[Biococoa-dev] More on BCSymbolSets

John Timmer jtimmer at bellatlantic.net
Fri Mar 4 20:08:41 EST 2005

>> For example, let's say we provide all combinations of symbol sets
>> using only
>> the single bases (ATCG), those plus N, those plus N and gap, those
>> plus, N,
>> gap, and undefined, etc.  You're easily up to about a dozen symbol
>> sets for
>> DNA alone.  Then you add RNA, and protein, and you're probably in the
>> area
>> of 25.
> 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?

>> I don't see how you can avoid iteration, but you feel you can, so
>> maybe i'm
>> missing something.  Your alternative, "containsNucleotides" is fine,
>> but we
>> already have the other system in place -  it's simple, and it works,
>> so I
>> don't see the need to redo it.
> What other system are you referring to?

The existing one, where we have an enumeration with a value associated with
the sequence.

Thanks for the links - I'll look into them tomorrow.


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