Uses of Interface org.biojava.bio.seq.io.agave.StAXContentHandler (BioJava-1.5-beta API)

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## 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` | `StAXContentHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)`
`void` | `StAXContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)`
`void` | `StAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)` Handles basic exit processing.
`void` | `StAXPropertyHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEMapLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEMapPositionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEElementIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVERelatedAnnotPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `StAXFeatureHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)` Element specific exit handler Subclass to do anything useful.
`void` | `AGAVEDbIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVESeqLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `StAXPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)` Element specific exit handler Subclass to do anything useful.
`void` | `AGAVEXrefPropPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEXrefsPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVESeqPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEEvidenceHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVESciPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEClassificationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEQueryRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEXrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEChromosomeHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEResultPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEBioSeqHandler.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` | `AGAVEContigHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)`
`void` | `AGAVEIdAliasPropHandler.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.

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