Uses of Interface org.biojava.utils.stax.StAXContentHandler (BioJava-1.5-beta API)

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## 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.

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