[BioPython] Rethinking Seq objects
Gavin Crooks
GECrooks at lbl.gov
Wed May 4 12:37:18 EDT 2005
On May 2, 2005, at 23:45, Michiel Jan Laurens de Hoon wrote:
> 1) Make Seq objects mutable, and get rid of MutableSeq. The Seq class
> and the MutableSeq class basically describe the same thing, except
> that one is read-only and the other one is not. If desired, we can add
> a readonly flag to the class to describe if it is mutable or not.
> (Given that e.g. Numerical Python arrays don't have such a flag, my
> feeling is that it is not really needed for Seq objects either). For
> performance reasons, the new Seq class will be implemented in C.
>
Although I agree that we don't need a Seq and a MutableSeq class, I
don't follow why we need a mutable sequence class at all. What's the
use case?
If, in the alternative, Seq was a simple immutable object then it could
be implemented as a light weight subclass of str, with an alphabet
attribute that is also a subclass of str. You'd edit it like you would
edit any string in python; split it into a list, do whatever
manipulations are necessary, and then join the list back together into
a new Seq.
Gavin Crooks
--
Gavin E. Crooks
Divisional Fellow tel: (510) 486-7721
Physical Biosciences aim:notastring
Lawrence Berkeley Natl. Lab http://threeplusone.com/
Berkeley, CA 94720, USA GECrooks at lbl.gov
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