Bio/AnnotatableI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::AnnotatableI
   4 #
   5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
   6 #
   7 # Copyright Hilmar Lapp
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::AnnotatableI - the base interface an annotatable object must implement
  16
  17 =head1 SYNOPSIS
  18
  19     use Bio::SeqIO;
  20     # get an annotatable object somehow: for example, Bio::SeqI objects
  21     # are annotatable
  22     my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
  23     while (my $seq = $seqio->next_seq()) {
  24         # $seq is-a Bio::AnnotatableI, hence:
  25         my $ann_coll = $seq->annotation();
  26         # $ann_coll is-a Bio::AnnotationCollectionI, hence:
  27         my @all_anns = $ann_coll->get_Annotations();
  28         # do something with the annotation objects
  29     }
  30
  31 =head1 DESCRIPTION
  32
  33 This is the base interface that all annotatable objects must implement. A
  34 good example is Bio::Seq which is an AnnotableI object.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules. Send your comments and suggestions preferably to
  42 the Bioperl mailing list.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Reporting Bugs
  48
  49 Report bugs to the Bioperl bug tracking system to help us keep track
  50 of the bugs and their resolution. Bug reports can be submitted via the
  51 web:
  52
  53   http://bugzilla.open-bio.org/
  54
  55 =head1 AUTHOR
  56
  57  Hilmar Lapp E<lt>hlapp@gmx.netE<gt>
  58  Allen Day E<lt>allenday@ucla.eduE<gt>
  59
  60 =head1 APPENDIX
  61
  62 The rest of the documentation details each of the object methods.
  63 Internal methods are usually preceded with a _
  64
  65 =cut
  66
  67
  68 # Let the code begin...
  69
  70
  71 package Bio::AnnotatableI;
  72 use strict;
  73
  74 use Bio::Annotation::Comment;
  75 use Bio::Annotation::DBLink;
  76 #use Bio::Annotation::OntologyTerm;
  77 use Bio::Annotation::Reference;
  78 use Bio::Annotation::SimpleValue;
  79
  80 use base qw(Bio::Root::RootI);
  81
  82 =head2 annotation
  83
  84  Title   : annotation
  85  Usage   : $obj->annotation($newval)
  86  Function: Get the annotation collection for this annotatable object.
  87  Example :
  88  Returns : a Bio::AnnotationCollectionI implementing object, or undef
  89  Args    : on set, new value (a Bio::AnnotationCollectionI
  90            implementing object, optional) (an implementation may not
  91            support changing the annotation collection)
  92
  93 See L<Bio::AnnotationCollectionI>
  94
  95 =cut
  96
  97 sub annotation{
  98   shift->throw_not_implemented();
  99 }
 100
 101 1;