lib/Bio/AnnotatableI.pm

   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 use strict;
  85
  86 use base qw(Bio::Root::RootI);
  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;