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
$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:
https://redmine.open-bio.org/projects/bioperl/
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)