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1 : fangfang 1.1 #
2 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :     # for Interpretations of Genomes. All Rights Reserved.
4 :     #
5 :     # This file is part of the SEED Toolkit.
6 :     #
7 :     # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 :     # Public License.
10 :     #
11 :     # You should have received a copy of the SEED Toolkit Public License
12 :     # along with this program; if not write to the University of Chicago
13 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :     # Genomes at veronika@thefig.info or download a copy from
15 :     # http://www.theseed.org/LICENSE.TXT.
16 :     #
17 :     package AT;
18 :    
19 :     use strict;
20 :    
21 :     use ERDB;
22 :     use Tracer;
23 :     use SeedUtils;
24 :     use ServerThing;
25 :    
26 :     use gjoalignment;
27 :    
28 :     sub new {
29 :     my ($class) = @_;
30 :     # Create the sapling object.
31 :     # my $at = ERDB::GetDatabase('AT');
32 :    
33 :     # Create the server object.
34 :     # my $retVal = { db => $at };
35 :     my $retVal = { };
36 :    
37 :     # Bless and return it.
38 :     bless $retVal, $class;
39 :     return $retVal;
40 :     }
41 :    
42 :     use constant METHODS => [qw(
43 :     align_seqs
44 :     )];
45 :    
46 :     sub methods {
47 :     my ($self) = @_;
48 :     return METHODS;
49 :     }
50 :    
51 :     sub align_seqs {
52 :     my ($self, $args) = @_;
53 :     my $rv;
54 :    
55 :     my $program = \&align_with_clustal;
56 :     if ($args->{tool} =~ /muscle/i) {
57 :     $program = \&align_with_muscle;
58 :     $args->{muscle} = "/home/fangfang/bin/muscle";
59 :     } elsif ($args->{tool} =~ /mafft/i) {
60 :     $program = \&align_with_mafft;
61 :     $args->{mafft} = "/home/fangfang/bin/mafft";
62 :     }
63 :    
64 :     $rv->{rv} = $program->($args->{seqs}, $args);
65 :     $rv->{args} = $args;
66 :     return $rv;
67 :     }
68 :    
69 :     1;

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