/ 
bioperl-1.5.2_005-RCb
/ Bio::Annotation::DBLink

NAME

Bio::Annotation::DBLink - untyped links between databases

SYNOPSIS

   $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);

DESCRIPTION

Provides an object which represents a link from one object to something in another database without prescribing what is in the other database.

Aside from Bio::AnnotationI, this class also implements Bio::IdentifiableI.

AUTHOR - Ewan Birney

Ewan Birney - birney@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : $dblink = Bio::Annotation::DBLink->new(-database =>"GenBank",
                                                 -primary_id => "M123456");
Function: Creates a new instance of this class.
Example :
Returns : A new instance of Bio::Annotation::DBLink.
Args    : Named parameters. At present, the following parameters are
          recognized.

            -database    the name of the database referenced by the xref
            -primary_id  the primary (main) id of the referenced entry
                         (usually this will be an accession number)
            -optional_id a secondary ID under which the referenced entry
                         is known in the same database
            -comment     comment text for the dbxref
            -tagname     the name of the tag under which to add this
                         instance to an annotation bundle (usually 'dblink')
            -namespace   synonymous with -database (also overrides)
            -version     version of the referenced entry
            -authority   attribute of the Bio::IdentifiableI interface
            -url         attribute of the Bio::IdentifiableI interface

AnnotationI implementing functions

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)

Specific accessors for DBLinks

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)

Methods for Bio::IdentifiableI compliance

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

url

Title   : url
Usage   : $url    = $obj->url()
Function: URL which is associated with this DB link
Returns : string, full URL descriptor

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