[Biojava-l] RE: [BioSQL-l] location in features

[Richard HOLLAND]

Hullo Martina.

I must admit I am confused. I have been using BioJava+BioSQL to load
Genbank records with features with no trouble, they always come out
again with no exceptions raised and none missing. I am using Oracle, but
this shouldn't make a difference as the SQL code that looks for features
is the same for all database types at present.

Can I ask what database type you are using (MySQL, Oracle etc.), and the
versions of BioJava and BioSQL you have?

I'd also suggest downloading biojava-live from CVS, if you haven't done
so already, and trying that to see if someone has already fixed your
problem.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gnf.org] 
> Sent: Thursday, April 28, 2005 2:51 AM
> To: Martina
> Cc: OBDA BioSQL; BioJava; Richard HOLLAND; Mark Schreiber
> Subject: Re: [BioSQL-l] location in features
> 
> 
> Hi Martina, people on the biojava mailing list will probably 
> be better 
> able to help you out. Also, Richard and Mark have been working on 
> getting Biojava interoperate better with the standard biosql schema. 
> They may know better where your issue is coming from.
> 
> 	-hilmar
> 
> On Apr 27, 2005, at 8:27 AM, Martina wrote:
> 
> > Hi,
> > I can't get rid of this exception:
> > org.biojava.bio.BioRuntimeException: BioSQL SeqFeature doesn't have 
> > any associated location spans. seqfeature_id=148
> >
> > Can anybody help me?
> >
> > put the sequence in:
> >
> > Sequence seq = DNATools.createDNASequence(sequence, "AF100928");
> > Feature.Template templSeq = new Feature.Template();
> > 		templSeq.source = "ncbi";
> > 		templSeq.type = "gen";
> > 		templSeq.location = Location.empty;
> > 		seq.createFeature(templSeq);
> > db.addSequence(seq);
> >
> > get it out:
> > seq = db.getSequence("AF100928");
> > System.out.println(seq.getName() + " contains " + 
> seq.countFeatures()
> > 					+ " features");	
> >
> > seq.getName() works fine, but the seq doesn't have any 
> features, but I 
> > can see them in the db.
> >
> > What am I missing here?
> >
> > Martina
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at open-bio.org
> > http://open-bio.org/mailman/listinfo/biosql-l
> >
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
>