[Biococoa-dev] mass calculator bug

Koen van der Drift kvddrift at earthlink.net
Sat Aug 28 11:54:30 EDT 2004

Hi John,

> 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.

If we keep the method private, we don't have to worry about that, I 
guess. We could implement a validateInput method that checks (using an 
NSScanner) if any character in the string are not allowed. Or we could 
use an BCAlphabet class that manages the symbols.  But in the meantime 
I'll leave it alone.

>> 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!

Ok, I will start working on that. I'll also replace 'sequence' with 

> Incidentally, have you done a "step into" in the debugger to see where
> things actually error out? And what's the error message?

If I step into the offending line I go straight to the assembly code, 
which is not very helpful (to me atlast :)

It has to do with how I obtain a reference to each BCSymbol, see my 
other post.

- Koen.

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