Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an Bio::AnnotationI, and defines a "as_text" method print "Annotation ",$key," stringified value ",$value->as_text,"\n"; # also defined hash_tree method, which allows data orientated # access into this object $hash = $value->hash_tree(); } } Bioperl implementation for Bio::AnnotationCollecitonI

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email birney@ebi.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $coll = Bio::Annotation::Collection->new() Function: Makes a new Annotation::Collection object. Returns : Bio::Annotation::Collection Args : none

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

get_Annotations
Title : get_Annotations Usage : my @annotations = $collection->get_Annotations('key') Function: Retrieves all the Bio::AnnotationI objects for one or more specific key(s). If no key is given, returns all annotation objects. The returned objects will have their tagname() attribute set to the key under which they were attached, unless the tagname was already set. Returns : list of Bio::AnnotationI - empty if no objects stored for a key Args : keys (list of strings) for annotations (optional)

get_all_Annotations
Title : get_all_Annotations Usage : Function: Similar to get_Annotations, but traverses and flattens nested annotation collections. This means that collections in the tree will be replaced by their components. Keys will not be passed on to nested collections. I.e., if the tag name of a nested collection matches the key, it will be flattened in its entirety. Hence, for un-nested annotation collections this will be identical to get_Annotations. Example : Returns : an array of L<Bio::AnnotationI> compliant objects Args : keys (list of strings) for annotations (optional)

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

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. 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

remove_Annotations
Title : remove_Annotations Usage : Function: Remove the annotations for the specified key from this collection. Example : Returns : an array Bio::AnnotationI compliant objects which were stored under the given key(s) Args : the key(s) (tag name(s), one or more strings) for which to remove annotations (optional; if none given, flushes all annotations)

flatten_Annotations
Title : flatten_Annotations Usage : Function: Flattens part or all of the annotations in this collection. This is a convenience method for getting the flattened annotation for the given keys, removing the annotation for those keys, and adding back the flattened array. This should not change anything for un-nested collections. Example : Returns : an array Bio::AnnotationI compliant objects which were stored under the given key(s) Args : list of keys (strings) the annotation for which to flatten, defaults to all keys if not given This is to allow nested annotation: you can a collection as an annotation object to an annotation collection.

as_text
Title : as_text Usage : Function: See L<Bio::AnnotationI> Example : Returns : a string Args : none

hash_tree
Title : hash_tree Usage : Function: See L<Bio::AnnotationI> Example : Returns : a hash reference Args : none

tagname
Title : tagname Usage : $obj->tagname($newval) Function: Get/set the tagname for this annotation value. Setting this is optional. If set, it obviates the need to provide a tag to Bio::AnnotationCollectionI when adding this object. When obtaining an AnnotationI object from the collection, the collection will set the value to the tag under which it was stored unless the object has a tag stored already. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional) Functions put in for backward compatibility with old Bio::Annotation.pm stuff

description
Title : description Usage : Function: Example : Returns : Args :

add_gene_name
Title : add_gene_name Usage : Function: Example : Returns : Args :

each_gene_name
Title : each_gene_name Usage : Function: Example : Returns : Args :

add_Reference
Title : add_Reference Usage : Function: Example : Returns : Args :

each_Reference
Title : each_Reference Usage : Function: Example : Returns : Args :

add_Comment
Title : add_Comment Usage : Function: Example : Returns : Args :

each_Comment
Title : each_Comment Usage : Function: Example : Returns : Args :

add_DBLink
Title : add_DBLink Usage : Function: Example : Returns : Args :

each_DBLink
Title : each_DBLink Usage : Function: Example : Returns : Args :

_typemap
Title : _typemap Usage : $obj->_typemap($newval) Function: Example : Returns : value of _typemap Args : newvalue (optional)