[Biococoa-dev] New Structure for BioCocoa part I

[Koen van der Drift]

On Jul 3, 2005, at 7:55 AM, Alexander Griekspoor wrote:

> Hi guys,
>
> My apologies for not having jumped in earlier, certainly towards Koen 
> and John I'm sorry, I should have given a summary of the WWDC meeting 
> much earlier. I understand that all of this comes out of the blue, but 
> understand us well, this is all still open for debate. In fact I hope 
> that we will discuss things more elaborate on the list in order to 
> come up with the best implementation. I'll try to summarise the topics 
> discussed at the WWDC and the thoughts behind them below.

Thanks Alex, for compiling this summary. It's good to see lively and 
hopefully fruitful discussion again on the list.

> The really only downside I think is the fact that programming the 
> implementations using strings is somewhat more complex, more c less 
> cocoa, more pointer fiddling, less enumerators. But since in many 
> occasions we already started that to "hack" things faster, and already 
> opted to do the conversions necessary to get at that point, I guess 
> it's not a problem so much. In fact, we can now use many standard char 
> implementations already available (and tested). Of course, if speed is 
> not an issue we can still do it the old way because there is still a 
> way to get the pointer to the symbol for any position.

I really like the idea of using an internal char[] for storing the 
sequence internally, it going to help a lot with implementing a lot of 
algorithms. Since we are using ObjectiveC, this all comes with the 
package, so no need to feel you are hacking things. And probably no 
more need for a BCScanner :)

cheers,

- Koen.