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

Packages that use OrthoPair

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

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

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

Modifier and Type	Class and Description
class	SimpleOrthoPair A no-frills implementation of the OrthoPair interface

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

Modifier and Type	Method and Description
OrthoPair	HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity) Create a computed orthology entry.
OrthoPair	SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)
OrthoPair	HomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref) Create a curated orthology entry.
OrthoPair	SimpleHomologeneDB.createOrthoPair(Orthologue first, Orthologue second, String ref)
OrthoPair	SimpleOrthoPairSet.Iterator.nextOrthoPair()
OrthoPair	OrthoPairSet.Iterator.nextOrthoPair()

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

Modifier and Type	Method and Description
boolean	OrthoPairFilter.accept(OrthoPair pair)
boolean	OrthoPairFilter.AcceptAll.accept(OrthoPair pair)
boolean	OrthoPairFilter.Not.accept(OrthoPair pair)
boolean	OrthoPairFilter.Or.accept(OrthoPair pair)
boolean	OrthoPairFilter.And.accept(OrthoPair pair)
boolean	OrthoPairFilter.Xor.accept(OrthoPair pair)
boolean	OrthoPairFilter.ByMinIdentity.accept(OrthoPair pair)
boolean	OrthoPairFilter.ByMaxIdentity.accept(OrthoPair pair)
boolean	OrthoPairFilter.BySimilarityType.accept(OrthoPair pair)
boolean	OrthoPairFilter.ByRef.accept(OrthoPair pair)
void	SimpleOrthoPairSet.addOrthoPair(OrthoPair orthology)
void	OrthoPairSet.addOrthoPair(OrthoPair orthology) adds a specified OrthoPair relationship to this group.
void	SimpleOrthoPairSet.removeOrthoPair(OrthoPair orthology)
void	OrthoPairSet.removeOrthoPair(OrthoPair orthology) removes a specified OrthoPair relationship from this group.