NAME

Bio::Tools::PSort::ModuleI - an interface class that all PSort modules should derive implement.

SYNOPSIS

    package Bio::Tools::PSort::Module::Foo;
    use Bio::Tools::PSort::Module;
    use vars qw(@ISA);
    @ISA = qw(Bio::Tools::PSort::Module;
    ...
    ...
    1;

DESCRIPTION

The module object contains functionality common to all PSort modules. This class is not intended to be instantiated on it's own, it only provides functionality common to all PSort modules.

METHODS

    $result = $module->run($seq);

The run method must be overridden in all derived classes. run() should accept a Bio::Tools::Seq object, and perform whatever analysis the module provides on the sequence, returning a bio::PSort::Scort object upon completion.

SEE ALSO

Bio::Tools::PSort, Bio::Tools::PSort::Pathway, Bio::Tools::PSort::Score

AUTHOR

 Fiona Brinkman, Cory Spencer <psort-list@sfu.ca>
 Brinkman Laboratory, Simon Fraser University, BC, CANADA

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.

LICENCE

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