Bio::Cluster::ClusterFactory.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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

DESCRIPTION

This object will build Bio::ClusterI objects generically.

FEEDBACK

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

APPENDIX

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