[Biococoa-dev] Optimizations

Alexander Griekspoor a.griekspoor at nki.nl
Wed Mar 16 13:13:39 EST 2005

On 16-mrt-05, at 1:29, John Timmer wrote:
>> Where do you want to use an NSSet, as a return value for findSequence?
>> The advantage of the array is that the found sequences are in the
>> 'right order'.
> Sorry for my lack of clarity.  Shark says that over 30% of the 
> execution
> time in the "findSequence" method is spent checking whether one symbol
> represents another.  Currently, that's done by checking whether the
> submitted symbol occurs in the array of represented symbols.  
> According to
> the docs, making the represented symbols a set instead of an array will
> speed this up significantly.

It would make sense to turn the representedsymbols as a NSSet, there's 
no specific order to keep in mind, so go ahead. Be careful though how 
to implement this in combination with the aminoacid template plist we 
use. I don't believe NSSet can be used directly in a plist, so you 
perhaps have to do the conversion from the array you get from the 

                         ** Alexander Griekspoor **
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