Thanks Deepak for updating us. I have just starting updating the latest version on my laptop.I am going through the code and I will update you what is wrong with this code. Your point though,seems valid.
Thanks, JD On 7/18/10, Deepak Sheoran <[email protected]> wrote: > The problem which I think Indu Pandey is having is with following > method from latest version of biojava: > > public RichSequence getRichSequence(String id) throws > IllegalIDException, BioException { > try { > // Build the query object > String queryText = "from Sequence where name = ?"; > **************///// instead of "name" it should be "accession" > Object query = this.createQuery.invoke(this.session, new > Object[]{queryText}); > // Set the parameters > query = this.setParameter.invoke(query, new Object[]{new > Integer(0), id}); > // Get the results > List result = (List)this.list.invoke(query,(Object[]) null); > // If the result doesn't just have a single entry, throw an > exception > if (result.size()==0) throw new IllegalIDException("Id not > found: "+id); > else if (result.size()>1) throw new > IllegalIDException("Multiple records found with that id - use > getRichSequences: "+id); > // Return the found object, if found - null if not. > return (RichSequence)result.get(0); > } catch (Exception e) { > // Throw the exception with our nice message > throw new RuntimeException("Error while trying to load by > id: "+id,e); > } > } > > Either biojava or Indu should change this method from having "name" to > "accession" because in biosql.bioentry table "name" and "accession" are > not same, in most case they are equal, but its not necessary. Thus even > if you are querying the database with a valid accession number you won't > get any record back in some cases. Also we should update the > documentation which indicate that it query "name" column from bioentry > table and not the accession column. > > Deepak Sheoran > > > > > > > On 7/17/2010 11:00 AM, [email protected] wrote: >> Send Biojava-l mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Biojava-l digest..." >> >> >> Today's Topics: >> >> 1. regarding code (indu pandey) >> 2. Re: regarding code (Richard Holland) >> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
