| Filename | /Users/ap13/perl5/lib/perl5/Bio/Annotation/Collection.pm |
| Statements | Executed 11 statements in 1.95ms |
| Calls | P | F | Exclusive Time |
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| 1 | 1 | 1 | 551µs | 1.05ms | Bio::Annotation::Collection::BEGIN@93 |
| 1 | 1 | 1 | 401µs | 511µs | Bio::Annotation::Collection::BEGIN@92 |
| 1 | 1 | 1 | 14µs | 28µs | Bio::Annotation::Collection::BEGIN@88 |
| 1 | 1 | 1 | 11µs | 535µs | Bio::Annotation::Collection::BEGIN@96 |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::__ANON__[:504] |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::_typemap |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::add_Annotation |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::add_Comment |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::add_DBLink |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::add_Reference |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::add_gene_name |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::as_text |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::description |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::display_text |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::each_Comment |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::each_DBLink |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::each_Reference |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::each_gene_name |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::flatten_Annotations |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::get_Annotations |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::get_all_Annotations |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::get_all_annotation_keys |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::get_nested_Annotations |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::get_num_of_annotations |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::hash_tree |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::new |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::remove_Annotations |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::Collection::tagname |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Annotation::Collection.pm | ||||
| 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::Annotation::Collection - Default Perl implementation of | ||||
| 17 | AnnotationCollectionI | ||||
| 18 | |||||
| 19 | =head1 SYNOPSIS | ||||
| 20 | |||||
| 21 | # get an AnnotationCollectionI somehow, eg | ||||
| 22 | |||||
| 23 | $ac = $seq->annotation(); | ||||
| 24 | |||||
| 25 | foreach $key ( $ac->get_all_annotation_keys() ) { | ||||
| 26 | @values = $ac->get_Annotations($key); | ||||
| 27 | foreach $value ( @values ) { | ||||
| 28 | # value is an Bio::AnnotationI, and defines a "as_text" method | ||||
| 29 | print "Annotation ",$key," stringified value ",$value->as_text,"\n"; | ||||
| 30 | |||||
| 31 | # also defined hash_tree method, which allows data orientated | ||||
| 32 | # access into this object | ||||
| 33 | $hash = $value->hash_tree(); | ||||
| 34 | } | ||||
| 35 | } | ||||
| 36 | |||||
| 37 | =head1 DESCRIPTION | ||||
| 38 | |||||
| 39 | Bioperl implementation for Bio::AnnotationCollectionI | ||||
| 40 | |||||
| 41 | =head1 FEEDBACK | ||||
| 42 | |||||
| 43 | =head2 Mailing Lists | ||||
| 44 | |||||
| 45 | User feedback is an integral part of the evolution of this and other | ||||
| 46 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
| 47 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
| 48 | |||||
| 49 | bioperl-l@bioperl.org - General discussion | ||||
| 50 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
| 51 | |||||
| 52 | =head2 Support | ||||
| 53 | |||||
| 54 | Please direct usage questions or support issues to the mailing list: | ||||
| 55 | |||||
| 56 | I<bioperl-l@bioperl.org> | ||||
| 57 | |||||
| 58 | rather than to the module maintainer directly. Many experienced and | ||||
| 59 | reponsive experts will be able look at the problem and quickly | ||||
| 60 | address it. Please include a thorough description of the problem | ||||
| 61 | with code and data examples if at all possible. | ||||
| 62 | |||||
| 63 | =head2 Reporting Bugs | ||||
| 64 | |||||
| 65 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 66 | the bugs and their resolution. Bug reports can be submitted via | ||||
| 67 | the web: | ||||
| 68 | |||||
| 69 | https://github.com/bioperl/bioperl-live/issues | ||||
| 70 | |||||
| 71 | =head1 AUTHOR - Ewan Birney | ||||
| 72 | |||||
| 73 | Email birney@ebi.ac.uk | ||||
| 74 | |||||
| 75 | =head1 APPENDIX | ||||
| 76 | |||||
| 77 | The rest of the documentation details each of the object | ||||
| 78 | methods. Internal methods are usually preceded with a _ | ||||
| 79 | |||||
| 80 | =cut | ||||
| 81 | |||||
| 82 | |||||
| 83 | # Let the code begin... | ||||
| 84 | |||||
| 85 | |||||
| 86 | package Bio::Annotation::Collection; | ||||
| 87 | |||||
| 88 | 2 | 29µs | 2 | 41µs | # spent 28µs (14+14) within Bio::Annotation::Collection::BEGIN@88 which was called:
# once (14µs+14µs) by Bio::SeqFeature::Generic::BEGIN@145 at line 88 # spent 28µs making 1 call to Bio::Annotation::Collection::BEGIN@88
# spent 14µs making 1 call to strict::import |
| 89 | |||||
| 90 | # Object preamble - inherits from Bio::Root::Root | ||||
| 91 | |||||
| 92 | 2 | 138µs | 1 | 511µs | # spent 511µs (401+110) within Bio::Annotation::Collection::BEGIN@92 which was called:
# once (401µs+110µs) by Bio::SeqFeature::Generic::BEGIN@145 at line 92 # spent 511µs making 1 call to Bio::Annotation::Collection::BEGIN@92 |
| 93 | 2 | 144µs | 1 | 1.05ms | # spent 1.05ms (551µs+495µs) within Bio::Annotation::Collection::BEGIN@93 which was called:
# once (551µs+495µs) by Bio::SeqFeature::Generic::BEGIN@145 at line 93 # spent 1.05ms making 1 call to Bio::Annotation::Collection::BEGIN@93 |
| 94 | |||||
| 95 | |||||
| 96 | 2 | 1.63ms | 2 | 1.06ms | # spent 535µs (11+524) within Bio::Annotation::Collection::BEGIN@96 which was called:
# once (11µs+524µs) by Bio::SeqFeature::Generic::BEGIN@145 at line 96 # spent 535µs making 1 call to Bio::Annotation::Collection::BEGIN@96
# spent 524µs making 1 call to base::import |
| 97 | |||||
| 98 | |||||
| 99 | =head2 new | ||||
| 100 | |||||
| 101 | Title : new | ||||
| 102 | Usage : $coll = Bio::Annotation::Collection->new() | ||||
| 103 | Function: Makes a new Annotation::Collection object. | ||||
| 104 | Returns : Bio::Annotation::Collection | ||||
| 105 | Args : none | ||||
| 106 | |||||
| 107 | =cut | ||||
| 108 | |||||
| 109 | sub new{ | ||||
| 110 | my ($class,@args) = @_; | ||||
| 111 | |||||
| 112 | my $self = $class->SUPER::new(@args); | ||||
| 113 | |||||
| 114 | $self->{'_annotation'} = {}; | ||||
| 115 | $self->_typemap(Bio::Annotation::TypeManager->new()); | ||||
| 116 | |||||
| 117 | return $self; | ||||
| 118 | } | ||||
| 119 | |||||
| 120 | |||||
| 121 | =head1 L<Bio::AnnotationCollectionI> implementing methods | ||||
| 122 | |||||
| 123 | =cut | ||||
| 124 | |||||
| 125 | =head2 get_all_annotation_keys | ||||
| 126 | |||||
| 127 | Title : get_all_annotation_keys | ||||
| 128 | Usage : $ac->get_all_annotation_keys() | ||||
| 129 | Function: gives back a list of annotation keys, which are simple text strings | ||||
| 130 | Returns : list of strings | ||||
| 131 | Args : none | ||||
| 132 | |||||
| 133 | =cut | ||||
| 134 | |||||
| 135 | sub get_all_annotation_keys{ | ||||
| 136 | my ($self) = @_; | ||||
| 137 | return keys %{$self->{'_annotation'}}; | ||||
| 138 | } | ||||
| 139 | |||||
| 140 | =head2 get_Annotations | ||||
| 141 | |||||
| 142 | Title : get_Annotations | ||||
| 143 | Usage : my @annotations = $collection->get_Annotations('key') | ||||
| 144 | Function: Retrieves all the Bio::AnnotationI objects for one or more | ||||
| 145 | specific key(s). | ||||
| 146 | |||||
| 147 | If no key is given, returns all annotation objects. | ||||
| 148 | |||||
| 149 | The returned objects will have their tagname() attribute set to | ||||
| 150 | the key under which they were attached, unless the tagname was | ||||
| 151 | already set. | ||||
| 152 | |||||
| 153 | Returns : list of Bio::AnnotationI - empty if no objects stored for a key | ||||
| 154 | Args : keys (list of strings) for annotations (optional) | ||||
| 155 | |||||
| 156 | =cut | ||||
| 157 | |||||
| 158 | sub get_Annotations{ | ||||
| 159 | my ($self,@keys) = @_; | ||||
| 160 | |||||
| 161 | my @anns = (); | ||||
| 162 | @keys = $self->get_all_annotation_keys() unless @keys; | ||||
| 163 | foreach my $key (@keys) { | ||||
| 164 | if(exists($self->{'_annotation'}->{$key})) { | ||||
| 165 | push(@anns, | ||||
| 166 | map { | ||||
| 167 | $_->tagname($key) if ! $_->tagname(); $_; | ||||
| 168 | } @{$self->{'_annotation'}->{$key}}); | ||||
| 169 | } | ||||
| 170 | } | ||||
| 171 | return @anns; | ||||
| 172 | } | ||||
| 173 | |||||
| 174 | |||||
| 175 | =head2 get_nested_Annotations | ||||
| 176 | |||||
| 177 | Title : get_nested_Annotations | ||||
| 178 | Usage : my @annotations = $collection->get_nested_Annotations( | ||||
| 179 | '-key' => \@keys, | ||||
| 180 | '-recursive => 1); | ||||
| 181 | Function: Retrieves all the Bio::AnnotationI objects for one or more | ||||
| 182 | specific key(s). If -recursive is set to true, traverses the nested | ||||
| 183 | annotation collections recursively and returns all annotations | ||||
| 184 | matching the key(s). | ||||
| 185 | |||||
| 186 | If no key is given, returns all annotation objects. | ||||
| 187 | |||||
| 188 | The returned objects will have their tagname() attribute set to | ||||
| 189 | the key under which they were attached, unless the tagname was | ||||
| 190 | already set. | ||||
| 191 | |||||
| 192 | Returns : list of Bio::AnnotationI - empty if no objects stored for a key | ||||
| 193 | Args : -keys => arrayref of keys to search for (optional) | ||||
| 194 | -recursive => boolean, whether or not to recursively traverse the | ||||
| 195 | nested annotations and return annotations with matching keys. | ||||
| 196 | |||||
| 197 | =cut | ||||
| 198 | |||||
| 199 | sub get_nested_Annotations { | ||||
| 200 | my ($self, @args) = @_; | ||||
| 201 | my ($keys, $recursive) = $self->_rearrange([qw(KEYS RECURSIVE)], @args); | ||||
| 202 | $self->verbose(1); | ||||
| 203 | |||||
| 204 | my @anns = (); | ||||
| 205 | # if not recursive behave exactly like get_Annotations() | ||||
| 206 | if (!$recursive) { | ||||
| 207 | my @keys = $keys? @$keys : $self->get_all_annotation_keys(); | ||||
| 208 | foreach my $key (@keys) { | ||||
| 209 | if(exists($self->{'_annotation'}->{$key})) { | ||||
| 210 | push(@anns, | ||||
| 211 | map { | ||||
| 212 | $_->tagname($key) if ! $_->tagname(); $_; | ||||
| 213 | } @{$self->{'_annotation'}->{$key}}); | ||||
| 214 | } | ||||
| 215 | } | ||||
| 216 | } | ||||
| 217 | # if recursive search for keys recursively | ||||
| 218 | else { | ||||
| 219 | my @allkeys = $self->get_all_annotation_keys(); | ||||
| 220 | foreach my $key (@allkeys) { | ||||
| 221 | my $keymatch = 0; | ||||
| 222 | foreach my $searchkey (@$keys) { | ||||
| 223 | if ($key eq $searchkey) { $keymatch = 1;} | ||||
| 224 | } | ||||
| 225 | if ($keymatch) { | ||||
| 226 | if(exists($self->{'_annotation'}->{$key})) { | ||||
| 227 | push(@anns, | ||||
| 228 | map { | ||||
| 229 | $_->tagname($key) if ! $_->tagname(); $_; | ||||
| 230 | } @{$self->{'_annotation'}->{$key}}); | ||||
| 231 | } | ||||
| 232 | } | ||||
| 233 | else { | ||||
| 234 | my @annotations = @{$self->{'_annotation'}->{$key}}; | ||||
| 235 | foreach (@annotations) { | ||||
| 236 | if ($_->isa("Bio::AnnotationCollectionI")) { | ||||
| 237 | push (@anns, | ||||
| 238 | $_->get_nested_Annotations('-keys' => $keys, '-recursive' => 1) | ||||
| 239 | ); | ||||
| 240 | } | ||||
| 241 | } | ||||
| 242 | } | ||||
| 243 | } | ||||
| 244 | } | ||||
| 245 | return @anns; | ||||
| 246 | } | ||||
| 247 | |||||
| 248 | =head2 get_all_Annotations | ||||
| 249 | |||||
| 250 | Title : get_all_Annotations | ||||
| 251 | Usage : | ||||
| 252 | Function: Similar to get_Annotations, but traverses and flattens nested | ||||
| 253 | annotation collections. This means that collections in the | ||||
| 254 | tree will be replaced by their components. | ||||
| 255 | |||||
| 256 | Keys will not be passed on to nested collections. I.e., if the | ||||
| 257 | tag name of a nested collection matches the key, it will be | ||||
| 258 | flattened in its entirety. | ||||
| 259 | |||||
| 260 | Hence, for un-nested annotation collections this will be identical | ||||
| 261 | to get_Annotations. | ||||
| 262 | Example : | ||||
| 263 | Returns : an array of L<Bio::AnnotationI> compliant objects | ||||
| 264 | Args : keys (list of strings) for annotations (optional) | ||||
| 265 | |||||
| 266 | |||||
| 267 | =cut | ||||
| 268 | |||||
| 269 | sub get_all_Annotations{ | ||||
| 270 | my ($self,@keys) = @_; | ||||
| 271 | |||||
| 272 | return map { | ||||
| 273 | $_->isa("Bio::AnnotationCollectionI") ? | ||||
| 274 | $_->get_all_Annotations() : $_; | ||||
| 275 | } $self->get_Annotations(@keys); | ||||
| 276 | } | ||||
| 277 | |||||
| 278 | |||||
| 279 | =head2 get_num_of_annotations | ||||
| 280 | |||||
| 281 | Title : get_num_of_annotations | ||||
| 282 | Usage : my $count = $collection->get_num_of_annotations() | ||||
| 283 | Function: Returns the count of all annotations stored in this collection | ||||
| 284 | Returns : integer | ||||
| 285 | Args : none | ||||
| 286 | |||||
| 287 | |||||
| 288 | =cut | ||||
| 289 | |||||
| 290 | sub get_num_of_annotations{ | ||||
| 291 | my ($self) = @_; | ||||
| 292 | my $count = 0; | ||||
| 293 | map { $count += scalar @$_ } values %{$self->{'_annotation'}}; | ||||
| 294 | return $count; | ||||
| 295 | } | ||||
| 296 | |||||
| 297 | =head1 Implementation specific functions - mainly for adding | ||||
| 298 | |||||
| 299 | =cut | ||||
| 300 | |||||
| 301 | =head2 add_Annotation | ||||
| 302 | |||||
| 303 | Title : add_Annotation | ||||
| 304 | Usage : $self->add_Annotation('reference',$object); | ||||
| 305 | $self->add_Annotation($object,'Bio::MyInterface::DiseaseI'); | ||||
| 306 | $self->add_Annotation($object); | ||||
| 307 | $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI'); | ||||
| 308 | Function: Adds an annotation for a specific key. | ||||
| 309 | |||||
| 310 | If the key is omitted, the object to be added must provide a value | ||||
| 311 | via its tagname(). | ||||
| 312 | |||||
| 313 | If the archetype is provided, this and future objects added under | ||||
| 314 | that tag have to comply with the archetype and will be rejected | ||||
| 315 | otherwise. | ||||
| 316 | |||||
| 317 | Returns : none | ||||
| 318 | Args : annotation key ('disease', 'dblink', ...) | ||||
| 319 | object to store (must be Bio::AnnotationI compliant) | ||||
| 320 | [optional] object archetype to map future storage of object | ||||
| 321 | of these types to | ||||
| 322 | |||||
| 323 | =cut | ||||
| 324 | |||||
| 325 | sub add_Annotation{ | ||||
| 326 | my ($self,$key,$object,$archetype) = @_; | ||||
| 327 | |||||
| 328 | # if there's no key we use the tagname() as key | ||||
| 329 | if(ref($key) && $key->isa("Bio::AnnotationI") && (!ref($object))) { | ||||
| 330 | $archetype = $object if defined($object); | ||||
| 331 | $object = $key; | ||||
| 332 | $key = $object->tagname(); | ||||
| 333 | $key = $key->name() if ref($key); # OntologyTermI | ||||
| 334 | $self->throw("Annotation object must have a tagname if key omitted") | ||||
| 335 | unless $key; | ||||
| 336 | } | ||||
| 337 | |||||
| 338 | if( !defined $object ) { | ||||
| 339 | $self->throw("Must have at least key and object in add_Annotation"); | ||||
| 340 | } | ||||
| 341 | |||||
| 342 | if( !ref $object ) { | ||||
| 343 | $self->throw("Must add an object. Use Bio::Annotation::{Comment,SimpleValue,OntologyTerm} for simple text additions"); | ||||
| 344 | } | ||||
| 345 | |||||
| 346 | if( !$object->isa("Bio::AnnotationI") ) { | ||||
| 347 | $self->throw("object must be AnnotationI compliant, otherwise we won't add it!"); | ||||
| 348 | } | ||||
| 349 | |||||
| 350 | # ok, now we are ready! If we don't have an archetype, set it | ||||
| 351 | # from the type of the object | ||||
| 352 | |||||
| 353 | if( !defined $archetype ) { | ||||
| 354 | $archetype = ref $object; | ||||
| 355 | } | ||||
| 356 | |||||
| 357 | # check typemap, storing if needed. | ||||
| 358 | my $stored_map = $self->_typemap->type_for_key($key); | ||||
| 359 | |||||
| 360 | if( defined $stored_map ) { | ||||
| 361 | # check validity, irregardless of archetype. A little cheeky | ||||
| 362 | # this means isa stuff is executed correctly | ||||
| 363 | |||||
| 364 | if( !$self->_typemap()->is_valid($key,$object) ) { | ||||
| 365 | $self->throw("Object $object was not valid with key $key. ". | ||||
| 366 | "If you were adding new keys in, perhaps you want to make use\n". | ||||
| 367 | "of the archetype method to allow registration to a more basic type"); | ||||
| 368 | } | ||||
| 369 | } else { | ||||
| 370 | $self->_typemap->_add_type_map($key,$archetype); | ||||
| 371 | } | ||||
| 372 | |||||
| 373 | # we are ok to store | ||||
| 374 | |||||
| 375 | if( !defined $self->{'_annotation'}->{$key} ) { | ||||
| 376 | $self->{'_annotation'}->{$key} = []; | ||||
| 377 | } | ||||
| 378 | |||||
| 379 | push(@{$self->{'_annotation'}->{$key}},$object); | ||||
| 380 | |||||
| 381 | return 1; | ||||
| 382 | } | ||||
| 383 | |||||
| 384 | =head2 remove_Annotations | ||||
| 385 | |||||
| 386 | Title : remove_Annotations | ||||
| 387 | Usage : | ||||
| 388 | Function: Remove the annotations for the specified key from this collection. | ||||
| 389 | Example : | ||||
| 390 | Returns : an array Bio::AnnotationI compliant objects which were stored | ||||
| 391 | under the given key(s) | ||||
| 392 | Args : the key(s) (tag name(s), one or more strings) for which to | ||||
| 393 | remove annotations (optional; if none given, flushes all | ||||
| 394 | annotations) | ||||
| 395 | |||||
| 396 | |||||
| 397 | =cut | ||||
| 398 | |||||
| 399 | sub remove_Annotations{ | ||||
| 400 | my ($self, @keys) = @_; | ||||
| 401 | |||||
| 402 | @keys = $self->get_all_annotation_keys() unless @keys; | ||||
| 403 | my @anns = $self->get_Annotations(@keys); | ||||
| 404 | # flush | ||||
| 405 | foreach my $key (@keys) { | ||||
| 406 | delete $self->{'_annotation'}->{$key}; | ||||
| 407 | delete $self->{'_typemap'}->{'_type'}->{$key}; | ||||
| 408 | } | ||||
| 409 | return @anns; | ||||
| 410 | } | ||||
| 411 | |||||
| 412 | =head2 flatten_Annotations | ||||
| 413 | |||||
| 414 | Title : flatten_Annotations | ||||
| 415 | Usage : | ||||
| 416 | Function: Flattens part or all of the annotations in this collection. | ||||
| 417 | |||||
| 418 | This is a convenience method for getting the flattened | ||||
| 419 | annotation for the given keys, removing the annotation for | ||||
| 420 | those keys, and adding back the flattened array. | ||||
| 421 | |||||
| 422 | This should not change anything for un-nested collections. | ||||
| 423 | Example : | ||||
| 424 | Returns : an array Bio::AnnotationI compliant objects which were stored | ||||
| 425 | under the given key(s) | ||||
| 426 | Args : list of keys (strings) the annotation for which to flatten, | ||||
| 427 | defaults to all keys if not given | ||||
| 428 | |||||
| 429 | |||||
| 430 | =cut | ||||
| 431 | |||||
| 432 | sub flatten_Annotations{ | ||||
| 433 | my ($self,@keys) = @_; | ||||
| 434 | |||||
| 435 | my @anns = $self->get_all_Annotations(@keys); | ||||
| 436 | my @origanns = $self->remove_Annotations(@keys); | ||||
| 437 | foreach (@anns) { | ||||
| 438 | $self->add_Annotation($_); | ||||
| 439 | } | ||||
| 440 | return @origanns; | ||||
| 441 | } | ||||
| 442 | |||||
| 443 | =head1 Bio::AnnotationI methods implementations | ||||
| 444 | |||||
| 445 | This is to allow nested annotation: you can use a collection as an | ||||
| 446 | annotation object for an annotation collection. | ||||
| 447 | |||||
| 448 | =cut | ||||
| 449 | |||||
| 450 | =head2 as_text | ||||
| 451 | |||||
| 452 | Title : as_text | ||||
| 453 | Usage : | ||||
| 454 | Function: See L<Bio::AnnotationI> | ||||
| 455 | Example : | ||||
| 456 | Returns : a string | ||||
| 457 | Args : none | ||||
| 458 | |||||
| 459 | |||||
| 460 | =cut | ||||
| 461 | |||||
| 462 | sub as_text{ | ||||
| 463 | my $self = shift; | ||||
| 464 | |||||
| 465 | my $txt = "Collection consisting of "; | ||||
| 466 | my @texts = (); | ||||
| 467 | foreach my $ann ($self->get_Annotations()) { | ||||
| 468 | push(@texts, $ann->as_text()); | ||||
| 469 | } | ||||
| 470 | if(@texts) { | ||||
| 471 | $txt .= join(", ", map { '['.$_.']'; } @texts); | ||||
| 472 | } else { | ||||
| 473 | $txt .= "no elements"; | ||||
| 474 | } | ||||
| 475 | return $txt; | ||||
| 476 | } | ||||
| 477 | |||||
| 478 | =head2 display_text | ||||
| 479 | |||||
| 480 | Title : display_text | ||||
| 481 | Usage : my $str = $ann->display_text(); | ||||
| 482 | Function: returns a string. Unlike as_text(), this method returns a string | ||||
| 483 | formatted as would be expected for te specific implementation. | ||||
| 484 | |||||
| 485 | One can pass a callback as an argument which allows custom text | ||||
| 486 | generation; the callback is passed the current instance and any text | ||||
| 487 | returned | ||||
| 488 | Example : | ||||
| 489 | Returns : a string | ||||
| 490 | Args : [optional] callback | ||||
| 491 | |||||
| 492 | =cut | ||||
| 493 | |||||
| 494 | { | ||||
| 495 | # this just calls the default display_text output for | ||||
| 496 | # any AnnotationI | ||||
| 497 | 1 | 600ns | my $DEFAULT_CB = sub { | ||
| 498 | my $obj = shift; | ||||
| 499 | my $txt; | ||||
| 500 | foreach my $ann ($obj->get_Annotations()) { | ||||
| 501 | $txt .= $ann->display_text()."\n"; | ||||
| 502 | } | ||||
| 503 | return $txt; | ||||
| 504 | 1 | 4µs | }; | ||
| 505 | |||||
| 506 | sub display_text { | ||||
| 507 | my ($self, $cb) = @_; | ||||
| 508 | $cb ||= $DEFAULT_CB; | ||||
| 509 | $self->throw("") if ref $cb ne 'CODE'; | ||||
| 510 | return $cb->($self); | ||||
| 511 | } | ||||
| 512 | } | ||||
| 513 | |||||
| 514 | |||||
| 515 | =head2 hash_tree | ||||
| 516 | |||||
| 517 | Title : hash_tree | ||||
| 518 | Usage : | ||||
| 519 | Function: See L<Bio::AnnotationI> | ||||
| 520 | Example : | ||||
| 521 | Returns : a hash reference | ||||
| 522 | Args : none | ||||
| 523 | |||||
| 524 | |||||
| 525 | =cut | ||||
| 526 | |||||
| 527 | sub hash_tree{ | ||||
| 528 | my $self = shift; | ||||
| 529 | my $tree = {}; | ||||
| 530 | |||||
| 531 | foreach my $key ($self->get_all_annotation_keys()) { | ||||
| 532 | # all contained objects will support hash_tree() | ||||
| 533 | # (they are AnnotationIs) | ||||
| 534 | $tree->{$key} = [$self->get_Annotations($key)]; | ||||
| 535 | } | ||||
| 536 | return $tree; | ||||
| 537 | } | ||||
| 538 | |||||
| 539 | =head2 tagname | ||||
| 540 | |||||
| 541 | Title : tagname | ||||
| 542 | Usage : $obj->tagname($newval) | ||||
| 543 | Function: Get/set the tagname for this annotation value. | ||||
| 544 | |||||
| 545 | Setting this is optional. If set, it obviates the need to | ||||
| 546 | provide a tag to Bio::AnnotationCollectionI when adding | ||||
| 547 | this object. When obtaining an AnnotationI object from the | ||||
| 548 | collection, the collection will set the value to the tag | ||||
| 549 | under which it was stored unless the object has a tag | ||||
| 550 | stored already. | ||||
| 551 | |||||
| 552 | Example : | ||||
| 553 | Returns : value of tagname (a scalar) | ||||
| 554 | Args : new value (a scalar, optional) | ||||
| 555 | |||||
| 556 | |||||
| 557 | =cut | ||||
| 558 | |||||
| 559 | sub tagname{ | ||||
| 560 | my $self = shift; | ||||
| 561 | |||||
| 562 | return $self->{'tagname'} = shift if @_; | ||||
| 563 | return $self->{'tagname'}; | ||||
| 564 | } | ||||
| 565 | |||||
| 566 | |||||
| 567 | =head1 Backward compatible functions | ||||
| 568 | |||||
| 569 | Functions put in for backward compatibility with old | ||||
| 570 | Bio::Annotation.pm stuff | ||||
| 571 | |||||
| 572 | =cut | ||||
| 573 | |||||
| 574 | =head2 description | ||||
| 575 | |||||
| 576 | Title : description | ||||
| 577 | Usage : | ||||
| 578 | Function: | ||||
| 579 | Example : | ||||
| 580 | Returns : | ||||
| 581 | Args : | ||||
| 582 | |||||
| 583 | |||||
| 584 | =cut | ||||
| 585 | |||||
| 586 | sub description{ | ||||
| 587 | my ($self,$value) = @_; | ||||
| 588 | |||||
| 589 | $self->deprecated("Using old style annotation call on new Annotation::Collection object"); | ||||
| 590 | |||||
| 591 | if( defined $value ) { | ||||
| 592 | my $val = Bio::Annotation::SimpleValue->new(); | ||||
| 593 | $val->value($value); | ||||
| 594 | $self->add_Annotation('description',$val); | ||||
| 595 | } | ||||
| 596 | |||||
| 597 | my ($desc) = $self->get_Annotations('description'); | ||||
| 598 | |||||
| 599 | # If no description tag exists, do not attempt to call value on undef: | ||||
| 600 | return $desc ? $desc->value : undef; | ||||
| 601 | } | ||||
| 602 | |||||
| 603 | |||||
| 604 | =head2 add_gene_name | ||||
| 605 | |||||
| 606 | Title : add_gene_name | ||||
| 607 | Usage : | ||||
| 608 | Function: | ||||
| 609 | Example : | ||||
| 610 | Returns : | ||||
| 611 | Args : | ||||
| 612 | |||||
| 613 | |||||
| 614 | =cut | ||||
| 615 | |||||
| 616 | sub add_gene_name{ | ||||
| 617 | my ($self,$value) = @_; | ||||
| 618 | |||||
| 619 | $self->deprecated("Old style add_gene_name called on new style Annotation::Collection"); | ||||
| 620 | |||||
| 621 | my $val = Bio::Annotation::SimpleValue->new(); | ||||
| 622 | $val->value($value); | ||||
| 623 | $self->add_Annotation('gene_name',$val); | ||||
| 624 | } | ||||
| 625 | |||||
| 626 | =head2 each_gene_name | ||||
| 627 | |||||
| 628 | Title : each_gene_name | ||||
| 629 | Usage : | ||||
| 630 | Function: | ||||
| 631 | Example : | ||||
| 632 | Returns : | ||||
| 633 | Args : | ||||
| 634 | |||||
| 635 | |||||
| 636 | =cut | ||||
| 637 | |||||
| 638 | sub each_gene_name{ | ||||
| 639 | my ($self) = @_; | ||||
| 640 | |||||
| 641 | $self->deprecated("Old style each_gene_name called on new style Annotation::Collection"); | ||||
| 642 | |||||
| 643 | my @out; | ||||
| 644 | my @gene = $self->get_Annotations('gene_name'); | ||||
| 645 | |||||
| 646 | foreach my $g ( @gene ) { | ||||
| 647 | push(@out,$g->value); | ||||
| 648 | } | ||||
| 649 | |||||
| 650 | return @out; | ||||
| 651 | } | ||||
| 652 | |||||
| 653 | =head2 add_Reference | ||||
| 654 | |||||
| 655 | Title : add_Reference | ||||
| 656 | Usage : | ||||
| 657 | Function: | ||||
| 658 | Example : | ||||
| 659 | Returns : | ||||
| 660 | Args : | ||||
| 661 | |||||
| 662 | |||||
| 663 | =cut | ||||
| 664 | |||||
| 665 | sub add_Reference{ | ||||
| 666 | my ($self, @values) = @_; | ||||
| 667 | |||||
| 668 | $self->deprecated("add_Reference (old style Annotation) on new style Annotation::Collection"); | ||||
| 669 | |||||
| 670 | # Allow multiple (or no) references to be passed, as per old method | ||||
| 671 | foreach my $value (@values) { | ||||
| 672 | $self->add_Annotation('reference',$value); | ||||
| 673 | } | ||||
| 674 | } | ||||
| 675 | |||||
| 676 | =head2 each_Reference | ||||
| 677 | |||||
| 678 | Title : each_Reference | ||||
| 679 | Usage : | ||||
| 680 | Function: | ||||
| 681 | Example : | ||||
| 682 | Returns : | ||||
| 683 | Args : | ||||
| 684 | |||||
| 685 | |||||
| 686 | =cut | ||||
| 687 | |||||
| 688 | sub each_Reference{ | ||||
| 689 | my ($self) = @_; | ||||
| 690 | |||||
| 691 | $self->deprecated("each_Reference (old style Annotation) on new style Annotation::Collection"); | ||||
| 692 | |||||
| 693 | return $self->get_Annotations('reference'); | ||||
| 694 | } | ||||
| 695 | |||||
| 696 | |||||
| 697 | =head2 add_Comment | ||||
| 698 | |||||
| 699 | Title : add_Comment | ||||
| 700 | Usage : | ||||
| 701 | Function: | ||||
| 702 | Example : | ||||
| 703 | Returns : | ||||
| 704 | Args : | ||||
| 705 | |||||
| 706 | |||||
| 707 | =cut | ||||
| 708 | |||||
| 709 | sub add_Comment{ | ||||
| 710 | my ($self,$value) = @_; | ||||
| 711 | |||||
| 712 | $self->deprecated("add_Comment (old style Annotation) on new style Annotation::Collection"); | ||||
| 713 | |||||
| 714 | $self->add_Annotation('comment',$value); | ||||
| 715 | |||||
| 716 | } | ||||
| 717 | |||||
| 718 | =head2 each_Comment | ||||
| 719 | |||||
| 720 | Title : each_Comment | ||||
| 721 | Usage : | ||||
| 722 | Function: | ||||
| 723 | Example : | ||||
| 724 | Returns : | ||||
| 725 | Args : | ||||
| 726 | |||||
| 727 | |||||
| 728 | =cut | ||||
| 729 | |||||
| 730 | sub each_Comment{ | ||||
| 731 | my ($self) = @_; | ||||
| 732 | |||||
| 733 | $self->deprecated("each_Comment (old style Annotation) on new style Annotation::Collection"); | ||||
| 734 | |||||
| 735 | return $self->get_Annotations('comment'); | ||||
| 736 | } | ||||
| 737 | |||||
| - - | |||||
| 740 | =head2 add_DBLink | ||||
| 741 | |||||
| 742 | Title : add_DBLink | ||||
| 743 | Usage : | ||||
| 744 | Function: | ||||
| 745 | Example : | ||||
| 746 | Returns : | ||||
| 747 | Args : | ||||
| 748 | |||||
| 749 | |||||
| 750 | =cut | ||||
| 751 | |||||
| 752 | sub add_DBLink{ | ||||
| 753 | my ($self,$value) = @_; | ||||
| 754 | |||||
| 755 | $self->deprecated("add_DBLink (old style Annotation) on new style Annotation::Collection"); | ||||
| 756 | |||||
| 757 | $self->add_Annotation('dblink',$value); | ||||
| 758 | |||||
| 759 | } | ||||
| 760 | |||||
| 761 | =head2 each_DBLink | ||||
| 762 | |||||
| 763 | Title : each_DBLink | ||||
| 764 | Usage : | ||||
| 765 | Function: | ||||
| 766 | Example : | ||||
| 767 | Returns : | ||||
| 768 | Args : | ||||
| 769 | |||||
| 770 | |||||
| 771 | =cut | ||||
| 772 | |||||
| 773 | sub each_DBLink{ | ||||
| 774 | my ($self) = @_; | ||||
| 775 | |||||
| 776 | $self->deprecated("each_DBLink (old style Annotation) on new style Annotation::Collection - use get_Annotations('dblink')"); | ||||
| 777 | |||||
| 778 | return $self->get_Annotations('dblink'); | ||||
| 779 | } | ||||
| 780 | |||||
| - - | |||||
| 783 | =head1 Implementation management functions | ||||
| 784 | |||||
| 785 | =cut | ||||
| 786 | |||||
| 787 | =head2 _typemap | ||||
| 788 | |||||
| 789 | Title : _typemap | ||||
| 790 | Usage : $obj->_typemap($newval) | ||||
| 791 | Function: | ||||
| 792 | Example : | ||||
| 793 | Returns : value of _typemap | ||||
| 794 | Args : newvalue (optional) | ||||
| 795 | |||||
| 796 | |||||
| 797 | =cut | ||||
| 798 | |||||
| 799 | sub _typemap{ | ||||
| 800 | my ($self,$value) = @_; | ||||
| 801 | if( defined $value) { | ||||
| 802 | $self->{'_typemap'} = $value; | ||||
| 803 | } | ||||
| 804 | return $self->{'_typemap'}; | ||||
| 805 | |||||
| 806 | } | ||||
| 807 | |||||
| 808 | 1 | 5µs | 1; |