Bio::DB::Persistent BioNamespace
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Summary
Bio::DB::Persistent::BioNamespace - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::DB::Persistent::PersistentObject
Bio::IdentifiableI
Inherit
Bio::DB::Persistent::PersistentObject Bio::IdentifiableI
Synopsis
Give standard usage here
Description
Describe the object here
Methods
newDescriptionCode
objDescriptionCode
identifiableDescriptionCode
object_idDescriptionCode
versionDescriptionCode
authorityDescriptionCode
namespaceDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::DB::Persistent::BioNamespace->new();
Function: Builds a new Bio::DB::Persistent::BioNamespace object
Returns : an instance of Bio::DB::Persistent::BioNamespace
Args :
objcodeprevnextTop
 Title   : obj
Usage : $obj->obj()
Function: Get the object that is made persistent through this adaptor.
Note that this implementation does not allow setting the object. Example : Returns : The object made persistent through this adaptor Args : None (set not supported)
identifiablecodeprevnextTop
 Title   : identifiable
Usage : $obj->identifiable($newval)
Function: Get/set the Bio::IdentifiableI compliant object from which to obtain
namespace and authority, and to which to forward all IdentifiableI
calls.
Example :
Returns : a Bio::IdentifiableI compliant object
Args : Optionally on set, a Bio::IdentifiableI compliant object
object_idcodeprevnextTop
 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
Returns : A scalar
versioncodeprevnextTop
 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
authoritycodeprevnextTop
 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
namespacecodeprevnextTop
 Title   : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
Returns : A scalar
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    my ($identifiable) = $self->_rearrange([qw(IDENTIFIABLE)], @args);

    $self->identifiable($identifiable) if $identifiable;

    return $self;
}
objdescriptionprevnextTop
sub obj {
    # we always point to ourselves
return shift;
}
identifiabledescriptionprevnextTop
sub identifiable {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->throw("Object of class ".ref($value)." does not implement ".
		     "Bio::IdentifiableI. Too bad.")
	    unless $value->isa("Bio::IdentifiableI");
	$self->{'identifiable'} = $value;
	$self->is_dirty(1);
    }
    return $self->{'identifiable'};
}
object_iddescriptionprevnextTop
sub object_id {
    my ($self, @args) = @_;
    $self->is_dirty(1) if @args;
    return $self->identifiable()->object_id(@args);
}
versiondescriptionprevnextTop
sub version {
    my ($self,@args) = @_;
    $self->is_dirty(1) if @args;
    return $self->identifiable()->version(@args);
}
authoritydescriptionprevnextTop
sub authority {
    my ($self,@args) = @_;
    $self->is_dirty(1) if @args;
    return $self->identifiable()->authority(@args);
}
namespacedescriptionprevnextTop
sub namespace {
    my ($self,@args) = @_;
    $self->is_dirty(1) if @args;
    return $self->identifiable()->namespace(@args);
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
 
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Methods for Bio::IdentifiableI complianceTop