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
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.
Interface Summary Interface Description StAXHandlerFactoryFactory for StAX content handlers.
Class Summary Class Description GAMEAnnotationHandlerHandles the GAME <annotation> element GAMEAspectHandlerHandles the GAME <aspect> element GAMEDbxrefHandlerHandles the GAME <dbxref> element GAMEFeatureSetHandlerHandles the GAME <feature_set> element this element is used to represent transcripts. GAMEFeatureSpanHandlerHandles the GAME <feature_span> element GAMEGeneHandlerHandles the GAME <annotation> element GAMEHandlerHandles the root GAME element GAMEPropertyHandlerHandles the GAME <dbxref> element GAMESeqHandlerHandles the GAME <seq> element GAMESeqRelHandlerHandles the GAME < > element GAMESpanHandlerHandles the GAME <> element. StAXFeatureHandlerStAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.