[Biopython-dev] "Features" of Bio.Clustalw

[Jeffrey Chang]

>  [Davide Marchignoli]
>  > I think that having a class like MultipleAlignCL is superior to passing
>  > the alignment arguments to a function as is for blastpgp or blastall.

[Brad Chapman]
[...]
>blastall and blastpgp are Jeff Chang's functions, so maybe he could
>comment on your idea to have classes to encompass their options. I'm
>not positive if he even likes the "command line in a class" idea :-).
>
>>  Finally it is a general mechanism and could be used to give a uniform
>>  interface to functions invoking external programs.
>>
>>  Do you think you would be interested in a patch implementing such
>>  behaviour? I think one could also retain compatibilty with the current
>>  interface.

Yes, I think that's a good idea, and one that I've used in other 
modules I've written.  However, I do still want a low-level interface 
mapped closely to the program where you pass in variables as 
parameters to the function.  If you have that, it's always possible 
to build other interfaces on top of it, as you suggest.  However, 
it's harder to go the other way around.

>class AbstractApplication:
>     """Generic interface for running applications from biopython.
>
>     This class shouldn't be called directly; it should be subclassed to
>     provide an implementation for a specific application.
>     """

Looks pretty cool.  The only thing that might be missing is some way 
of dealing with the output.  That way, you can pass around 
applications that you can call, and it will return usable objects. 
But maybe that should be done in a decorator class.

Jeff