package Bio::Tools::Signal::Report;

# 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);

  return $self;
}

sub cleavage_site {
  my $self = shift;

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

sub is_lipoprotein {
  my $self = shift;

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

sub localization {
  my $self = shift;

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

sub hmm_score {
  my $self = shift;

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

sub hmm_pvalue {
  my $self = shift;

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

sub svm_prediction {
  my $self = shift;

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

sub signal_peptide {
  my $self = shift;

  return ($self->{islipo} || ($self->{hmmpvalue} < 0.01) ||
	  (($self->{hmmpvalue} < 0.05) && $self->{svmpred})) ? 1 : 0;
}

1;