File Coverage

blib/lib/Bio/CUA/CUB.pm
Criterion Covered Total %
statement 14 14 100.0
branch 2 2 100.0
condition n/a
subroutine 5 5 100.0
pod 1 1 100.0
total 22 22 100.0


line stmt bran cond sub pod time code
1             package Bio::CUA::CUB;
2              
3 3     3   1338 use 5.006;
  3         8  
4 3     3   11 use strict;
  3         4  
  3         59  
5 3     3   11 use warnings;
  3         14  
  3         101  
6 3     3   13 use parent qw/Bio::CUA::Summarizer/;
  3         3  
  3         19  
7              
8             =head1 NAME
9              
10             Bio::CUA::CUB - This is the parent class for all classs processing
11             codon usage bias (CUB).
12              
13              
14             =head1 SYNOPSIS
15              
16             At present, this class largely inherits from
17             L. The class may be updated in future depending
18             on the needs of new analyses.
19              
20             Please refer to its child classes L and
21             L for usage of methods.
22              
23             =head1 METHODS
24              
25             =head2 no_atg
26              
27             Title : no_atg
28             Usage : $status = $self->no_atg([$newVal])
29             Function: get/set the status whether ATG should be excluded in tAI
30             calculation.
31             Returns : current status after updating
32             Args : optional. 1 for true, 0 for false
33              
34             =cut
35              
36             sub no_atg
37             {
38 2     2 1 3 my ($self, $val) = @_;
39 2 100       12 $self->set_tag('no_atg',$val) if(defined($val));
40 2         7 return $self->get_tag('no_atg');
41             }
42              
43              
44             =head1 AUTHOR
45              
46             Zhenguo Zhang, C<< >>
47              
48             =head1 BUGS
49              
50             Please report any bugs or feature requests to C, or through
51             the web interface at L. I will be notified, and then you'll
52             automatically be notified of progress on your bug as I make changes.
53              
54              
55             =head1 SUPPORT
56              
57             You can find documentation for this class with the perldoc command.
58              
59             perldoc Bio::CUA::CUB
60              
61              
62             You can also look for information at:
63              
64             =over 4
65              
66             =item * RT: CPAN's request tracker (report bugs here)
67              
68             L
69              
70             =item * AnnoCPAN: Annotated CPAN documentation
71              
72             L
73              
74             =item * CPAN Ratings
75              
76             L
77              
78             =item * Search CPAN
79              
80             L
81              
82             =back
83              
84              
85             =head1 ACKNOWLEDGEMENTS
86              
87              
88             =head1 LICENSE AND COPYRIGHT
89              
90             Copyright 2015 Zhenguo Zhang.
91              
92             This program is free software: you can redistribute it and/or modify
93             it under the terms of the GNU General Public License as published by
94             the Free Software Foundation, either version 3 of the License, or
95             (at your option) any later version.
96              
97             This program is distributed in the hope that it will be useful,
98             but WITHOUT ANY WARRANTY; without even the implied warranty of
99             MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
100             GNU General Public License for more details.
101              
102             You should have received a copy of the GNU General Public License
103             along with this program. If not, see L.
104              
105              
106             =cut
107              
108             1; # End of Bio::CUA::CUB