[Biococoa-dev] BCSequence implementation

Alexander Griekspoor mek at mekentosj.com
Thu Feb 24 04:32:34 EST 2005

On 24-feb-05, at 6:56, Charles PARNOT wrote:

> * NSArray of BCSymbols vs arrays of chars: I am on John and Alex's 
> side; the object might be bigger, but not much much bigger; 
> performance may be an issue at some point but it is difficult to 
> really predict what is going to happen until you face the issue; in 
> which case translating back and forth to a different structure might 
> make sense if the performance is an issue  (in that I don't completely 
> agree with Alex)

I was talking here specifically about the conversion to NSString and 
back. I guess, most of us have previously used NSString for their 
sequence related methods like reverse complement for example. So the 
easiest way to implement your old work would be BCSequence -> NSString 
-> your old code -> NSString -> BCSequence. The whole argument I wanted 
to make is that in my opinion NSString does/should not have an 
advantage over our BCSequence, in contrast it should perform worse 
because of the benefits we described previously (if that isn't the case 
then we should make it that way, a primary condition). Both are cocoa 
objects. So the point I wanted to make is that if we implement old-code 
based on NSString, we should convert it to work natively with 
BCSequence objects (otherwise you'll get the same situation John just 
described about the overhead if you work natively with char arrays). 
BUT having said that, if a critical bottleneck can be resolved  by 
using more primitive C type structures like char arrays or the Core 
Foundation classes, yes then it might make sense to do a conversion. 

                      ** Alexander Griekspoor **
                The Netherlands Cancer Institute
                Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                  AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

    The requirements said: Windows 2000 or better.
    So I got a Macintosh.


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