Has someone benchmarked this?
I could easily stand corrected on this (not tested by me), but I'd
look for a way to touch the variable outPutData "by reference" (in
other words touching as little as possible).
"Put into", I think, has more overhead. In a situation with so much
data, every little bit helps.
I know that in HC, when you put somevariable into tOutVariable, that
the entire tOutVariable gets recreated, not just appended.
Ken Ray has a demonstration of the the use of "by reference" but does
not allude to any speed improvement.
http://www.sonsothunder.com/devres/revolution/tips/scrp003.htm
Also again I could be corrected, but perhaps moving the data from
field "massList" into a variable might speed things up a bit. I'm
wondering that ANY referring to any field from inside such a long
loop is a possible time consumer.
another thing -- the last line in the loop
put "====================" & return after outputData
perhaps that could be a constant, defined at the top of the script
constant kBarDisplay = "===================="
then use this in the loop
put kBarDisplay & return after outputData
this one might have negligible difference, but I haven't tested this.
Thanks to everyone who responded (Mark Schonewille, Mark Smith,
Viktoras Didziulis, Robert Brenstein, apologies if I forgot anyone)
- a whole range of solutions, including arrays, databases and 'just'
variables. Anyway, I coded up the brute force method without any
finess... here's the business bit of the script with some frippery...
put "NEW SEARCH, MASS = " & pepMass & " at " & ppm & " ppm
error" & return after outputData
I ran a brutal test, of 45,000 lines in massList and 16,000 lines in seqDB
My crude attempt seems to be capable, even running within the Rev
IDE, of completing the 720million comparisons in about 30minutes
(OK, admittedly CoreDuo 2.66GHz, 2GB RAM). That's 24million a
minute! (I deliberately put some searches that would match at the
end of seqDB, to be sure I searched through most of the file each
time). I am pretty happy with this, and I'd be looking for at least
a 10-fold gain in speed to code up a harder solution.
Do you experts thing a 10-fold gain is feasible? 100-fold?
Rob
________________________________
Prof R J Beynon[h]
Proteomics and Functional Genomics Group
Faculty of Veterinary Science
University of Liverpool
Crown Street, Liverpool L69 7ZJ
________________________________
Phone: +44 151 794 4312
Fax: +44 151 794 4243
Email: [EMAIL PROTECTED]
http://www.liv.ac.uk/pfg
________________________________
This email was sent on Sun, 15 Jul, 2007 at 8:58 PM.
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stephen barncard
s a n f r a n c i s c o
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