologue` `OrthoPair.getSecondOrthologue()` gets the first orthologue in the orthology relationship.
`Orthologue` `SimpleOrthologueSet.Iterator.nextOrthologue()`
`Orthologue` `OrthologueSet.Iterator.nextOrthologue()`

Methods in org.biojava.bio.program.homologene with parameters of type Orthologue
`boolean` `OrthologueFilter.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.AcceptAll.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.Not.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.Or.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.And.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.Xor.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.ByTaxonID.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.ByTaxon.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.ByLocusID.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.ByHomologeneID.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.ByAccession.accept(Orthologue ortho)`
`boolean` `OrthologueFilter.ByTitle.accept(Orthologue ortho)`
`void` `SimpleOrthologueSet.addOrthologue(Orthologue ortho)`
`void` `OrthologueSet.addOrthologue(Orthologue ortho)` Add an orthologue to the set.
`OrthoPair` `SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)`
`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` `HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)` Create a curated orthology entry.
`void` `SimpleOrthologueSet.removeOrthologue(Orthologue ortho)`
`void` `OrthologueSet.removeOrthologue(Orthologue ortho)` Remove an orthologue from the set.

Constructors in org.biojava.bio.program.homologene with parameters of type Orthologue
`SimpleOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)` constructor for the computed form of an orthology relationship.
`SimpleOrthoPair(Orthologue first, Orthologue second, String ref)` constructor for the curated form of an orthology relationship