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Man Pages

Manual Reference Pages  -  BIO::ANNOTATIONI (3)

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Bio::AnnotationI - Annotation interface



  # generally you get AnnotationIs from AnnotationCollectionIs

   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 support.


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 should return an anonymous hash with XML-like formatting:

   $hash = $annotation->hash_tree();

The formatting is as follows.

  (1) For each key in the hash, if the value is a referenced 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 reference to a hash
          Recurse again from point (1)
  (4) else
          Assume 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 inherit off some super-generic interface for representing things in the hash.


    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.


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

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:

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 shouldnt 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)

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perl v5.20.3 BIO::ANNOTATIONI (3) 2016-04-05

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