[BioPython] what should I do next?

[Brad Chapman]

>>Right now I'm integrating the existing corba server with your 
sequence 
>>code so that it actually does something :)
> 
> Cool!  I haven't really looked at Ewan's proposal for a while, so
> I didn't know how it would work together.

It looks like what is in the Bio module now supports the 
AnonymousSeq, PrimarySeq and PrimarySeqIterator interfaces, at least 
for info in fasta files, so that is really cool.

> That interface is likely to change.  I'm thinking about adapters
> to make it work with "pure" FASTA records (description and sequence)
> or hypothetical sequence records (where the format of the description
> line means something).
> 
> BTW, the most stable interfaces are the ones tested by the regression
> suite.  The next most stable are used by those modules.  If it
> isn't touched by the regression code, it is most likely to change.

I don't mind things changing, so feel free to modify the interfaces 
(as if I could stop you :) The corba code is in serious flux, so it is 
no big deal to make changes to reflect interface changes (plus right 
now I'm doing ugly things like reaching into internal class variables, 
so I deserve to have the code break :).

>>I would be 
>>interested in seeing more support for the corba interface and for 
>>building this up.
> 
> You are using Fnorb, right?  As I recall, that's not for commercial
> use without paying, yes?  Since I'm trying to do this commercially
> (hopefully), I've been looking at ILU and pyomniorb.  I got stuck
> in the latter trying to figure out memory management.  Keep meaning
> to send email to the authors....

Yeah, a serious problem with the current server code is that it is 
pretty highly dependent on Fnorb. I'm hoping to try and fix this so 
that any number of orbs could we used. My thoughts were to try and 
support Fnorb, ORBit-python, ILU, and omniORBpy (although that thing 
is a beast to compile), so that everyone can be happy. The mapping has 
been standardized, so hopefully this will work...

Brad