[Biococoa-dev] Update

[John Timmer]

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.

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).

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.

Cheers,

John

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