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

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

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

Modifier and Type	Interface and 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 and 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 and 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 and 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 and 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 and Description
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	SequenceContentHandlerBase.endElement(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	StAXFeatureHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.
void	GAMESpanPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	GAMEFeatureSpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
void	GAMEFeatureSetHandler.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	GAMEAnnotationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler)
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 and Description
class	GAMEAspectHandler Handles the GAME <aspect> element
class	GAMEDbxrefHandler Handles the GAME <dbxref> element
class	GAMEFeatureSpanHandler.SeqRelHandler
class	GAMEGeneHandler Handles the GAME <annotation> 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.

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

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

Uses of StAXContentHandler in org.biojava.utils.stax

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

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

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

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