Filename | /Users/ap13/perl5/lib/perl5/Bio/IdentifiableI.pm |
Statements | Executed 5 statements in 329µs |
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1 | 1 | 1 | 21µs | 46µs | BEGIN@93 | Bio::IdentifiableI::
1 | 1 | 1 | 11µs | 95µs | BEGIN@96 | Bio::IdentifiableI::
0 | 0 | 0 | 0s | 0s | authority | Bio::IdentifiableI::
0 | 0 | 0 | 0s | 0s | lsid_string | Bio::IdentifiableI::
0 | 0 | 0 | 0s | 0s | namespace | Bio::IdentifiableI::
0 | 0 | 0 | 0s | 0s | namespace_string | Bio::IdentifiableI::
0 | 0 | 0 | 0s | 0s | object_id | Bio::IdentifiableI::
0 | 0 | 0 | 0s | 0s | version | Bio::IdentifiableI::
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1 | # | ||||
2 | # This module is licensed under the same terms as Perl itself. You use, | ||||
3 | # modify, and redistribute it under the terms of the Perl Artistic License. | ||||
4 | # | ||||
5 | |||||
6 | =head1 NAME | ||||
7 | |||||
8 | Bio::IdentifiableI - interface for objects with identifiers | ||||
9 | |||||
10 | =head1 SYNOPSIS | ||||
11 | |||||
12 | # to test this is an identifiable object | ||||
13 | |||||
14 | $obj->isa("Bio::IdentifiableI") || | ||||
15 | $obj->throw("$obj does not implement the Bio::IdentifiableI interface"); | ||||
16 | |||||
17 | # Accessors | ||||
18 | |||||
19 | $object_id = $obj->object_id(); | ||||
20 | $namespace = $obj->namespace(); | ||||
21 | $authority = $obj->authority(); | ||||
22 | $version = $obj->version(); | ||||
23 | # Gets authority:namespace:object_id | ||||
24 | $lsid = $obj->lsid_string(); | ||||
25 | # Gets namespace:object_id.version | ||||
26 | $ns_string = $obj->namespace_string(); | ||||
27 | |||||
28 | =head1 DESCRIPTION | ||||
29 | |||||
30 | This interface describes methods expected on identifiable objects, i.e. | ||||
31 | ones which have identifiers expected to make sense across a number of | ||||
32 | instances and/or domains. This interface is modeled after pretty much | ||||
33 | ubiquitous ideas for names in bioinformatics being | ||||
34 | |||||
35 | databasename:object_id.version | ||||
36 | |||||
37 | Example: | ||||
38 | |||||
39 | swissprot:P012334.2 | ||||
40 | |||||
41 | or: | ||||
42 | |||||
43 | GO:0007048 | ||||
44 | |||||
45 | The object will also work with LSID proposals which adds the concept of an | ||||
46 | authority, being the DNS name of the organisation assigning the namespace. | ||||
47 | See L<http://lsid.sourceforge.net/>. | ||||
48 | |||||
49 | Helper functions are provided to make useful strings: | ||||
50 | |||||
51 | lsid_string - string complying to the LSID standard | ||||
52 | |||||
53 | namespace_string - string complying to the usual convention of | ||||
54 | namespace:object_id.version | ||||
55 | |||||
56 | =head1 FEEDBACK | ||||
57 | |||||
58 | =head2 Mailing Lists | ||||
59 | |||||
60 | User feedback is an integral part of the evolution of this and other | ||||
61 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
62 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
63 | |||||
64 | bioperl-l@bioperl.org - General discussion | ||||
65 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
66 | |||||
67 | =head2 Support | ||||
68 | |||||
69 | Please direct usage questions or support issues to the mailing list: | ||||
70 | |||||
71 | I<bioperl-l@bioperl.org> | ||||
72 | |||||
73 | rather than to the module maintainer directly. Many experienced and | ||||
74 | reponsive experts will be able look at the problem and quickly | ||||
75 | address it. Please include a thorough description of the problem | ||||
76 | with code and data examples if at all possible. | ||||
77 | |||||
78 | =head2 Reporting Bugs | ||||
79 | |||||
80 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
81 | the bugs and their resolution. Bug reports can be submitted via the | ||||
82 | web: | ||||
83 | |||||
84 | https://github.com/bioperl/bioperl-live/issues | ||||
85 | |||||
86 | =head1 AUTHOR - Ewan Birney | ||||
87 | |||||
88 | Email birney@ebi.ac.uk | ||||
89 | |||||
90 | =cut | ||||
91 | |||||
92 | package Bio::IdentifiableI; | ||||
93 | 2 | 39µs | 2 | 72µs | # spent 46µs (21+26) within Bio::IdentifiableI::BEGIN@93 which was called:
# once (21µs+26µs) by base::import at line 93 # spent 46µs making 1 call to Bio::IdentifiableI::BEGIN@93
# spent 26µs making 1 call to strict::import |
94 | |||||
95 | |||||
96 | 2 | 287µs | 2 | 95µs | # spent 95µs (11+84) within Bio::IdentifiableI::BEGIN@96 which was called:
# once (11µs+84µs) by base::import at line 96 # spent 95µs making 1 call to Bio::IdentifiableI::BEGIN@96
# spent 84µs making 1 call to base::import, recursion: max depth 2, sum of overlapping time 84µs |
97 | |||||
98 | =head1 Implementation Specific Functions | ||||
99 | |||||
100 | These functions are the ones that a specific implementation must | ||||
101 | define. | ||||
102 | |||||
103 | =head2 object_id | ||||
104 | |||||
105 | Title : object_id | ||||
106 | Usage : $string = $obj->object_id() | ||||
107 | Function: a string which represents the stable primary identifier | ||||
108 | in this namespace of this object. For DNA sequences this | ||||
109 | is its accession_number, similarly for protein sequences | ||||
110 | Returns : A scalar | ||||
111 | Status : Virtual | ||||
112 | |||||
113 | =cut | ||||
114 | |||||
115 | sub object_id { | ||||
116 | my ($self) = @_; | ||||
117 | $self->throw_not_implemented(); | ||||
118 | } | ||||
119 | |||||
120 | =head2 version | ||||
121 | |||||
122 | Title : version | ||||
123 | Usage : $version = $obj->version() | ||||
124 | Function: a number which differentiates between versions of | ||||
125 | the same object. Higher numbers are considered to be | ||||
126 | later and more relevant, but a single object described | ||||
127 | the same identifier should represent the same concept | ||||
128 | Returns : A number | ||||
129 | Status : Virtual | ||||
130 | |||||
131 | =cut | ||||
132 | |||||
133 | sub version { | ||||
134 | my ($self) = @_; | ||||
135 | $self->throw_not_implemented(); | ||||
136 | } | ||||
137 | |||||
138 | |||||
139 | =head2 authority | ||||
140 | |||||
141 | Title : authority | ||||
142 | Usage : $authority = $obj->authority() | ||||
143 | Function: a string which represents the organisation which | ||||
144 | granted the namespace, written as the DNS name for | ||||
145 | organisation (eg, wormbase.org) | ||||
146 | Returns : A scalar | ||||
147 | Status : Virtual | ||||
148 | |||||
149 | =cut | ||||
150 | |||||
151 | sub authority { | ||||
152 | my ($self) = @_; | ||||
153 | $self->throw_not_implemented(); | ||||
154 | } | ||||
155 | |||||
156 | |||||
157 | =head2 namespace | ||||
158 | |||||
159 | Title : namespace | ||||
160 | Usage : $string = $obj->namespace() | ||||
161 | Function: A string representing the name space this identifier | ||||
162 | is valid in, often the database name or the name | ||||
163 | describing the collection | ||||
164 | Returns : A scalar | ||||
165 | Status : Virtual | ||||
166 | |||||
167 | =cut | ||||
168 | |||||
169 | sub namespace { | ||||
170 | my ($self) = @_; | ||||
171 | $self->throw_not_implemented(); | ||||
172 | } | ||||
173 | |||||
174 | |||||
175 | =head1 Implementation optional functions | ||||
176 | |||||
177 | These functions are helper functions that are provided by | ||||
178 | the interface but can be overridden if so wished | ||||
179 | |||||
180 | =head2 lsid_string | ||||
181 | |||||
182 | Title : lsid_string | ||||
183 | Usage : $string = $obj->lsid_string() | ||||
184 | Function: a string which gives the LSID standard | ||||
185 | notation for the identifier of interest | ||||
186 | |||||
187 | |||||
188 | Returns : A scalar | ||||
189 | |||||
190 | =cut | ||||
191 | |||||
192 | sub lsid_string { | ||||
193 | my ($self) = @_; | ||||
194 | |||||
195 | return $self->authority.":".$self->namespace.":".$self->object_id; | ||||
196 | } | ||||
197 | |||||
- - | |||||
200 | =head2 namespace_string | ||||
201 | |||||
202 | Title : namespace_string | ||||
203 | Usage : $string = $obj->namespace_string() | ||||
204 | Function: a string which gives the common notation of | ||||
205 | namespace:object_id.version | ||||
206 | Returns : A scalar | ||||
207 | |||||
208 | =cut | ||||
209 | |||||
210 | sub namespace_string { | ||||
211 | my ($self) = @_; | ||||
212 | |||||
213 | return $self->namespace.":".$self->object_id . | ||||
214 | (defined($self->version()) ? ".".$self->version : ''); | ||||
215 | } | ||||
216 | |||||
217 | 1 | 3µs | 1; |