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1 # $Id: AnnotatableI.pm,v 1.2 2002/12/31 13:09:06 birney Exp $
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2 #
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3 # BioPerl module for Bio::AnnotatableI
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4 #
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5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::AnnotatableI - the base interface an annotatable object must implement
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::SeqIO;
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20 # get an annotatable object somehow: for example, Bio::SeqI objects
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21 # are annotatable
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22 my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank);
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23 while (my $seq = $seqio->next_seq()) {
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24 # $seq is-a Bio::AnnotatableI, hence:
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25 my $ann_coll = $seq->annotation();
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26 # $ann_coll is-a Bio::AnnotationCollectionI, hence:
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27 my @all_anns = $ann_coll->get_Annotations();
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28 # do something with the annotation objects
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29 }
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30
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31 =head1 DESCRIPTION
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32
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33 This is the base interface that all annotatable objects must implement. A good
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34 example is Bio::Seq which is an AnnotableI object; if you are a little confused
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35 about what this module does, start a Bio::Seq.
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36
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37 =head1 FEEDBACK
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38
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39 =head2 Mailing Lists
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40
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41 User feedback is an integral part of the evolution of this and other
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42 Bioperl modules. Send your comments and suggestions preferably to
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43 the Bioperl mailing list. Your participation is much appreciated.
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44
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45 bioperl-l@bioperl.org - General discussion
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46 http://bioperl.org/MailList.shtml - About the mailing lists
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47
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48 =head2 Reporting Bugs
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49
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50 Report bugs to the Bioperl bug tracking system to help us keep track
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51 of the bugs and their resolution. Bug reports can be submitted via
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52 email or the web:
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53
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54 bioperl-bugs@bioperl.org
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55 http://bioperl.org/bioperl-bugs/
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56
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57 =head1 AUTHOR - Hilmar Lapp
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58
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59 Email hlapp at gmx.net
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60
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61 Describe contact details here
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62
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63 =head1 CONTRIBUTORS
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64
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65 Additional contributors names and emails here
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66
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67 =head1 APPENDIX
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68
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69 The rest of the documentation details each of the object methods.
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70 Internal methods are usually preceded with a _
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71
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72 =cut
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73
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74
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75 # Let the code begin...
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76
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77
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78 package Bio::AnnotatableI;
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79 use vars qw(@ISA);
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80 use strict;
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81 use Carp;
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82 use Bio::Root::RootI;
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83
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84 @ISA = qw( Bio::Root::RootI );
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85
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86 =head2 annotation
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87
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88 Title : annotation
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89 Usage : $obj->annotation($newval)
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90 Function: Get the annotation collection (see L<Bio::AnnotationCollectionI>)
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91 for this annotatable object.
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92 Example :
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93 Returns : a Bio::AnnotationCollectionI implementing object, or undef
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94 Args : on set, new value (a Bio::AnnotationCollectionI
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95 implementing object, optional) (an implementation may not
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96 support changing the annotation collection)
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97
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98
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99 =cut
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100
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101 sub annotation{
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102 shift->throw_not_implemented();
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103 }
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104
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105
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106
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107 1;
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