[Biococoa-dev] Digest tool
Koen van der Drift
kvddrift at earthlink.net
Sun Feb 27 16:31:35 EST 2005
On Feb 27, 2005, at 10:51 AM, John Timmer wrote:
> he first case handles no ambiguity, the second handles ambiguous
> bases, the third is when the site includes a stretch of N’s, and the
> final case has ambiguity and N’s. In each case, several enzymes may
> recognize the same sequence, so there’s an test and a call to mark
> everything from the “same sites” array.
Just thinking aloud here. Maybe if we design the appropriate
BCSymbolSet for each case, we can just have one method (or while-loop
in John's snippet). I haven't studied his code that closely, though, so
I might be way of. However in any case, the combination
BCScanner/BCSymbolSet to replace NSScanner/NCCharacterSet is definitely
something to keep in mind.
- Koen.
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