biococoa at bioworxx.com
Sun Mar 13 08:58:31 EST 2005
> They are also. But they're used to separate code within the same .h/.m
> file as well.
> Phil, the problem Koen and I have as far as I can speak for the two of
> us, is that we don't really see the structure you have in mind with
> the categories.
> Charles is right, the class-subclass layering only has use if there's
> code that can be grouped together between in this case different
> algorithms. So, if there is lots of code to share between let's say a
> smith-waterman and needleman-wunsch alignment then it makes sense to
> create a superclass for all algorithms. If there's hardly any, than
> there's not much use.
> So to clear things up from my side:
> BCAlignment becomes BCSequenceAlignment, this is the net result of an
> alignment, some way to store them in the end
> Then the question is what do we call for instance a Smith-Waterman
> local alignment and does it make sense to let them derive from a
> BCAlignmentAlgorithm (I believe Koen had a better name) superclass.
Ok, i don't see anything a multiple alignment and a pairwise alignment
have in common. Ok clustal uses Pairwise alignments to compute a non
optimal multiple alignment for example, but we don't need a super -
> Finally, the categories. I'm not sure where this would fit in, but the
> reason I said to just incorporate the convenience method in the class
> was based on the idea that given a class named
> BCSmithWatermanAlgorithm (to mention a horrible name), it would just
> have a class method:
> + (BCSequenceAlignment *)alignmentOfSequences: (NSArray *)sequences
> criteria: (NSDictionary *) dict; (to mention another horrible method
> I don't really see where the categories come in and what structure
> Phil had in mind.. Does this make my remarks more clear?
My idea was just to put all alignment algorithms into
BCSequenceAlignment as convenient methods. The BCSequenceAlignment can
represent multiple & pairwise alignments, so
the categories just came in to make it more readable, nothing else ;-)
Hope this was understandable
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