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

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.program.homologene.AbstractOrthologueSet (implements org.biojava.bio.program.homologene.OrthologueSet)
      - org.biojava.bio.program.homologene.SimpleOrthologueSet
    - org.biojava.bio.program.homologene.AbstractOrthoPairSet (implements org.biojava.bio.program.homologene.OrthoPairSet)
      - org.biojava.bio.program.homologene.SimpleOrthoPairSet
  - org.biojava.bio.program.homologene.AbstractOrthoPairCollection (implements org.biojava.bio.program.homologene.OrthoPairCollection)
    - org.biojava.bio.program.homologene.SimpleOrthoPairCollection
      - org.biojava.bio.program.homologene.SimpleHomologeneDB (implements org.biojava.bio.program.homologene.HomologeneDB)
  - org.biojava.bio.program.homologene.HomologeneTools
  - org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.And (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByAccession (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.ByTitle (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.Not (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.Or (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthologueFilter.Xor (implements org.biojava.bio.program.homologene.OrthologueFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.And (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.ByRef (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.Not (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.Or (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairFilter.Xor (implements org.biojava.bio.program.homologene.OrthoPairFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.And (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.Not (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.Or (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor (implements org.biojava.bio.program.homologene.OrthoPairSetFilter)
  - org.biojava.bio.program.homologene.SimilarityType.PlaceHolder (implements org.biojava.bio.program.homologene.SimilarityType)
  - org.biojava.bio.program.homologene.SimpleHomologeneBuilder (implements org.biojava.bio.program.homologene.HomologeneBuilder)
  - org.biojava.bio.program.homologene.SimpleOrthologue (implements org.biojava.bio.program.homologene.Orthologue)
  - org.biojava.bio.program.homologene.SimpleOrthologueSet.Iterator (implements org.biojava.bio.program.homologene.OrthologueSet.Iterator)
  - org.biojava.bio.program.homologene.SimpleOrthoPair (implements org.biojava.bio.program.homologene.OrthoPair)
  - org.biojava.bio.program.homologene.SimpleOrthoPairCollection.Iterator (implements org.biojava.bio.program.homologene.OrthoPairCollection.Iterator)
  - org.biojava.bio.program.homologene.SimpleOrthoPairSet.Iterator (implements org.biojava.bio.program.homologene.OrthoPairSet.Iterator)
  - org.biojava.bio.program.homologene.Taxon.TaxonStub (implements org.biojava.bio.program.homologene.Taxon)
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - org.biojava.bio.BioException
        - org.biojava.bio.program.homologene.DuplicateTaxonException

## Interface Hierarchy

- org.biojava.bio.program.homologene.HomologeneBuilder
- org.biojava.bio.program.homologene.HomologeneDB
- org.biojava.bio.program.homologene.Orthologue
- org.biojava.bio.program.homologene.OrthologueFilter
- org.biojava.bio.program.homologene.OrthologueSet
- org.biojava.bio.program.homologene.OrthologueSet.Iterator
- org.biojava.bio.program.homologene.OrthoPair
- org.biojava.bio.program.homologene.OrthoPairCollection
- org.biojava.bio.program.homologene.OrthoPairCollection.Iterator
- org.biojava.bio.program.homologene.OrthoPairFilter
- org.biojava.bio.program.homologene.OrthoPairSet
- org.biojava.bio.program.homologene.OrthoPairSet.Iterator
- org.biojava.bio.program.homologene.OrthoPairSetFilter
- org.biojava.bio.program.homologene.SimilarityType
- org.biojava.bio.program.homologene.Taxon