[Biococoa-dev] Optimizations

Koen van der Drift kvddrift at earthlink.net
Tue Mar 15 20:20:47 EST 2005

On Mar 15, 2005, at 7:29 PM, John Timmer wrote:

> 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.
> Returning an array from the method doesn't enter into this issue, and
> definitely should not be changed.
> I may be obsessing about this, but my tests earlier today showed that 
> the
> non-strict version of the code to take 4-5X the time to execute 
> compared to
> the strict one.  In a 1.2Kb sequence, it's the difference between 
> barely
> perceptible and wondering whether something's broken.

Ah, I see what you mean now, and yes, a BCSymbolSet could be much 
faster. I think the symbolsets are ready for use (is that right, 
Charles?). What's missing so far is that they have not been implemented 
to the BCSequence code yet.

- Koen.

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