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

Murad Nayal murad@godel.bioc.columbia.edu
Tue, 12 Dec 2000 10:22:32 +0100

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?

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

3- how many times can one say object in one sentence and still have it
mean something.

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