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Bio::Factory::ObjectFactory.3pm

NAME

Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory

SYNOPSIS

     use Bio::Factory::ObjectFactory;
 
     my $factory = Bio::Factory::ObjectFactory->new(-type => 'Bio::Ontology::GOterm');
     my $term = $factory->create_object(-name => 'peroxisome',
                                        -ontology => 'Gene Factory',
                                        -identifier => 'GO:0005777');
 
 

DESCRIPTION

This object will build Bio::Root::RootI 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

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.

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::Factory::ObjectFactory->new();
  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.
 
 

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.
 
 

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)
 
 

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)
 
 

_validate_type

  Title   : _validate_type
  Usage   : $factory->_validate_type($object)
  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.
 
            The default implementation here will throw an exception
            if the supplied object does not inherit from the interface
            provided by the interface() method.
 
  Args    : A hash reference blessed into the specified type, allowing
            queries like isa().