The revamped BioJava/BioSQL classes will expose the rank to the user for all tables which have ranks.
cheers, Richard -----Original Message----- From: [EMAIL PROTECTED] on behalf of Simon Foote Sent: Wed 6/22/2005 12:15 AM To: Martina Cc: Hilmar Lapp; [EMAIL PROTECTED]; BioJava; [EMAIL PROTECTED] Subject: Re: [Biojava-l] Re: [BioSQL-l] _removeSequence Hi Martina, In fact you can, as rank is the field that allows this to happen. In Biojava, currently it's just a linearily incremented number such that you can have the same type and source IDs for a given bioentry. For example, adding a Genbank entry with 10 CDS features for 1 bioentry will give you identical keys for bioentry_id, type_term_id and source_term_id, but will have a rank of 1 - 10 for each. Simon Martina wrote: > That means, that I can't have 2 features refering to the same bioentry > with the same type (= type_term_id)and source (=source_term_id) but > different parent features because of the composite key bioentry_id in > the seqfeature table? Or what does "rank" in that table mean (its part > of that key), how can I get different ranks? > > Martina > > Hilmar Lapp wrote: > >> The Biojava people will respond to this. Note though that >> Term_Relationship is for storing subject-predicate-object triples of >> terms, so I'm not sure why you want to use it for storing/associating >> annotation. Maybe you meant bioentry_qualifier_value? >> >> -hilmar >> >> On Jun 21, 2005, at 3:10 AM, Martina wrote: >> >>> >>>> Yes. When you insert a sequence you must be prepared that when >>>> inserting its ontology term or tag/value annotation the term may >>>> already be present because another bioentry uses it too. >>> >>> >>> >>> Ok, the proper way is to catch the SQLException in BIOSQLFeature, >>> test if it is a Dublicate key entry, get the identifier of the term >>> (would that be the BioSQLfeatureId ?) and insert it in the >>> term_relationship table? And there is no nice BioJava method for >>> this, I have to do it "manually", like conn.prepareStatement(..) and >>> stuff? BioJava spoiled me so! >>> >>> Martina >>> > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l -- Bioinformatics Programmer Pathogen Genomics Institute for Biological Sciences National Research Council of Canada [T] 613-990-0561 [F] 613-952-9092 [EMAIL PROTECTED] _______________________________________________ BioSQL-l mailing list [EMAIL PROTECTED] http://open-bio.org/mailman/listinfo/biosql-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
