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 buffered > > MySQL table, which is searched by a MySQL UDF, which does the bitstring > > comparison on the fingerprints. > > Stefan, do I remember correctly that this can be done in a fraction of a > > second? > > > > Of course, one can do this by reading the fingerprints from the database > > into memory (at startup and then every now and then updated by a cron > > job) and doing the fingerprint screening with regular java. That should > > 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 a second. Not sure if this would take longer via jdbc. Never tried the comparision in java, so I can't say how long it takes. Stefan > > Cheers, > > .../Ola -- Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 My public PGP key is available at http://pgp.mit.edu ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_idv37&alloc_id865&op=click _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
