maint: restructure to use Dist::Zilla
[bioperl-live.git] / lib / Bio / Annotation / Collection.pm
blob224ad959a01b130059da241c8d3ef8a90003d959
2 # BioPerl module for Bio::Annotation::Collection.pm
4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
8 # Copyright Ewan Birney
10 # You may distribute this module under the same terms as perl itself
12 # POD documentation - main docs before the code
14 =head1 NAME
16 Bio::Annotation::Collection - Default Perl implementation of
17 AnnotationCollectionI
19 =head1 SYNOPSIS
21 # get an AnnotationCollectionI somehow, eg
23 $ac = $seq->annotation();
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";
31 # also defined hash_tree method, which allows data orientated
32 # access into this object
33 $hash = $value->hash_tree();
37 =head1 DESCRIPTION
39 Bioperl implementation for Bio::AnnotationCollectionI
41 =head1 FEEDBACK
43 =head2 Mailing Lists
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.
49 bioperl-l@bioperl.org - General discussion
50 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
52 =head2 Support
54 Please direct usage questions or support issues to the mailing list:
56 I<bioperl-l@bioperl.org>
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.
63 =head2 Reporting Bugs
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:
69 https://github.com/bioperl/bioperl-live/issues
71 =head1 AUTHOR - Ewan Birney
73 Email birney@ebi.ac.uk
75 =head1 APPENDIX
77 The rest of the documentation details each of the object
78 methods. Internal methods are usually preceded with a _
80 =cut
83 # Let the code begin...
86 package Bio::Annotation::Collection;
88 use strict;
90 # Object preamble - inherits from Bio::Root::Root
92 use Bio::Annotation::TypeManager;
93 use Bio::Annotation::SimpleValue;
96 use base qw(Bio::Root::Root Bio::AnnotationCollectionI Bio::AnnotationI);
99 =head2 new
101 Title : new
102 Usage : $coll = Bio::Annotation::Collection->new()
103 Function: Makes a new Annotation::Collection object.
104 Returns : Bio::Annotation::Collection
105 Args : none
107 =cut
109 sub new{
110 my ($class,@args) = @_;
112 my $self = $class->SUPER::new(@args);
114 $self->{'_annotation'} = {};
115 $self->_typemap(Bio::Annotation::TypeManager->new());
117 return $self;
121 =head1 L<Bio::AnnotationCollectionI> implementing methods
123 =cut
125 =head2 get_all_annotation_keys
127 Title : get_all_annotation_keys
128 Usage : $ac->get_all_annotation_keys()
129 Function: gives back a list of annotation keys, which are simple text strings
130 Returns : list of strings
131 Args : none
133 =cut
135 sub get_all_annotation_keys{
136 my ($self) = @_;
137 return keys %{$self->{'_annotation'}};
140 =head2 get_Annotations
142 Title : get_Annotations
143 Usage : my @annotations = $collection->get_Annotations('key')
144 Function: Retrieves all the Bio::AnnotationI objects for one or more
145 specific key(s).
147 If no key is given, returns all annotation objects.
149 The returned objects will have their tagname() attribute set to
150 the key under which they were attached, unless the tagname was
151 already set.
153 Returns : list of Bio::AnnotationI - empty if no objects stored for a key
154 Args : keys (list of strings) for annotations (optional)
156 =cut
158 sub get_Annotations{
159 my ($self,@keys) = @_;
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}});
171 return @anns;
175 =head2 get_nested_Annotations
177 Title : get_nested_Annotations
178 Usage : my @annotations = $collection->get_nested_Annotations(
179 '-key' => \@keys,
180 '-recursive => 1);
181 Function: Retrieves all the Bio::AnnotationI objects for one or more
182 specific key(s). If -recursive is set to true, traverses the nested
183 annotation collections recursively and returns all annotations
184 matching the key(s).
186 If no key is given, returns all annotation objects.
188 The returned objects will have their tagname() attribute set to
189 the key under which they were attached, unless the tagname was
190 already set.
192 Returns : list of Bio::AnnotationI - empty if no objects stored for a key
193 Args : -keys => arrayref of keys to search for (optional)
194 -recursive => boolean, whether or not to recursively traverse the
195 nested annotations and return annotations with matching keys.
197 =cut
199 sub get_nested_Annotations {
200 my ($self, @args) = @_;
201 my ($keys, $recursive) = $self->_rearrange([qw(KEYS RECURSIVE)], @args);
202 $self->verbose(1);
204 my @anns = ();
205 # if not recursive behave exactly like get_Annotations()
206 if (!$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}});
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) { $keymatch = 1;}
225 if ($keymatch) {
226 if(exists($self->{'_annotation'}->{$key})) {
227 push(@anns,
228 map {
229 $_->tagname($key) if ! $_->tagname(); $_;
230 } @{$self->{'_annotation'}->{$key}});
233 else {
234 my @annotations = @{$self->{'_annotation'}->{$key}};
235 foreach (@annotations) {
236 if ($_->isa("Bio::AnnotationCollectionI")) {
237 push (@anns,
238 $_->get_nested_Annotations('-keys' => $keys, '-recursive' => 1)
245 return @anns;
248 =head2 get_all_Annotations
250 Title : get_all_Annotations
251 Usage :
252 Function: Similar to get_Annotations, but traverses and flattens nested
253 annotation collections. This means that collections in the
254 tree will be replaced by their components.
256 Keys will not be passed on to nested collections. I.e., if the
257 tag name of a nested collection matches the key, it will be
258 flattened in its entirety.
260 Hence, for un-nested annotation collections this will be identical
261 to get_Annotations.
262 Example :
263 Returns : an array of L<Bio::AnnotationI> compliant objects
264 Args : keys (list of strings) for annotations (optional)
267 =cut
269 sub get_all_Annotations{
270 my ($self,@keys) = @_;
272 return map {
273 $_->isa("Bio::AnnotationCollectionI") ?
274 $_->get_all_Annotations() : $_;
275 } $self->get_Annotations(@keys);
279 =head2 get_num_of_annotations
281 Title : get_num_of_annotations
282 Usage : my $count = $collection->get_num_of_annotations()
283 Function: Returns the count of all annotations stored in this collection
284 Returns : integer
285 Args : none
288 =cut
290 sub get_num_of_annotations{
291 my ($self) = @_;
292 my $count = 0;
293 map { $count += scalar @$_ } values %{$self->{'_annotation'}};
294 return $count;
297 =head1 Implementation specific functions - mainly for adding
299 =cut
301 =head2 add_Annotation
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.
310 If the key is omitted, the object to be added must provide a value
311 via its tagname().
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.
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
323 =cut
325 sub add_Annotation{
326 my ($self,$key,$object,$archetype) = @_;
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;
338 if( !defined $object ) {
339 $self->throw("Must have at least key and object in add_Annotation");
342 if( !ref $object ) {
343 $self->throw("Must add an object. Use Bio::Annotation::{Comment,SimpleValue,OntologyTerm} for simple text additions");
346 if( !$object->isa("Bio::AnnotationI") ) {
347 $self->throw("object must be AnnotationI compliant, otherwise we won't add it!");
350 # ok, now we are ready! If we don't have an archetype, set it
351 # from the type of the object
353 if( !defined $archetype ) {
354 $archetype = ref $object;
357 # check typemap, storing if needed.
358 my $stored_map = $self->_typemap->type_for_key($key);
360 if( defined $stored_map ) {
361 # check validity, irregardless of archetype. A little cheeky
362 # this means isa stuff is executed correctly
364 if( !$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");
369 } else {
370 $self->_typemap->_add_type_map($key,$archetype);
373 # we are ok to store
375 if( !defined $self->{'_annotation'}->{$key} ) {
376 $self->{'_annotation'}->{$key} = [];
379 push(@{$self->{'_annotation'}->{$key}},$object);
381 return 1;
384 =head2 remove_Annotations
386 Title : remove_Annotations
387 Usage :
388 Function: Remove the annotations for the specified key from this collection.
389 Example :
390 Returns : an array Bio::AnnotationI compliant objects which were stored
391 under the given key(s)
392 Args : the key(s) (tag name(s), one or more strings) for which to
393 remove annotations (optional; if none given, flushes all
394 annotations)
397 =cut
399 sub remove_Annotations{
400 my ($self, @keys) = @_;
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};
409 return @anns;
412 =head2 flatten_Annotations
414 Title : flatten_Annotations
415 Usage :
416 Function: Flattens part or all of the annotations in this collection.
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.
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
430 =cut
432 sub flatten_Annotations{
433 my ($self,@keys) = @_;
435 my @anns = $self->get_all_Annotations(@keys);
436 my @origanns = $self->remove_Annotations(@keys);
437 foreach (@anns) {
438 $self->add_Annotation($_);
440 return @origanns;
443 =head1 Bio::AnnotationI methods implementations
445 This is to allow nested annotation: you can use a collection as an
446 annotation object for an annotation collection.
448 =cut
450 =head2 as_text
452 Title : as_text
453 Usage :
454 Function: See L<Bio::AnnotationI>
455 Example :
456 Returns : a string
457 Args : none
460 =cut
462 sub as_text{
463 my $self = shift;
465 my $txt = "Collection consisting of ";
466 my @texts = ();
467 foreach my $ann ($self->get_Annotations()) {
468 push(@texts, $ann->as_text());
470 if(@texts) {
471 $txt .= join(", ", map { '['.$_.']'; } @texts);
472 } else {
473 $txt .= "no elements";
475 return $txt;
478 =head2 display_text
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.
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
492 =cut
495 # this just calls the default display_text output for
496 # any AnnotationI
497 my $DEFAULT_CB = sub {
498 my $obj = shift;
499 my $txt;
500 foreach my $ann ($obj->get_Annotations()) {
501 $txt .= $ann->display_text()."\n";
503 return $txt;
506 sub display_text {
507 my ($self, $cb) = @_;
508 $cb ||= $DEFAULT_CB;
509 $self->throw("") if ref $cb ne 'CODE';
510 return $cb->($self);
515 =head2 hash_tree
517 Title : hash_tree
518 Usage :
519 Function: See L<Bio::AnnotationI>
520 Example :
521 Returns : a hash reference
522 Args : none
525 =cut
527 sub hash_tree{
528 my $self = shift;
529 my $tree = {};
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)];
536 return $tree;
539 =head2 tagname
541 Title : tagname
542 Usage : $obj->tagname($newval)
543 Function: Get/set the tagname for this annotation value.
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.
552 Example :
553 Returns : value of tagname (a scalar)
554 Args : new value (a scalar, optional)
557 =cut
559 sub tagname{
560 my $self = shift;
562 return $self->{'tagname'} = shift if @_;
563 return $self->{'tagname'};
567 =head1 Backward compatible functions
569 Functions put in for backward compatibility with old
570 Bio::Annotation.pm stuff
572 =cut
574 =head2 description
576 Title : description
577 Usage :
578 Function:
579 Example :
580 Returns :
581 Args :
584 =cut
586 sub description{
587 my ($self,$value) = @_;
589 $self->deprecated("Using old style annotation call on new Annotation::Collection object");
591 if( defined $value ) {
592 my $val = Bio::Annotation::SimpleValue->new();
593 $val->value($value);
594 $self->add_Annotation('description',$val);
597 my ($desc) = $self->get_Annotations('description');
599 # If no description tag exists, do not attempt to call value on undef:
600 return $desc ? $desc->value : undef;
604 =head2 add_gene_name
606 Title : add_gene_name
607 Usage :
608 Function:
609 Example :
610 Returns :
611 Args :
614 =cut
616 sub add_gene_name{
617 my ($self,$value) = @_;
619 $self->deprecated("Old style add_gene_name called on new style Annotation::Collection");
621 my $val = Bio::Annotation::SimpleValue->new();
622 $val->value($value);
623 $self->add_Annotation('gene_name',$val);
626 =head2 each_gene_name
628 Title : each_gene_name
629 Usage :
630 Function:
631 Example :
632 Returns :
633 Args :
636 =cut
638 sub each_gene_name{
639 my ($self) = @_;
641 $self->deprecated("Old style each_gene_name called on new style Annotation::Collection");
643 my @out;
644 my @gene = $self->get_Annotations('gene_name');
646 foreach my $g ( @gene ) {
647 push(@out,$g->value);
650 return @out;
653 =head2 add_Reference
655 Title : add_Reference
656 Usage :
657 Function:
658 Example :
659 Returns :
660 Args :
663 =cut
665 sub add_Reference{
666 my ($self, @values) = @_;
668 $self->deprecated("add_Reference (old style Annotation) on new style Annotation::Collection");
670 # Allow multiple (or no) references to be passed, as per old method
671 foreach my $value (@values) {
672 $self->add_Annotation('reference',$value);
676 =head2 each_Reference
678 Title : each_Reference
679 Usage :
680 Function:
681 Example :
682 Returns :
683 Args :
686 =cut
688 sub each_Reference{
689 my ($self) = @_;
691 $self->deprecated("each_Reference (old style Annotation) on new style Annotation::Collection");
693 return $self->get_Annotations('reference');
697 =head2 add_Comment
699 Title : add_Comment
700 Usage :
701 Function:
702 Example :
703 Returns :
704 Args :
707 =cut
709 sub add_Comment{
710 my ($self,$value) = @_;
712 $self->deprecated("add_Comment (old style Annotation) on new style Annotation::Collection");
714 $self->add_Annotation('comment',$value);
718 =head2 each_Comment
720 Title : each_Comment
721 Usage :
722 Function:
723 Example :
724 Returns :
725 Args :
728 =cut
730 sub each_Comment{
731 my ($self) = @_;
733 $self->deprecated("each_Comment (old style Annotation) on new style Annotation::Collection");
735 return $self->get_Annotations('comment');
740 =head2 add_DBLink
742 Title : add_DBLink
743 Usage :
744 Function:
745 Example :
746 Returns :
747 Args :
750 =cut
752 sub add_DBLink{
753 my ($self,$value) = @_;
755 $self->deprecated("add_DBLink (old style Annotation) on new style Annotation::Collection");
757 $self->add_Annotation('dblink',$value);
761 =head2 each_DBLink
763 Title : each_DBLink
764 Usage :
765 Function:
766 Example :
767 Returns :
768 Args :
771 =cut
773 sub each_DBLink{
774 my ($self) = @_;
776 $self->deprecated("each_DBLink (old style Annotation) on new style Annotation::Collection - use get_Annotations('dblink')");
778 return $self->get_Annotations('dblink');
783 =head1 Implementation management functions
785 =cut
787 =head2 _typemap
789 Title : _typemap
790 Usage : $obj->_typemap($newval)
791 Function:
792 Example :
793 Returns : value of _typemap
794 Args : newvalue (optional)
797 =cut
799 sub _typemap{
800 my ($self,$value) = @_;
801 if( defined $value) {
802 $self->{'_typemap'} = $value;
804 return $self->{'_typemap'};