[Bioperl-l] Pise/bioperl

[Aaron J Mackey]

On Thu, 10 Jan 2002, Jason Stajich wrote:

> my $clustal = $pisefactory->get_Application_Handle('clustalw');
> my $res = $clustal->align(-data => [$seq1,$seq2]);

Just two simple design comments:

1) get_Application_Handle could just be application(), no?  Yes, I
understand what a handle is, but no need to make things more confusing.
Other good words might be instantiate(), startup(), etc. (I like
doubleclick(), but I'm a GUI sorta guy I guess; just kidding).

2) $application->run() vs. $app->align(), $app->convert(), etc; $clustal
is a good example of a program that can do a couple of different things,
even with the same "input" (Yes I realize that part of your input
parameters could be a flag telling clustalw what to do; I guess that's
part of PISE's job.  At the same time, you should be able to AUTOLOAD
those "run" methods, and have them usable as such).

I think this is great work though, and could really open things up (I've
always been very impressed with PISE and similar efforts).

-Aaron