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

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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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