# 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: ArrayDesign.pm 340 2010-07-23 13:19:27Z tfrayner $
package Bio::MAGETAB::ArrayDesign;
use Moose;
use MooseX::FollowPBP;
use MooseX::Types::Moose qw(Str ArrayRef);
use Bio::MAGETAB::Types qw(Uri);
BEGIN { extends 'Bio::MAGETAB::DatabaseEntry' };
has 'name' => ( is => 'rw',
isa => Str,
required => 1 );
has 'version' => ( is => 'rw',
isa => Str,
clearer => 'clear_version',
predicate => 'has_version',
required => 0 );
has 'uri' => ( is => 'rw',
isa => Uri,
clearer => 'clear_uri',
predicate => 'has_uri',
coerce => 1,
required => 0 );
has 'provider' => ( is => 'rw',
isa => Str,
clearer => 'clear_provider',
predicate => 'has_provider',
required => 0 );
has 'technologyType' => ( is => 'rw',
isa => 'Bio::MAGETAB::ControlledTerm',
clearer => 'clear_technologyType',
predicate => 'has_technologyType',
required => 0 );
has 'surfaceType' => ( is => 'rw',
isa => 'Bio::MAGETAB::ControlledTerm',
clearer => 'clear_surfaceType',
predicate => 'has_surfaceType',
required => 0 );
has 'substrateType' => ( is => 'rw',
isa => 'Bio::MAGETAB::ControlledTerm',
clearer => 'clear_substrateType',
predicate => 'has_substrateType',
required => 0 );
has 'printingProtocol' => ( is => 'rw',
isa => Str,
clearer => 'clear_printingProtocol',
predicate => 'has_printingProtocol',
required => 0 );
has 'sequencePolymerType' => ( is => 'rw',
isa => 'Bio::MAGETAB::ControlledTerm',
clearer => 'clear_sequencePolymerType',
predicate => 'has_sequencePolymerType',
required => 0 );
has 'designElements' => ( is => 'rw',
isa => ArrayRef['Bio::MAGETAB::DesignElement'],
auto_deref => 1,
clearer => 'clear_designElements',
predicate => 'has_designElements',
required => 0 );
has 'comments' => ( is => 'rw',
isa => ArrayRef['Bio::MAGETAB::Comment'],
auto_deref => 1,
clearer => 'clear_comments',
predicate => 'has_comments',
required => 0 );
__PACKAGE__->meta->make_immutable();
no Moose;
=pod
=head1 NAME
Bio::MAGETAB::ArrayDesign - MAGE-TAB array design class
=head1 SYNOPSIS
use Bio::MAGETAB::ArrayDesign;
=head1 DESCRIPTION
This class is used to store information about array designs in
MAGE-TAB. This class can represent information from an ADF, or a
reference to an array design in a database. See
the L<DatabaseEntry|Bio::MAGETAB::DatabaseEntry> class for superclass methods.
=head1 ATTRIBUTES
=over 2
=item name (required)
The name of the array design (data type: String).
=item version (optional)
The version of the array design (data type: String).
=item uri (optional)
A URI for the array design (data type: Uri).
=item provider (optional)
The provider (typically the manufacturer) of the array design (data
type: String).
=item technologyType (optional)
The technology type of the array (data type:
Bio::MAGETAB::ControlledTerm).
=item surfaceType (optional)
The surface type of the array (data type:
Bio::MAGETAB::ControlledTerm).
=item substrateType (optional)
The substrate type of the array (data type:
Bio::MAGETAB::ControlledTerm).
=item printingProtocol (optional)
The protocol used for printing the array (data type: String).
=item sequencePolymerType (optional)
The sequence polymer type of the array (data type:
Bio::MAGETAB::ControlledTerm).
=item designElements (optional)
A list of array design elements (Features, Reporters and
CompositeElements) describing the array (data type:
Bio::MAGETAB::DesignElement).
=item comments (optional)
A list of user-defined comments for the array design (data type:
Bio::MAGETAB::Comment).
=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::DatabaseEntry>
=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;