[Biococoa-dev] BCPairwiseAlignment & BCScoreMatrix

[Philipp Seibel]

Am 12.03.2005 um 08:51 schrieb Alexander Griekspoor:

> Yeah, I was about to raise the same question yesterday, I also thought 
> that the BCAlignment would be the general "algorithm" class, and 
> BCPairwiseAlignment one of it subclasses But, as far as I can see what 
> Phil had in mind, they're two completely different things. 
> BCPairwiseAlignment does the job, and BCAlignment is what it returns. 
> It is the result of an alignment. Now, I think Koen has a point that 
> this is quite confusing. First, indeed their maybe a benefit if we 
> implement a general algorithm class BCAlignmentAlgorithm or something 
> and have subclasses that implement the different alignments (NW, 
> Smith-W). And have its name be more distinct from the alignment class. 
> Phil, do you know NeoBio, a java framework for alignments, they also 
> use classes throughout and maybe you can see how they gave names to 
> them (not saying they're better though)...
> Cheers,
> Alex

Ok we should discuss this point in more detail. I think it's logical to 
have a structure like this:

								BCPairwiseAlignmentAlgorithm
								/
BCAlignmentAlgorithm (Protocol or class)
								\
								BCMultipleAlignmentAlgorithm

oh nice ascii art ;-). And inside the alignmentalgorithm classes we 
have static methods to perform different kind of algorithms. If they 
get to complex to have the methods inside one class, we could either do 
something like class clusters or we simply pack them in different .m 
files with different categories. Would be more objective-c like than 
the NeoBio thing.

Phil