File Coverage

Bio/AnnotatableI.pm
Criterion Covered Total %
statement 6 7 85.7
branch n/a
condition n/a
subroutine 2 3 66.6
pod 1 1 100.0
total 9 11 81.8


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::AnnotatableI
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::AnnotatableI - the base interface an annotatable object must implement
17              
18             =head1 SYNOPSIS
19              
20             use Bio::SeqIO;
21             # get an annotatable object somehow: for example, Bio::SeqI objects
22             # are annotatable
23             my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
24             while (my $seq = $seqio->next_seq()) {
25             # $seq is-a Bio::AnnotatableI, hence:
26             my $ann_coll = $seq->annotation();
27             # $ann_coll is-a Bio::AnnotationCollectionI, hence:
28             my @all_anns = $ann_coll->get_Annotations();
29             # do something with the annotation objects
30             }
31              
32             =head1 DESCRIPTION
33              
34             This is the base interface that all annotatable objects must implement. A
35             good example is Bio::Seq which is an AnnotableI object.
36              
37             =head1 FEEDBACK
38              
39             =head2 Mailing Lists
40              
41             User feedback is an integral part of the evolution of this and other
42             Bioperl modules. Send your comments and suggestions preferably to
43             the Bioperl mailing list. Your participation is much appreciated.
44              
45             bioperl-l@bioperl.org - General discussion
46             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
47              
48             =head2 Support
49              
50             Please direct usage questions or support issues to the mailing list:
51              
52             I
53              
54             rather than to the module maintainer directly. Many experienced and
55             reponsive experts will be able look at the problem and quickly
56             address it. Please include a thorough description of the problem
57             with code and data examples if at all possible.
58              
59             =head2 Reporting Bugs
60              
61             Report bugs to the Bioperl bug tracking system to help us keep track
62             of the bugs and their resolution. Bug reports can be submitted via the
63             web:
64              
65             https://github.com/bioperl/bioperl-live/issues
66              
67             =head1 AUTHOR
68              
69             Hilmar Lapp Ehlapp@gmx.netE
70             Allen Day Eallenday@ucla.eduE
71              
72             =head1 APPENDIX
73              
74             The rest of the documentation details each of the object methods.
75             Internal methods are usually preceded with a _
76              
77             =cut
78              
79              
80             # Let the code begin...
81              
82              
83             package Bio::AnnotatableI;
84 196     196   898 use strict;
  196         261  
  196         4791  
85              
86 196     196   1386 use base qw(Bio::Root::RootI);
  196         297  
  196         14680  
87              
88             =head2 annotation
89              
90             Title : annotation
91             Usage : $obj->annotation($newval)
92             Function: Get the annotation collection for this annotatable object.
93             Example :
94             Returns : a Bio::AnnotationCollectionI implementing object, or undef
95             Args : on set, new value (a Bio::AnnotationCollectionI
96             implementing object, optional) (an implementation may not
97             support changing the annotation collection)
98              
99             See L
100              
101             =cut
102              
103             sub annotation{
104 0     0 1   shift->throw_not_implemented();
105             }
106              
107             1;