[Biococoa-dev] Update

[Koen van der Drift]

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 
> symbols
> and BCSequenceNucleotides.  I've modified the corresponding BCSequence 
> and
> 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 
> returning
> "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 
> demo
> doesn't crash (though it produces a very short peptide, so it may not 
> be
> 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 
> rationalizing
> 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.

- Koen.