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

[Martina]

I'm using MySQL, biojava-1.4pre1, biosql,v 1.40

Richard HOLLAND wrote:

> 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
>>-------------------------------------------------------------
>>
> 
>