[Biococoa-dev] BCPairwiseAlignment

[Philipp Seibel]

>> Not sure if I like the name BCAlignmentAlgorithm, it screams for 
>> typo's ;)  We could have the result named BCAlignmentResult or 
>> BCSequenceAlignment.
>>
> I agree with you. I like the BCSequenceAlignment version.

So there is my new idea:

You can see a alignment-algorithms as convenient constructors of a 
BCAlignment (or BCSequenceAlignment), so we could have categories for 
BCAlignment like

@interface BCAlignment ( PairwiseAlignment )

+ (BCAlignment *)needlemanWunschAlignment......
+ (BCAlignment *)smithWatermanAlignment....

@end


@interface BCAlignment ( MultipleAlignment )

+ (BCAlignment *)clustalWAlignment.....

@end

so everybody who wants to add alignment algorithms do that in additions 
(categories).

Just another idea ....


Phil