[Biococoa-dev] Using an untyped class sequence

[Koen van der Drift]

On Jul 5, 2005, at 6:35 PM, Koen van der Drift wrote:

> My main reason for liking the single class so much is that it is easy 
> to maintain and allows a high degree of modularity.

Just to follow up on that.

I was digging through some of the mailing list archives of the 
biopython project and came upon some interesting messages about the 
same issue. Especially this one:

http://portal.open-bio.org/pipermail/biopython/1999-October/000091.html

One point that I haven't thought of yet, is that if you use typed 
sequences, you could easily keep adding subclasses, eg 
mutable/immutable, strict/nonstrict, ambiguous/unambiguous, and you 
quickly increase the number of subclasses and therefore maintenance. 
With only one sequence class and symbolsets for all different sequence 
types, this is a non-issue.  In fact, you can even allow for 
user-defines sequence types, where the user supplies a symbolset. This 
could contain for instance some specialized, modified residues. Also, 
it would be very easy to change the sequencetype for a BCSequence 
object. This could for instance happen in a sequence editor, where user 
decides that the input is actually DNA, and not a protein.

Anyway, if the majority wants to subclasses, then that's fine with me. 
However, lets stick with the current subclasses, and create variations 
through the symbolsets.

cheers,

- Koen.