[Biococoa-dev] can't compile framework

[Koen van der Drift]

On Mar 8, 2005, at 3:08 PM, Philipp Seibel wrote:

> I want to start with the BCAlignment stuff and there are many things 
> to discuss:
>
> 1. what exactly do we want an BCAlignment to be ?
> 	A slim Datastructure for different Alignment algorithms
> 	Or a comfortable datastructure, which is perhaps not very useful for 
> programs concentrating on performance


Although I have not much experience with alignments, I would suggest 
that we go for the first option. If programmed cleverly, it should 
allow for expansion to more sophisticated calculations. This expansion 
can be done within BioCocoa, or by the user of the framework.

>
> 2. We need a BCMatrix (protocol or class) for substitution matrices

Could you please explain this in a littile more detail? My 
understanding of alignment calculations is that these are very 
complicated and need a lot of processing power (correct me if I am 
wrong). Therefore we should consider using C directly, without much 
overhead of ObjC classes.

- Koen.