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 TypeMethodDescriptionvoidBlastXMLParser.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 TypeClassDescriptionclassAlignmentStAXHandlerhandles the BlastLikeAlignment element of BioJava BlastLike XML.classHeaderStAXHandlerhandles the Header element of BioJava BlastLike XML.classAlignmentStAXHandlerhandles the Hit element of BioJava BlastLike XML.classHSPStAXHandlerhandles the HSP element of BioJava BlastLike XML.classHSPSummaryStAXHandlerhandles the HSPSummary element of BioJava BlastLike XML.classSeqSimilarityStAXAdapteris a handler for XML conforming to the BioJava BlastLike DTD.classSeqSimilarityStAXHandleris 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) getHandlerreturns an appropriateStAXContentHandlerimplementation containing a reference to a parent context.Methods in org.biojava.bio.program.ssbind with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoidSeqSimilarityStAXAdapter.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidSeqSimilarityStAXHandler.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 TypeClassDescriptionclassStAX handler for the basicfeaturetype of XFF.classHandler to the XFF location type.classStAX handler for xff:prop detail elements.classStAX handler for XFF strandedFeature type.classStAX 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 StAXContentHandlerFeatureHandler.getLocationHandler()protected StAXContentHandlerFeatureHandler.getOldIDHandler()XFFPartHandlerFactory.getPartHandler(XFFFeatureSetHandler xffenv) Return a suitable StAX content handler.protected StAXContentHandlerFeatureHandler.getSourceHandler()protected StAXContentHandlerFeatureHandler.getTypeHandler()Methods in org.biojava.bio.program.xff with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoidFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) StAX callback for element ends.voidLocationHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidXFFFeatureSetHandler.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 interfaceHandler for an individualCollectionConstraintin an AnnotationType.static interfaceHandler for an individualPropertyConstraintin an AnnotationType.static interfaceStAXContentHandler for a particular type of FeatureFilter.Classes in org.biojava.bio.seq.io.filterxml that implement StAXContentHandlerModifier and TypeClassDescriptionclassStAX handler for parsing AnnotationTypes in FilterXML documents.Methods in org.biojava.bio.seq.io.filterxml with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoidXMLAnnotationTypeHandler.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 TypeClassDescriptionclassHandles the GAME <annotation> elementclassHandles the GAME <aspect> elementclassDeals with database crossreferencesclassStAX handler for GAME <description> elements.classHandles the <feature_set> elementclassHandles the GAMEelement classHandles the <feature_span> elementclassHandles the GAME <gene> elementclassHandles the root GAME elementclassHandles the GAME <map_position> element Currently, it just ignores it!classStAX handler for the GAME <name> element.classStAX handler for GAME <residues> elements.classHandles the GAME <seq> elementclassHandles the GAME <aspect> elementclassHandles the GAME <span> element Currently, it just ignores it!classStAX handler for GAME <type> elements.classStAX handler for elements containing sequenceclassStAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.classStAX 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 TypeMethodDescriptionvoidSequenceContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidStAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) Handles basic exit processing.voidStAXPropertyHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidGAMEAnnotationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidGAMEDbxrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) when exiting, put the DbXrefElement into the annotation bundlevoidGAMEFeatureSetHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidGAMEFeatureSpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidGAMESpanPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidStAXFeatureHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.voidStAXPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.protected voidStAXFeatureHandler.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 TypeClassDescriptionclassHandles the GAME <annotation> elementclassHandles the GAME <aspect> elementclassHandles the GAME <dbxref> elementclassHandles the GAME <feature_set> element this element is used to represent transcripts.classHandles the GAME <feature_span> elementclassclassHandles the GAME <annotation> elementclassHandles the root GAME elementclassHandles the GAME <dbxref> elementclassHandles the GAME <seq> elementclassHandles the GAME <> element classHandles the GAME <> element.classStAX 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 TypeMethodDescriptionvoidStAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) Handles basic exit processing.voidGAMEAnnotationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEAspectHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEDbxrefHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEFeatureSetHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEFeatureSpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEFeatureSpanHandler.SeqRelHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEGeneHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMEPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMESeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler staxHandler) voidGAMESeqRelHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidGAMESpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler) voidStAXFeatureHandler.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 TypeClassDescriptionclassStAX handler for any element which just contains a string representation of an boolean.classStAX handler for any element which just contains a string representation of a byte.classStAX handler for any element which just contains a string representation of a char.classStAX handler for any element which just contains a string representation of a double.classStAX handler for any element which just contains a string representation of a float.classStAX handler for any element which just contains a string representation of an integer.classStAX handler for any element which just contains a string representation of a long.classSimple implementation of theStAXContentHandlerinterface, with empty implementations for all the methods.classStAX handler for any element which just contains a string.Methods in org.biojava.utils.stax with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoidDelegationManager.delegate(StAXContentHandler handler) voidBooleanElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidByteElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidCharElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidDoubleElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidFloatElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidIntElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidLongElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidStAXContentHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate) voidStAXContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate) voidStringElementHandlerBase.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.