[Biococoa-dev] BCScanner

John Timmer jtimmer at bellatlantic.net
Tue Mar 15 19:38:36 EST 2005

> This dates back to an early discussion, where it was suggested that it
> would be nice if we have a NSScanner equivalent that deals with native
> BCSequences. I think Alex made the initial interface of BCScanner, I
> just started to add some implementation. See this thread:
> http://bioinformatics.org/pipermail/biococoa-dev/2004-September/
> 000286.html
> If we use a plain NSScanner, we add two conversion steps between a
> BCSequence and its string which could add some overhead:
> BCSequence -> string -> NSScanner -> strings -> BCSequences.

Right, and I agree with that completely.  But my thought was more as to
whether a scanner-type object is needed at all for digests, since Scanners
are useful for reading ordered objects one at a time.  The products of a
digest aren't necessarily ordered in any way.  I would have thought a digest
should generate an array containing all fragments at once, through a process

Pocessed by BCFindSequence -> array of ranges
BCSequence  subSequenceInRange -> individual digest fragments

A scanner seems like overkill for this need.


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