package GDxBase::GeneModel::Specification;

=head1 NAME

 GDxBase::GeneModel::Specification

=head1 SYNOPSIS

 A base class for all gene models - not for direct use.

=head1 DESCRIPTION

 A generic class for the display of gene models.
 This class alone is not sufficient to display a gene model; in fact,
 there's not much in it all at the moment. A more specific subclass,
 such as GDxBase::GeneModel::Specification::GFF, must be defined to override the 'get_features'
 method. The criteria for the format of the features that are returned
 by subclasses are fairly liberal - for rendering, the features are passed
 directly to the 'add_track' method of the Bio::Graphics::Panel, which is
 pretty good at displaying anything you throw at it in a sensible way.


 Last Revision: 9-Aug-06

=head1 See Also

 GDxBase::GeneModel::Collection
 GDxBase::GeneModel::Specification::GFF
 GDxBase::GeneModel::Specification::Consensus
 GDxBase::GeneModel::Specification::Summary

=head1 Author

 James Allen
 Email: james.allen@cimr.cam.ac.uk

=head1 Copyright

 Copyright 2006 James Allen, DIL

=cut

use warnings;
use strict;
use Carp;

use Class::AutoClass;

our @ISA = "Class::AutoClass";

our (@AUTO_ATTRIBUTES, %DEFAULTS);
@AUTO_ATTRIBUTES = qw(source);
%DEFAULTS = ();

Class::AutoClass::declare(__PACKAGE__);

################################################################################

=head1 METHODS

=cut

=head2 _init_self

 Title:		_init_self
 Function:	Create a new GDxBase::GeneModel::Specification object
 Usage:		$gm = GDxBase::GeneModel::Specification->new($source)
 Args:		source - mandatory, e.g. EnsEMBL, UCSC
 Returns:	A GDxBase::GeneModel::Specification object

=cut

sub _init_self {
	my $self = shift;

	confess "A source (e.g. Ensembl) must be supplied" unless $self->source;
}

################################################################################

=head2 get_features

 Title:		get_features
 Function:	Return a set of features for the gene (and possibly build)
		specified in a GDxBase::GeneModel::Collection object
 Usage:		($features, $start, $stop) =
			GDxBase::GeneModel::Specification->get_features($gmc, $config_values)
 Args:		gmc - mandatory, a GDxBase::GeneModel::Collection object
		config_values - optional, a hash of config-ini settings
 Returns:	An array of feature objects
		The start and stop values for the gene model as integer values
 Notes:		Must be overridden in a subclass

=cut

sub get_features {
	confess "The 'get_features' method must be overridden in a subclass.\n";
}

################################################################################
1;