AnnotationCollectionI documentation.

   # 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();
       }
   }

Annotation Collections are a way of storing a series of "interesting
facts" about something. We call an "interesting fact" in Bioperl an
Annotation (this differs from a Sequence Feature, which is called
a Sequence Feature and may or may not have an Annotation Collection).
A benefit of this approach is that all sorts of simple, interesting
observations can be collected, the possibility is endless.
The Bioperl approach is that the "interesting facts" are represented by
Bio::AnnotationI objects. The interface Bio::AnnotationI guarantees
two methods

   $obj->as_text(); # string formated to display to users

and

   $obj->hash_tree(); # hash with defined rules for data-orientated discovery

The hash_tree method is designed to play well with XML output and
other "nested-tag-of-data-values", think BoulderIO and/or Ace stuff. For more
information see Bio::AnnotationI.
Annotations are stored in AnnotationCollections, each Annotation under a
different "tag". The tags allow simple discovery of the available annotations,
and in some cases (like the tag "gene_name") indicate how to interpret the
data underneath the tag. The tag is only one tag deep and each tag can have an
array of values.
In addition, AnnotationCollections are guaranteed to maintain consistent
types of objects under each tag - at least that each object complies to one
interface. The "standard" AnnotationCollection insists the following rules
are set up:

  Tag            Object
  ---            ------
  comment        Bio::Annotation::Comment
  dblink         Bio::Annotation::DBLink
  description    Bio::Annotation::SimpleValue
  gene_name      Bio::Annotation::SimpleValue
  ontology_term  Bio::Annotation::OntologyTerm
  reference      Bio::Annotation::Reference

These tags are the implict tags that the SeqIO system needs to round-trip
GenBank/EMBL/Swissprot.
However, you as a user and us collectively as a community can grow the
"standard" tag mapping over time and specifically for a particular
area.

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

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

Usage :
Function: Remove the annotations for the specified key from this collection.
Returns : an list of 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)

get_all_annotation_keys	Description	Code
get_Annotations	Description	Code
add_Annotation	Description	Code
remove_Annotations	Description	Code
get_num_of_annotations	Description	Code