Package org.biojava.bio.seq.io.game
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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ClassDescriptionSimple interface for filtering SAX/StAX startElement eventsFilter elements by local name (not recommended).Filter elements by name and namespace.Filter elements on the existence of a specified attribute.Handles the GAME <annotation> elementHandles the GAME <aspect> elementDeals with database crossreferencesStAX handler for GAME <description> elements.An interface that can be tested for by nested handlers when trying to do a callback.Handles the <feature_set> elementHandles the GAME
element Handles the <feature_span> elementHandles the GAME <gene> elementHandles the root GAME elementHandles the GAME <map_position> element Currently, it just ignores it!An interface that can be tested for by nested handlers when trying to do a callback.StAX handler for the GAME <name> element.StAX handler for GAME <residues> elements.Handles the GAME <seq> elementHandles the GAME <aspect> elementHandles the GAME <span> element Currently, it just ignores it!An interface that can be tested for by nested handlers when trying to do a callback.StAX handler for GAME <type> elements.StAX handler for elements containing sequenceStAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.Factory for StAX content handlers.StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.