[Biococoa-dev] BCScanner

[John Timmer]

>> BCSequence
>> Pocessed by BCFindSequence -> array of ranges
>> BCSequence  subSequenceInRange -> individual digest fragments
>> 
>> A scanner seems like overkill for this need.
>> 
> 
> The nice thing of a scanner is that you can pass it a
> symbolset/characterset, containing all the various locations where a
> sequence has to be cut. At least this is how I use it for proteins in
> my own app. Eg trypsin cuts at K and R, if we pass KR to findSequence,
> it will look for that actual sequence. If we pass it as a symbolset to
> a scanner, it will look for each individual symbol, which is what we
> want.

Ah, I hadn't thought of that case.  I keep thinking in nucleotide terms,
where every possible combination of nucleotides is represented by a single
symbol.  This might be another case where splitting the tool two ways (one
for aa's, one for nt's) could be justified by performance profiling.

JT

_______________________________________________
This mind intentionally left blank