[Bioperl-l] Re: [Biocorba-l] Bioperl biocorba server code checked in

[Jason Stajich]

I fixed these bugs.  Brad if you can run your code some more to see if
this fixes your observed bugs.  I added some more tests to the local
server/client code to test the different cases of SeqFeature.  I know
there needs to be more tests and they ought to be done in a nice perl
manner, I'll see if I can plug away some more later.

On Sat, 10 Feb 2001, Ewan Birney wrote:

> > * Seq::get_SeqFeatures_in_region[_by_type] -- was raising
> > UnableToProcess errors instead of OutOfRange errors.
> > 
fixed 

> 
> 
> > * Seq::get_SeqFeatures_in_region[_by_type] -- trying to use 
> > range->contains on a SeqFeature object and not a range object. Changed
> > to create a range for the SeqFeature, and then check.
added requisite 'use Bio::Range' as well
> > 
> > Not fixed
> > ---------
> > * Seq::get_SeqFeatures_in_region/by_type -- All of these functions first
> > make a call to all_Features, which retrieves BioCorba objects, and not
> > bioperl objects. Then when you try to get a SeqFeature out of a Vector 
> > or Iterator created with these objects, the SeqFeature constructor will
> > die with: "Must have poa and seq into Seq Feature." I didn't want to
> > get too into this, since this would involve rewriting parts of these 
> > implementations -- I'm not sure about the best way to handle it.

fixed.  Calls directly to the underlying _seq method to create the array
of seqs directly.  
> > 
> > * PrimarySeq/AnonymousSeq implementation -- one issue with the way you
> > implemented these as one class is that if a client tries to narrow a
> > PrimarySeq object to the AnonymousSeq interface (which it should be able
> > to do), the server will die since it has no AnonymousSeq implementation
> > to narrow to. The solution to this would be to implement AnonymousSeq
> > separately and then inherit from it with PrimarySeq.
fixed, added AnonymousSeq
> > 
> > * Unknown::query_interface -- Anything I do here causes the server to 
> > crash :-<. If you try to return anything but a CORBA::Object, ORBit
> > will complain about having problems marshalling the object, and if you
> > try to return a CORBA::Object, the server seg-faults. I don't know what
> > to do to just keep this from blowing up. Any thoughts?
> > 

I'll have to think about this, I'm not sure.

> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/