Raw content of Bio::Biblio::Ref
<![CDATA[# $Id: Ref.pm,v 1.5 2002/10/22 07:45:11 lapp Exp $
#
# BioPerl module for Bio::Biblio::Ref
#
# Cared for by Martin Senger <senger@ebi.ac.uk>
# For copyright and disclaimer see below.
# POD documentation - main docs before the code
=head1 NAME
Bio::Biblio::Ref - Representation of a bibliographic reference
=head1 SYNOPSIS
$obj = new Bio::Biblio::Ref (-type => 'Letter',
-title => 'Onegin to Tatiana');
--- OR ---
$obj = new Bio::Biblio::Ref;
$obj->type ('Letter');
=head1 DESCRIPTION
A storage object for a general bibliographic reference (a citation).
See its place in the class hierarchy in
http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
=head2 Attributes
The following attributes are specific to this class,
and they are inherited by all citation types.
author_list_complete values: 'Y' (default) or 'N'
authors type: array ref of Bio::Biblio::Provider's
cross_references type: array ref of Bio::Annotation::DBLink's
cross_references_list_complete values: 'Y' (default) or 'N'
abstract
abstract_language
abstract_type
codes type: hash ref
contributors type: array ref of Bio::Biblio::Provider's
date
date_completed
date_created
date_revised
format
identifier
keywords
language
last_modified_date
publisher type: Bio::Biblio::Provider
repository_subset
rights
spatial_location
subject_headings type: hash ref
subject_headings_source
temporal_period
title
toc
toc_type
type
=head1 SEE ALSO
=over
=item *
OpenBQS home page: http://industry.ebi.ac.uk/openBQS
=item *
Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
=back
=head1 FEEDBACK
=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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHORS
Heikki Lehvaslaiho (heikki@ebi.ac.uk),
Martin Senger (senger@ebi.ac.uk)
=head1 COPYRIGHT
Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are preceded with a _
=cut
# Let the code begin...
package Bio::Biblio::Ref;
use strict;
use vars qw(@ISA $AUTOLOAD);
use Bio::Biblio::BiblioBase;
use Bio::Annotation::DBLink;
@ISA = qw(Bio::Biblio::BiblioBase);
#
# a closure with a list of allowed attribute names (these names
# correspond with the allowed 'get' and 'set' methods); each name also
# keep what type the attribute should be (use 'undef' if it is a
# simple scalar)
#
{
my %_allowed =
(
_author_list_complete => undef,
_authors => 'ARRAY', # of Bio::Biblio::Provider
_cross_references => 'ARRAY', # of Bio::Annotation::DBLink
_cross_references_list_complete => undef,
_abstract => undef,
_abstract_language => undef,
_abstract_type => undef,
_codes => 'HASH',
_contributors => 'ARRAY', # of Bio::Biblio::Provider
_date => undef,
_date_completed => undef,
_date_created => undef,
_date_revised => undef,
_format => undef,
_identifier => undef,
_keywords => 'HASH',
_language => undef,
_last_modified_date => undef,
_publisher => 'Bio::Biblio::Provider',
_repository_subset => undef,
_rights => undef,
_spatial_location => undef,
_subject_headings => 'HASH',
_subject_headings_source => undef,
_temporal_period => undef,
_title => undef,
_toc => undef,
_toc_type => undef,
_type => undef,
);
# return 1 if $attr is allowed to be set/get in this class
sub _accessible {
my ($self, $attr) = @_;
exists $_allowed{$attr};
}
# return an expected type of given $attr
sub _attr_type {
my ($self, $attr) = @_;
$_allowed{$attr};
}
}
=head2 add_cross_reference
Usage : $self->add_cross_reference
(new Bio::Annotation::DBLink (-database => 'EMBL',
-primary_id => 'V00808');
Function: adding a link to a database entry
Returns : new value of 'cross_references'
Args : an object of type Bio::Annotation::DBLink
=cut
sub add_cross_reference {
my ($self, $value) = @_;
$self->throw ($self->_wrong_type_msg (ref $value, 'Bio::Annotation::DBLink'))
unless (UNIVERSAL::isa ($value, 'Bio::Annotation::DBLink'));
(defined $self->cross_references) ?
push (@{ $self->cross_references }, $value) :
return $self->cross_references ( [$value] );
return $self->cross_references;
}
=head2 add_author
Usage : $self->add_author (new Bio::Biblio::Person (-lastname => 'Novak');
Function: adding an author to a list of authors
Returns : new value of 'authors' (a full list)
Args : an object of type Bio::Biblio::Provider
=cut
sub add_author {
my ($self, $value) = @_;
$self->throw ($self->_wrong_type_msg (ref $value, 'Bio::Biblio::Provider'))
unless (UNIVERSAL::isa ($value, 'Bio::Biblio::Provider'));
(defined $self->authors) ?
push (@{ $self->authors }, $value) :
return $self->authors ( [$value] );
return $self->authors;
}
=head2 add_contributor
Usage : $self->add_contributor (new Bio::Biblio::Person (-lastname => 'Novak');
Function: adding a contributor to a list of contributors
Returns : new value of 'contributors' (a full list)
Args : an object of type Bio::Biblio::Provider
=cut
sub add_contributor {
my ($self, $value) = @_;
$self->throw ($self->_wrong_type_msg (ref $value, 'Bio::Biblio::Provider'))
unless (UNIVERSAL::isa ($value, 'Bio::Biblio::Provider'));
(defined $self->contributors) ?
push (@{ $self->contributors }, $value) :
return $self->contributors ( [$value] );
return $self->contributors;
}
1;
__END__
]]>