[Biococoa-dev] more ramblings

John Timmer jtimmer at bellatlantic.net
Fri Dec 3 17:08:20 EST 2004

>> BTW, what's the difference between 'strict', 'skippingnonbases' and
>> 'unambiguous' ?
> Basically they're the same thing, and yes, we should rename them to be
> similar I think...

I'm largely sitting this discussion out (my boss just sent in her latest
revisions to my paper, so I'll be sitting it out for the near future as
well), but just to prove I am paying some attention:

Strict and unambiguous would be the same - all symbols represent a single
entity.  SkippingNonBases isn't - that's what the "undefined" character is
for.  It is used when a character doesn't represent a symbol, ambiguous or

Renaming the concepts is fine, but we need at least two of the concepts
around (3 if you count the opposite of unambiguous as a separate concept).
And that's not even contemplating gapped sequences....


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