[Biococoa-dev] BCNucleotideRNA

Alexander Griekspoor a.griekspoor at nki.nl
Thu Sep 23 04:21:30 EDT 2004


In your nucleotideRNA class, you take the nucleotides.plist and then 
cleverly replace everything T for U. But next, in the actual 
instantiating you do this:

  tempDict = [baseDefinitions objectForKey: @"T"];
     if ( tempDict != nil  && [tempDict isKindOfClass: [NSDictionary 
class]] ) {
         uridineRepresentation = [[BCNucleotideRNA alloc]  
initWithSymbol: 'U'];
         [baseDefinitions removeObjectForKey: @"T"];

That should be [baseDefinitions objectForKey: @"U"]; then isn't it? 
Haven't changed it though...

Op 23-sep-04 om 2:38 heeft John Timmer het volgende geschreven:

>> - Is it necessary to duplicate all the code from BCNucleotideDNA,
>> except for the uridine instead of thymidine? Why not have a class
>> BCNucleotide that takes care of everything, and just have two
>> subclasses with the small differences?
> That was my long-term intention.  I just wanted to get things working
> quickly so that I could get translation and codons handled.  Once I was
> happy with how they worked, I figured I could go back and sort out a 
> better
> class structure.  Even so, all the base methods have to be separate 
> for DNA
> and RNA, as they need to return something different so that == works as
> expected, so the classes won't shrink as much as I'd have hoped.
>> -  The method molecularWeight is deprecated, please don't keep adding
>> it. We now use BCToolsMassCalculator for all MW calculations.
> Sorry, that didn't exist when I left on vacation, and as you noticed, I
> simply copied the DNA file over.  I'll delete it the next time I have 
> time
> for some coding.
>> - There is no need to use #import <Cocoa/Cocoa.h>, for the 
>> BCFoundation
>> classes <Foundation/Foundation.h> is sufficient.
> Yeah, that's just what comes when you create a new class with Xcode.  I
> tried to go back and catch all of them, but I guess I missed a few.  
> For
> something like this, you should feel free to just correct it.  The same
> things can be said for this:
>> - Please use the Copyright line as in the other files
> Cheers,
> John
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                       ** Alexander Griekspoor **
                 The Netherlands Cancer Institute
                 Department of Tumorbiology (H4)
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                     E-mail: a.griekspoor at nki.nl
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