Bio::Annotation::DBLink(3pm)				User Contributed Perl Documentation			      Bio::Annotation::DBLink(3pm)

NAME

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

SYNOPSIS

	  $link1 = Bio::Annotation::DBLink->new(-database => 'TSC',
					       -primary_id => 'TSC0000030'
					       );

	  #or

	  $link2 = Bio::Annotation::DBLink->new();
	  $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')
		    -type	 the type of information in the referenced entry
				 (e.g. protein, mRNA, structure)
		    -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	:

   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 te specific implementation.

		  One can pass a callback as an argument which allows custom text
		  generation; the callback is passed the current instance and any text
		  returned
	Example :
	Returns : a string
	Args	: [optional] callback

   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)

   type
	Title	: type
	Usage	: $self->type($newval)
	Function: get/set of type
		  Sets or gets the type of this dblink.
	Example : $self->type('protein')
	Returns : value of type
	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

perl v5.14.2							    2012-03-02					      Bio::Annotation::DBLink(3pm)