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

Packages that use StAXContentHandler

Package	Description
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

Modifier and Type	Class	Description
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

Modifier and Type	Method	Description
StAXContentHandler	StAXHandlerFactory.getHandler(StAXFeatureHandler staxenv)	Return a suitable StAX content handler.

Methods in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler

Modifier and Type	Method	Description
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	AGAVEBioSeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEChromosomeHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEClassificationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEContigHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEDbIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEElementIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEEvidenceHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEIdAliasPropHandler.endElementHandler(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	AGAVEMatchRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEQualifierPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEQueryRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVERelatedAnnotPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEResultPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVESciPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVESeqLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVESeqPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEXrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEXrefPropPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	AGAVEXrefsPropHandler.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	StAXPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)	Element specific exit handler Subclass to do anything useful.
protected void	StAXFeatureHandler.push(StAXContentHandler handler)	Push StAXContentHandler object onto stack

Constructors in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler

Constructor	Description
SAX2StAXAdaptor(StAXContentHandler rootHandler)	Construct a new SAX Content handler which wraps a StAX handler.