Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory

BioPerl documentation Contained in the BioPerl distribution.

Index

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NAME

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Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory

SYNOPSIS

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    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 = Bio::Cluster::ClusterFactory->new(-type => 'Bio::Cluster::UniGene');
    my $clu = $factory->create_object(-description => 'NAT',
                                      -display_id  => 'Hs.2');

DESCRIPTION

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This object will build Bio::ClusterI objects generically.

FEEDBACK

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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/wiki/Mailing_lists  - About the mailing lists

Support

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 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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp

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Email hlapp at gmx.net

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::Cluster::ClusterFactory->new();
 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.

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

_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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Cluster::ClusterFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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



# Let the code begin...


package Bio::Cluster::ClusterFactory;
use strict;

use Bio::Root::Root;

use base qw(Bio::Factory::ObjectFactory);


sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    $self->interface("Bio::ClusterI");
    $self->type($self->type) if $self->type;

    return $self;
}



sub create_object {
   my ($self,@args) = @_;

   my $type = $self->type();
   if(! $type) {
       # we need to guess this
       $type = $self->_guess_type(@args);
       $self->throw("No cluster type set and unable to guess.") unless $type;
       $self->type($type);
   }
   return $type->new(-verbose => $self->verbose, @args);
}


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;
}

1;