On Monday 09 Jun 2003 6:43 pm, Y D Sun wrote: > > -----Original Message----- > > From: Thomas Down [mailto:[EMAIL PROTECTED] > > Sent: 09 June 2003 18:27 > > To: Y D Sun > > Cc: [EMAIL PROTECTED] > > Subject: Re: [Biojava-l] Elapsed time of feature filtering > > > > > > Just to double-check... I presume you're still talking about > > code of the form: > > > > SequenceDB seqdb = new BioSQLSequenceDB(...); > > Sequence seq = seqdb.getSequence("foo"); > > FeatureHolder cds = seq.filter(new FeatureFilter.ByType("CDS")); > > Yes. > > > If the time to do that shows any strong dependancy on the > > number of sequences in the database, I'd suggest that this is > > (very) strong evidence of missing/corrupted indices. Are you > > using the tweaked schema I sent to you last week? Are you > > still of PostgreSQL, or have you tried MySQL? > > I am using the schema you sent to me on Friday 6 June and PostgreSQL. I > create a new database and run the new scheme you sent to me along with > biosqldb-assembly-pg.sql and biosql-accelerators-pg.sql downloaded from > http://biojava.org/download/biosql/. I haven't tried MySQL. > I think biosqldb-assembly-pg.sql and biosql-accelerators-pg.sql from that URL were specifically created for the old schema. I haven't had a look to see if they are applicable to the new one. They may well be inappropriate. Thomas?
Regards, David Huen _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
