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.