How about 'name = ? or accession = ?' - solves both in that case.
On 18 Jul 2010, at 00:05, Deepak Sheoran 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
>
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
