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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 : fangfang 1.2
24 :     use gjoalignment;
25 :    
26 :     use AlignTree;
27 : fangfang 1.1 use SeedUtils;
28 :     use ServerThing;
29 :    
30 :     sub new {
31 :     my ($class) = @_;
32 :     # Create the sapling object.
33 :     # my $at = ERDB::GetDatabase('AT');
34 :    
35 :     # Create the server object.
36 :     # my $retVal = { db => $at };
37 :     my $retVal = { };
38 :    
39 :     # Bless and return it.
40 :     bless $retVal, $class;
41 :     return $retVal;
42 :     }
43 :    
44 :     use constant METHODS => [qw(
45 :     align_seqs
46 : fangfang 1.2 trim_ali
47 : fangfang 1.3 psiblast_search
48 : fangfang 1.4 make_tree
49 : fangfang 1.1 )];
50 :    
51 :     sub methods {
52 :     my ($self) = @_;
53 :     return METHODS;
54 :     }
55 :    
56 :     sub align_seqs {
57 : fangfang 1.2 my ($self, $opts) = @_;
58 :     my $ali = AlignTree::align_sequences($opts);
59 :     return { rv => $ali };
60 :     }
61 : fangfang 1.1
62 : fangfang 1.2 sub trim_ali {
63 :     my ($self, $opts) = @_;
64 :     my $trim = AlignTree::trim_alignment($opts);
65 :     return { rv => $trim };
66 : fangfang 1.1 }
67 :    
68 : fangfang 1.3 sub psiblast_search {
69 :     my ($self, $opts) = @_;
70 :     my ($trim, $report) = AlignTree::psiblast_search($opts);
71 :     return $opts->{report} ? { rv => $trim, report => $report } : { rv => $trim };
72 :     }
73 :    
74 : fangfang 1.4 sub make_tree {
75 :     my ($self, $opts) = @_;
76 :     my ($tree, $stats) = AlignTree::make_tree($opts);
77 :     return { rv => $tree, stats => $stats };
78 :     }
79 :    
80 : fangfang 1.1 1;

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