| 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 | Bio::Annotation::SimpleValue::BEGIN@76 |
| 1 | 1 | 1 | 9µs | 466µs | Bio::Annotation::SimpleValue::BEGIN@82 |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::__ANON__[:151] |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::as_text |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::display_text |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::hash_tree |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::new |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::tag_term |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::tagname |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::SimpleValue::value |
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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; |