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Revision 1.1 - (download) (as text) (annotate)
Wed Oct 27 16:21:57 2010 UTC (9 years, 8 months ago) by fangfang
Branch: MAIN
Initial import of Alignment and Tree module

#
# 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 AT;

use strict;

use ERDB;
use Tracer;
use SeedUtils;
use ServerThing;

use gjoalignment;

sub new {
    my ($class) = @_;
    # Create the sapling object.
    # my $at = ERDB::GetDatabase('AT');

    # Create the server object.
    # my $retVal = { db => $at };
    my $retVal = { };

    # Bless and return it.
    bless $retVal, $class;
    return $retVal;
}

use constant METHODS => [qw(
                            align_seqs
                           )];

sub methods {
    my ($self) = @_;
    return METHODS;
}

sub align_seqs {
    my ($self, $args) = @_;
    my $rv;

    my $program = \&align_with_clustal;
    if ($args->{tool} =~ /muscle/i) {
        $program = \&align_with_muscle;
        $args->{muscle} = "/home/fangfang/bin/muscle";
    } elsif ($args->{tool} =~ /mafft/i) {
        $program = \&align_with_mafft;
        $args->{mafft} = "/home/fangfang/bin/mafft";
    }

    $rv->{rv} = $program->($args->{seqs}, $args);
    $rv->{args} = $args;
    return $rv;
}

1;

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