Koen van der Drift
kvddrift at earthlink.net
Fri Feb 25 19:38:24 EST 2005
On Feb 25, 2005, at 7:23 PM, John Timmer wrote:
> Okay, I'm ready to do a major update. I've created BCNucleotides as
> and BCSequenceNucleotides. I've modified the corresponding BCSequence
> Symbol subclasses for DNA and RNA. I've modified BCSymbol to move
> complementation down to the subclass, while adding "isCompoundSymbol"
> to it.
> I added "containsCompoundSymbols" to BCAbstractSequence accordingly.
> I had to modify the Complement tool - if its sequence is a protein, it
> returns a copy of that protein (in keeping with Koen's idea of
> "self" when it can't return anything else). If it's not, it uses
> BCNucleotides to create the complement.
That was actually Charles' idea ;-)
> I can't guarantee everything's working properly, but the translation
> doesn't crash (though it produces a very short peptide, so it may not
> working perfectly).
It already does that, maybe we should a different DNA sequence?
> Any objections before I commit this? I may not be done with
> things up from the subclasses, but I think the worst of it is now
> done. I
> won't commit until I hear from Charles and Koen, who seem to be
> working the
> most on things right now.
No objections from me.
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