# 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: Protocol.pm 340 2010-07-23 13:19:27Z tfrayner $
package Bio::MAGETAB::Protocol;
use Moose;
use MooseX::FollowPBP;
use MooseX::Types::Moose qw( Str );
BEGIN { extends 'Bio::MAGETAB::DatabaseEntry' };
has 'name' => ( is => 'rw',
isa => Str,
required => 1 );
has 'text' => ( is => 'rw',
isa => Str,
clearer => 'clear_text',
predicate => 'has_text',
required => 0 );
has 'software' => ( is => 'rw',
isa => Str,
clearer => 'clear_software',
predicate => 'has_software',
required => 0 );
has 'hardware' => ( is => 'rw',
isa => Str,
clearer => 'clear_hardware',
predicate => 'has_hardware',
required => 0 );
has 'protocolType' => ( is => 'rw',
isa => 'Bio::MAGETAB::ControlledTerm',
clearer => 'clear_protocolType',
predicate => 'has_protocolType',
required => 0 );
has 'contact' => ( is => 'rw',
isa => Str,
clearer => 'clear_contact',
predicate => 'has_contact',
required => 0 );
__PACKAGE__->meta->make_immutable();
no Moose;
=pod
=head1 NAME
Bio::MAGETAB::Protocol - MAGE-TAB protocol class
=head1 SYNOPSIS
use Bio::MAGETAB::Protocol;
=head1 DESCRIPTION
This class is used to describe experimental protocols in MAGE-TAB. It
can either contain all the information about a protocol itself, or it
can link to a protocol entry in a suitable database via its
superclass. See the L<DatabaseEntry|Bio::MAGETAB::DatabaseEntry> class for superclass methods.
=head1 ATTRIBUTES
=over 2
=item name (required)
The name of the protocol (data type: String).
=item text (optional)
A free-text description of the protocol, giving all the steps in the
procedure (data type: String).
=item software (optional)
The software used in the protocol. Multiple softwares must be
concatenated into a single value (data type: String).
=item hardware (optional)
The hardware used in the protocol. Multiple hardwares must be
concatenated into a single value (data type: String).
=item protocolType (optional)
The type of the protocol ('nucleic_acid_extraction','labeling' etc.;
data type: Bio::MAGETAB::ControlledTerm).
=item contact (optional)
A contact for more information on the protocol. Multiple contacts must
be concatenated into a single value (data type: String).
=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;