jtimmer at bellatlantic.net
Sat Sep 4 10:22:27 EDT 2004
> I seem to be missing BCGeneticCodeName, I get a bunch of errors related
> to that. Did you forget to commit that file?
I told Xcode to add it, but I had created a "Translation" folder, so it
failed to add this properly. I've gone in and fixed things manually now.
Sorry about that
>> The time is down by a bit, but not a whole lot (maybe about 10-15% -
>> just under .4 seconds now). ObjC_msgSend is down to about 23%, and
>> whether a base in the codon represents one in the sequence is up to
>> 17.5%. Since that's the most important step, I view this as a bit of
> maybe you can speed up by changing this:
> [theOutput setString: [aString addSpacesToStringWithInterval:5]];
> to this:
> [theOutput setString: aString];
No, I was checking timings separate from generating the output to
specifically avoid this sort of thing.
Anyway, I checked in code that cuts the time spent translating more than in
half. I did some thinking and I'm pretty sure that the way the code's
written, if one potential codon matches, there's not a chance that a codon
for a different a.a. would also match. There's a chance my thinking's
wrong, so if anybody has sequences filled with ambiguous bases, I recommend
giving it a try and let me know if there are any inaccuracies.
Given that I'm happy with the speed now, I'll spend some time cleaning up
the codons/genetic codes and then work on creating a BCSequenceCodon.
This mind intentionally left blank
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