Bio::Annotation
DBLink
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Summary
Bio::Annotation::DBLink - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Inherit
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
Methods
Methods description
Title : as_text
Usage :
Function:
Example :
Returns :
Args : |
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 : 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 : database
Usage : $self->database($newval)
Function: set/get on the database string. Databases are just
a string here which can then be interpretted elsewhere
Example :
Returns : value of database
Args : newvalue (optional) |
Title : hash_tree
Usage :
Function:
Example :
Returns :
Args : |
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 |
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 : 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 : 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 : 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 : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Returns : A number |
Methods code
sub as_text
{ my ($self) = @_;
return "Direct database link to ".$self->primary_id." in database ".$self->database; } | sub authority
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'authority'} = $value;
}
return $obj->{'authority'};} | sub comment
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'comment'} = $value;
}
return $self->{'comment'};} | sub database
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'database'} = $value;
}
return $self->{'database'};} | sub hash_tree
{ my ($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 $h;} | sub namespace
{ return shift->database(@_);
}
1; } | sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($database, $primary_id, $optional_id, $comment, $tag, $ns, $auth, $v) =
$self->_rearrange([qw(DATABASE
PRIMARY_ID
OPTIONAL_ID
COMMENT
TAGNAME
NAMESPACE
AUTHORITY
VERSION
)], @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);
$ns && $self->namespace($ns);
$auth && $self->authority($auth);
defined($v) && $self->version($v);
return $self;} | sub object_id
{ return shift->primary_id(@_); } | sub optional_id
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'optional_id'} = $value;
}
return $self->{'optional_id'};} | sub primary_id
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'primary_id'} = $value;
}
return $self->{'primary_id'};} | sub tagname
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'tagname'} = $value;
}
return $self->{'tagname'};} | sub version
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'_version'} = $value;
}
return $self->{'_version'};} | 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 |