[Biococoa-dev] BCPairwiseAlignment

[Philipp Seibel]

>>
> 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 - 
subclass structure.

> 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 
> name).
> 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

Phil