[Biopython] Biopython on Jython

[Peter]

Hi Kyle,

You probably noticed I merged some of your fixes to get (the non C and
non NumPy bits of) Biopython to work on Jython, but not all. Could you
update your github branch to the trunk at some point? That would help
in picking up more of your fixes.

Many of the issues related to large python methods exceeding JVM size
restrictions, something which Jython was going to try and fix in 2.5.1
(but didn't seem to be solved in the release candidate I was trying),
see e.g. http://bugs.jython.org/issue527524
Do you (Kyle) know about more about the Jython plans and if/when they
might resolve this? I would prefer to avoid any ugly Jython specific
fixes in Biopython - especially if the next release of Jython may
resolve many of these points.

Thanks,

Peter