[Biococoa-dev] Using an untyped class sequence
Koen van der Drift
kvddrift at earthlink.net
Wed Jul 6 18:12:55 EDT 2005
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:
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.
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