Uses of Interface
org.biojava.utils.stax.StAXContentHandler
Packages that use StAXContentHandler
Package
Description
Parsers for the XML output from NCBI blast.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Event-driven parsing system for the Extensible Feature Format (XFF).
Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
The Stack API for XML (StAX).
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Uses of StAXContentHandler in org.biojava.bio.program.sax.blastxml
Classes in org.biojava.bio.program.sax.blastxml that implement StAXContentHandlerMethods in org.biojava.bio.program.sax.blastxml with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
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 StAXContentHandlerModifier and TypeClassDescriptionclass
AlignmentStAXHandler
handles the BlastLikeAlignment element of BioJava BlastLike XML.class
HeaderStAXHandler
handles the Header element of BioJava BlastLike XML.class
AlignmentStAXHandler
handles the Hit element of BioJava BlastLike XML.class
HSPStAXHandler
handles the HSP element of BioJava BlastLike XML.class
HSPSummaryStAXHandler
handles the HSPSummary element of BioJava BlastLike XML.class
SeqSimilarityStAXAdapter
is a handler for XML conforming to the BioJava BlastLike DTD.class
SeqSimilarityStAXHandler
is a base class for creating modular StAX handlers which send callbacks to aSeqSimilarityStAXAdapter
.Methods in org.biojava.bio.program.ssbind that return StAXContentHandlerModifier and TypeMethodDescriptionStAXHandlerFactory.getHandler
(SeqSimilarityStAXAdapter ssContext) getHandler
returns an appropriateStAXContentHandler
implementation containing a reference to a parent context.Methods in org.biojava.bio.program.ssbind with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
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 StAXContentHandlerModifier and TypeClassDescriptionclass
StAX handler for the basicfeature
type of XFF.class
Handler to the XFF location type.class
StAX handler for xff:prop detail elements.class
StAX handler for XFF strandedFeature type.class
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 StAXContentHandlerModifier and TypeMethodDescriptionprotected StAXContentHandler
FeatureHandler.getLocationHandler()
protected StAXContentHandler
FeatureHandler.getOldIDHandler()
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 StAXContentHandlerModifier and TypeMethodDescriptionvoid
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.filterxmlModifier and TypeInterfaceDescriptionstatic interface
Handler for an individualCollectionConstraint
in an AnnotationType.static interface
Handler for an individualPropertyConstraint
in an AnnotationType.static interface
StAXContentHandler for a particular type of FeatureFilter.Classes in org.biojava.bio.seq.io.filterxml that implement StAXContentHandlerModifier and TypeClassDescriptionclass
StAX handler for parsing AnnotationTypes in FilterXML documents.Methods in org.biojava.bio.seq.io.filterxml with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
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 StAXContentHandlerModifier and TypeClassDescriptionclass
Handles the GAME <annotation> elementclass
Handles the GAME <aspect> elementclass
Deals with database crossreferencesclass
StAX handler for GAME <description> elements.class
Handles the <feature_set> elementclass
Handles the GAMEelement class
Handles the <feature_span> elementclass
Handles the GAME <gene> elementclass
Handles the root GAME elementclass
Handles the GAME <map_position> element Currently, it just ignores it!class
StAX handler for the GAME <name> element.class
StAX handler for GAME <residues> elements.class
Handles the GAME <seq> elementclass
Handles the GAME <aspect> elementclass
Handles the GAME <span> element Currently, it just ignores it!class
StAX handler for GAME <type> elements.class
StAX handler for elements containing sequenceclass
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.class
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.Methods in org.biojava.bio.seq.io.game that return StAXContentHandlerModifier and TypeMethodDescriptionStAXHandlerFactory.getHandler
(StAXFeatureHandler staxenv) Return a suitable StAX content handler.Methods in org.biojava.bio.seq.io.game with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
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 bundlevoid
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 StAXContentHandlerModifier and TypeClassDescriptionclass
Handles the GAME <annotation> elementclass
Handles the GAME <aspect> elementclass
Handles the GAME <dbxref> elementclass
Handles the GAME <feature_set> element this element is used to represent transcripts.class
Handles the GAME <feature_span> elementclass
class
Handles the GAME <annotation> elementclass
Handles the root GAME elementclass
Handles the GAME <dbxref> elementclass
Handles the GAME <seq> elementclass
Handles the GAME <> element class
Handles the GAME <> element.class
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.Methods in org.biojava.bio.seq.io.game12 that return StAXContentHandlerModifier and TypeMethodDescriptionStAXHandlerFactory.getHandler
(StAXFeatureHandler staxenv) Return a suitable StAX content handler.Methods in org.biojava.bio.seq.io.game12 with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
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 StAXContentHandlerModifier and TypeClassDescriptionclass
StAX handler for any element which just contains a string representation of an boolean.class
StAX handler for any element which just contains a string representation of a byte.class
StAX handler for any element which just contains a string representation of a char.class
StAX handler for any element which just contains a string representation of a double.class
StAX handler for any element which just contains a string representation of a float.class
StAX handler for any element which just contains a string representation of an integer.class
StAX handler for any element which just contains a string representation of a long.class
Simple implementation of theStAXContentHandler
interface, with empty implementations for all the methods.class
StAX handler for any element which just contains a string.Methods in org.biojava.utils.stax with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
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 StAXContentHandlerModifierConstructorDescriptionSAX2StAXAdaptor
(StAXContentHandler rootHandler) Construct a new SAX Content handler which wraps a StAX handler.