[BioCocoa-dev] Peptides...

Koen van der Drift kvddrift at earthlink.net
Sat Mar 19 07:52:48 EST 2005


I can't build it, get a lot of build errors:

BioCocoa/BCFoundation.h: No such file or directory
BioCocoa/BCAppKit.h: No such file or directory

I also linked to the framework on my HD, but that didn't help.

- Koen.

On Mar 19, 2005, at 7:22 AM, Alexander Griekspoor wrote:

> Hi everyone,
> Someone in our institute asked me to create a little Cocoa app for a  
> specific problem he had. Given a certain protein sequence and the  
> weight for a peptide reported by the mass spec, which peptide would be  
> the closest match?
> Of course an ideal situation to use BioCocoa ;-)
> I've used a modified version of our translation demo, which can be  
> downloaded here:
> http://www.mekentosj.com/temporary/Peptides.zip
> Please check it out and perhaps we can add the example or parts of it  
> to the framework.
> Often using the framework is the best way to discover problems or come  
> up with new ideas (so I guess I better start working on the demo app  
> we plan to make), so here are a few suggestions/changes I'd like to  
> feed back in the repository but not before you have agreed to do so...
> 1) In this case I have one sequence of which I want to calculate the  
> mass of many peptides. So I wanted to cache the BCToolMassCalculator  
> and ask it for the mass of a certain range. To avoid the overhead of  
> having to create a subsequence first, instantiate a new  
> BCToolMassCalculator from it and calculate the mass, I've added a  
> simple method:
> -(NSArray *)calculateMassForRange: (NSRange)aRange;
> and changed the original calculateMass method to a convenience method:
> --(NSArray *)calculateMass{
> 	return [self calculateMassForRange: NSMakeRange(0, [[self sequence]  
> length])];
> }
> As BCToolMassCalculator uses BCToolSymbolCounter (very elegant Koen!)  
> I've added the same method there as well:
> - (NSCountedSet *)countSymbols;
> - (NSCountedSet *)countSymbolsForRange: (NSRange)aRange;
> 2) I noticed that the BCSequenceView still needs a lot of works. For  
> one, it can display line numbers (not so useful), but it wrongly  
> displays symbol numbers. Also many things are not configurable yet  
> (like the indent of the spacing). Also, none of the selection, marking  
> etc methods take the spaces into account, so for a start I added an  
> override of the setSelectedRange:  method:
> - (void)setSelectedRange:(NSRange)charRange{
> 	int start = charRange.location;
> 	int end = charRange.location + charRange.length;
> 	start += start/10;
> 	end += end/10;
> 	[super setSelectedRange: NSMakeRange(start, end-start)];
> }
> Again, the 10 here should become configurable later.. I'd like to  
> spend some time on this one further, and see what we can do... (it's  
> also required for the demo app).
> Finally, I think the program is acceptable fast for the purpose I made  
> it for (it calculates the mass of approx. 1200 peptides a second on my  
> 1.5Ghz G4), but I'm sure it can be a lot faster if we optimize the  
> symbolcounter where it spends most of its time (doing a lot of object  
> messaging). But first I'll let the guy who asked me to help play with  
> it, I challenged him to come up with something dramatically faster ;-)
> Cheers,
> Alex
> *********************************************************
>                     ** Alexander Griekspoor **
> *********************************************************
>               The Netherlands Cancer Institute
>               Department of Tumorbiology (H4)
>          Plesmanlaan 121, 1066 CX, Amsterdam
>                    Tel:  + 31 20 - 512 2023
>                   Fax:  + 31 20 - 512 2029
>                   AIM: mekentosj at mac.com
>                  E-mail: a.griekspoor at nki.nl
>               Web: http://www.mekentosj.com
>               4Peaks - For Peaks, Four Peaks.
>        2004 Winner of the Apple Design Awards
>                Best Mac OS X Student Product
>              http://www.mekentosj.com/4peaks
> *********************************************************______________ 
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