Summary

Bio::AnnotationI - Annotation interface

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  # generally you get AnnotationI's from AnnotationCollectionI's

   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";
          # you can also use a generic hash_tree method for getting 
          # stuff out say into XML format
          $hash_tree = $value->hash_tree();
       }
   }

Description

Interface all annotations must support. There are two things that each annotation
has to support.

  $annotation->as_text()

Annotations have to support an "as_text" method. This should be a
single text string, without newlines representing the annotation,
mainly for human readability. It is not aimed at being able to
store/represent the annotation
The second method allows annotations to at least attempt to represent
themselves as pure data for storage/display/whatever. The method
hash_tree

   $hash = $annotation->hash_tree();

should return an anonymous hash with "XML-like" formatting. The
formatting is as follows.

  (1) For each key in the hash, if the value is a reference'd array -

      (2) For each element of the array if the value is a object - 
          Assumme the object has the method "hash_tree";
      (3) else if the value is a referene to a hash
          Recurse again from point (1)
      (4) else 
          Assumme the value is a scalar, and handle it directly as text

   (5) else (if not an array) apply rules 2,3 and 4 to value

The XML path in tags is represented by the keys taken in the
hashes. When arrays are encountered they are all present in the path
level of this tag
This is a pretty "natural" representation of an object tree in an XML
style, without forcing everything to inheriet off some super-generic
interface for representing things in the hash.

Methods

Methods description

 Title   : as_text
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : hash_tree
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

Methods code

sub as_text {

   my ($self) = @_;

   $self->throw("Implementing object did not provide as_text function");

}

sub hash_tree {

   my ($self,@args) = @_;

   $self->throw("Implementing object did not provide hash_tree method");

}

General documentation

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@bio.perl.org

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@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

Email birney@ebi.ac.uk
Describe contact details here

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