[Biococoa-dev] testing alignements

Charles PARNOT charles.parnot at stanford.edu
Mon Mar 21 14:52:22 EST 2005

At 9:49 +0100 3/21/05, Alexander Griekspoor wrote:
>>I profiled the code in Shark (on my old iMac G3 400), and found it spends ~35% of the time reading the score matrix. I don't know if it is worth changing the char mapping to find if things are improved? What do you think, guys?
>I would say that depends on a number of things I guess. Let me explain:
>- how well is the code performing right now? Is it slow?

I don't know what fast or slow is supposed to be ;-)
Faster than my eye can follow!

>- is this the only major part the code spends it time in and the rest is fragmented? Then yes, if there's something else where the algorithm stays 50% of the time in, I would first focus on that process
Yes, this is the situation at this point. The rest of the time is spread out over several instructions.

>- are there real reasons to believe that remapping will significantly speed up things, then it's worth trying (don't forget to take the time remapping takes into account for a fair comparison)
I don't know.
I suppose at this point, we would need to write a separate class for the mapping to do fair comparisons and easily test different options, but maybe we will wait for more results from other algorithms and see what our needs are.

Wait and see... I will go back to my 'agenda' for now and work on BCSequence with BCSymbolSet :-)


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Charles Parnot
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