org.biojava.bio.program.homologene (BioJava-1.5-beta API)
Keywords: org.biojava.bio.program.homologene package

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## 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.

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