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 _

as_text
Title : as_text Usage : Function: Example : Returns : Args :

hash_tree
Title : hash_tree Usage : Function: Example : Returns : Args :

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)

database
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)

primary_id
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)

optional_id
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)

comment
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)

object_id
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

version
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

authority
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

namespace
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