[Bioperl-l] my todo list

Jason Stajich jason@chg.mc.duke.edu
Wed, 28 Feb 2001 12:37:48 -0500 (EST)

On Wed, 28 Feb 2001, Hilmar Lapp wrote:

> Jason Stajich wrote:
> > 
> > On Tue, 27 Feb 2001, Jason Stajich wrote:
> > 
> > > I am looking at the tempfile creation and cleanup, it seems to work in the
> > > test case I built in t/Tempfile.t, but I will try and investigate further.
> > > So later this afternoon I hope to close the following bugs off:
> > >
> > > - bug #246 (location parsing not working for certain cases with a
> > >   specified seq_id)
> > fixed
> > > - tempfiles not being cleaned up properly.
> > 
> > Fixed, I had added an empty DESTROY method to Bio::Root::RootI, since
> Now I see. The DESTROY in IO.pm wasn't executed because it came
> second in multiple inheritance, right? Does this mean that a
> DESTROY method is potentially harmful in RootI.pm? Not good, even
> though we don't need it yet. So, assuming my guess of the reason
> is right, can we add a method _io_cleanup() (or whatever name, but
> not a very common one) to IO.pm, and in RootI.pm a DESTROY method
> that calls $self->_io_cleanup() if $self->can('_io_cleanup').

Exactly!  This took a little digging.  I think the choice may be dependent
on the order in the ISA.  This is why C++ only allows inheritance from a
single object.  Actually proper behavior would be to either change the
order of the ISA list so the Root::IO comes first OR make the object just
inherit from Bio::Root::IO since IO isa Bio::Root::RootI.  OF course that
is not really as clean as I would like it to be but would work.

> Not very clean though. Just an idea. My feeling is that the
> requirement of keeping DESTROY out of RootI.pm calls for trouble. 

Me too.  We can do chained DESTROY, but that will only work if RootI is
last in the ISA list ( I *think* that will work)..

> > 
> > > - additional bugs for biocorba that Brad C has found.  (these are in
> > >   bioperl-corba-server code).
> > Not done, low priority, release should be done first. IMHO.
> Exactly. (Hoping that the bugs are rather not in the BioPerl code;
> otherwise we'll do a quick 0.7.1 :-)
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
> -----------------------------------------------------------------

Jason Stajich
Center for Human Genetics
Duke University Medical Center