Raw content of Bio::Factory::ObjectFactory
<![CDATA[# $Id: ObjectFactory.pm,v 1.1.2.1 2003/03/27 10:07:56 lapp Exp $
#
# BioPerl module for Bio::Factory::ObjectFactory
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2003.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory
=head1 SYNOPSIS
use Bio::Factory::ObjectFactory;
my $factory = new Bio::Factory::ObjectFactory(-type => 'Bio::Ontology::GOterm');
my $term = $factory->create_object(-name => 'peroxisome',
-ontology => 'Gene Factory',
-identifier => 'GO:0005777');
=head1 DESCRIPTION
This object will build L<Bio::Root::RootI> objects generically.
=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 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 CONTRIBUTORS
This is mostly copy-and-paste with subsequent adaptation from
Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
to him.
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Factory::ObjectFactory;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Factory::ObjectFactoryI;
@ISA = qw(Bio::Root::Root Bio::Factory::ObjectFactoryI);
=head2 new
Title : new
Usage : my $obj = new Bio::Factory::ObjectFactory();
Function: Builds a new Bio::Factory::ObjectFactory object
Returns : Bio::Factory::ObjectFactory
Args : -type => string, name of a L<Bio::Root::RootI> derived class.
There is no default.
-interface => string, name of the interface or class any type
specified needs to at least implement.
The default is Bio::Root::RootI.
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($type,$interface) = $self->_rearrange([qw(TYPE INTERFACE)], @args);
$self->{'_loaded_types'} = {};
$self->interface($interface || "Bio::Root::RootI");
$self->type($type) if $type;
return $self;
}
=head2 create_object
Title : create_object
Usage : my $seq = $factory->create_object(<named parameters>);
Function: Instantiates a new object of the previously set type.
This object allows us to genericize the instantiation of
objects.
You must have provided -type at instantiation, or have
called type($mytype) before you can call this method.
Returns : an object of the type returned by type()
The return type is configurable using new(-type =>"..."),
or by calling $self->type("My::Fancy::Class").
Args : Initialization parameters specific to the type of
object we want. Check the POD of the class you set as type.
=cut
sub create_object {
my ($self,@args) = @_;
my $type = $self->type(); # type has already been loaded upon set
return $type->new(-verbose => $self->verbose, @args);
}
=head2 type
Title : type
Usage : $obj->type($newval)
Function: Get/set the type of object to be created.
This may be changed at any time during the lifetime of this
factory.
Returns : value of type (a string)
Args : newvalue (optional, a string)
=cut
sub type{
my $self = shift;
if(@_) {
my $type = shift;
if($type && (! $self->{'_loaded_types'}->{$type})) {
eval {
$self->_load_module($type);
};
if( $@ ) {
$self->throw("module for '$type' failed to load: ".
$@);
}
my $o = bless {},$type;
if(!$self->_validate_type($o)) { # this may throw an exception
$self->throw("'$type' is not valid for factory ".ref($self));
}
$self->{'_loaded_types'}->{$type} = 1;
}
return $self->{'type'} = $type;
}
return $self->{'type'};
}
=head2 interface
Title : interface
Usage : $obj->interface($newval)
Function: Get/set the interface or base class that supplied types
must at least implement (inherit from).
Example :
Returns : value of interface (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub interface{
my $self = shift;
my $interface = shift;
if($interface) {
return $self->{'interface'} = $interface;
}
return $self->{'interface'};
}
=head2 _validate_type
Title : _validate_type
Usage :
Function: Called to let derived factories validate the type set
via type().
The default implementation here checks whether the supplied
object skeleton implements the interface set via -interface
upon factory instantiation.
Example :
Returns : TRUE if the type is to be considered valid, and FALSE otherwise.
Instead of returning FALSE this method may also just throw
an informative exception.
Args : A hash reference blessed into the specified type, allowing
queries like isa().
=cut
sub _validate_type{
my ($self,$obj) = @_;
if(! $obj->isa($self->interface())) {
$self->throw("invalid type: '".ref($obj).
"' does not implement '".$self->interface()."'");
}
return 1;
}
#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*create = \&create_object;
1;
]]>