[Biojava-l] GAME parser and Ragbag

[David Huen]

Hi,
As per Thomas Down's suggestion, the above were moved to
org.biojava.bio.seq.io.game and org.biojava.bio.seq.ragbag respectively.
The move seemed to end smoothly (though it got a bit rough in the middle)
and my compile check at the end went OK.  Please contact me if anything
has gone wrong as a result.

Changes:-
(a) I made changes in org.biojava.bio.seq.io to support a
SimpleAssemblyBuilder class.  I can revert these if they cause problems.

(b) Ragbag now extended to cover GAME, EMBL, Genbank and XFF formats.
Annotation directory works on assemblies too.  It should be possible to
mix formats at will - that's been tested.  I will probably change the
name of RagbagDirectoryHandler to RagbagAssembly, it seems more sensible. 
New demos will be uploaded soon.  WARNING: Still experimental software,
use at your own peril.


Regards,
David Huen, Dept. of Genetics, Univ. of Cambridge