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Bio::Annotation::DBLink.3pm

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