[Biococoa-dev] More on BCSymbolSets

Charles PARNOT charles.parnot at stanford.edu
Fri Mar 4 01:44:22 EST 2005

> >> Regarding the naming conventions, BCSequenceDNA for the class,
>>> BCDNASequence for the type, it is indeed quite confusing; how about
>>> BCSequenceTypeDNA et al.?
>> *If* we decide to keep it, that would indeed be better, yes.
>Renaming it's fine, but we HAVE to keep it.  There are going to be literally
>dozens of symbol sets, plus the potential for user-generated sets, and I
>would not want to loop through all the possibilities just to find out
>whether a sequence could be translated or complemented.

I totally agree with John. It will already be useful for us, but for the user it is critical. If we let the sequence type be checked using the class, you have a number of potential big issues:
* testing for class equality e.g. [sequence class]==[BCSequenceDNA], can be broken if the class is a subclass
* using isKindOfClass method is also dangerous if the class tree changes
* how about BCSequence?? The user should not have to know that at runtime, they could be one of the other class, while [someSequence sequenceType] is simple

Now, what do you guys think of a 'sequenceType' on the symbolSet as well that control what kind of symbols can get in, and that allows us to check the compatibility of a sequence and a symbolSet before initialization?


Help science go fast forward:

Charles Parnot
charles.parnot at stanford.edu

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