[Bioperl-l] my todo list

[Ewan Birney]

On Wed, 28 Feb 2001, Jason Stajich wrote:

> 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').

I think it is considered "Bad Manners" in Perl to AUTOLOAD a DESTROY
function, which is where this comes from.

This sort of thing makes me dispair of Perl as a OOP lanugage. But that
for another thread entirely...


> 
> 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 :-)
> seconded.  
> > 
> > 	Hilmar
> > -- 
> > -----------------------------------------------------------------
> > Hilmar Lapp                              email: hlapp@gmx.net
> > GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
> > -----------------------------------------------------------------
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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