Bioperl: Q: Objects in C++ or Java

[Ewan Birney]

On Thu, 17 Jun 1999, Richard Bruskiewich wrote:


> On Thu, 17 Jun 1999, gert thijs wrote:
> 
> > Hello,
> > 
> > I know this question is slightly off topic, but I presume some of you are also
> > working with other programming languages. Does anyone know where I can find
> > some object classes in C++ or Java to access GENBANK or EMBL to download DNA
> > sequences? 
> > Or if those don't exist, do you know where I can find information on how to
> > write my own objects to access databases.

You can check out CORBA access to the EBI database via
http://corba.ebi.ac.uk/. I wrote my own slimmed down C-client to this
(called cfetch) which is linked in at
http://corba.ebi.ac.uk/EMBL_demos.html. It uses ORBit as the ORB (which is
my *favourite* ORB, but I am biased...).

Problem - the EBI CORBA server is not kept 100% up to date with the EMBL
database yet (annoyingly). This has been promised for a while... 


Writing a C++ client should be fine but a little long winded. I know that
Artemis uses this (check out web pages at 
http://www.sanger.ac.uk/Software/Artemis/) via Java. Both Kim Rutherford
(kmr@sanger.ac.uk) and Michele Clamp (michele@sanger.ac.uk) have Java code
for EMBL/swissprot feature tables, and are very good coders. You could
get in touch with them...


For generic C object based libraries - the Wise2 package has an underlying
object model which can be loaded into Perl via XS. I like it... but I am
the author of it <grin>. Go to http://www.sanger.ac.uk/Software/Wise2/
if you want and... well... probably ask why anyone would write a software
package like this in C ;).




> > 
> > Thanks,
> > 
> > Gert Thijs
> > 
> > 
> > 
> > -- 
> > ==========================================================
> > + Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
> > +                                                        +
> > + Dept. Elektrotechniek ESAT-SISTA                       +
> > + Kardinaal Mercierlaan, 94                              +
> > + B-3001 HEVERLEE  Belgium                               +
> > + Tel :  +32-16-32 18 84 ---- Fax : +32-16-32 19 70      +
> > ==========================================================
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> 
> ========================================================
> Dr. Richard Bruskiewich		<rbsk@sanger.ac.uk>
> 	WWW: http://www.sanger.ac.uk/Users/rbsk/
> Human Analysis/Bioinformatics
> The Sanger Centre		Tel:  +44-(0)1223-834244
> Wellcome Trust Genome Campus,	Fax:  +44-(0)1223-494919
> Hinxton, Cambridge   CB10 1SA
> United Kingdom
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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