[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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