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1 | # | ||||
2 | # BioPerl module for Bio::AnnotatableI | ||||
3 | # | ||||
4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
5 | # | ||||
6 | # Cared for by Hilmar Lapp <hlapp at gmx.net> | ||||
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<bioperl-l@bioperl.org> | ||||
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 E<lt>hlapp@gmx.netE<gt> | ||||
70 | Allen Day E<lt>allenday@ucla.eduE<gt> | ||||
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 | 2 | 24µs | 2 | 36µs | # spent 24µs (12+12) within Bio::AnnotatableI::BEGIN@84 which was called:
# once (12µs+12µs) by base::import at line 84 # spent 24µs making 1 call to Bio::AnnotatableI::BEGIN@84
# spent 12µs making 1 call to strict::import |
85 | |||||
86 | 2 | 46µs | 2 | 63µs | # spent 63µs (8+56) within Bio::AnnotatableI::BEGIN@86 which was called:
# once (8µs+56µs) by base::import at line 86 # spent 63µs making 1 call to Bio::AnnotatableI::BEGIN@86
# spent 56µs making 1 call to base::import, recursion: max depth 3, sum of overlapping time 56µs |
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<Bio::AnnotationCollectionI> | ||||
100 | |||||
101 | =cut | ||||
102 | |||||
103 | sub annotation{ | ||||
104 | shift->throw_not_implemented(); | ||||
105 | } | ||||
106 | |||||
107 | 1 | 2µs | 1; |