[Biococoa-dev] more on Peptides

[Koen van der Drift]

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.