File Coverage

Bio/AnnotationI.pm
Criterion Covered Total %
statement 6 10 60.0
branch n/a
condition n/a
subroutine 2 6 33.3
pod 4 4 100.0
total 12 20 60.0


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::AnnotationI
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Ewan Birney
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
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;
116 195     195   1283 use strict;
  195         378  
  195         5433  
117              
118             # Object preamble - inherits from Bio::Root::Root
119              
120 195     195   890 use base qw(Bio::Root::RootI);
  195         305  
  195         23336  
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 0     0 1   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 0     0 1   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 0     0 1   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 0     0 1   shift->throw_not_implemented();
202             }
203              
204             1;