[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.
Absolutely.
Alex
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** Alexander Griekspoor **
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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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