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Revision 1.1 - (download) (as text) (annotate)
Fri Apr 1 20:45:58 2011 UTC (8 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_release_3_0_4, mgrast_dev_06072011, mgrast_dev_08022011, rast_rel_2014_0912, mgrast_dev_04012011, myrast_rel40, rast_rel_2014_0729, mgrast_dev_05262011, mgrast_release_3_1_2, mgrast_release_3_1_1, rast_rel_2011_0928, mgrast_dev_04132011, mgrast_dev_04052011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_10262011, mgrast_dev_04082011, mgrast_release_3_1_0, mgrast_release_3_0_3, HEAD
New alignment/tree server stuff.

#	This is a SAS Component.
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
# This file is part of the SEED Toolkit.
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License.
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.

package ALITREserver;

    use strict;
    use base qw(ClientThing);

=head1 Alignment/Tree Server Helper Object

=head2 Description

This module is used to call the alignment/tree server, which is a 
server for extracting alignment and tree data. Each server
function corresponds to a method of this object. In other words, all
L<ALITRE/Primary Methods> are also methods here.


=head3 new

    my $ss = ALITREserver->new(%options);

Construct a new ALITREserver object. The following options are supported.

=over 4

=item url

URL for the sapling server. This option may be used to redirect requests to a
test version of the server, or to an older server script.

=item singleton

If TRUE, results from methods will be returned in singleton mode. In singleton
mode, if a single result comes back, it will come back as a scalar rather than
as a hash value accessible via an incoming ID.



sub new {
    # Get the parameters.
    my ($class, @options) = @_;
    # Fix the option hash.
    my %options = ClientThing::FixOptions(@options);
    # Compute the URL.
    $options{url} = ClientThing::ComputeURL($options{url}, 'alitre_server.cgi',
    # Construct the subclass.
    return $class->SUPER::new(ALITRE => %options);


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