Bio/AnnotationI.pm

   1 # $Id$
   2
   3 #
   4 # BioPerl module for Bio::AnnotationI
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   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::AnnotationI - Annotation interface
  17
  18 =head1 SYNOPSIS
  19
  20   # generally you get AnnotationI's from AnnotationCollectionI's
  21
  22    foreach $key ( $ac->get_all_annotation_keys() ) {
  23        @values = $ac->get_Annotations($key);
  24        foreach $value ( @values ) {
  25           # value is an Bio::AnnotationI, and defines a "as_text" method
  26           print "Annotation ",$key," stringified value ",$value->as_text,"\n";
  27           # you can also use a generic hash_tree method for getting
  28           # stuff out say into XML format
  29           $hash_tree = $value->hash_tree();
  30        }
  31    }
  32
  33
  34 =head1 DESCRIPTION
  35
  36 Interface all annotations must support. There are two things that each
  37 annotation has to support.
  38
  39   $annotation->as_text()
  40
  41 Annotations have to support an "as_text" method. This should be a
  42 single text string, without newlines representing the annotation,
  43 mainly for human readability. It is not aimed at being able to
  44 store/represent the annotation.
  45
  46 The second method allows annotations to at least attempt to represent
  47 themselves as pure data for storage/display/whatever. The method
  48 hash_tree
  49
  50    $hash = $annotation->hash_tree();
  51
  52 should return an anonymous hash with "XML-like" formatting. The
  53 formatting is as follows.
  54
  55   (1) For each key in the hash, if the value is a reference'd array -
  56
  57       (2) For each element of the array if the value is a object -
  58           Assume the object has the method "hash_tree";
  59       (3) else if the value is a referene to a hash
  60           Recurse again from point (1)
  61       (4) else
  62           Assumme the value is a scalar, and handle it directly as text
  63
  64    (5) else (if not an array) apply rules 2,3 and 4 to value
  65
  66 The XML path in tags is represented by the keys taken in the
  67 hashes. When arrays are encountered they are all present in the path
  68 level of this tag
  69
  70 This is a pretty "natural" representation of an object tree in an XML
  71 style, without forcing everything to inheriet off some super-generic
  72 interface for representing things in the hash.
  73
  74 =head1 FEEDBACK
  75
  76 =head2 Mailing Lists
  77
  78 User feedback is an integral part of the evolution of this
  79 and other Bioperl modules. Send your comments and suggestions preferably
  80  to one of the Bioperl mailing lists.
  81 Your participation is much appreciated.
  82
  83   bioperl-l@bioperl.org
  84
  85 =head2 Reporting Bugs
  86
  87 Report bugs to the Bioperl bug tracking system to help us keep track
  88 the bugs and their resolution.  Bug reports can be submitted via the
  89 web:
  90
  91   http://bugzilla.open-bio.org/
  92
  93 =head1 AUTHOR - Ewan Birney
  94
  95 Email birney@ebi.ac.uk
  96
  97 =head1 APPENDIX
  98
  99 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
 100
 101 =cut
 102
 103 #'
 104 # Let the code begin...
 105
 106
 107 package Bio::AnnotationI;
 108 use strict;
 109
 110 # Object preamble - inherits from Bio::Root::Root
 111
 112
 113
 114 use base qw(Bio::Root::RootI);
 115
 116
 117 =head2 as_text
 118
 119  Title   : as_text
 120  Usage   :
 121  Function: single text string, without newlines representing the
 122            annotation, mainly for human readability. It is not aimed
 123            at being able to store/represent the annotation.
 124  Example :
 125  Returns : a string
 126  Args    : none
 127
 128
 129 =cut
 130
 131 sub as_text{
 132     shift->throw_not_implemented();
 133 }
 134
 135 =head2 display_text
 136
 137  Title   : display_text
 138  Usage   : my $str = $ann->display_text();
 139  Function: returns a string. Unlike as_text(), this method returns a string
 140            formatted as would be expected for the specific implementation.
 141
 142            Implementations should allow passing a callback as an argument which
 143            allows custom text generation; the callback will be passed the
 144            current implementation.
 145
 146            Note that this is meant to be used as a simple representation
 147            of the annotation data but probably shouldn't be used in cases
 148            where more complex comparisons are needed or where data is
 149            stored.
 150  Example :
 151  Returns : a string
 152  Args    : [optional] callback
 153
 154 =cut
 155
 156 sub display_text {
 157     shift->throw_not_implemented();
 158 }
 159
 160 =head2 hash_tree
 161
 162  Title   : hash_tree
 163  Usage   :
 164  Function: should return an anonymous hash with "XML-like" formatting
 165  Example :
 166  Returns : a hash reference
 167  Args    : none
 168
 169
 170 =cut
 171
 172 sub hash_tree{
 173     shift->throw_not_implemented();
 174 }
 175
 176 =head2 tagname
 177
 178  Title   : tagname
 179  Usage   : $obj->tagname($newval)
 180  Function: Get/set the tagname for this annotation value.
 181
 182            Setting this is optional. If set, it obviates the need to
 183            provide a tag to Bio::AnnotationCollectionI when adding
 184            this object. When obtaining an AnnotationI object from the
 185            collection, the collection will set the value to the tag
 186            under which it was stored unless the object has a tag
 187            stored already.
 188
 189  Example :
 190  Returns : value of tagname (a scalar)
 191  Args    : new value (a scalar, optional)
 192
 193
 194 =cut
 195
 196 sub tagname{
 197     shift->throw_not_implemented();
 198 }
 199
 200 1;