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

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

See: Description

Interface Summary

Interface	Description
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

Class	Description
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.