[Biococoa-dev] BCSymbol Nomenclature

John Timmer jtimmer at bellatlantic.net
Fri Aug 20 13:33:52 EDT 2004

A modest proposal, since I'm thinking of header doc-ing everything this
evening (and I'm the second oldest, so it's my turn ;) :

symbol provides a 1 letter code as a unichar
symbolString provides that as a string
name provides the chemical name for the item

We move all initialization methods into the subclasses, since Koen and I are
writing them and handling them somewhat differently.

We'll drop the "setName:" method, since Koen doesn't want to do that either.

I'd like to create a standard "gap" and "non-chemical" symbol for the bases,
and thought they should parallel what's done with amino acids (the
non-chemical is for situations where a long string is provided and needs to
be translated into objects - the user may need to know where problems are).
I also don't want them to conflict with a "stop" amino acid, which would be
needed for translating an entire frame.

For stop, I propose:
Symbol: X
Name: stop

For gap:
symbol: -
name: gap

For non-chemical:
name: undefined
symbol: ?

I'm not sold on any of these (especially the last), so I invite comments.



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