[Biojava-l] Elapsed time of feature filtering

[Y D Sun]

> -----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.

George

>     Thomas.
>