[Biojava-l] Error loading ontology terms

[Richard HOLLAND]

It was never removed, at least not that I'm aware of. Are you using
biojava-live or biojava-1.4, or even 1.3? It should work in 1.4 and
biojava-live, or at least that's the theory. If not, then could you post
complete stacktraces for each of the two kinds of error you mention?

Note that in release 1.5, the whole of org.biojava.bio.seq.db.biosql and
large parts of org.biojava.bio.seq.io will be deprecated, having been
superceded by various parts of org.biojavax. See the
docs/docbook/BioJavaX.xml DocBook document in biojava-live and the
JavaDocs for org.biojavax for details.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Matthew Pocock
> Sent: Thursday, November 24, 2005 11:30 PM
> To: biojava-l at biojava.org
> Cc: Felix Dreher
> Subject: Re: [Biojava-l] Error loading ontology terms
> 
> 
> We had the same problem. We fixed it in a copy of biojava, 
> but my cvs account 
> has been suspended. Somebody there with commit privilages 
> that will roll our 
> fix back in?
> 
> Matthew
> 
> On Thursday 24 November 2005 13:51, Felix Dreher wrote:
> > Hello,
> >
> > we have a problem with the connection to a BioSQL Database.
> > When we start our application for the very first time and 
> try to connect
> > to the Database, it throws an SQLException "Connection is closed."
> > After that, when we simply repeat the process, everything 
> works fine and
> > one can store Sequences in the DB.
> > But when we stop the whole project (which is a 
> JavaServerPages Project
> > inside the Tomcat-Container) and restart it, a new error message
> > appears: "Error loading ontology terms."
> >
> > Maybe somebody has a hint....
> >
> > Greetings,
> > Felix
> >
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