Uses of Class
org.biojava.utils.stax.StAXContentHandlerBase

Packages that use StAXContentHandlerBase
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.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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
 class BlastXMLParser
          This class parses NCBI Blast XML output.
(package private)  class org.biojava.bio.program.sax.blastxml.StAXFeatureHandler
          StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
 

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

Subclasses of StAXContentHandlerBase in org.biojava.bio.program.ssbind
 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
 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
 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
 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
 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 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
 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.bio.seq.ragbag
 

Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.ragbag
 class RagbagMap
          This class is an object that encapsulates all information present in a Map file in a Ragbag directory.
 

Uses of StAXContentHandlerBase in org.biojava.utils.stax
 

Subclasses of StAXContentHandlerBase in org.biojava.utils.stax
 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.