[BioPython] Clustalw multiple alignment

[Brad Chapman]

Jeff wrote:
> Put the clustalw stuff in Bio.ClustalW. We'll reserve Bio.Align (or
> something like it) for generalized alignment code.
 
Hmmm... I also have a generic base class (called Alignment right now) for
trying to represent Alignments in general in Biopython. I thought it
would be a good idea to try and see if we can have some of the general
functionality that you should have for any kind of alignment in this
class, and then inherit from this to deal with specific alignment
formats. 
 
Right now I only inherited from this to deal with the clustal format, but
there are conceivably a lot more formats to deal with (bioperl has code
to deal with 8 different formats that alignments can be stored in!).
 
So if we put the clustalw specific stuff in clustalw, do you want the
generic class to go in Align? 
 
Or do you think I should be going about this in a different way?
 
Brad