[Biococoa-dev] ambiguous symbols

[Koen van der Drift]

>
> There's two challenges here - one is that the nucleotides have 
> complements
> and the amino acids don't, as you pointed out in the quote just below. 
>  A
> second is that the relationships have to be made to members of a 
> specific
> subclass - ie, a BCNucleotideDNA should only complement others from its
> subclass.  I'd guess you could get around this by figuring out what 
> kind of
> class self is, but I don't know enough about how ObjC handles 
> inheritance to
> know how well this would work - does an object know what class it is 
> when
> it's executing functions in it's super?
>
> Clearly, we could just declare that method in the super and implement 
> it in
> each subclass.  Since you're doing the work, how are you hoping to 
> handle
> it, Koen?

For now, I've left the method in the super class empty, and put all the 
code in the subclasses. But I think we can at least put the code that 
fills represents and representedBy in the superclass. I will check that 
later. When similar code gets repeated in the various subclasses, it 
definitely is a candidate to go into the super. (This was also the 
reason for my plea a few weeks ago to put all the rangeOfSubsequence 
methods in BCSequence only. But now that BCFindSequence is in place, we 
probably can remove rangeOfSubsequence et al completely).

>
>  As far as I can tell,
> there's no need to access the "Name" value in this method.  The code 
> should
> probably start somewhere around the line:
>
>     infoArray = [baseInfo objectForKey: @"Represents"];
>

Ah, thanks. Will fix that.


>> if ([represents count] == 1)
>>
>> Is this also correct?
>
> That would work, but if we're adding the code to handle the ambiguity 
> in the
> superclass, we could probably move this method up to the superclass, 
> too.

I already did :)


> You may want to reverse the logic, though, as "isAmbiguous" seems 
> (pardon me
> here) less ambiguous than "isSingleSymbol" in terms of method names 
> that
> clearly indicate the function.

You mean to use:

if ([represents count] >1) ?


thanks for the input,

- Koen.