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

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

void	SimpleOrthologueSet.addOrthologue(Orthologue ortho)
void	SimpleOrthologueSet.removeOrthologue(Orthologue ortho)
OrthoPair	SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
OrthoPair	SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)
void	OrthologueSet.addOrthologue(Orthologue ortho) Add an orthologue to the set.
void	OrthologueSet.removeOrthologue(Orthologue ortho) Remove an orthologue from the set.
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)
OrthoPair	HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) Create a computed orthology entry.
OrthoPair	HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref) Create a curated orthology entry.

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