libbio-perl-perl 1.7.2-2 / usr / share / perl5 / Bio / AnnotationCollectionI.pm

#
# BioPerl module for Bio::AnnotationCollectionI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::AnnotationCollectionI - Interface for annotation collections

=head1 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();
       }
   }

=head1 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 L<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.


=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 one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org

=head2 Support 

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

I<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.

=head2 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

=head1 AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

=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::AnnotationCollectionI;
use strict;

# Interface preamble - inherits from Bio::Root::RootI


use base qw(Bio::Root::RootI);

=head1 ACCESSOR METHODS

Use these for Bio::AnnotationI object access.

=cut

=head2 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{
    shift->throw_not_implemented();
}


=head2 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{
    shift->throw_not_implemented();
}

=head2 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

=cut

sub add_Annotation {
  shift->throw_not_implemented();
}

=head2 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)

=cut

sub remove_Annotations{
  shift->throw_not_implemented();
}

=head2 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{
    shift->throw_not_implemented();
}

1;