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package Bio::Tools::PSort::XMLRPC::Client;
# 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 RPC::XML::Client;
use RPC::XML;
use Bio::Tools::PSort::Report::Result;
use Bio::Tools::PSort::Report;
use Bio::Root::Root;
use strict;
use vars qw(@ISA);
@ISA = qw(Bio::Root::Root);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# Get any of the parameters passed to the constructor.
my ($server,$method) = $self->_rearrange([qw(SERVER METHOD)], @args);
# Set some default values if they weren't received in the constructor.
$self->{server} = $server || 'http://localhost/RPC';
$self->{method} = $method || 'psort.classify';
# Create a new XML-RPC client.
$self->{client} = RPC::XML::Client->new($self->{server});
return $self;
}
sub classify {
my ($self, $seq, $path) = @_;
my ($req, $rep, $res);
# Create the structure of the request we're going to send.
$req = { seq => $seq->seq,
path => { input => $path->{input} || 'all',
analysis => $path->{analysis} || 'all',
output => $path->{output} || 'all' }};
$res = $self->{client}->send_request($self->{method}, $req);
# Check to see if we received a reference to an object from the send_request.
# (If we didn't, then there was a client side send error - check parameters
# passed to the RPC::XML::Client constructor.)
if(ref($res)) {
if(! $res->is_fault) {
my $res = $res->value;
my $rep = new Bio::Tools::PSort::Report(-seq => $seq);
for my $path (keys(%{$res})) {
my %res = ( );
for my $mod (keys(%{$res->{$path}})) {
my @res;
for(@{$res->{$path}->{$mod}}) {
my @locs = split(',', $_->{localization});
push(@res, new Bio::Tools::PSort::Report::Result(
-loc => \@locs,
-score => $_->{score} || 0,
-details => $_->{details}));
}
$res{$mod} = \@res;
}
$rep->add_results($path, %res);
}
return $rep;
} else {
# Fault was returned, throw an exception.
$self->throw("XML-RPC fault: " . $res->string);
}
} else {
$self->throw("XML-RPC client side send error");
}
}
1;
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