Provided by: libbio-perl-perl_1.6.923-1_all bug


       Bio::AnnotationI - Annotation interface


         # 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();


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


       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.


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AUTHOR - Ewan Birney



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

        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

        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
        Example :
        Returns : a string
        Args    : [optional] callback

        Title   : hash_tree
        Usage   :
        Function: should return an anonymous hash with "XML-like" formatting
        Example :
        Returns : a hash reference
        Args    : none

        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)