Filename | /Users/ap13/perl5/lib/perl5/Bio/Annotation/SimpleValue.pm |
Statements | Executed 7 statements in 450µs |
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1 | 1 | 1 | 15µs | 29µs | BEGIN@76 | Bio::Annotation::SimpleValue::
1 | 1 | 1 | 9µs | 466µs | BEGIN@82 | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | __ANON__[:151] | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | as_text | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | display_text | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | hash_tree | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | new | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | tag_term | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | tagname | Bio::Annotation::SimpleValue::
0 | 0 | 0 | 0s | 0s | value | Bio::Annotation::SimpleValue::
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1 | # | ||||
2 | # BioPerl module for Bio::Annotation::SimpleValue | ||||
3 | # | ||||
4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
5 | # | ||||
6 | # Cared for by bioperl <bioperl-l@bioperl.org> | ||||
7 | # | ||||
8 | # Copyright bioperl | ||||
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::Annotation::SimpleValue - A simple scalar | ||||
17 | |||||
18 | =head1 SYNOPSIS | ||||
19 | |||||
20 | use Bio::Annotation::SimpleValue; | ||||
21 | use Bio::Annotation::Collection; | ||||
22 | |||||
23 | my $col = Bio::Annotation::Collection->new(); | ||||
24 | my $sv = Bio::Annotation::SimpleValue->new(-value => 'someval'); | ||||
25 | $col->add_Annotation('tagname', $sv); | ||||
26 | |||||
27 | =head1 DESCRIPTION | ||||
28 | |||||
29 | Scalar value annotation object | ||||
30 | |||||
31 | =head1 FEEDBACK | ||||
32 | |||||
33 | =head2 Mailing Lists | ||||
34 | |||||
35 | User feedback is an integral part of the evolution of this and other | ||||
36 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
37 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
38 | |||||
39 | bioperl-l@bioperl.org - General discussion | ||||
40 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
41 | |||||
42 | =head2 Support | ||||
43 | |||||
44 | Please direct usage questions or support issues to the mailing list: | ||||
45 | |||||
46 | I<bioperl-l@bioperl.org> | ||||
47 | |||||
48 | rather than to the module maintainer directly. Many experienced and | ||||
49 | reponsive experts will be able look at the problem and quickly | ||||
50 | address it. Please include a thorough description of the problem | ||||
51 | with code and data examples if at all possible. | ||||
52 | |||||
53 | =head2 Reporting Bugs | ||||
54 | |||||
55 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
56 | the bugs and their resolution. Bug reports can be submitted via | ||||
57 | the web: | ||||
58 | |||||
59 | https://github.com/bioperl/bioperl-live/issues | ||||
60 | |||||
61 | =head1 AUTHOR - Ewan Birney | ||||
62 | |||||
63 | Email birney@ebi.ac.uk | ||||
64 | |||||
65 | =head1 APPENDIX | ||||
66 | |||||
67 | The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ | ||||
68 | |||||
69 | =cut | ||||
70 | |||||
71 | |||||
72 | # Let the code begin... | ||||
73 | |||||
74 | |||||
75 | package Bio::Annotation::SimpleValue; | ||||
76 | 2 | 29µs | 2 | 42µs | # spent 29µs (15+13) within Bio::Annotation::SimpleValue::BEGIN@76 which was called:
# once (15µs+13µs) by Bio::Annotation::Collection::BEGIN@93 at line 76 # spent 29µs making 1 call to Bio::Annotation::SimpleValue::BEGIN@76
# spent 13µs making 1 call to strict::import |
77 | |||||
78 | # Object preamble - inherits from Bio::Root::Root | ||||
79 | |||||
80 | #use Bio::Ontology::TermI; | ||||
81 | |||||
82 | 2 | 415µs | 2 | 924µs | # spent 466µs (9+458) within Bio::Annotation::SimpleValue::BEGIN@82 which was called:
# once (9µs+458µs) by Bio::Annotation::Collection::BEGIN@93 at line 82 # spent 466µs making 1 call to Bio::Annotation::SimpleValue::BEGIN@82
# spent 458µs making 1 call to base::import |
83 | |||||
84 | =head2 new | ||||
85 | |||||
86 | Title : new | ||||
87 | Usage : my $sv = Bio::Annotation::SimpleValue->new(); | ||||
88 | Function: Instantiate a new SimpleValue object | ||||
89 | Returns : Bio::Annotation::SimpleValue object | ||||
90 | Args : -value => $value to initialize the object data field [optional] | ||||
91 | -tagname => $tag to initialize the tagname [optional] | ||||
92 | -tag_term => ontology term representation of the tag [optional] | ||||
93 | |||||
94 | =cut | ||||
95 | |||||
96 | sub new{ | ||||
97 | my ($class,@args) = @_; | ||||
98 | |||||
99 | my $self = $class->SUPER::new(@args); | ||||
100 | |||||
101 | my ($value,$tag,$term) = | ||||
102 | $self->_rearrange([qw(VALUE TAGNAME TAG_TERM)], @args); | ||||
103 | |||||
104 | # set the term first | ||||
105 | defined $term && $self->tag_term($term); | ||||
106 | defined $value && $self->value($value); | ||||
107 | defined $tag && $self->tagname($tag); | ||||
108 | |||||
109 | return $self; | ||||
110 | } | ||||
111 | |||||
112 | |||||
113 | =head1 AnnotationI implementing functions | ||||
114 | |||||
115 | =cut | ||||
116 | |||||
117 | =head2 as_text | ||||
118 | |||||
119 | Title : as_text | ||||
120 | Usage : my $text = $obj->as_text | ||||
121 | Function: return the string "Value: $v" where $v is the value | ||||
122 | Returns : string | ||||
123 | Args : none | ||||
124 | |||||
125 | |||||
126 | =cut | ||||
127 | |||||
128 | sub as_text{ | ||||
129 | my ($self) = @_; | ||||
130 | |||||
131 | return "Value: ".$self->value; | ||||
132 | } | ||||
133 | |||||
134 | =head2 display_text | ||||
135 | |||||
136 | Title : display_text | ||||
137 | Usage : my $str = $ann->display_text(); | ||||
138 | Function: returns a string. Unlike as_text(), this method returns a string | ||||
139 | formatted as would be expected for te specific implementation. | ||||
140 | |||||
141 | One can pass a callback as an argument which allows custom text | ||||
142 | generation; the callback is passed the current instance and any text | ||||
143 | returned | ||||
144 | Example : | ||||
145 | Returns : a string | ||||
146 | Args : [optional] callback | ||||
147 | |||||
148 | =cut | ||||
149 | |||||
150 | { | ||||
151 | 2 | 3µs | my $DEFAULT_CB = sub { $_[0]->value}; | ||
152 | |||||
153 | sub display_text { | ||||
154 | my ($self, $cb) = @_; | ||||
155 | $cb ||= $DEFAULT_CB; | ||||
156 | $self->throw("Callback must be a code reference") if ref $cb ne 'CODE'; | ||||
157 | return $cb->($self); | ||||
158 | } | ||||
159 | |||||
160 | } | ||||
161 | |||||
162 | =head2 hash_tree | ||||
163 | |||||
164 | Title : hash_tree | ||||
165 | Usage : my $hashtree = $value->hash_tree | ||||
166 | Function: For supporting the AnnotationI interface just returns the value | ||||
167 | as a hashref with the key 'value' pointing to the value | ||||
168 | Returns : hashrf | ||||
169 | Args : none | ||||
170 | |||||
171 | |||||
172 | =cut | ||||
173 | |||||
174 | sub hash_tree{ | ||||
175 | my $self = shift; | ||||
176 | |||||
177 | my $h = {}; | ||||
178 | $h->{'value'} = $self->value; | ||||
179 | return $h; | ||||
180 | } | ||||
181 | |||||
182 | =head2 tagname | ||||
183 | |||||
184 | Title : tagname | ||||
185 | Usage : $obj->tagname($newval) | ||||
186 | Function: Get/set the tagname for this annotation value. | ||||
187 | |||||
188 | Setting this is optional. If set, it obviates the need to | ||||
189 | provide a tag to AnnotationCollection when adding this | ||||
190 | object. | ||||
191 | |||||
192 | Example : | ||||
193 | Returns : value of tagname (a scalar) | ||||
194 | Args : new value (a scalar, optional) | ||||
195 | |||||
196 | |||||
197 | =cut | ||||
198 | |||||
199 | sub tagname{ | ||||
200 | my $self = shift; | ||||
201 | |||||
202 | # check for presence of an ontology term | ||||
203 | if($self->{'_tag_term'}) { | ||||
204 | # keep a copy in case the term is removed later | ||||
205 | $self->{'tagname'} = $_[0] if @_; | ||||
206 | # delegate to the ontology term object | ||||
207 | return $self->tag_term->name(@_); | ||||
208 | } | ||||
209 | return $self->{'tagname'} = shift if @_; | ||||
210 | return $self->{'tagname'}; | ||||
211 | } | ||||
212 | |||||
213 | |||||
214 | =head1 Specific accessors for SimpleValue | ||||
215 | |||||
216 | =cut | ||||
217 | |||||
218 | =head2 value | ||||
219 | |||||
220 | Title : value | ||||
221 | Usage : $obj->value($newval) | ||||
222 | Function: Get/Set the value for simplevalue | ||||
223 | Returns : value of value | ||||
224 | Args : newvalue (optional) | ||||
225 | |||||
226 | |||||
227 | =cut | ||||
228 | |||||
229 | sub value{ | ||||
230 | my ($self,$value) = @_; | ||||
231 | |||||
232 | if( defined $value) { | ||||
233 | $self->{'value'} = $value; | ||||
234 | } | ||||
235 | return $self->{'value'}; | ||||
236 | } | ||||
237 | |||||
238 | =head2 tag_term | ||||
239 | |||||
240 | Title : tag_term | ||||
241 | Usage : $obj->tag_term($newval) | ||||
242 | Function: Get/set the L<Bio::Ontology::TermI> object representing | ||||
243 | the tag name. | ||||
244 | |||||
245 | This is so you can specifically relate the tag of this | ||||
246 | annotation to an entry in an ontology. You may want to do | ||||
247 | this to associate an identifier with the tag, or a | ||||
248 | particular category, such that you can better match the tag | ||||
249 | against a controlled vocabulary. | ||||
250 | |||||
251 | This accessor will return undef if it has never been set | ||||
252 | before in order to allow this annotation to stay | ||||
253 | light-weight if an ontology term representation of the tag | ||||
254 | is not needed. Once it is set to a valid value, tagname() | ||||
255 | will actually delegate to the name() of this term. | ||||
256 | |||||
257 | Example : | ||||
258 | Returns : a L<Bio::Ontology::TermI> compliant object, or undef | ||||
259 | Args : on set, new value (a L<Bio::Ontology::TermI> compliant | ||||
260 | object or undef, optional) | ||||
261 | |||||
262 | |||||
263 | =cut | ||||
264 | |||||
265 | sub tag_term{ | ||||
266 | my $self = shift; | ||||
267 | |||||
268 | return $self->{'_tag_term'} = shift if @_; | ||||
269 | return $self->{'_tag_term'}; | ||||
270 | } | ||||
271 | |||||
272 | 1 | 4µs | 1; |