[Biococoa-dev] Translation

John Timmer jtimmer at bellatlantic.net
Wed Sep 1 20:04:11 EDT 2004

> Ugh - the code works and is a lot cleaner and easier to follow, but takes
> twice as long.  Looks like I'm going to have to learn to use the performance
> tools to figure out where the hangups are.
> I'm at home, so I can't commit it to CVS, but I'll send everything necessary
> for anyone who wants to look it over.

I had a brief window where bioinformatics.org appeared, and I added a bunch
of stuff then, so the code may be visible.  It requires a different .plist
format which I didn't manage to upload, though, so it is currently

Shark turned out to be incredibly easy to use.  I just looped through the
translation 100 times while sampling, and out popped a list of what's being
done sorted by percent of CPU use.  About 28% of the time is being used by
ObjC_msgSend, another 17% or so with array index related stuff.

This isn't really surprising, given that we've injected another object layer
(the codons) into the process.  I'm thinking I might be able to remove the
BCSequenceDNA from the codon and just store all three bases as variables,
and pull the array out of the sequence being translated and deal with the
base array directly - both of these should cut down on the messaging

Hopefully, a positive report later this evening -


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