[Biojava-l] regarding code (Richard Holland)

[Richard Holland]

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, biojava-l-request at lists.open-bio.org wrote:
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>>    1. regarding code (indu pandey)
>>    2. Re: regarding code (Richard Holland)
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/