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 and 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 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.

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

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

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 StAXContentHandlerBase

Modifier and Type	Method and 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 and 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 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.

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

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

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.

Uses of StAXContentHandlerBase in org.biojava.utils.stax

Subclasses of StAXContentHandlerBase in org.biojava.utils.stax

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