Bio::Annotation
DBLink
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Summary
Bio::Annotation::DBLink - untyped links between databases
Package variables
Privates (from "my" definitions)
$DEFAULT_CB = sub { (($_[0]->database ? $_[0]->database . ':' : '' ) . ($_[0]->primary_id ? $_[0]->primary_id : '') . ($_[0]->version ? '.' . $_[0]->version : '')) || '' }
Inherit
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.
Methods
Methods description
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 |
Title : as_text
Usage :
Function:
Example :
Returns :
Args : |
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 |
Title : hash_tree
Usage :
Function:
Example :
Returns :
Args : |
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) |
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) |
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) |
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) |
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) |
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) |
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 |
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 |
Title : url
Usage : $url = $obj->url()
Function: URL which is associated with this DB link
Returns : string, full URL descriptor |
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 |
Title : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
For DBLink this is the same as database().
Returns : A scalar |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($database,$primary_id,$optional_id,$comment,$tag,$type,$ns,$auth,$v,$url) =
$self->_rearrange([qw(DATABASE
PRIMARY_ID
OPTIONAL_ID
COMMENT
TAGNAME
TYPE
NAMESPACE
AUTHORITY
VERSION
URL
)], @args);
$database && $self->database($database);
$primary_id && $self->primary_id($primary_id);
$optional_id && $self->optional_id($optional_id);
$comment && $self->comment($comment);
$tag && $self->tagname($tag);
$type && $self->type($type);
$ns && $self->namespace($ns);
$auth && $self->authority($auth);
defined($v) && $self->version($v);
defined($url) && $self->url($url);
return $self;} | sub as_text
{ my ($self) = @_;
return "Direct database link to ".$self->primary_id
.($self->version ? ".".$self->version : "")
.($self->optional_id ? " (".$self->optional_id.")" : "")
." in database ".$self->database;} | sub display_text
{ my ($self, $cb) = @_;
$cb ||= $DEFAULT_CB;
$self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
return $cb->($self);
}} | sub hash_tree
{ my ($self) = @_;
my $h = {};
$h->{'database'} = $self->database;
$h->{'primary_id'} = $self->primary_id;
if( defined $self->optional_id ) {
$h->{'optional_id'} = $self->optional_id;
}
if( defined $self->comment ) {
$h->{'comment'} = $self->comment;
}
return $h;} | sub tagname
{ my $self = shift;
return $self->{'tagname'} = shift if @_;
return $self->{'tagname'};} | sub database
{ my $self = shift;
return $self->{'database'} = shift if @_;
return $self->{'database'};} | sub primary_id
{ my $self = shift;
return $self->{'primary_id'} = shift if @_;
return $self->{'primary_id'};} | sub optional_id
{ my $self = shift;
return $self->{'optional_id'} = shift if @_;
return $self->{'optional_id'};} | sub comment
{ my $self = shift;
return $self->{'comment'} = shift if @_;
return $self->{'comment'};} | sub type
{ my $self = shift;
return $self->{'type'} = shift if @_;
return $self->{'type'};} | sub object_id
{ return shift->primary_id(@_); } | sub version
{ my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'};} | sub url
{ my $self = shift;
return $self->{'url'} = shift if @_;
return $self->{'url'};} | sub authority
{ my $self = shift;
return $self->{'authority'} = shift if @_;
return $self->{'authority'};} | sub namespace
{ return shift->database(@_);
}
1; } | General documentation
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| AnnotationI implementing functions | Top |
| Specific accessors for DBLinks | Top |
| Methods for Bio::IdentifiableI compliance | Top |