[Biococoa-dev] more on Peptides
Koen van der Drift
kvddrift at earthlink.net
Thu Mar 31 10:23:56 EST 2005
Hi,
Right now the Peptides example uses the Results class for the peptides
that were found. Since we are using the BioCocoa framwork (d'oh),
shouldn't we be using the BCSequenceProtein class instead? To see if
this would make a speed difference, I added a new class to the target,
Peptide, which now is a subclass of BCSequenceProtein. Also in the
theController.m I had to make some changes, however, I have bracketed
these with a #define that can be set to 0 or 1 to use the Peptide or
Result class, respectively. It is located at the top the
theController.m:
#define USE_RESULT_CLASS 0
Looking at the speed (on an iMac G3 400 MHz), and these settings:
peptide mass: 876
charge: 2
accuracy: 150 ppm -> actually this should be called tolerance, I will
commit that too with the extra code
Using the Peptide class averages at 2.5 sec, using the Result class
averages at 2.4 sec. So there is not much of a difference on my iMac.
What are others opinion on this?
cheers,
- Koen.
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