[Biococoa-dev] sequence wrappers

[John Timmer]

In terms of design of this class, how will it differ from a regular
NSMutableArray?  The existing class isn't too much more complex than an
array other than in terms of the sequence-type specific code.  I'm not
trying to be argumentative, but more performance oriented.  If we're only
adding a couple of methods, there should be much less overhead to adding a
category to NSMutableArray (you wouldn't be calling methods through as many
objects to get to the actual sequence array).

That said, the idea of having annotations and features be a part of the
sequence specific subclasses allows some interesting possibilities, so I am
intrigued....

JT

 
> How about the following change in our class structure to accomodate the
> sequence wrapper nomenclature:
> 
> We create a new, bare sequence class, which only function is to
> maintain an array of BCSymbols. A possible name is BCSimpleSequence or
> BCSymbolList, or whatever. Part of the current code in BCSequence could
> go in that class. Then we subclass that to BCSequence, which has
> annotations and features. This is then subclassed to the current
> subclasses. One advantage: no long ugly class names such as
> BCSequenceProteinAnnotated, etc.
>


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