Package org.biojava.bio.seq.io.game12

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

See: Description

Interface Summary

Interface	Description
StAXHandlerFactory	Factory for StAX content handlers.

Class Summary

Class	Description
GAMEAnnotationHandler	Handles the GAME <annotation> element
GAMEAspectHandler	Handles the GAME <aspect> element
GAMEDbxrefHandler	Handles the GAME <dbxref> element
GAMEFeatureSetHandler	Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSpanHandler	Handles the GAME <feature_span> element
GAMEGeneHandler	Handles the GAME <annotation> element
GAMEHandler	Handles the root GAME element
GAMEPropertyHandler	Handles the GAME <dbxref> element
GAMESeqHandler	Handles the GAME <seq> element
GAMESeqRelHandler	Handles the GAME <> element
GAMESpanHandler	Handles the GAME <> element.
StAXFeatureHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.

Package org.biojava.bio.seq.io.game12 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 an update that is targetted at the GAME 1.2 proposal. It was written specifically to parse annotation files from the Gadfly Drosophila Genome Annotation Project although it can probably be readily extended to other GAME files.

You should be aware that this parser doesn't set locations in the templates for and elements. These are inferred from the exons represented in elements and the data is not readily available to the parent element during the parser run. In my only implementation, I have a pass in the makeSequence method of the SeqIOListener class that goes thru' to resolve these details.

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.