Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::AnnotationCollectionI - Interface for annotation collections

SYNOPSIS

          # 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();
              }
          }

DESCRIPTION

       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 formatted 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.

FEEDBACK

   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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

       Email birney@ebi.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

ACCESSOR METHODS

       Use these for Bio::AnnotationI object access.

   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()
        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

   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()
        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_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