Uses of Interface
org.biojava.bio.seq.io.agave.StAXContentHandler
Packages that use StAXContentHandler
Package
Description
Classes for converting between AGAVE XML and BioJava objects.
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Uses of StAXContentHandler in org.biojava.bio.seq.io.agave
Classes in org.biojava.bio.seq.io.agave that implement StAXContentHandlerModifier and TypeClassDescriptionclassDeals with alternate sequence IDsclassclassclassHandles the AGAVE <bio_sequence> elementclassHandles the AGAVE <bio_sequence> elementclassHandles the AGAVE <cds> elementclassHandles the AGAVE <chromosome> elementclassclassclassclassHandles the AGAVE <contig> elementclassDeals with database crossreferencesclassDeals with database crossreferencesclassclassclassclassclassclassclassHandles the root AGAVE element modified for agave formatclassclassDeals with AGAVE keywordsclassclassclassDeals with match_alignclassDeals with match_descclassDeals with match_regionclassHandles the AGAVE <mrna> elementclassDeals with noteclassHandles the AGAVE <predicted_protein> elementclassclassclassclassclassclasssci_propertyclassseq_featureclassseq_locationclasssequence_mapclassDeals with sequence codeclasstranscriptclassunordered_fragmentsclassMoves view attributes into annotation properties.classhandle AGAVE xrefclassxref_propertyclassDeals with database crossreferences (xrefs)classSimple implementation of theStAXContentHandlerinterface, with empty implementations for all the methods.classStAX 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.agave that return StAXContentHandlerModifier and TypeMethodDescriptionStAXHandlerFactory.getHandler(StAXFeatureHandler staxenv) Return a suitable StAX content handler.Methods in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoidDelegationManager.delegate(StAXContentHandler handler) voidStAXContentHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate) voidStAXContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate) voidStAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) Handles basic exit processing.voidStAXPropertyHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEBioSeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEChromosomeHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEClassificationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEContigHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEDbIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEElementIdPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEEvidenceHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEIdAliasPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEMapLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEMapPositionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEMatchRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEQualifierPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEQueryRegionPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVERelatedAnnotPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEResultPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVESciPropertyPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVESeqLocationPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVESeqPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEXrefPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEXrefPropPropHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler handler) voidAGAVEXrefsPropHandler.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 stackConstructors in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandlerModifierConstructorDescriptionSAX2StAXAdaptor(StAXContentHandler rootHandler) Construct a new SAX Content handler which wraps a StAX handler.