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.\" ========================================================================
.\"
.IX Title "Bio::Annotation::DBLink 3pm"
.TH Bio::Annotation::DBLink 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Annotation::DBLink \- untyped links between databases
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&   $link1 = Bio::Annotation::DBLink\->new(\-database => \*(AqTSC\*(Aq,
\&                                        \-primary_id => \*(AqTSC0000030\*(Aq
\&                                        );
\&
\&   #or 
\&
\&   $link2 = Bio::Annotation::DBLink\->new();
\&   $link2\->database(\*(AqdbSNP\*(Aq);
\&   $link2\->primary_id(\*(Aq2367\*(Aq);
\&
\&   # DBLink is\-a Bio::AnnotationI object, can be added to annotation
\&   # collections, e.g. the one on features or seqs
\&   $feat\->annotation\->add_Annotation(\*(Aqdblink\*(Aq, $link2);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Provides an object which represents a link from one object to something
in another database without prescribing what is in the other database.
.PP
Aside from Bio::AnnotationI, this class also implements
Bio::IdentifiableI.
.SH "AUTHOR \- Ewan Birney"
.IX Header "AUTHOR - Ewan Birney"
Ewan Birney \- birney@ebi.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 8
\& 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 \*(Aqdblink\*(Aq)
\&             \-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
.Ve
.SH "AnnotationI implementing functions"
.IX Header "AnnotationI implementing functions"
.SS "as_text"
.IX Subsection "as_text"
.Vb 6
\& Title   : as_text
\& Usage   :
\& Function:
\& Example :
\& Returns : 
\& Args    :
.Ve
.SS "display_text"
.IX Subsection "display_text"
.Vb 4
\& 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
.Ve
.SS "hash_tree"
.IX Subsection "hash_tree"
.Vb 6
\& Title   : hash_tree
\& Usage   :
\& Function:
\& Example :
\& Returns : 
\& Args    :
.Ve
.SS "tagname"
.IX Subsection "tagname"
.Vb 3
\& 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)
.Ve
.SH "Specific accessors for DBLinks"
.IX Header "Specific accessors for DBLinks"
.SS "database"
.IX Subsection "database"
.Vb 7
\& 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)
.Ve
.SS "primary_id"
.IX Subsection "primary_id"
.Vb 9
\& 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)
.Ve
.SS "optional_id"
.IX Subsection "optional_id"
.Vb 3
\& 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\*(Aqs content to provide precise mappings.
\&
\& Example : 
\& Returns : value of optional_id
\& Args    : newvalue (optional)
.Ve
.SS "comment"
.IX Subsection "comment"
.Vb 7
\& 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)
.Ve
.SS "type"
.IX Subsection "type"
.Vb 7
\& Title   : type
\& Usage   : $self\->type($newval)
\& Function: get/set of type
\&           Sets or gets the type of this dblink.
\& Example : $self\->type(\*(Aqprotein\*(Aq)
\& Returns : value of type
\& Args    : newvalue (optional)
.Ve
.SH "Methods for Bio::IdentifiableI compliance"
.IX Header "Methods for Bio::IdentifiableI compliance"
.SS "object_id"
.IX Subsection "object_id"
.Vb 5
\& 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
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& 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
.Ve
.SS "url"
.IX Subsection "url"
.Vb 4
\& Title   : url
\& Usage   : $url    = $obj\->url()
\& Function: URL which is associated with this DB link
\& Returns : string, full URL descriptor
.Ve
.SS "authority"
.IX Subsection "authority"
.Vb 5
\& 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
.Ve
.SS "namespace"
.IX Subsection "namespace"
.Vb 5
\& 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
.Ve