lib/Bio/AnnotationI.pm

   1 #
   2 # BioPerl module for Bio::AnnotationI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   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 =head1 DESCRIPTION
  34
  35 Interface all annotations must support. There are two things that each
  36 annotation has to support.
  37
  38   $annotation->as_text()
  39
  40 Annotations have to support an "as_text" method. This should be a
  41 single text string, without newlines representing the annotation,
  42 mainly for human readability. It is not aimed at being able to
  43 store/represent the annotation.
  44
  45 The second method allows annotations to at least attempt to represent
  46 themselves as pure data for storage/display/whatever. The method
  47 hash_tree should return an anonymous hash with "XML-like" formatting:
  48
  49    $hash = $annotation->hash_tree();
  50
  51 The formatting is as follows.
  52
  53   (1) For each key in the hash, if the value is a reference'd array -
  54
  55   (2) For each element of the array if the value is a object -
  56           Assume the object has the method "hash_tree";
  57   (3) else if the value is a reference to a hash
  58           Recurse again from point (1)
  59   (4) else
  60           Assume the value is a scalar, and handle it directly as text
  61   (5) else (if not an array) apply rules 2,3 and 4 to value
  62
  63 The XML path in tags is represented by the keys taken in the
  64 hashes. When arrays are encountered they are all present in the path
  65 level of this tag
  66
  67 This is a pretty "natural" representation of an object tree in an XML
  68 style, without forcing everything to inherit off some super-generic
  69 interface for representing things in the hash.
  70
  71 =head1 FEEDBACK
  72
  73 =head2 Mailing Lists
  74
  75 User feedback is an integral part of the evolution of this
  76 and other Bioperl modules. Send your comments and suggestions preferably
  77  to one of the Bioperl mailing lists.
  78 Your participation is much appreciated.
  79
  80   bioperl-l@bioperl.org
  81
  82 =head2 Support
  83
  84 Please direct usage questions or support issues to the mailing list:
  85
  86 I<bioperl-l@bioperl.org>
  87
  88 rather than to the module maintainer directly. Many experienced and
  89 reponsive experts will be able look at the problem and quickly
  90 address it. Please include a thorough description of the problem
  91 with code and data examples if at all possible.
  92
  93 =head2 Reporting Bugs
  94
  95 Report bugs to the Bioperl bug tracking system to help us keep track
  96 the bugs and their resolution.  Bug reports can be submitted via the
  97 web:
  98
  99   https://github.com/bioperl/bioperl-live/issues
 100
 101 =head1 AUTHOR - Ewan Birney
 102
 103 Email birney@ebi.ac.uk
 104
 105 =head1 APPENDIX
 106
 107 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
 108
 109 =cut
 110
 111 #'
 112 # Let the code begin...
 113
 114
 115 package Bio::AnnotationI;
 116 use strict;
 117
 118 # Object preamble - inherits from Bio::Root::Root
 119
 120 use base qw(Bio::Root::RootI);
 121
 122 =head2 as_text
 123
 124  Title   : as_text
 125  Usage   :
 126  Function: single text string, without newlines representing the
 127            annotation, mainly for human readability. It is not aimed
 128            at being able to store/represent the annotation.
 129  Example :
 130  Returns : a string
 131  Args    : none
 132
 133
 134 =cut
 135
 136 sub as_text{
 137     shift->throw_not_implemented();
 138 }
 139
 140 =head2 display_text
 141
 142  Title   : display_text
 143  Usage   : my $str = $ann->display_text();
 144  Function: returns a string. Unlike as_text(), this method returns a string
 145            formatted as would be expected for the specific implementation.
 146
 147            Implementations should allow passing a callback as an argument which
 148            allows custom text generation; the callback will be passed the
 149            current implementation.
 150
 151            Note that this is meant to be used as a simple representation
 152            of the annotation data but probably shouldn't be used in cases
 153            where more complex comparisons are needed or where data is
 154            stored.
 155  Example :
 156  Returns : a string
 157  Args    : [optional] callback
 158
 159 =cut
 160
 161 sub display_text {
 162     shift->throw_not_implemented();
 163 }
 164
 165 =head2 hash_tree
 166
 167  Title   : hash_tree
 168  Usage   :
 169  Function: should return an anonymous hash with "XML-like" formatting
 170  Example :
 171  Returns : a hash reference
 172  Args    : none
 173
 174 =cut
 175
 176 sub hash_tree{
 177     shift->throw_not_implemented();
 178 }
 179
 180 =head2 tagname
 181
 182  Title   : tagname
 183  Usage   : $obj->tagname($newval)
 184  Function: Get/set the tagname for this annotation value.
 185
 186            Setting this is optional. If set, it obviates the need to
 187            provide a tag to Bio::AnnotationCollectionI when adding
 188            this object. When obtaining an AnnotationI object from the
 189            collection, the collection will set the value to the tag
 190            under which it was stored unless the object has a tag
 191            stored already.
 192
 193  Example :
 194  Returns : value of tagname (a scalar)
 195  Args    : new value (a scalar, optional)
 196
 197
 198 =cut
 199
 200 sub tagname{
 201     shift->throw_not_implemented();
 202 }
 203
 204 1;