[Biojava-l] Elapsed time of feature filtering

[David Huen]

On Monday 09 Jun 2003 6:43 pm, Y D Sun wrote:
> > -----Original Message-----
> > From: Thomas Down [mailto:thomas at derkholm.net]
> > Sent: 09 June 2003 18:27
> > To: Y D Sun
> > Cc: biojava-l at biojava.org
> > 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