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Statements | Executed 11 statements in 1.95ms |
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1 | 1 | 1 | 551µs | 1.05ms | BEGIN@93 | Bio::Annotation::Collection::
1 | 1 | 1 | 401µs | 511µs | BEGIN@92 | Bio::Annotation::Collection::
1 | 1 | 1 | 14µs | 28µs | BEGIN@88 | Bio::Annotation::Collection::
1 | 1 | 1 | 11µs | 535µs | BEGIN@96 | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | __ANON__[:504] | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | _typemap | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | add_Annotation | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | add_Comment | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | add_DBLink | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | add_Reference | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | add_gene_name | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | as_text | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | description | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | display_text | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | each_Comment | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | each_DBLink | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | each_Reference | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | each_gene_name | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | flatten_Annotations | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | get_Annotations | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | get_all_Annotations | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | get_all_annotation_keys | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | get_nested_Annotations | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | get_num_of_annotations | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | hash_tree | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | new | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | remove_Annotations | Bio::Annotation::Collection::
0 | 0 | 0 | 0s | 0s | tagname | Bio::Annotation::Collection::
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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; |