[Biococoa-dev] More on BCSymbolSets

John Timmer jtimmer at bellatlantic.net
Sat Mar 5 12:20:32 EST 2005

> On Mar 4, 2005, at 8:08 PM, John Timmer wrote:
>>> But each set will only have nucleotides or amino acids. They are not
>>> intended to mix.
>> Okay, so we will have no user-defined sets, and I would go in, grab the
>> first symbol, and test what type of symbol it is?  Wouldn't that get
>> into
>> issues like testing its class, which Charles indicated might not be
>> the best
>> way of determining this?
> That's a good point. So we could move the BCSequenceType ivar to
> BCSymbolSet.

Yes, and just make the method that's now in BCSequence a convenience
call-through to that.  To maintain key/value coding, we could just have the
setter method do nothing.

> BTW, With the line 'They are not intended to mix' I didn't mean that
> there cannot be user-defined sets. Just meant that I don't see a
> situation where a symbol set is created containing both amino acids and
> nucleotides. That would be 'distorting biology', to use your own words
> :)
Exactly.  Which is why I expect it will happen, and want the code to be
robust enough to cope with it.  It still amazes me, the bugs people find
when the app gets distributed to more than a dozen people.


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