Uses of Interface
org.biojava.utils.stax.StAXContentHandler

Packages that use StAXContentHandler
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 StAXContentHandler in org.biojava.bio.program.sax.blastxml
 

Classes in org.biojava.bio.program.sax.blastxml that implement StAXContentHandler
 class BlastXMLParser
          This class parses NCBI Blast XML output.
 

Methods in org.biojava.bio.program.sax.blastxml with parameters of type StAXContentHandler
 void 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 StAXContentHandler
 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.
 

Methods in org.biojava.bio.program.ssbind that return StAXContentHandler
 StAXContentHandler StAXHandlerFactory.getHandler(SeqSimilarityStAXAdapter ssContext)
          getHandler returns an appropriate StAXContentHandler implementation containing a reference to a parent context.
 

Methods in org.biojava.bio.program.ssbind with parameters of type StAXContentHandler
 void SeqSimilarityStAXHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void SeqSimilarityStAXAdapter.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 StAXContentHandler
 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 StAXContentHandler
protected  StAXContentHandler FeatureHandler.getLocationHandler()
           
protected  StAXContentHandler FeatureHandler.getOldIDHandler()
           
 StAXContentHandler 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 StAXContentHandler
 void FeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
          StAX callback for element ends.
 void XFFFeatureSetHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void LocationHandlerBase.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.filterxml
static interface XMLAnnotationTypeHandler.CollectionConstraintHandler
          Handler for an individual CollectionConstraint in an AnnotationType.
static interface XMLAnnotationTypeHandler.PropertyConstraintHandler
          Handler for an individual PropertyConstraint in an AnnotationType.
static interface XMLFilterHandler.FilterHandler
          StAXContentHandler for a particular type of FeatureFilter.
 

Classes in org.biojava.bio.seq.io.filterxml that implement StAXContentHandler
 class XMLAnnotationTypeHandler
          StAX handler for parsing AnnotationTypes in FilterXML documents.
 

Methods in org.biojava.bio.seq.io.filterxml with parameters of type StAXContentHandler
 void 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 StAXContentHandler
 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.
 

Methods in org.biojava.bio.seq.io.game that return StAXContentHandler
 StAXContentHandler StAXHandlerFactory.getHandler(StAXFeatureHandler staxenv)
          Return a suitable StAX content handler.
 

Methods in org.biojava.bio.seq.io.game with parameters of type StAXContentHandler
 void StAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
          Handles basic exit processing.
 void SequenceContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void StAXPropertyHandler.endElement(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.
 void 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 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 bundle
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 StAXContentHandler
 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.
 

Methods in org.biojava.bio.seq.io.game12 that return StAXContentHandler
 StAXContentHandler StAXHandlerFactory.getHandler(StAXFeatureHandler staxenv)
          Return a suitable StAX content handler.
 

Methods in org.biojava.bio.seq.io.game12 with parameters of type StAXContentHandler
 void StAXFeatureHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
          Handles basic exit processing.
 void GAMESeqRelHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
           
 void GAMEAspectHandler.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 GAMEDbxrefHandler.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.
 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 GAMESeqHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler staxHandler)
           
 void GAMESpanHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
           
 void GAMEAnnotationHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
           
 void GAMEPropertyHandler.endElementHandler(String nsURI, String localName, String qName, StAXContentHandler contentHandler)
           
 

Uses of StAXContentHandler in org.biojava.utils.stax
 

Classes in org.biojava.utils.stax that implement StAXContentHandler
 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 StAXContentHandlerBase
          Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
 class StringElementHandlerBase
          StAX handler for any element which just contains a string.
 

Methods in org.biojava.utils.stax with parameters of type StAXContentHandler
 void DelegationManager.delegate(StAXContentHandler handler)
           
 void StAXContentHandler.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)
           
 void IntElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void StAXContentHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler delegate)
           
 void StringElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void LongElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 void BooleanElementHandlerBase.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 ByteElementHandlerBase.endElement(String nsURI, String localName, String qName, StAXContentHandler handler)
           
 

Constructors in org.biojava.utils.stax with parameters of type StAXContentHandler
SAX2StAXAdaptor(StAXContentHandler rootHandler)
          Construct a new SAX Content handler which wraps a StAX handler.