[Biococoa-dev] Translation

[John Timmer]

> 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% -
>> it's
>> just under .4 seconds now).  ObjC_msgSend is down to about 23%, and
>> testing
>> whether a base in the codon represents one in the sequence is up to
>> about
>> 17.5%.  Since that's the most important step, I view this as a bit of
>> progress.
> 
> 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.

Cheers,

John

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