[Biococoa-dev] more on Peptides

Charles PARNOT charles.parnot at stanford.edu
Thu Mar 31 11:51:41 EST 2005

The difference in speed does not look significant to me, so yes, we could use a BCPeptide class if this is useful!


At 10:23 -0500 3/31/05, Koen van der Drift wrote:
>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:
>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?
>- Koen.
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>Biococoa-dev at bioinformatics.org

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