Bio::AnnotationI

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 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 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 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.

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.

  [email protected]

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email [email protected]

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)