[Biococoa-dev] Base test

John Timmer jtimmer at bellatlantic.net
Sat Aug 14 11:10:18 EDT 2004

> Koen,
> The problem is not so much with complement bases but with the fact that
> the nucleotide alphabet contains ambiguous bases, bases that represent
> a group of bases. Examples are N for aNy base, but also R for puRine
> bases (A and G), W for Weak bases (A and T), etc. Therefore, each
> symbol has a -(NSArray *)matches; method that returns all bases that
> belong to this base (it returns only self if the base is atomic (A, C,
> G and T). A similar setup can be choosen for the complements of course,
> but perhaps it's indeed better to just return the complement ambiguous
> base. So N would return N as complement, W would return S as
> complement. I don't know if John plans to follow this latter setup
> actually, but he will probably tell us. In the protein world one could
> have a "stop" amino acid which would be ambiguous for the three stop
> codons we have, although another complicated factor would be species
> specificity.
> I hope this helps, but perhaps I completely misunderstood the question.
> Alex

That was more or less my plan.  You can get complement, which is the direct
complement (strict subset - N only really complements N), and the full set
of complements (where N complements anything).  I'll also have a
"represents" and "representedBy" method - N represents anything, but is
really only represented by N, while C represents only C, but can be
represented by C, S, Y, N, etc.

There's situations where I can imagine needing any one of these, so there's
no reason not to implement all of them - do all the work in the base class,
so that nobody ever has to repeat it.



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