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Summary

Bio::Ontology::TermFactory - Instantiates a new
Bio::Ontology::TermI (or derived class) through a factory

Package variables

Included modules

Inherit

Bio::Factory::ObjectFactory

Synopsis

    use Bio::Ontology::TermFactory;

    # the default type is Bio::Ontology::Term
    my $factory = Bio::Ontology::TermFactory->new(
                        -type => 'Bio::Ontology::GOterm');
    my $term = $factory->create_object(-name => 'peroxisome',
                                       -ontology => 'Gene Ontology',
                                       -identifier => 'GO:0005777');

Description

This object will build Bio::Ontology::TermI objects generically.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Ontology::TermFactory->new();
 Function: Builds a new Bio::Ontology::TermFactory object 
 Returns : Bio::Ontology::TermFactory
 Args    : -type => string, name of a Bio::Ontology::TermI derived class.
                    The default is Bio::Ontology::Term.

Methods code

sub new {

    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
  
    # make sure this matches our requirements
    $self->interface("Bio::Ontology::TermI");
    $self->type($self->type() || "Bio::Ontology::Term");

    return $self;

}

General documentation

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

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.

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/

Email hlapp at gmx.net

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

 Title   : create_object
 Usage   : my $term = $factory->create_object(<named parameters>);
 Function: Instantiates new Bio::Ontology::TermI (or one of its child classes)

           This object allows us to genericize the instantiation of
           Term objects.

 Returns : Bio::Ontology::TermI compliant object
           The return type is configurable using new(-type =>"...").
 Args    : initialization parameters specific to the type of term
           object we want.  Typically 
           -name        => $name
           -identifier  => identifier for the term
           -ontology    => ontology for the term

See Bio::Ontology::TermI.