Bio AnnotationI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::AnnotationI - Annotation interface
Package variables
No package variables defined.
  # 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 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 = $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.
Methods description
as_textcode    nextTop
 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 stored. 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)
Methods code
sub as_text {
sub display_text {
sub hash_tree {
sub tagname {

General documentation
Mailing ListsTop
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.
Support Top
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 BugsTop
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
AUTHOR - Ewan BirneyTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _