[Bioperl-l] Alignment::Clustalw and Bio::RootI

[Jason Stajich]

On Tue, 12 Dec 2000, Murad Nayal wrote:

> 
> 
> I am trying to do something that I probably shouldn't. I am trying to
> combine some 0.7 modules, specifically Bio::Tools::Alignment::Clustalw
> and support modules, with the current 0.62 release. one immediate
> problem I have encountered is that Clustalw inherits from Root::RootI
> (not from Object). However RootI in 0.62 does not have a new method (it
> does in 0.7). (hence I can't instantiate a Clustalw).
> 
> the questions:
> 
> 1- is Root::Object being phased out?
Yes! 

> 2- how foolish is it to start mingling 0.62 and 0.7 objects. I really
> need a clustalw wrapper and don't want to write one since it is already
> available in 0.7. I suppose if I replace RootI 0.62 with RootI 0.7, then
> 0.62 objects (which inherit from Object) will hook into Object methods
> while 0.7 objects (really just Clustalw and co) will access the RootI
> methods!!. 

Going to be very difficult if not impossible to mix versions right now.  
Once we started down this path, we acknowledged there would be a lot of
incompatibilities between versions because of Root::Object dependence. You
will have an easier time checking out the main branch and learning with
that then struggling with compatibility issues.  The Clustal module is
just a wrapper around the clustalw program, are you trying to do something
so tricky that you can't just run clustalw separately and then feed it
into AlignIO (oh shoot, which is only on main-trunk too, well....).

Let me know if I can help steer you in the right direction.  Peter S (the
author) is away on vacation for a few more weeks so I agreed to stand
watch on the AlignIO and Bio::Tools::Alignment in the meantime.

> 
> 3- how many times can one say object in one sentence and still have it
> mean something.
obfuscation obviates obfuscation
> 
> 
> many thanks for the feedback.
>  
> 
> 
> -- 
> Murad Nayal M.D. Ph.D.
> Department of Biochemistry and Molecular Biophysics
> College of Physicians and Surgeons of Columbia University
> 630 West 168th Street. New York, NY 10032
> Tel: 212-305-6884	Fax: 212-305-6926
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> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/