org.biojava.bio.seq.io.game (BioJava-1.5-beta API)
Keywords: org.biojava.bio.seq.io.game package

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## Package org.biojava.bio.seq.io.game

Event-driven parsing system for the Gene Annotation Markup Elements (GAME).

See:
Description

Interface Summary
ElementRecognizer | Simple interface for filtering SAX/StAX startElement events
GAMEFeatureCallbackItf | An interface that can be tested for by nested handlers when trying to do a callback.
GAMENameCallbackItf | An interface that can be tested for by nested handlers when trying to do a callback.
GAMETranscriptCallbackItf | An interface that can be tested for by nested handlers when trying to do a callback.
StAXHandlerFactory | Factory for StAX content handlers.

Class Summary
ElementRecognizer.AllElementRecognizer |
ElementRecognizer.ByLocalName | Filter elements by local name (not recommended).
ElementRecognizer.ByNSName | Filter elements by name and namespace.
ElementRecognizer.HasAttribute | Filter elements on the existence of a specified attribute.
GAMEAnnotationHandler | Handles the GAME <annotation> element
GAMEAspectPropHandler | Handles the GAME <aspect> element
GAMEDbxrefPropHandler | Deals with database crossreferences
GAMEDescriptionPropHandler | StAX handler for GAME <description> elements.
GAMEFeatureSetHandler | Handles the <feature_set> element
GAMEFeatureSetPropHandler | Handles the GAME element
GAMEFeatureSpanHandler | Handles the <feature_span> element
GAMEGenePropHandler | Handles the GAME <gene> element
GAMEHandler | Handles the root GAME element
GAMEMapPosPropHandler | Handles the GAME <map_position> element Currently, it just ignores it!
GAMENamePropHandler | StAX handler for the GAME <name> element.
GAMEResiduesPropHandler | StAX handler for GAME <residues> elements.
GAMESeqPropHandler | Handles the GAME <seq> element
GAMESeqRelPropHandler | Handles the GAME <aspect> element
GAMESpanPropHandler | Handles the GAME <span> element Currently, it just ignores it!
GAMETypePropHandler | StAX handler for GAME <type> elements.
SequenceContentHandlerBase | StAX handler for elements containing sequence
StAXFeatureHandler | StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXPropertyHandler | StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.

## Package org.biojava.bio.seq.io.game Description

Event-driven parsing system for the Gene Annotation Markup Elements (GAME). It uses the StAX API developed by Thomase Down and is extensively derived from code he and others wrote for the XFF parser. This is currently targetted at the GAME 1.001 proposal. For more information, see The GAME specification page.

Be aware that a newer GAME proposal has since been released. This release is targetted at the Gadfly Drosophila annotations which are GAME 1.001 documents. I make no claims that they will work for other input files although they can be readily extended to cover other GAME structures.

There are two base classes in this release. The first is the StAXFeatureHandler which is the base class for elements that intend to create new Feature objects. Then there is the StAXPropertyHandler class that is base class for element handlers that only extend properties of the existing feature. All classes should be subclassed from one of these.

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