Mercurial > repos > matteoc > agame_custom_tools
comparison pfamScan/Bio/Pfam/HMM/HMMSequence.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::HMMSequence; | |
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 | |
13 has sumEvalue => ( | |
14 isa => 'evalue', | |
15 is => 'rw', | |
16 ); | |
17 | |
18 | |
19 has H2mode => ( | |
20 isa => 'Str', | |
21 is => 'rw' | |
22 ); | |
23 | |
24 has sumScore => ( | |
25 isa => 'Num', | |
26 is => 'rw', | |
27 ); | |
28 | |
29 has desc => ( | |
30 isa => 'Str', | |
31 is => 'rw', | |
32 required => 1 | |
33 ); | |
34 | |
35 has numberHits => ( | |
36 isa => 'Int', | |
37 is => 'rw', | |
38 required => 1 | |
39 ); | |
40 | |
41 | |
42 | |
43 has 'exp' => ( | |
44 isa => 'Num', | |
45 is => 'rw' | |
46 ); | |
47 | |
48 | |
49 has hmmUnits => ( | |
50 isa => "ArrayRef[ Bio::Pfam::HMM::HMMUnit ]", | |
51 is => 'rw', | |
52 default => sub { [] } | |
53 ); | |
54 | |
55 | |
56 #------------------------------------------------------------------------------- | |
57 =head1 Subroutines | |
58 | |
59 =head2 addHMMUnit | |
60 | |
61 Title : addHMMUnit | |
62 Usage : $hmmseq->addHMMUnit($hmmUnit) | |
63 Function : Adds a hmmUnit to a sequence. It checks that the variable passed in is a Bio::Pfam::HMM::HMMUnit oject | |
64 Args : A Bio::Pfam::HMM::HMMUnit oject | |
65 Returns : Nothing | |
66 | |
67 =cut | |
68 | |
69 sub addHMMUnit { | |
70 my ( $self, $hmmUnit ) = @_; | |
71 if($hmmUnit->isa("Bio::Pfam::HMM::HMMUnit")){ | |
72 push(@{$self->hmmUnits}, $hmmUnit); | |
73 }else{ | |
74 warn "$hmmUnit is not a Bio::Pfam::HMM::HMMUnit, not added\n"; | |
75 } | |
76 } | |
77 | |
78 | |
79 __PACKAGE__->meta->make_immutable; | |
80 | |
81 =head1 COPYRIGHT | |
82 | |
83 Copyright (c) 2007: Genome Research Ltd. | |
84 | |
85 Authors: Rob Finn (rdf@sanger.ac.uk), John Tate (jt6@sanger.ac.uk) | |
86 | |
87 This is free software; you can redistribute it and/or modify it under | |
88 the terms of the GNU General Public License as published by the Free Software | |
89 Foundation; either version 2 of the License, or (at your option) any later | |
90 version. | |
91 | |
92 This program is distributed in the hope that it will be useful, but WITHOUT | |
93 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | |
94 FOR A PARTICULAR PURPOSE. See the GNU General Public License for more | |
95 details. | |
96 | |
97 You should have received a copy of the GNU General Public License along with | |
98 this program. If not, see <http://www.gnu.org/licenses/>. | |
99 | |
100 =cut | |
101 | |
102 1; |