package Bio::Tools::Run::HMMTOP::Helix;

# 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 strict;

our @ISA = qw(Bio::Root::Root);

sub new {
  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);

  my ($s, $e, $p) = $self->_rearrange([ qw(START END) ], @args);

  $self->{start}  = $s || $self->throw("No start position provided");
  $self->{end}    = $e || $self->throw("No end position provided");

  return $self;
}

sub start {
  my $self = shift;

  (@_) ? $self->{start} = shift : $self->{start};
}

sub end {
  my $self = shift;

  (@_) ? $self->{end} = shift : $self->{end};
}

1;

__END__