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# $Id$
# BioPerl module for Bio::BioEntry
# Please direct questions and support issues to <>
# Cared for by Hilmar Lapp <hlapp at>
# Copyright Hilmar Lapp
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::BioEntry - DESCRIPTION of Object
Give standard usage here
Describe the object here
=head2 Mailing Lists
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. - General discussion - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
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.
=head2 Reporting Bugs
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:
=head1 AUTHOR - Hilmar Lapp
Email hlapp at
Describe contact details here
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
# Let the code begin...
package Bio::BioEntry;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::IdentifiableI;
use Bio::DescribableI;
@ISA = qw(Bio::Root::Root Bio::IdentifiableI Bio::DescribableI);
=head2 new
Title : new
Usage : my $obj = Bio::BioEntry->new();
Function: Builds a new Bio::BioEntry object
Returns : an instance of Bio::BioEntry
Args :
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($objid, $ns, $auth, $v, $display_id, $desc) =
$self->object_id($objid) if $objid;
$self->namespace($ns) if $ns;
$self->authority($auth) if $auth;
$self->version($v) if $v;
$self->display_name($display_id) if $display_id;
$self->description($desc) if $desc;
return $self;
=head1 Methods for Bio::IdentifiableI compliance
=head2 object_id
Title : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object. For DNA sequences this
is its accession_number, similarly for protein sequences
This is aliased to accession_number().
Returns : A scalar
sub object_id {
my ($self, $value) = @_;
if( defined $value) {
$self->{'object_id'} = $value;
return $self->{'object_id'};
=head2 version
Title : version
Usage : $version = $obj->version()
Function: a number which differentiates between versions of
the same object. Higher numbers are considered to be
later and more relevant, but a single object described
the same identifier should represent the same concept
Returns : A number
sub version{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_version'} = $value;
return $self->{'_version'};
=head2 authority
Title : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg,
Returns : A scalar
sub authority {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'authority'} = $value;
return $obj->{'authority'};
=head2 namespace
Title : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection
Returns : A scalar
sub namespace{
my ($self,$value) = @_;
if( defined $value) {
$self->{'namespace'} = $value;
return $self->{'namespace'} || "";
=head1 Methods for Bio::DescribableI compliance
=head2 display_name
Title : display_name
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user
the string should have no spaces (ideally, though a cautious
user of this interface would not assumme this) and should be
less than thirty characters (though again, double checking
this is a good idea)
This is aliased to display_id().
Returns : A scalar
sub display_name {
my ($self,$value) = @_;
if( defined $value) {
$self->{'_display_name'} = $value;
return $self->{'_display_name'};
=head2 description
Title : description
Usage : $string = $obj->description()
Function: A text string suitable for displaying to the user a
description. This string is likely to have spaces, but
should not have any newlines or formatting - just plain
text. The string should not be greater than 255 characters
and clients can feel justified at truncating strings at 255
characters for the purposes of display
This is aliased to desc().
Returns : A scalar
sub description {
my ($self,$value) = @_;
if( defined $value) {
$self->{'_description'} = $value;
return $self->{'_description'};
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