Uses of Class
org.biojava.utils.stax.StAXContentHandlerBase

Packages that use StAXContentHandlerBase

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 StAXContentHandlerBase in org.biojava.bio.program.sax.blastxml

Subclasses of StAXContentHandlerBase in org.biojava.bio.program.sax.blastxml

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

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

Subclasses of StAXContentHandlerBase in org.biojava.bio.program.ssbind

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.

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

Subclasses of StAXContentHandlerBase in org.biojava.bio.program.xff

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 StAXContentHandlerBase

Modifier and Type	Method	Description
StAXContentHandlerBase	XFFFeatureSetHandler.getDetailsHandler()	Return a handler for the XFF details element.

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

Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.io.filterxml

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

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

Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.io.game

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.

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

Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.io.game12

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.

Uses of StAXContentHandlerBase in org.biojava.utils.stax

Subclasses of StAXContentHandlerBase in org.biojava.utils.stax

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	StringElementHandlerBase	StAX handler for any element which just contains a string.