[BioCocoa-dev] Peptides...
Alexander Griekspoor
mek at mekentosj.com
Sat Mar 19 09:07:45 EST 2005
Ok, don't ask why, but for some reason XCode can't find the build
framework anymore if you open the project on another machine. The trick
is to delete the reference in the xcode project and add the framework
again (be sure to also add it to the Copy Files build phase in the
Target to make the app standalone.
It doesn't even help if you add the framework "relative to the
project". Anyone a clue?
Also, I forgot to build it as with the deployment build style so the
build app doesn't work also.
I changed that in the version now available at:
http://www.mekentosj.com/temporary/Peptides.zip
But you still have to re-add the framework again.
The build app itself can be downloaded from:
http://www.mekentosj.com/temporary/Peptides_app.zip
if you just want to get an idea of the app...
Hope this helps,
Alex
On 19-mrt-05, at 13:52, Koen van der Drift wrote:
> Alex,
>
> I can't build it, get a lot of build errors:
>
> /Users/koen/Desktop/Peptides/theController.m:10:34:
> BioCocoa/BCFoundation.h: No such file or directory
> /Users/koen/Desktop/Peptides/theController.m:11:30:
> 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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>> Biococoa-dev at bioinformatics.org
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>
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>
*********************************************************
** 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
iRNAi, do you?
http://www.mekentosj.com/irnai
*********************************************************
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