Filename | /Users/ap13/perl5/lib/perl5/Bio/AnnotationI.pm |
Statements | Executed 5 statements in 142µs |
Calls | P | F | Exclusive Time |
Inclusive Time |
Subroutine |
---|---|---|---|---|---|
1 | 1 | 1 | 13µs | 26µs | BEGIN@116 | Bio::AnnotationI::
1 | 1 | 1 | 9µs | 77µs | BEGIN@120 | Bio::AnnotationI::
0 | 0 | 0 | 0s | 0s | as_text | Bio::AnnotationI::
0 | 0 | 0 | 0s | 0s | display_text | Bio::AnnotationI::
0 | 0 | 0 | 0s | 0s | hash_tree | Bio::AnnotationI::
0 | 0 | 0 | 0s | 0s | tagname | Bio::AnnotationI::
Line | State ments |
Time on line |
Calls | Time in subs |
Code |
---|---|---|---|---|---|
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 | 2 | 27µs | 2 | 39µs | # spent 26µs (13+13) within Bio::AnnotationI::BEGIN@116 which was called:
# once (13µs+13µs) by base::import at line 116 # spent 26µs making 1 call to Bio::AnnotationI::BEGIN@116
# spent 13µs making 1 call to strict::import |
117 | |||||
118 | # Object preamble - inherits from Bio::Root::Root | ||||
119 | |||||
120 | 2 | 113µs | 2 | 77µs | # spent 77µs (9+67) within Bio::AnnotationI::BEGIN@120 which was called:
# once (9µs+67µs) by base::import at line 120 # spent 77µs making 1 call to Bio::AnnotationI::BEGIN@120
# spent 68µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 68µs |
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 | 2µs | 1; |