## Package org.biojava.bio.program.homologene

Support classes for Homologene data.

See:
Description

Interface Summary
HomologeneBuilder: an interface for Homologene dataset Builders
HomologeneDB: Homologene is a NCBI dataset that curates sets of orthologues from the reference model organisms.
Orthologue: this entry contains data about the orthologue.
OrthologueFilter
OrthologueSet: Interface for classes that store and manipulate orthologues.
OrthologueSet.Iterator: An iterator for the contents of an OrthologueSet.
OrthoPair: Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
OrthoPairCollection: Interface for a Set of OrthoPairSets
OrthoPairCollection.Iterator: Iterator for a OrthoPairCollection
OrthoPairFilter
OrthoPairSet: represents the Homologene Group.
OrthoPairSet.Iterator
OrthoPairSetFilter
SimilarityType: Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
Taxon

Class Summary
AbstractOrthologueSet
AbstractOrthoPairCollection: An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairSet: represents the Homologene Group.
HomologeneTools: Homologene is a NCBI dataset that curates sets of orthologues from the reference model ogranisms.
OrthologueFilter.AcceptAll
OrthologueFilter.And
OrthologueFilter.ByAccession
OrthologueFilter.ByHomologeneID
OrthologueFilter.ByLocusID
OrthologueFilter.ByTaxon
OrthologueFilter.ByTaxonID
OrthologueFilter.ByTitle
OrthologueFilter.Not
OrthologueFilter.Or
OrthologueFilter.Xor
OrthoPairFilter.AcceptAll
OrthoPairFilter.And
OrthoPairFilter.ByMaxIdentity
OrthoPairFilter.ByMinIdentity
OrthoPairFilter.ByRef
OrthoPairFilter.BySimilarityType
OrthoPairFilter.Not
OrthoPairFilter.Or
OrthoPairFilter.Xor
OrthoPairSetFilter.AcceptAll
OrthoPairSetFilter.AllPairsInCollection: all OrthoPairs must meet the requirement defined by filter.
OrthoPairSetFilter.And
OrthoPairSetFilter.ByMinIdentity
OrthoPairSetFilter.ByTaxon
OrthoPairSetFilter.Not
OrthoPairSetFilter.Or
OrthoPairSetFilter.SomePairsInCollection: at least one OrthoPair must meet the requirement defined by filter.
OrthoPairSetFilter.Xor
SimilarityType.PlaceHolder
SimpleHomologeneBuilder: A simple no-frills implementation of the HomologeneBuilder interface.
SimpleHomologeneDB
SimpleOrthologue: this entry contains data about the orthologue.
SimpleOrthologueSet
SimpleOrthoPair: A no-frills implementation of the OrthoPair interface
SimpleOrthoPairCollection
SimpleOrthoPairSet: a no-frills implementation of a Homologene Group
Taxon.TaxonStub

Exception Summary
DuplicateTaxonException

## Package org.biojava.bio.program.homologene Description

Support classes for Homologene data. A work-in-progress with rudimentary support.