[Biojava-l] GAME-1.001 StAX parser version 1E-06

[Dr S.M. Huen]

I have uploaded a version of a work-in-progress version of a parser for
GAME-XML version 1.001 to:-

http://www.huen.org.uk/david/game-all.tgz

It includes the previously mentioned patches for XXXElementHandlerBase
which are necessary for handling Gadlfy files as well as a small demo
program (dumps Feature.Templates with a dummy SeqIOListener) and a test
file from Gadfly (at which it is targetted anyway).

The manifest is:-
demos/game/
demos/game/AE002734.game
demos/game/README.txt
demos/game/SeqIOTatler.java
demos/game/TestGAME.java
src/org/biojava/bio/program/game/
src/org/biojava/bio/program/game/StAXFeatureHandler.java
src/org/biojava/bio/program/game/ElementRecognizer.java
src/org/biojava/bio/program/game/GAMEHandler.java
src/org/biojava/bio/program/game/StAXHandlerFactory.java
src/org/biojava/bio/program/game/GAMENamePropHandler.java
src/org/biojava/bio/program/game/GAMEGenePropHandler.java
src/org/biojava/bio/program/game/GAMETypePropHandler.java
src/org/biojava/bio/program/game/StAXPropertyHandler.java
src/org/biojava/bio/program/game/GAMESeqPropHandler.java
src/org/biojava/bio/program/game/GAMESeqRelPropHandler.java
src/org/biojava/bio/program/game/GAMEMapPosPropHandler.java
src/org/biojava/bio/program/game/package.html
src/org/biojava/bio/program/game/GAMESpanPropHandler.java
src/org/biojava/bio/program/game/package.inf
src/org/biojava/bio/program/game/GAMEAspectPropHandler.java
src/org/biojava/bio/program/game/GAMEAnnotationHandler.java
src/org/biojava/bio/program/game/GAMEStartEndCallbackItf.java
src/org/biojava/bio/program/game/GAMEStartEndPropHandler.java
src/org/biojava/bio/program/game/StAXAdditions.note
src/org/biojava/bio/program/game/GAMEFeatureSetPropHandler.java
src/org/biojava/bio/program/game/GAMEFeatureSpanHandler.java
src/org/biojava/bio/program/game/GAMETranscriptCallbackItf.java
src/org/biojava/bio/program/game/GAMENameCallbackItf.java
src/org/biojava/bio/program/game/GAMEFeatureSetHandler.java
src/org/biojava/bio/program/game/GAMEFeatureCallbackItf.java
src/org/biojava/bio/program/game/GAMEDescriptionPropHandler.java
src/org/biojava/utils/stax/IntElementHandlerBase.java
src/org/biojava/utils/stax/FloatElementHandlerBase.java
src/org/biojava/utils/stax/LongElementHandlerBase.java
src/org/biojava/utils/stax/DoubleElementHandlerBase.java

To use, cd to biojava-live and execute tar xzvf game-all.tgz to update
your tree.  cd to demos/game to run test demo as per instructions there.

The code may be subject to a fair bit more revision.  Use at your own
risk.  A number of assumptions were made as to how elements in GAME should
map to features in Biojava which may not suit your taste.  It'll suit mine
more and more! ;-)

Could a CVS commit be done by one who can please after appropriate
inspection?

Regards,
David Huen, Dept. of Genetics, Univ of Genetics, U.K.