Raw content of Bio::Cluster::ClusterFactory
<![CDATA[# $Id: ClusterFactory.pm,v 1.2 2002/10/31 09:45:39 lapp Exp $
#
# BioPerl module for Bio::Cluster::ClusterFactory
#
# 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, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# 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::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory
=head1 SYNOPSIS
use Bio::Cluster::ClusterFactory;
# if you don't provide a default type, the factory will try
# some guesswork based on display_id and namespace
my $factory = new Bio::Cluster::ClusterFactory(-type => 'Bio::Cluster::UniGene');
my $clu = $factory->create_object(-description => 'NAT',
-display_id => 'Hs.2');
=head1 DESCRIPTION
This object will build L<Bio::ClusterI> 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::Cluster::ClusterFactory;
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 $obj = new Bio::Cluster::ClusterFactory();
Function: Builds a new Bio::Cluster::ClusterFactory object
Returns : Bio::Cluster::ClusterFactory
Args : -type => string, name of a ClusterI derived class.
If not provided, the factory will have to guess
from ID and namespace, which may or may not be
successful.
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($type) = $self->_rearrange([qw(TYPE)], @args);
$self->{'_loaded_types'} = {};
$self->type($type) if $type;
return $self;
}
=head2 create_object
Title : create_object
Usage : my $seq = $factory->create_object(<named parameters>);
Function: Instantiates new Bio::ClusterI (or one of its child classes)
This object allows us to genericize the instantiation of
cluster objects.
Returns : L<Bio::ClusterI> compliant object
The return type is configurable using new(-type =>"...").
Args : initialization parameters specific to the type of cluster
object we want. Typically
-display_id => $name
-description => description of the cluster
-members => arrayref, members of the cluster
=cut
sub create_object {
my ($self,@args) = @_;
my $type = $self->type();
if(! $type) {
# we need to guess this
$type = $self->_guess_type(@args);
if(! $type) {
$self->throw("No cluster type set and unable to guess.");
}
# load dynamically if it hasn't been loaded yet
if(! $self->{'_loaded_types'}->{$type}) {
eval {
$self->_load_module($type);
$self->{'_loaded_types'}->{$type} = 1;
};
if($@) {
$self->throw("Bio::ClusterI implementation $type ".
"failed to load: ".$@);
}
}
}
return $type->new(-verbose => $self->verbose, @args);
}
=head2 type
Title : type
Usage : $obj->type($newval)
Function: Get/set the type of L<Bio::ClusterI> object to be created.
This may be changed at any time during the lifetime of this
factory.
Returns : value of type
Args : newvalue (optional)
=cut
sub type{
my $self = shift;
if(@_) {
my $type = shift;
if($type && (! $self->{'_loaded_types'}->{$type})) {
eval {
$self->_load_module($type);
};
if( $@ ) {
$self->throw("Cluster implementation '$type' failed to load: ".
$@);
}
my $a = bless {},$type;
if( ! $a->isa('Bio::ClusterI') ) {
$self->throw("'$type' does not implement Bio::ClusterI. ".
"Too bad.");
}
$self->{'_loaded_types'}->{$type} = 1;
}
return $self->{'type'} = $type;
}
return $self->{'type'};
}
=head2 _guess_type
Title : _guess_type
Usage :
Function: Guesses the right type of L<Bio::ClusterI> implementation
based on initialization parameters for the prospective
object.
Example :
Returns : the type (a string, the module name)
Args : initialization parameters to be passed to the prospective
cluster object
=cut
sub _guess_type{
my ($self,@args) = @_;
my $type;
# we can only guess from a certain number of arguments
my ($dispid, $ns, $members) =
$self->_rearrange([qw(DISPLAY_ID
NAMESPACE
MEMBERS
)], @args);
# Unigene namespace or ID?
if($ns && (lc($ns) eq "unigene")) {
$type = 'Bio::Cluster::UniGene';
} elsif($dispid && ($dispid =~ /^Hs\.[0-9]/)) {
$type = 'Bio::Cluster::UniGene';
}
# what else could we look for?
return $type;
}
#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*create = \&create_object;
1;
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