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
 117 use strict;
 118
 119 # Object preamble - inherits from Bio::Root::Root
 120
 121 use base qw(Bio::Root::RootI);
 122
 123 =head2 as_text
 124
 125  Title   : as_text
 126  Usage   :
 127  Function: single text string, without newlines representing the
 128            annotation, mainly for human readability. It is not aimed
 129            at being able to store/represent the annotation.
 130  Example :
 131  Returns : a string
 132  Args    : none
 133
 134
 135 =cut
 136
 137 sub as_text{
 138     shift->throw_not_implemented();
 139 }
 140
 141 =head2 display_text
 142
 143  Title   : display_text
 144  Usage   : my $str = $ann->display_text();
 145  Function: returns a string. Unlike as_text(), this method returns a string
 146            formatted as would be expected for the specific implementation.
 147
 148            Implementations should allow passing a callback as an argument which
 149            allows custom text generation; the callback will be passed the
 150            current implementation.
 151
 152            Note that this is meant to be used as a simple representation
 153            of the annotation data but probably shouldn't be used in cases
 154            where more complex comparisons are needed or where data is
 155            stored.
 156  Example :
 157  Returns : a string
 158  Args    : [optional] callback
 159
 160 =cut
 161
 162 sub display_text {
 163     shift->throw_not_implemented();
 164 }
 165
 166 =head2 hash_tree
 167
 168  Title   : hash_tree
 169  Usage   :
 170  Function: should return an anonymous hash with "XML-like" formatting
 171  Example :
 172  Returns : a hash reference
 173  Args    : none
 174
 175 =cut
 176
 177 sub hash_tree{
 178     shift->throw_not_implemented();
 179 }
 180
 181 =head2 tagname
 182
 183  Title   : tagname
 184  Usage   : $obj->tagname($newval)
 185  Function: Get/set the tagname for this annotation value.
 186
 187            Setting this is optional. If set, it obviates the need to
 188            provide a tag to Bio::AnnotationCollectionI when adding
 189            this object. When obtaining an AnnotationI object from the
 190            collection, the collection will set the value to the tag
 191            under which it was stored unless the object has a tag
 192            stored already.
 193
 194  Example :
 195  Returns : value of tagname (a scalar)
 196  Args    : new value (a scalar, optional)
 197
 198
 199 =cut
 200
 201 sub tagname{
 202     shift->throw_not_implemented();
 203 }
 204
 205 1;