# Copyright 2008-2010 Tim Rayner
#
# This file is part of Bio::MAGETAB.
#
# Bio::MAGETAB is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# Bio::MAGETAB is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Bio::MAGETAB. If not, see <http://www.gnu.org/licenses/>.
#
# $Id: Material.pm 340 2010-07-23 13:19:27Z tfrayner $
package Bio::MAGETAB::Material;
use Moose;
use MooseX::FollowPBP;
use MooseX::Types::Moose qw( Str ArrayRef );
BEGIN { extends 'Bio::MAGETAB::Node'; };
# This is an abstract class; block direct instantiation.
sub BUILD {
my ( $self, $params ) = @_;
if ( blessed $self eq __PACKAGE__ ) {
confess("ERROR: Attempt to instantiate abstract class " . __PACKAGE__);
}
return;
}
has 'name' => ( is => 'rw',
isa => Str,
required => 1 );
has 'materialType' => ( is => 'rw',
isa => 'Bio::MAGETAB::ControlledTerm',
clearer => 'clear_materialType',
predicate => 'has_materialType',
required => 0 );
has 'description' => ( is => 'rw',
isa => Str,
clearer => 'clear_description',
predicate => 'has_description',
required => 0 );
has 'characteristics' => ( is => 'rw',
isa => ArrayRef['Bio::MAGETAB::ControlledTerm'],
auto_deref => 1,
clearer => 'clear_characteristics',
predicate => 'has_characteristics',
required => 0 );
has 'measurements' => ( is => 'rw',
isa => ArrayRef['Bio::MAGETAB::Measurement'],
auto_deref => 1,
clearer => 'clear_measurements',
predicate => 'has_measurements',
required => 0 );
__PACKAGE__->meta->make_immutable();
no Moose;
=pod
=head1 NAME
Bio::MAGETAB::Material - Abstract material class
=head1 SYNOPSIS
use Bio::MAGETAB::Material;
=head1 DESCRIPTION
This class is an abstract class from which all MAGE-TAB Material
classes (Source, Sample, Extract, LabeledExtract) are derived. It
cannot be instantiated directly. See the L<Node|Bio::MAGETAB::Node> class for
superclass methods.
=head1 ATTRIBUTES
=over 2
=item name (required)
The name of the material (data type: String).
=item materialType (optional)
The type of the material (e.g. 'whole_organism', 'organism_part',
'RNA' etc.), usually from a suitable ontology (data type:
Bio::MAGETAB::ControlledTerm).
=item description (optional)
A free-text description of the material. In general the use of this
attribute is discouraged due to the difficulty of computationally
parsing natural languages (data type: String).
=item characteristics (optional)
A list of characteristics of the material. These may describe any
aspect of the material, and should ideally be taken from an
appropriate ontology (data type: Bio::MAGETAB::ControlledTerm).
=item measurements (optional)
A list of measurements of the material. These may describe any
measurable property of the material. Units are handled by the
Measurement class (data type: Bio::MAGETAB::Measurement).
=back
=head1 METHODS
Each attribute has accessor (get_*) and mutator (set_*) methods, and
also predicate (has_*) and clearer (clear_*) methods where the
attribute is optional. Where an attribute represents a one-to-many
relationship the mutator accepts an arrayref and the accessor returns
an array.
=head1 SEE ALSO
L<Bio::MAGETAB::Node>
=head1 AUTHOR
Tim F. Rayner <tfrayner@gmail.com>
=head1 LICENSE
This library is released under version 2 of the GNU General Public
License (GPL).
=cut
1;