[Biococoa-dev] mass calculator bug
Alexander Griekspoor
mek at mekentosj.com
Sun Aug 29 16:30:53 EDT 2004
>> 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.
I think the initWithSequence method should be a public one, like
NSString's initWithString. See my mail "safety vs speed" why I think
we don't have to worry for a different reason. But the validateSequence
method you propose would be a very welcome addition which would help
the developer to make sure he feeds us a proper sequence object. We
leave him the choice then if he wants to trade some speed for safety.
>>> 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
> 'sequenceArray'.
Very nice!
> 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 :)
As BCSymbol supports -description now, can you check that the
enumerator at least returns symbols by putting in a NSLog(@"%@",
aSymbol); ?
Alex
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** Alexander Griekspoor **
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The Netherlands Cancer Institute
Department of Tumorbiology (H4)
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E-mail: a.griekspoor at nki.nl
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