[Biojava-l] regarding code (Richard Holland)

[jitesh dundas]

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 <sheoran143 at gmail.com> 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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