1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
|
=head1 NAME
Bio::Tools::PSort::ModuleI - an interface class that all PSort modules should derive
implement.
=head1 SYNOPSIS
package Bio::Tools::PSort::Module::Foo;
use Bio::Tools::PSort::Module;
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module;
...
...
1;
=head1 DESCRIPTION
The module object contains functionality common to all PSort modules. This
class is not intended to be instantiated on it's own, it only provides
functionality common to all PSort modules.
=head1 METHODS
$result = $module->run($seq);
The run method must be overridden in all derived classes. run() should accept
a Bio::Tools::Seq object, and perform whatever analysis the module provides on the
sequence, returning a bio::PSort::Scort object upon completion.
=head1 SEE ALSO
Bio::Tools::PSort, Bio::Tools::PSort::Pathway, Bio::Tools::PSort::Score
=head1 AUTHOR
Fiona Brinkman, Cory Spencer <psort-list@sfu.ca>
Brinkman Laboratory, Simon Fraser University, BC, CANADA
=head1 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.
=head1 LICENCE
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
=cut
package Bio::Tools::PSort::ModuleI;
use Bio::Root::Root;
use vars qw(@ISA);
@ISA = qw(Bio::Root::Root);
use strict;
sub module_name {
my $self = shift;
$self->throw_not_implemented;
}
sub module_description {
my $self = shift;
$self->throw_not_implemented();
}
sub module_type {
my $self = shift;
SWITCH: {
$self->isa("Bio::Tools::PSort::Module::InputI") && return 'input';
$self->isa("Bio::Tools::PSort::Module::AnalysisI") && return 'analysis';
$self->isa("Bio::Tools::PSort::Module::OutputI") && return 'output';
return 'unknown';
}
}
sub run {
my $self = shift;
$self->throw_not_implemented();
}
sub _run {
my ($self, $rpt) = @_;
my $res;
$res = $self->run($rpt);
return $res;
}
1;
|
