[Biococoa-dev] mass calculator bug

Alexander Griekspoor mek at mekentosj.com
Sat Aug 28 15:29:09 EDT 2004

Sorry guys, I'm somewhere else right now and don't have the time to really go into details, which I will 
a.s.a.p. (somewhere tomorrow).... Hope it doesn't slow things down to much.


---------- Original Message ----------------------------------
From: John Timmer <jtimmer at bellatlantic.net>
Date:  Sat, 28 Aug 2004 11:13:27 -0400

>The following was left over from when I started with a DNA sequence class
>before deciding what would be generally useful and moved to the superclass -
>I had used "sequenceArray" instead of "sequence", but forgot to change it in
>this location.  The idea behind it (and a lot else that I code) is to
>prevent a user from doing something stupid, accidentally or maliciously.
>Since we can't control what's in the array the user is handing us when it's
>a raw array (as opposed to when we're handed a sequence) we need to make
>sure that its contents will work with all the methods we're using on the
>contents - hence the test for BCSymbols.
>> John,  you implemented this method setSequence as follows:
>> - (void)setSequence:(NSMutableArray *)anArray
>> {
>>      [sequenceArray release];
>>      sequenceArray = [[NSMutableArray alloc] init];
>>      NSEnumerator *theEnumerator = [sequenceArray objectEnumerator];
>>      id aSymbol;
>>      while ( aSymbol = [theEnumerator nextObject] ) {
>>          if ( [aSymbol isKindOfClass: [BCSymbol class]] )
>>              [sequenceArray addObject: aSymbol];
>>      }
>> }
>> Is it possible to move all the rangeOfSubsequence variants that are now
>> in BCSequeneDNA to BCSequence? I think the same code can be useful for
>> proteins as well.
>Please do!  And please fix my experimentation with the adenosine @"A" -> 'A'
>conversion.  And rename anything you feel is necessary, as long as you're
>careful with the find and replace!
>It looks like I won't have CVS access all weekend (Koen, if you're annoyed
>at Earthlink, I'm annoyed at Verizon), so I'll be working on something new
>instead of contributing to the work on sequences, copying, and coding.
>Incidentally, have you done a "step into" in the debugger to see where
>things actually error out? And what's the error message?
>This mind intentionally left blank
>Biococoa-dev mailing list
>Biococoa-dev at bioinformatics.org

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