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

Classes for converting between AGAVE XML and BioJava objects.

See:
Description

Interface Summary
AGAVEAnnotFilter: This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory
AGAVEBioSeqCallbackItf: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECallbackItf: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeCallbackItf: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigCallbackItf: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEDbIdCallbackItf: this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf
AGAVEEvidenceCallbackItf
AGAVEFeatureCallbackItf: An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEIdAliasCallbackItf
AGAVEXrefCallbackItf
DelegationManager: Interface which exposes delegation services offered by a StAX event source.
ElementRecognizer: This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
SequenceHandler: mark interface
StAXContentHandler: Interface for StAX content handlers.
StAXHandlerFactory: Factory for StAX content handlers.

Class Summary
Agave2AgaveAnnotFilter: Dumping the data from biojava with source of agave into agave format
AGAVEAltIdsPropHandler: Deals with alternate sequence IDs
AGAVEAnnotationsHandler
AGAVEAssemblyHandler
AGAVEBioSeqHandler: Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler: Handles the AGAVE <bio_sequence> element
AGAVECdsHandler: Handles the AGAVE <cds> element
AGAVEChromosomeHandler: Handles the AGAVE <chromosome> element
AGAVEClassificationHandler
AGAVECompResultHandler
AGAVEComputationHandler
AGAVEContigHandler: Handles the AGAVE <contig> element
AGAVEDbId
AGAVEDbIdPropHandler: Deals with database crossreferences
AGAVEDescPropHandler: Deals with database crossreferences
AGAVEElementIdPropHandler
AGAVEEvidenceHandler
AGAVEExonsPropHandler
AGAVEFragmentOrderHandler
AGAVEFragmentOrientationHandler
AGAVEGeneHandler
AGAVEHandler: Handles the root AGAVE element modified for agave format
AGAVEIdAlias
AGAVEIdAliasPropHandler
AGAVEKeywordPropHandler: Deals with AGAVE keywords
AGAVEMapLocation
AGAVEMapLocationPropHandler
AGAVEMapPosition
AGAVEMapPositionPropHandler
AGAVEMatchAlignPropHandler: Deals with match_align
AGAVEMatchDescPropHandler: Deals with match_desc
AGAVEMatchRegion: match_region
AGAVEMatchRegionPropHandler: Deals with match_region
AGAVEMrnaHandler: Handles the AGAVE <mrna> element
AGAVENotePropHandler: Deals with note
AGAVEPredictedProteinHandler: Handles the AGAVE <predicted_protein> element
AGAVEProperty
AGAVEQualifierPropHandler
AGAVEQueryRegion
AGAVEQueryRegionPropHandler
AGAVERelatedAnnot
AGAVERelatedAnnotPropHandler
AGAVEResultGroupHandler
AGAVEResultPropertyPropHandler
AGAVESciPropertyPropHandler: sci_property
AGAVESeqFeatureHandler: seq_feature
AGAVESeqLocationPropHandler: seq_location
AGAVESeqMapHandler: sequence_map
AGAVESeqPropHandler: Deals with sequence code
AGAVETranscriptHandler: transcript
AGAVEUnorderedFragmentsHandler: unordered_fragments
AGAVEViewPropHandler: Moves view attributes into annotation properties.
AgaveWriter: Writes Sequence into AGAVE XML document.
AGAVEXref: xref
AGAVEXrefPropHandler: handle AGAVE xref
AGAVEXrefPropPropHandler: xref_property
AGAVEXrefs: xrefs
AGAVEXrefsPropHandler: Deals with database crossreferences (xrefs)
ElementRecognizer.AllElementRecognizer
ElementRecognizer.ByLocalName: Filter elements by local name (not recommended).
ElementRecognizer.ByNSName: Filter elements by name and namespace.
ElementRecognizer.HasAttribute: Filter elements on the existence of a specified attribute.
Embl2AgaveAnnotFilter: Map EMBL data into AGAVE format
SAX2StAXAdaptor: Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SimpleAnnotFilter: Basic implementation of AGAVEAnnotFilter
StAXContentHandlerBase: Simple implementation of the `StAXContentHandler` interface, with empty implementations for all the methods.
StAXFeatureHandler: StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXPropertyHandler: StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
UtilHelper: Just make the property follow the common case

## Package org.biojava.bio.seq.io.agave Description

Classes for converting between AGAVE XML and BioJava objects. Use AGAVEHandler with a SAX parser to parse AGAVE XML into BioJava Sequences, and use AgaveWriter to write BioJava Sequences into AGAVE format. When writing BioJava to AGAVE we need to specify how the data in BioJava stored. Two conversion filters are implemented. The Agave2AgaveAnnotFilter helps write data that was parsed from AGAVE, and Embl2AgaveAnnotFilter helps write data that was parsed from EMBL. This package uses a modified version of the BioJava StAX parser architecture that supports nested features.