## Uses of Interface
org.biojava.bio.seq.io.agave.StAXContentHandler

Packages that use StAXContentHandler
org.biojava.bio.seq.io.agave: Classes for converting between AGAVE XML and BioJava objects.

Uses of StAXContentHandler in org.biojava.bio.seq.io.agave

Classes in org.biojava.bio.seq.io.agave that implement StAXContentHandler
`class` `AGAVEAltIdsPropHandler` Deals with alternate sequence IDs
`class` `AGAVEAnnotationsHandler`
`class` `AGAVEAssemblyHandler`
`class` `AGAVEBioSeqHandler` Handles the AGAVE <bio_sequence> element
`class` `AGAVEBioSequenceHandler` Handles the AGAVE <bio_sequence> element
`class` `AGAVECdsHandler` Handles the AGAVE <cds> element
`class` `AGAVEChromosomeHandler` Handles the AGAVE <chromosome> element
`class` `AGAVEClassificationHandler`
`class` `AGAVECompResultHandler`
`class` `AGAVEComputationHandler`
`class` `AGAVEContigHandler` Handles the AGAVE <contig> element
`class` `AGAVEDbIdPropHandler` Deals with database crossreferences
`class` `AGAVEDescPropHandler` Deals with database crossreferences
`class` `AGAVEElementIdPropHandler`
`class` `AGAVEEvidenceHandler`
`class` `AGAVEExonsPropHandler`
`class` `AGAVEFragmentOrderHandler`
`class` `AGAVEFragmentOrientationHandler`
`class` `AGAVEGeneHandler`
`class` `AGAVEHandler` Handles the root AGAVE element modified for agave format
`class` `AGAVEIdAliasPropHandler`
`class` `AGAVEKeywordPropHandler` Deals with AGAVE keywords
`class` `AGAVEMapLocationPropHandler`
`class` `AGAVEMapPositionPropHandler`
`class` `AGAVEMatchAlignPropHandler` Deals with match_align
`class` `AGAVEMatchDescPropHandler` Deals with match_desc
`class` `AGAVEMatchRegionPropHandler` Deals with match_region
`class` `AGAVEMrnaHandler` Handles the AGAVE <mrna> element
`class` `AGAVENotePropHandler` Deals with note
`class` `AGAVEPredictedProteinHandler` Handles the AGAVE <predicted_protein> element
`class` `AGAVEQualifierPropHandler`
`class` `AGAVEQueryRegionPropHandler`
`class` `AGAVERelatedAnnotPropHandler`
`class` `AGAVEResultGroupHandler`
`class` `AGAVEResultPropertyPropHandler`
`class` `AGAVESciPropertyPropHandler` sci_property
`class` `AGAVESeqFeatureHandler` seq_feature
`class` `AGAVESeqLocationPropHandler` seq_location
`class` `AGAVESeqMapHandler` sequence_map
`class` `AGAVESeqPropHandler` Deals with sequence code
`class` `AGAVETranscriptHandler` transcript
`class` `AGAVEUnorderedFragmentsHandler` unordered_fragments
`class` `AGAVEViewPropHandler` Moves view attributes into annotation properties.
`class` `AGAVEXrefPropHandler` handle AGAVE xref
`class` `AGAVEXrefPropPropHandler` xref_property
`class` `AGAVEXrefsPropHandler` Deals with database crossreferences (xrefs)
`class` `StAXContentHandlerBase` Simple implementation of the `StAXContentHandler` interface, with empty implementations for all the methods.
`class` `StAXFeatureHandler` StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
`class` `StAXPropertyHandler` StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.

Methods in org.biojava.bio.seq.io.agave that return StAXContentHandler
`StAXContentHandler` `StAXHandlerFactory.getHandler(StAXFeatureHandler staxenv)` Return a suitable StAX content handler.

Methods in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler
`void` `DelegationManager.delegate(StAXContentHandler handler)`
`void` `StAXPropertyHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `StAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)` Handles basic exit processing.
`void` `StAXContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)`
`void` `StAXContentHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)`
`void` `StAXPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)` Element specific exit handler Subclass to do anything useful.
`void` `StAXFeatureHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)` Element specific exit handler Subclass to do anything useful.
`void` `AGAVEXrefsPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEXrefPropPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEXrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVESeqPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVESeqLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVESciPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEResultPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVERelatedAnnotPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEQueryRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEQualifierPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEMatchRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEMapPositionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEMapLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEIdAliasPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEEvidenceHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEElementIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEDbIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEContigHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEClassificationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEChromosomeHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` `AGAVEBioSeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`protected void` `StAXFeatureHandler.push(StAXContentHandler handler)` Push StAXContentHandler object onto stack

Constructors in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler
`SAX2StAXAdaptor(StAXContentHandler rootHandler)` Construct a new SAX Content handler which wraps a StAX handler.