Package org.biojava.bio.seq.io.game
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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Interface Summary Interface Description ElementRecognizer Simple interface for filtering SAX/StAX startElement eventsGAMEFeatureCallbackItf 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> elementGAMEAspectPropHandler Handles the GAME <aspect> elementGAMEDbxrefPropHandler Deals with database crossreferencesGAMEDescriptionPropHandler StAX handler for GAME <description> elements.GAMEFeatureSetHandler Handles the <feature_set> elementGAMEFeatureSetPropHandler Handles the GAMEelement GAMEFeatureSpanHandler Handles the <feature_span> elementGAMEGenePropHandler Handles the GAME <gene> elementGAMEHandler Handles the root GAME elementGAMEMapPosPropHandler 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> elementGAMESeqRelPropHandler Handles the GAME <aspect> elementGAMESpanPropHandler Handles the GAME <span> element Currently, it just ignores it!GAMETypePropHandler StAX handler for GAME <type> elements.SequenceContentHandlerBase StAX handler for elements containing sequenceStAXFeatureHandler StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.StAXPropertyHandler StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.