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package Bio::Tools::Motif::Pattern;
# This program 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.
# This program 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 this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
# OVERVIEW
# PSORT-B is described in Gardy, J.L. et al (2003). PSORT-B:
# improving protein subcellular localization prediction for
# Gram-negative bacteria. Nuc Acids Res 31(13):3613-17. Please
# cite this publication if you use PSORT-B in your research.
# The standalone version of PSORT-B is distributed under the GNU
# General Public Licence (Gnu GPL) (see the LICENSE file included
# in the download) by the Brinkman Laboratory, Simon Fraser
# University, Burnaby, B.C., Canada.
# This standalone version of PSORT-B has initially been developed
# for the Linux environment.
# This document describes the installation of the PSORT-B version
# 1.1.4 command line program and the PSORT-B server packages. For
# most purposes, following the installation instructions for the
# command line version will be sufficient.
# For further information, please contact psort-mail@sfu.ca.
use Bio::Root::Root;
use Carp;
use strict;
our @ISA = qw(Bio::Root::Root);
our $VERSION = '0.01';
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# Get the parameters we've been passed.
my ($id,$loc,$regexp,$comment) =
$self->_rearrange([qw(MOTIFID LOCALIZATION REGEXP COMMENT)], @args);
$self->{localization} = $loc;
$self->{motif_id} = $id;
$self->{regexp} = $regexp;
$self->{comment} = $comment;
return $self;
}
sub motif_id {
my $self = shift;
return (@_) ? $self->{motif_id} = shift : $self->{motif_id};
}
sub localization {
my $self = shift;
return (@_) ? $self->{localization} = shift : $self->{localization};
}
sub regexp {
my $self = shift;
return (@_) ? $self->{regexp} = shift : $self->{regexp};
}
sub comment {
my $self = shift;
return (@_) ? $self->{comment} = shift : $self->{comment};
}
=head1 NAME
Bio::Tools::Motif::Pattern - Represents a pattern used by the
Bio::Tools::Motif module.
=head1 SYNOPSIS
use Bio::Tools::Motif::Pattern;
# Create a new object.
$m = new Bio::Tools::Motif::Pattern(-motifid => 'P07110',
-localization => 'OuterMembrane',
-regexp => '(GG.G.D.*){4}',
-comment => 'FIMBRIAL_USHER Pattern');
# Accessor methods.
$val = $m->motif_id();
$val = $m->localization();
$val = $m->regexp();
$val = $m->comment();
=head1 AUTHOR
Cory Spencer <cspencer@sfu.ca>
=head1 SEE ALSO
Bio::Tools::Motif
=head1 ACKNOWLEGEMENTS
Thanks go out to Fiona Brinkman, Jennifer Gardy and the other members of the
Simon Fraser University Brinkman laboratory.
=cut
1;
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