File Coverage

Bio/SeqFeature/Gene/ExonI.pm
Criterion Covered Total %
statement 6 10 60.0
branch n/a
condition n/a
subroutine 2 4 50.0
pod 2 2 100.0
total 10 16 62.5


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::SeqFeature::Gene::ExonI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Hilmar Lapp
7             #
8             # Copyright Hilmar Lapp
9             #
10             # You may distribute this module under the same terms as perl itself
11              
12             # POD documentation - main docs before the code
13              
14             =head1 NAME
15              
16             Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon
17              
18             =head1 SYNOPSIS
19              
20             See documentation of methods.
21              
22             =head1 DESCRIPTION
23              
24             A feature representing an exon. An exon in this definition is
25             transcribed and at least for one particular transcript not spliced out
26             of the pre-mRNA. However, it does not necessarily code for amino acid.
27              
28             =head1 FEEDBACK
29              
30             =head2 Mailing Lists
31              
32             User feedback is an integral part of the evolution of this
33             and other Bioperl modules. Send your comments and suggestions preferably
34             to one of the Bioperl mailing lists.
35             Your participation is much appreciated.
36              
37             bioperl-l@bioperl.org - General discussion
38             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
39              
40             =head2 Support
41              
42             Please direct usage questions or support issues to the mailing list:
43              
44             I
45              
46             rather than to the module maintainer directly. Many experienced and
47             reponsive experts will be able look at the problem and quickly
48             address it. Please include a thorough description of the problem
49             with code and data examples if at all possible.
50              
51             =head2 Reporting Bugs
52              
53             Report bugs to the Bioperl bug tracking system to help us keep track
54             the bugs and their resolution. Bug reports can be submitted via the
55             web:
56              
57             https://github.com/bioperl/bioperl-live/issues
58              
59             =head1 AUTHOR - Hilmar Lapp
60              
61             Email hlapp@gmx.net
62              
63             =head1 APPENDIX
64              
65             The rest of the documentation details each of the object methods.
66             Internal methods are usually preceded with a _
67              
68             =cut
69              
70              
71             # Let the code begin...
72              
73              
74             package Bio::SeqFeature::Gene::ExonI;
75 9     9   41 use strict;
  9         9  
  9         280  
76              
77 9     9   30 use base qw(Bio::SeqFeatureI);
  9         9  
  9         896  
78              
79              
80             =head2 is_coding
81              
82             Title : is_coding
83             Usage : if($exon->is_coding()) {
84             # do something
85             }
86             Function: Whether or not the exon codes for amino acid.
87             Returns : TRUE if the object represents a feature translated into protein,
88             and FALSE otherwise.
89             Args :
90              
91              
92             =cut
93              
94             sub is_coding {
95 0     0 1   my ($self) = @_;
96 0           $self->throw_not_implemented();
97             }
98              
99             =head2 cds
100              
101             Title : cds()
102             Usage : $cds = $exon->cds();
103             Function: Get the coding sequence of the exon as a sequence object.
104              
105             The returned sequence object must be in frame 0, i.e., the first
106             base starts a codon.
107              
108             An implementation may return undef, indicating that a coding
109             sequence does not exist, e.g. for a UTR (untranslated region).
110              
111             Returns : A L implementing object.
112             Args :
113              
114              
115             =cut
116              
117             sub cds {
118 0     0 1   my ($self) = @_;
119 0           $self->throw_not_implemented();
120             }
121              
122             1;