[BioCocoa-dev] Peptides...
Koen van der Drift
kvddrift at earthlink.net
Sat Mar 19 16:17:21 EST 2005
Hi,
I found a bug in the display of the peptides, it is an error between
0-based and 1-based calculations. If I select a peptide in the right
pane, in the left pane the peptide shown is one position off (too
high). First I tried changing that in the search code, but tht is not
right because all calculations are 0-based. So it has to be changed in
the display code:
- (void)tableViewSelectionDidChange:(NSNotification *)aNotification{
// is there a selection?
if ([[aNotification object] selectedRow] == -1) return;
else {
NSRange aRange;
// which result is selected?
Result *res = [results objectAtIndex: [tv selectedRow]];
// select the location of the peptide in the inputview
aRange = [res range];
aRange.location -= 1;
[theInput setSelectedRange: aRange];
}
}
As you already mentioned in the comments, the code can be sped up by
using a search window of the average MW of an amino acid (= 110 Da),
+/- 10% (or maybe 15%).
- Koen.
On Mar 19, 2005, at 9:07 AM, Alexander Griekspoor wrote:
> 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
>>>
>>> *********************************************************____________
>>> ___________________________________
>>> Biococoa-dev mailing list
>>> Biococoa-dev at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>>
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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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> Biococoa-dev at bioinformatics.org
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