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 and 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 and 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 and Description
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

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