Re: SV: Re: SV: Re: [Cdk-user] Where is the DBReader class

[Stefan K. <ste...@un...>]

Am Friday 30 December 2005 23:59 schrieb Ola Spjuth:
> On Fri, 2005-12-30 at 15:34, Christoph Steinbeck wrote:
> > You need some way of in-memory presreening for fast substructure
> > searching. And this cannot be done efficiently with SQL functions.
> > In NMRShiftDB, we do this with fingerprints stored in a special buffe=
red
> > MySQL table, which is searched by a MySQL UDF, which does the bitstri=
ng
> > comparison on the fingerprints.
> > Stefan, do I remember correctly that this can be done in a fraction o=
f a
> > second?
> >
> > Of course, one can do this by reading the fingerprints from the datab=
ase
> > into memory (at startup and then every now and then updated by a cron
> > job) and doing the fingerprint screening with regular java. That shou=
ld
> > work equally well.
>
> How long does it take to read a reasonable-sized table of fingerprints
> stored as bit-strings into memory? How long does the actual comparison
> take (in java, not UDF)? Just curious...

Hard to say. A select for the fingerprints on 15000 nmrshiftdb rows takes=
 half=20
a second. Not sure if this would take longer via jdbc. Never tried the=20
comparision in java, so I can't say how long it takes.
Stefan

>
> Cheers,
>
>    .../Ola

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
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