Raw content of Bio::SeqFeature::AnnotationAdaptor # $Id: AnnotationAdaptor.pm,v 1.4 2002/11/11 18:16:31 lapp Exp $ # # BioPerl module for Bio::SeqFeature::AnnotationAdaptor # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # # (c) Hilmar Lapp, hlapp at gmx.net, 2002. # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. # # You may distribute this module under the same terms as perl itself. # Refer to the Perl Artistic License (see the license accompanying this # software package, or see http://www.perl.com/language/misc/Artistic.html) # for the terms under which you may use, modify, and redistribute this module. # # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. # # POD documentation - main docs before the code =head1 NAME Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation =head1 SYNOPSIS use Bio::SeqFeature::Generic; use Bio::SeqFeature::AnnotationAdaptor; # obtain a SeqFeatureI implementing object somehow my $feat = Bio::SeqFeature::Generic->new(-start => 10, -end => 20); # add tag/value annotation $feat->add_tag_value("mytag", "value of tag mytag"); $feat->add_tag_value("mytag", "another value of tag mytag"); # Bio::SeqFeature::Generic also provides annotation(), which returns a # Bio::AnnotationCollectionI compliant object $feat->annotation->add_Annotation("dbxref", $dblink); # to integrate tag/value annotation with AnnotationCollectionI # annotation, use this adaptor, which also implements # Bio::AnnotationCollectionI my $anncoll = Bio::SeqFeature::AnnotationAdaptor(-feature => $feat); # this will now return tag/value pairs as # Bio::Annotation::SimpleValue objects my @anns = $anncoll->get_Annotations("mytag"); # other added before annotation is available too my @dblinks = $anncoll->get_Annotations("dbxref"); # also supports transparent adding of tag/value pairs in # Bio::AnnotationI flavor my $tagval = Bio::Annotation::SimpleValue->new(-value => "some value", -tagname => "some tag"); $anncoll->add_Annotation($tagval); # this is now also available from the feature's tag/value system my @vals = $feat->each_tag_value("some tag"); =head1 DESCRIPTION L<Bio::SeqFeatureI> defines light-weight annotation of features through tag/value pairs. Conversely, L<Bio::AnnotationCollectionI> together with L<Bio::AnnotationI> defines an annotation bag, which is better typed, but more heavy-weight because it contains every single piece of annotation as objects. The frequently used base implementation of Bio::SeqFeatureI, Bio::SeqFeature::Generic, defines an additional slot for AnnotationCollectionI-compliant annotation. This adaptor provides a L<Bio::AnnotationCollectionI> compliant, unified, and integrated view on the annotation of L<Bio::SeqFeatureI> objects, including tag/value pairs, and annotation through the annotation() method, if the object supports it. Code using this adaptor does not need to worry about the different ways of possibly annotating a SeqFeatureI object, but can instead assume that it strictly follows the AnnotationCollectionI scheme. The price to pay is that retrieving and adding annotation will always use objects instead of light-weight tag/value pairs. In other words, this adaptor allows us to keep the best of both worlds. If you create tens of thousands of feature objects, and your only annotation is tag/value pairs, you are best off using the features' native tag/value system. If you create a smaller number of features, but with rich and typed annotation mixed with tag/value pairs, this adaptor may be for you. Since its implementation is by double-composition, you only need to create one instance of the adaptor. In order to transparently annotate a feature object, set the feature using the feature() method. Every annotation you add will be added to the feature object, and hence will not be lost when you set feature() to the next object. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::AnnotationAdaptor; use vars qw(@ISA); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::Root::Root; use Bio::AnnotatableI; use Bio::AnnotationCollectionI; use Bio::Annotation::SimpleValue; @ISA = qw(Bio::Root::Root Bio::AnnotationCollectionI Bio::AnnotatableI); =head2 new Title : new Usage : my $obj = new Bio::SeqFeature::AnnotationAdaptor(); Function: Builds a new Bio::SeqFeature::AnnotationAdaptor object Returns : an instance of Bio::SeqFeature::AnnotationAdaptor Args : Named parameters -feature the Bio::SeqFeatureI implementing object to adapt (mandatory to be passed here, or set via feature() before calling other methods) -annotation the Bio::AnnotationCollectionI implementing object for storing richer annotation (this will default to the $feature->annotation() if it supports it) -tagvalue_factory the object factory to use for creating tag/value pair representing objects =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($feat,$anncoll,$fact) = $self->_rearrange([qw(FEATURE ANNOTATION TAGVALUE_FACTORY)], @args); $self->feature($feat) if $feat; $self->annotation($anncoll) if $feat; $self->tagvalue_object_factory($fact) if $fact; return $self; } =head2 feature Title : feature Usage : $obj->feature($newval) Function: Get/set the feature that this object adapts to an AnnotationCollectionI. Example : Returns : value of feature (a Bio::SeqFeatureI compliant object) Args : new value (a Bio::SeqFeatureI compliant object, optional) =cut sub feature{ my ($self,$value) = @_; if( defined $value) { $self->{'feature'} = $value; } return $self->{'feature'}; } =head2 annotation Title : annotation Usage : $obj->annotation($newval) Function: Get/set the AnnotationCollectionI implementing object used by this adaptor to store additional annotation that cannot be stored by the SeqFeatureI itself. If requested before having been set, the value will default to the annotation object of the feature if it has one. Example : Returns : value of annotation (a Bio::AnnotationCollectionI compliant object) Args : new value (a Bio::AnnotationCollectionI compliant object, optional) =cut sub annotation{ my ($self,$value) = @_; if( defined $value) { $self->{'annotation'} = $value; } if((! exists($self->{'annotation'})) && $self->feature()->can('annotation')) { return $self->feature()->annotation(); } return $self->{'annotation'}; } =head1 AnnotationCollectionI implementing methods =cut =head2 get_all_annotation_keys Title : get_all_annotation_keys Usage : $ac->get_all_annotation_keys() Function: gives back a list of annotation keys, which are simple text strings Returns : list of strings Args : none =cut sub get_all_annotation_keys{ my ($self) = @_; my @keys = (); # get the tags from the feature object push(@keys, $self->feature()->all_tags()); # ask the annotation implementation in addition, while avoiding duplicates if($self->annotation()) { push(@keys, grep { ! $self->feature->has_tag($_); } $self->annotation()->get_all_annotation_keys()); } # done return @keys; } =head2 get_Annotations Title : get_Annotations Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for a specific key Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : string which is key for annotations =cut sub get_Annotations{ my ($self, $key) = @_; my @anns = (); # if the feature has tag/value pair for this key as the tag if($self->feature()->has_tag($key)) { my $fact = $self->tagvalue_object_factory(); # add each tag/value pair as a SimpleValue object foreach my $val ($self->feature()->each_tag_value($key)) { my $ann; if($fact) { $ann = $fact->create_object(-value => $val, -tagname => $key); } else { $ann = Bio::Annotation::SimpleValue->new(-value => $val, -tagname => $key); } push(@anns, $ann); } } # add what is in the annotation implementation if any if($self->annotation()) { push(@anns, $self->annotation->get_Annotations($key)); } # done return @anns; } =head2 get_num_of_annotations Title : get_num_of_annotations Usage : my $count = $collection->get_num_of_annotations() Function: Returns the count of all annotations stored in this collection Returns : integer Args : none =cut sub get_num_of_annotations{ my ($self) = @_; # first, count the number of tags on the feature my $num_anns = 0; foreach ($self->feature()->all_tags()) { $num_anns += $self->feature()->each_tag_value($_); } # add from the annotation implementation if any if($self->annotation()) { $num_anns += $self->annotation()->get_num_of_annotations(); } # done return $num_anns; } =head1 Implementation specific functions - to allow adding =cut =head2 add_Annotation Title : add_Annotation Usage : $self->add_Annotation('reference',$object); $self->add_Annotation($object,'Bio::MyInterface::DiseaseI'); $self->add_Annotation($object); $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI'); Function: Adds an annotation for a specific key. If the key is omitted, the object to be added must provide a value via its tagname(). If the archetype is provided, this and future objects added under that tag have to comply with the archetype and will be rejected otherwise. This implementation will add all Bio::Annotation::SimpleValue objects to the adapted features as tag/value pairs. Caveat: this may potentially result in information loss if a derived object is supplied. Returns : none Args : annotation key ('disease', 'dblink', ...) object to store (must be Bio::AnnotationI compliant) [optional] object archetype to map future storage of object of these types to =cut sub add_Annotation{ my ($self,$key,$object,$archetype) = @_; # if there's no key we use the tagname() as key if(ref($key) && $key->isa("Bio::AnnotationI") && (! ($object && ref($object)))) { $archetype = $object if $object; $object = $key; $key = $object->tagname(); $key = $key->name() if $key && ref($key); # OntologyTermI $self->throw("Annotation object must have a tagname if key omitted") unless $key; } if( !defined $object ) { $self->throw("Must have at least key and object in add_Annotation"); } if( ! (ref($object) && $object->isa("Bio::AnnotationI")) ) { $self->throw("object must be a Bio::AnnotationI compliant object, otherwise we wont add it!"); } # ready to add -- if it's a SimpleValue, we add to the feature's tags, # otherwise we'll add to the annotation collection implementation if($object->isa("Bio::Annotation::SimpleValue") && $self->feature()->can('add_tag_value')) { return $self->feature()->add_tag_value($key, $object->value()); } else { my $anncoll = $self->annotation(); if(! $anncoll) { $anncoll = Bio::Annotation::Collection->new(); $self->annotation($anncoll); } if($anncoll->can('add_Annotation')) { return $anncoll->add_Annotation($key,$object,$archetype); } $self->throw("Annotation implementation does not allow adding!"); } } =head1 Additional methods =cut =head2 tagvalue_object_factory Title : tagvalue_object_factory Usage : $obj->tagval_object_factory($newval) Function: Get/set the object factory to use for creating objects that represent tag/value pairs (e.g., Bio::Annotation::SimpleValue). The object to be created is expected to follow Bio::Annotation::SimpleValue in terms of supported arguments at creation time, and the methods. Example : Returns : A Bio::Factory::ObjectFactoryI compliant object Args : new value (a Bio::Factory::ObjectFactoryI compliant object, optional) =cut sub tagvalue_object_factory{ my ($self,$value) = @_; if( defined $value) { $self->{'tagval_object_factory'} = $value; } return $self->{'tagval_object_factory'}; } 1;