Mercurial > repos > matteoc > agame_custom_tools
comparison pfamScan/Bio/Pfam/HMM/HMMUnit.pm @ 0:68a3648c7d91 draft default tip
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author | matteoc |
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date | Thu, 22 Dec 2016 04:45:31 -0500 |
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-1:000000000000 | 0:68a3648c7d91 |
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1 | |
2 package Bio::Pfam::HMM::HMMUnit; | |
3 | |
4 use strict; | |
5 use warnings; | |
6 | |
7 use Moose; | |
8 use Moose::Util::TypeConstraints; | |
9 | |
10 extends 'Bio::Pfam::HMM::HMMMatch'; | |
11 | |
12 subtype 'Domain' | |
13 => as 'Int' | |
14 => where { $_ > 0 }; | |
15 | |
16 #coerce 'Domain' | |
17 # => from 'Str' | |
18 # => via { | |
19 # my $d; | |
20 # if(/(\d+)\/\d+/){ | |
21 # $d = $1; | |
22 # } | |
23 # return $d; | |
24 # }; | |
25 # | |
26 | |
27 #subtype 'proteinCoos' | |
28 # => as 'Int' | |
29 # => where { $_ > 0 && $_ < 100000 } | |
30 # => message { 'Protein coordinates are expected to be positive and less the 100,000'}; | |
31 | |
32 | |
33 has 'seqEvalue' => ( | |
34 isa => 'Num', | |
35 is => 'rw', | |
36 ); | |
37 | |
38 has 'domain' => ( | |
39 isa => 'Domain', | |
40 is => 'rw' | |
41 ); | |
42 | |
43 has 'seqFrom' => ( | |
44 isa => 'Int', | |
45 is => 'rw', | |
46 required => 1 | |
47 ); | |
48 | |
49 has 'seqTo' => ( | |
50 isa => 'Int', | |
51 is => 'rw', | |
52 required => 1 | |
53 ); | |
54 | |
55 #has 'indEvalue' => ( | |
56 # isa => 'evalue', | |
57 # is => 'rw', | |
58 # required => 1, | |
59 #); | |
60 | |
61 has 'domEvalue' => ( | |
62 isa => 'evalue', | |
63 is => 'rw', | |
64 ); | |
65 | |
66 has 'hmmalign' => ( | |
67 isa => 'HashRef', | |
68 is => 'rw', | |
69 default => sub { {} }, | |
70 ); | |
71 | |
72 has 'hmmFrom' => ( | |
73 isa => 'Int', | |
74 is => 'rw', | |
75 required => 1 | |
76 ); | |
77 | |
78 has 'hmmTo' => ( | |
79 isa => 'Int', | |
80 is => 'rw', | |
81 required => 1 | |
82 ); | |
83 | |
84 has 'envFrom' => ( | |
85 isa => 'Int', | |
86 is => 'rw' | |
87 ); | |
88 | |
89 has 'envTo' => ( | |
90 isa => 'Int', | |
91 is => 'rw' | |
92 ); | |
93 | |
94 has 'coreFrom' => ( | |
95 isa => 'Str', | |
96 is => 'rw' | |
97 ); | |
98 | |
99 has 'coreTo' => ( | |
100 isa => 'Str', | |
101 is => 'rw' | |
102 ); | |
103 | |
104 has 'aliAcc' => ( | |
105 isa => 'Num', | |
106 is => 'rw' | |
107 ); | |
108 | |
109 has 'sig' => ( | |
110 isa => 'Int', | |
111 is => 'rw' | |
112 ); | |
113 | |
114 | |
115 __PACKAGE__->meta->make_immutable; | |
116 | |
117 =head1 COPYRIGHT | |
118 | |
119 Copyright (c) 2007: Genome Research Ltd. | |
120 | |
121 Authors: Rob Finn (rdf@sanger.ac.uk), John Tate (jt6@sanger.ac.uk) | |
122 | |
123 This is free software; you can redistribute it and/or modify it under | |
124 the terms of the GNU General Public License as published by the Free Software | |
125 Foundation; either version 2 of the License, or (at your option) any later | |
126 version. | |
127 | |
128 This program is distributed in the hope that it will be useful, but WITHOUT | |
129 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | |
130 FOR A PARTICULAR PURPOSE. See the GNU General Public License for more | |
131 details. | |
132 | |
133 You should have received a copy of the GNU General Public License along with | |
134 this program. If not, see <http://www.gnu.org/licenses/>. | |
135 | |
136 =cut | |
137 | |
138 1; |