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[bioperl-live.git] / Bio / AnnotationI.pm
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2 # BioPerl module for Bio::AnnotationI
4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
8 # Copyright Ewan Birney
10 # You may distribute this module under the same terms as perl itself
12 # POD documentation - main docs before the code
14 =head1 NAME
16 Bio::AnnotationI - Annotation interface
18 =head1 SYNOPSIS
20 # generally you get AnnotationI's from AnnotationCollectionI's
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();
33 =head1 DESCRIPTION
35 Interface all annotations must support. There are two things that each
36 annotation has to support.
38 $annotation->as_text()
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.
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:
49 $hash = $annotation->hash_tree();
51 The formatting is as follows.
53 (1) For each key in the hash, if the value is a reference'd array -
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
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
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.
71 =head1 FEEDBACK
73 =head2 Mailing Lists
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.
80 bioperl-l@bioperl.org
82 =head2 Support
84 Please direct usage questions or support issues to the mailing list:
86 I<bioperl-l@bioperl.org>
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.
93 =head2 Reporting Bugs
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:
99 https://github.com/bioperl/bioperl-live/issues
101 =head1 AUTHOR - Ewan Birney
103 Email birney@ebi.ac.uk
105 =head1 APPENDIX
107 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
109 =cut
112 # Let the code begin...
115 package Bio::AnnotationI;
116 use strict;
118 # Object preamble - inherits from Bio::Root::Root
120 use base qw(Bio::Root::RootI);
122 =head2 as_text
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
134 =cut
136 sub as_text{
137 shift->throw_not_implemented();
140 =head2 display_text
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.
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.
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
159 =cut
161 sub display_text {
162 shift->throw_not_implemented();
165 =head2 hash_tree
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
174 =cut
176 sub hash_tree{
177 shift->throw_not_implemented();
180 =head2 tagname
182 Title : tagname
183 Usage : $obj->tagname($newval)
184 Function: Get/set the tagname for this annotation value.
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.
193 Example :
194 Returns : value of tagname (a scalar)
195 Args : new value (a scalar, optional)
198 =cut
200 sub tagname{
201 shift->throw_not_implemented();