NAME

       Bio::AnnotationI - Annotation interface

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 -
                 Assume 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.

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://redmine.open-bio.org/projects/bioperl/

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 _

   as_text
        Title   : as_text
        Usage   :
        Function: single text string, without newlines representing the
                  annotation, mainly for human readability. It is not aimed
                  at being able to store/represent the annotation.
        Example :
        Returns : a string
        Args    : none

   display_text
        Title   : display_text
        Usage   : my $str = $ann->display_text();
        Function: returns a string. Unlike as_text(), this method returns a string
                  formatted as would be expected for the specific implementation.

                  Implementations should allow passing a callback as an argument which
                  allows custom text generation; the callback will be passed the
                  current implementation.

                  Note that this is meant to be used as a simple representation
                  of the annotation data but probably shouldn't be used in cases
                  where more complex comparisons are needed or where data is
                  stored.
        Example :
        Returns : a string
        Args    : [optional] callback

   hash_tree
        Title   : hash_tree
        Usage   :
        Function: should return an anonymous hash with "XML-like" formatting
        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)