[Biococoa-dev] (no subject)

Philipp Seibel biococoa at bioworxx.com
Mon Mar 14 03:46:44 EST 2005

Am 14.03.2005 um 09:31 schrieb Alexander Griekspoor:

> On 14-mrt-05, at 9:13, Charles PARNOT wrote:
>> At 9:28 AM +0100 3/12/05, Alexander Griekspoor wrote:
>>> Sounds awesome Charles, great ideas. I guess many algorithms can 
>>> benefit from this approach. It's indeed very wise to "standardize" 
>>> this conversion path and provide some "legal" form to go from 
>>> symbols to c structures and vice versa for performance reasons in 
>>> the case that native use of BCSequences is not possible or does not 
>>> suffice.
>>> Alex
>> At 10:41 PM +0100 3/13/05, Alexander Griekspoor wrote:
>>> Hmmm, somehow I totally miss the reason the remapping. Why would it 
>>> be leaner/faster?
> You are right, sounds pretty contradictory (and is to some extent as 
> Koen made a good point which made me think about it again and see 
> things differently a bit). The point is that I do see the need for a 
> CONVERTION of BCSequences to c structures (i.e., c arrays) that's 
> clear. However I do not see the need for REMAPPING char symbols to 
> different characters.

This is a good point for large sequences. Could be much faster just to 
call +stringWithCString, but we will see.
Oh this discussion is going to make me schizo, too.

> Given that, and Koen's remark, I do not see why this would need a 
> special object and can't be done in two or 3 methods in BCSequence 
> itself. Hope that makes my schizophrenia more explainable ;-) More to 
> follow...

btw: i still like charles version better ;-)


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