| Filename | /Users/ap13/perl5/lib/perl5/Bio/IdentifiableI.pm |
| Statements | Executed 5 statements in 329µs |
| Calls | P | F | Exclusive Time |
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| 1 | 1 | 1 | 21µs | 46µs | Bio::IdentifiableI::BEGIN@93 |
| 1 | 1 | 1 | 11µs | 95µs | Bio::IdentifiableI::BEGIN@96 |
| 0 | 0 | 0 | 0s | 0s | Bio::IdentifiableI::authority |
| 0 | 0 | 0 | 0s | 0s | Bio::IdentifiableI::lsid_string |
| 0 | 0 | 0 | 0s | 0s | Bio::IdentifiableI::namespace |
| 0 | 0 | 0 | 0s | 0s | Bio::IdentifiableI::namespace_string |
| 0 | 0 | 0 | 0s | 0s | Bio::IdentifiableI::object_id |
| 0 | 0 | 0 | 0s | 0s | Bio::IdentifiableI::version |
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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; |