[Bioperl-l] SeqIO parsing

[Allen Smith]

On Sep 24,  2:49pm, Hilmar Lapp wrote:
> On Tuesday, September 24, 2002, at 09:01 AM, Ewan Birney wrote:

> >
> > this scheme in my mind has one *SERIOUS* gotcha. People *have* to write
> > their @ISA's with their implementation tree *first* and their interface
> > inheritance second. Is this ok with people?
> >
> 
> It should be the style everyone employs already. Otherwise you set 
> yourself up for trouble anyway (how would you avoid the interface 
> method stub that throws an exception from being invoked if you put 
> the interface first?).

I'm wanting to make sure that I (and hopefully others!) understand what
you're meaning here. So, in creating a module, the layout should be
something like:

In Bio::Matrix::Substitution:

	use Bio::Root::Root;
	use Bio::Root::IO;
	use Bio::Matrix::SubstitutionI;

	[...]

	@ISA = qw(Bio::Root::Root Bio::Root::IO Bio::Matrix::SubstitutionI);

In Bio::Matrix::SubstitutionI:

	use Bio::Root::RootI;

	[...]

	@ISA = qw(Bio::Root::RootI);

	[bunch of functions, _not_ including 'new' (or the similar 'newIO'), 
	which all look something like:

		sub string {
			my $self = shift;
			$self->throw_not_implemented();
		}
	I do have the problem with this that it appears to lessen the
	utility of $object->can('something'), as I understand it - it would
	be only for optional functions, then?]

This at least seems to work in my preliminary testing, but I'm afraid that I 
find the whole implementation/interface distinction - actually, object
orientation in general - difficult to get, so I'm nervous about this...

	Thanks,

	-Allen

-- 
Allen Smith			http://cesario.rutgers.edu/easmith/
September 11, 2001		A Day That Shall Live In Infamy II
"They that can give up essential liberty to obtain a little temporary
safety deserve neither liberty nor safety." - Benjamin Franklin