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 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. ---------------------------------------------
-----Original Message-----
From: Hilmar Lapp [mailto:[EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 -------------------------------------------------------------
_______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
