Bio::Annotation::DBLink - DESCRIPTION of Object
$link1 = new Bio::Annotation::DBLink(-database => 'TSC',
-primary_id => 'TSC0000030'
);
#or
$link2 = new Bio::Annotation::DBLink();
$link2->database('dbSNP');
$link2->primary_id('2367');
# DBLink is-a Bio::AnnotationI object, can be added to annotation
# collections, e.g. the one on features or seqs
$feat->annotation->add_Annotation('dblink', $link2);
Provides an object which represents a link from one object to something in another database without prescribing what is in the other database
Ewan Birney - birney@ebi.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : as_text Usage : Function: Example : Returns : Args :
Title : hash_tree Usage : Function: Example : Returns : Args :
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)
Title : database
Usage : $self->database($newval)
Function: set/get on the database string. Databases are just
a string here which can then be interpreted elsewhere
Example :
Returns : value of database
Args : newvalue (optional)
Title : primary_id
Usage : $self->primary_id($newval)
Function: set/get on the primary id (a string)
The primary id is the main identifier used for this object in
the database. Good examples would be accession numbers. The id
is meant to be the main, stable identifier for this object
Example :
Returns : value of primary_id
Args : newvalue (optional)
Title : optional_id
Usage : $self->optional_id($newval)
Function: get/set for the optional_id (a string)
optional id is a slot for people to use as they wish. The
main issue is that some databases do not have a clean
single string identifier scheme. It is hoped that the
primary_id can behave like a reasonably sane "single string
identifier" of objects, and people can use/abuse optional
ids to their heart's content to provide precise mappings.
Example :
Returns : value of optional_id
Args : newvalue (optional)
Title : comment
Usage : $self->comment($newval)
Function: get/set of comments (comment object)
Sets or gets comments of this dblink, which is sometimes relevant
Example :
Returns : value of comment (Bio::Annotation::Comment)
Args : newvalue (optional)
Title : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object. For DNA sequences this
is its accession_number, similarly for protein sequences
This is aliased to primary_id().
Returns : A scalar
Title : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Returns : A number
Title : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
Returns : A scalar
Title : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
For DBLink this is the same as database().
Returns : A scalar
