Bio::AnnotationI(3) User Contributed Perl Documentation Bio::AnnotationI(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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)
perl v5.14.1 2011-07-22 Bio::AnnotationI(3)
