Package org.biojava.bio.program.homologene

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

Interface Summary

Interface	Description
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

Class	Description
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

Exception	Description
DuplicateTaxonException