[Biojava-l] Getting feature by qualifier_value

[Augusto Fernandes Vellozo]

Hi Richard,

The problem is to obtain the sequence object, because the sequence object I
require depends on the seqfeature_qualifier_value.
I don't have the sequence object, i need to search and obtain the sequence
related to one value stored in seqfeature_qualifier_value.
I know how to do this using SQL query directly, but i don't know how do this
using hibernate.

Thanks,

Augusto

2008/9/12 Richard Holland <holland at eaglegenomics.com>

> Augusto,
>
> If you can adapt Zagato's code to load the sequence object you
> require, then you will find the seqfeature_qualifier_value entries are
> accessible by iterating over the sequence object's features then
> within each feature iterating over the Notes.
>
> cheers,
> RIchard
>
> 2008/9/11 Zagato <zagato.gekko at gmail.com>:
> > The proccess to get an object using hibernate it's something like this:
> >
> > TestClass // This is the class
> > objTestClass // this is the object from the class
> >
> > @@@@@@@@@@
> >
> > TestClass objTestClass = null;
> > hbn_session.clear();
> > Query query = hbn_session.createQuery( "from TestClass where attribute =
> > :attribute" );
> > query.setParameter("attribute", 55); // Here you set the value for the
> > specific where..
> > List list = query.list(); // You get the result that match
> > if( list.size() == 1 )
> >                        objTestClass = (TestClass)list.get(0);
> >
> > Remenber, you must have the map file in xml to hibernate, i don't
> remember
> > well but in the documentacion from biojava it's a better example...
> > (
> http://www.biojava.org/wiki/BioJava:Cookbook#BioSQL_and_Sequence_Databases
> )
> >
> > I hope this helps you.. Bye !!!
> >
> > Alan Jairo Acosta
> >
> >
> > On Thu, Sep 11, 2008 at 4:54 AM, Augusto Fernandes Vellozo <
> > augustovmail-java at yahoo.com.br> wrote:
> >
> >> Hi all.
> >>
> >> I don't know very well hibernate, and I am with problems to do one query
> >> into database BIOSQL using Biojavax.
> >>
> >> Given one organism (NVBITaxon), I need to get the feature with one
> specific
> >> value of one property (field value of table SeqFeature_qualifier_value).
> >>
> >> Please, somebody knows how can i do this?
> >>
> >> Thanks a lot,
> >>
> >> --
> >> Augusto F. Vellozo
> >>
> >>
> >>
> >> --
> >> Augusto F. Vellozo
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
> >
> >
> > --
> > Farewell.
> > http://www.youtube.com/zagatogekko
> > ruby << __EOF__
> >  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
> > __EOF__
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> Richard Holland, BSc
> Finance Director, Eagle Genomics Ltd
> M: +44 7500 438846 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>



-- 
Augusto F. Vellozo