Uses of Interface
org.biojava.utils.stax.StAXContentHandler

Packages that use StAXContentHandler

Package	Description
org.biojava.bio.program.sax.blastxml	Parsers for the XML output from NCBI blast.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.seq.io.filterxml	Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.utils.stax	The Stack API for XML (StAX).

Uses of StAXContentHandler in org.biojava.bio.program.sax.blastxml

Classes in org.biojava.bio.program.sax.blastxml that implement StAXContentHandler

Modifier and Type	Class	Description
class	BlastXMLParser	This class parses NCBI Blast XML output.

Methods in org.biojava.bio.program.sax.blastxml with parameters of type StAXContentHandler

Modifier and Type	Method	Description
void	BlastXMLParser.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)

Uses of StAXContentHandler in org.biojava.bio.program.ssbind

Classes in org.biojava.bio.program.ssbind that implement StAXContentHandler

Modifier and Type	Class	Description
class	AlignmentStAXHandler	AlignmentStAXHandler handles the BlastLikeAlignment element of BioJava BlastLike XML.
class	HeaderStAXHandler	HeaderStAXHandler handles the Header element of BioJava BlastLike XML.
class	HitStAXHandler	AlignmentStAXHandler handles the Hit element of BioJava BlastLike XML.
class	HSPStAXHandler	HSPStAXHandler handles the HSP element of BioJava BlastLike XML.
class	HSPSummaryStAXHandler	HSPSummaryStAXHandler handles the HSPSummary element of BioJava BlastLike XML.
class	SeqSimilarityStAXAdapter	SeqSimilarityStAXAdapter is a handler for XML conforming to the BioJava BlastLike DTD.
class	SeqSimilarityStAXHandler	SeqSimilarityStAXHandler is a base class for creating modular StAX handlers which send callbacks to a SeqSimilarityStAXAdapter.

Methods in org.biojava.bio.program.ssbind that return StAXContentHandler

Modifier and Type	Method	Description
StAXContentHandler	StAXHandlerFactory.getHandler(SeqSimilarityStAXAdapter ssContext)	getHandler returns an appropriate StAXContentHandler implementation containing a reference to a parent context.

Methods in org.biojava.bio.program.ssbind with parameters of type StAXContentHandler

Modifier and Type	Method	Description
void	SeqSimilarityStAXAdapter.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	SeqSimilarityStAXHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)

Uses of StAXContentHandler in org.biojava.bio.program.xff

Classes in org.biojava.bio.program.xff that implement StAXContentHandler

Modifier and Type	Class	Description
class	FeatureHandler	StAX handler for the basic feature type of XFF.
class	LocationHandlerBase	Handler to the XFF location type.
class	PropDetailHandler	StAX handler for xff:prop detail elements.
class	StrandedFeatureHandler	StAX handler for XFF strandedFeature type.
class	XFFFeatureSetHandler	StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events.

Methods in org.biojava.bio.program.xff that return StAXContentHandler

Modifier and Type	Method	Description
protected StAXContentHandler	FeatureHandler.getLocationHandler()
protected StAXContentHandler	FeatureHandler.getOldIDHandler()
StAXContentHandler	XFFPartHandlerFactory.getPartHandler(XFFFeatureSetHandler xffenv)	Return a suitable StAX content handler.
protected StAXContentHandler	FeatureHandler.getSourceHandler()
protected StAXContentHandler	FeatureHandler.getTypeHandler()

Methods in org.biojava.bio.program.xff with parameters of type StAXContentHandler

Modifier and Type	Method	Description
void	FeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)	StAX callback for element ends.
void	LocationHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	XFFFeatureSetHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)

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

Subinterfaces of StAXContentHandler in org.biojava.bio.seq.io.filterxml

Modifier and Type	Interface	Description
static interface	XMLAnnotationTypeHandler.CollectionConstraintHandler	Handler for an individual CollectionConstraint in an AnnotationType.
static interface	XMLAnnotationTypeHandler.PropertyConstraintHandler	Handler for an individual PropertyConstraint in an AnnotationType.
static interface	XMLFilterHandler.FilterHandler	StAXContentHandler for a particular type of FeatureFilter.

Classes in org.biojava.bio.seq.io.filterxml that implement StAXContentHandler

Modifier and Type	Class	Description
class	XMLAnnotationTypeHandler	StAX handler for parsing AnnotationTypes in FilterXML documents.

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

Modifier and Type	Method	Description
void	XMLAnnotationTypeHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)

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

Classes in org.biojava.bio.seq.io.game that implement StAXContentHandler

Modifier and Type	Class	Description
class	GAMEAnnotationHandler	Handles the GAME <annotation> element
class	GAMEAspectPropHandler	Handles the GAME <aspect> element
class	GAMEDbxrefPropHandler	Deals with database crossreferences
class	GAMEDescriptionPropHandler	StAX handler for GAME <description> elements.
class	GAMEFeatureSetHandler	Handles the <feature_set> element
class	GAMEFeatureSetPropHandler	Handles the GAME element
class	GAMEFeatureSpanHandler	Handles the <feature_span> element
class	GAMEGenePropHandler	Handles the GAME <gene> element
class	GAMEHandler	Handles the root GAME element
class	GAMEMapPosPropHandler	Handles the GAME <map_position> element Currently, it just ignores it!
class	GAMENamePropHandler	StAX handler for the GAME <name> element.
class	GAMEResiduesPropHandler	StAX handler for GAME <residues> elements.
class	GAMESeqPropHandler	Handles the GAME <seq> element
class	GAMESeqRelPropHandler	Handles the GAME <aspect> element
class	GAMESpanPropHandler	Handles the GAME <span> element Currently, it just ignores it!
class	GAMETypePropHandler	StAX handler for GAME <type> elements.
class	SequenceContentHandlerBase	StAX handler for elements containing sequence
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.game 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.game with parameters of type StAXContentHandler

Modifier and Type	Method	Description
void	SequenceContentHandlerBase.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	StAXPropertyHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	GAMEAnnotationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	GAMEDbxrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)	when exiting, put the DbXrefElement into the annotation bundle
void	GAMEFeatureSetHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	GAMEFeatureSpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	GAMESpanPropHandler.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

Uses of StAXContentHandler in org.biojava.bio.seq.io.game12

Classes in org.biojava.bio.seq.io.game12 that implement StAXContentHandler

Modifier and Type	Class	Description
class	GAMEAnnotationHandler	Handles the GAME <annotation> element
class	GAMEAspectHandler	Handles the GAME <aspect> element
class	GAMEDbxrefHandler	Handles the GAME <dbxref> element
class	GAMEFeatureSetHandler	Handles the GAME <feature_set> element this element is used to represent transcripts.
class	GAMEFeatureSpanHandler	Handles the GAME <feature_span> element
class	GAMEFeatureSpanHandler.SeqRelHandler
class	GAMEGeneHandler	Handles the GAME <annotation> element
class	GAMEHandler	Handles the root GAME element
class	GAMEPropertyHandler	Handles the GAME <dbxref> element
class	GAMESeqHandler	Handles the GAME <seq> element
class	GAMESeqRelHandler	Handles the GAME <> element
class	GAMESpanHandler	Handles the GAME <> element.
class	StAXFeatureHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.

Methods in org.biojava.bio.seq.io.game12 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.game12 with parameters of type StAXContentHandler

Modifier and Type	Method	Description
void	StAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)	Handles basic exit processing.
void	GAMEAnnotationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEAspectHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEDbxrefHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEFeatureSetHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEFeatureSpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEFeatureSpanHandler.SeqRelHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEGeneHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMEPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMESeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler staxHandler)
void	GAMESeqRelHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	GAMESpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
void	StAXFeatureHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)	Element specific exit handler Subclass to do anything useful.

Uses of StAXContentHandler in org.biojava.utils.stax

Classes in org.biojava.utils.stax that implement StAXContentHandler

Modifier and Type	Class	Description
class	BooleanElementHandlerBase	StAX handler for any element which just contains a string representation of an boolean.
class	ByteElementHandlerBase	StAX handler for any element which just contains a string representation of a byte.
class	CharElementHandlerBase	StAX handler for any element which just contains a string representation of a char.
class	DoubleElementHandlerBase	StAX handler for any element which just contains a string representation of a double.
class	FloatElementHandlerBase	StAX handler for any element which just contains a string representation of a float.
class	IntElementHandlerBase	StAX handler for any element which just contains a string representation of an integer.
class	LongElementHandlerBase	StAX handler for any element which just contains a string representation of a long.
class	StAXContentHandlerBase	Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
class	StringElementHandlerBase	StAX handler for any element which just contains a string.

Methods in org.biojava.utils.stax with parameters of type StAXContentHandler

Modifier and Type	Method	Description
void	DelegationManager.delegate(StAXContentHandler handler)
void	BooleanElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	ByteElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	CharElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	DoubleElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	FloatElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	IntElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
void	LongElementHandlerBase.endElement(String nsURI, String localName, String qName, 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	StringElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)

Constructors in org.biojava.utils.stax with parameters of type StAXContentHandler

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