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:
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Today's Topics:
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