| Filename | /Users/ap13/perl5/lib/perl5/Bio/AnnotatableI.pm |
| Statements | Executed 5 statements in 72µs |
| Calls | P | F | Exclusive Time |
Inclusive Time |
Subroutine |
|---|---|---|---|---|---|
| 1 | 1 | 1 | 12µs | 24µs | Bio::AnnotatableI::BEGIN@84 |
| 1 | 1 | 1 | 8µs | 63µs | Bio::AnnotatableI::BEGIN@86 |
| 0 | 0 | 0 | 0s | 0s | Bio::AnnotatableI::annotation |
| Line | State ments |
Time on line |
Calls | Time in subs |
Code |
|---|---|---|---|---|---|
| 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; |