[Biococoa-dev] Update

[John Timmer]

Okay, Koen's suggested fixes are now in place, along with a few others.  One
key difference is that I've now separated base representations and
complementation.    This is relevant to the following:
> - BCNucleotide should call it's super method in
> initializeComplementRelationships, otherwise the 'represents' etc never
> gets set up.
Now, BCSymbol has the methods that handle representing multiple symbols, and
these relationships are initialized in that class as needed.  BCNucleotide
has the complements, and they're initialized there as needed.  So, in the
end, there's not a need to call super - you can do a complement without
knowing the representations and vice versa.


Next up, I'd like to start cleaning up the mess I put in place in the
translation code.  I know Koen's done some tweaking there, but some of it
still looks almost as bad as when I wrote it, and I'd imagine it's not been
updated to handle BCAbstractSequences.  Has anyone who's looked it over
recently got any suggestions as to priorities or necessities?

JT

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