## Hierarchy For Package org.biojava.bio.seq.io.agave

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.bio.seq.io.agave.AGAVEDbId
  - org.biojava.bio.seq.io.agave.AGAVEIdAlias
  - org.biojava.bio.seq.io.agave.AGAVEMapLocation
  - org.biojava.bio.seq.io.agave.AGAVEMapPosition
  - org.biojava.bio.seq.io.agave.AGAVEMatchRegion
  - org.biojava.bio.seq.io.agave.AGAVEProperty
  - org.biojava.bio.seq.io.agave.AGAVEQueryRegion
  - org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
  - org.biojava.bio.seq.io.agave.AgaveWriter
  - org.biojava.bio.seq.io.agave.AgaveWriter.Indent
  - org.biojava.bio.seq.io.agave.AGAVEXref
  - org.biojava.bio.seq.io.agave.AGAVEXrefs
  - org.biojava.bio.seq.io.agave.ElementRecognizer.AllElementRecognizer (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.ByLocalName (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.ByNSName (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.ElementRecognizer.HasAttribute (implements org.biojava.bio.seq.io.agave.ElementRecognizer)
  - org.biojava.bio.seq.io.agave.SAX2StAXAdaptor (implements org.xml.sax.ContentHandler)
  - org.biojava.bio.seq.io.agave.SimpleAnnotFilter (implements org.biojava.bio.seq.io.agave.AGAVEAnnotFilter)
    - org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
    - org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
  - org.biojava.bio.seq.io.agave.StAXContentHandlerBase (implements org.biojava.bio.seq.io.agave.StAXContentHandler)
    - org.biojava.bio.seq.io.agave.StAXFeatureHandler
      - org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler (implements org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler (implements org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
      - org.biojava.bio.seq.io.agave.AGAVECdsHandler
      - org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler (implements org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEClassificationHandler (implements org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVECompResultHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEComputationHandler
      - org.biojava.bio.seq.io.agave.AGAVEContigHandler (implements org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf, org.biojava.bio.seq.io.agave.SequenceHandler)
      - org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
      - org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEGeneHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEHandler (implements org.biojava.bio.seq.io.agave.AGAVECallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
      - org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
      - org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
      - org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler (implements org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
      - org.biojava.bio.seq.io.agave.AGAVETranscriptHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
    - org.biojava.bio.seq.io.agave.StAXPropertyHandler
      - org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
      - org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVENotePropHandler
      - org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
      - org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
      - org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
      - org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
      - org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf)
      - org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
      - org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler (implements org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf, org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf)
  - org.biojava.bio.seq.io.agave.UtilHelper

## Interface Hierarchy

- org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
- org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
- org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
- org.biojava.bio.seq.io.agave.AGAVECallbackItf
- org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
- org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
- org.biojava.bio.seq.io.agave.DelegationManager
- org.biojava.bio.seq.io.agave.ElementRecognizer
- org.biojava.bio.seq.io.agave.SequenceHandler
- org.biojava.bio.seq.io.agave.StAXContentHandler
- org.biojava.bio.seq.io.agave.StAXHandlerFactory