Summary

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

Package variables

Included modules

Inherit

Bio::Factory::ObjectFactoryI Bio::Root::Root

Synopsis

    use Bio::Ontology::TermFactory;
    # the default type is Bio::Ontology::Term
    my $factory = new Bio::Ontology::TermFactory(-type => 'Bio::Ontology::GOterm');
    my $clu = $factory->create_object(-name => 'peroxisome',
                                      -category => 'cellular component',
                                      -identifier => 'GO:0005777');

Description

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

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Ontology::TermFactory();
 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.

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

           This object allows us to genericize the instantiation of
           cluster 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
           -category     => category for the term

 Title   : type
 Usage   : $obj->type($newval)
 Function: Get/set the type of Bio::AnnotationI object to be created.

           This may be changed at any time during the lifetime of this
           factory.

 Returns : value of type
 Args    : newvalue (optional)

Methods code

sub new {

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

    my $self = $class->SUPER::new(@args);
  
    my ($type) = $self->_rearrange([qw(TYPE)], @args);

    $self->{'_loaded_types'} = {};
    $type = "Bio::Ontology::Term" unless $type;
    $self->type($type) if $type;

    return $self;

}

sub create_object {

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

   my $type = $self->type(); # type has already been loaded upon set
   return $type->new(-verbose => $self->verbose, @args);

}

sub type {

    my $self = shift;

    if(@_) {
	my $type = shift;
	if($type && (! $self->{'_loaded_types'}->{$type})) {
	    eval {
		$self->_load_module($type);
	    };
	    if( $@ ) {
		$self->throw("Term implementation '$type' failed to load: ".
			     $@);
	    }
	    my $a = bless {},$type;
	    if( ! $a->isa('Bio::Ontology::TermI') ) {
		$self->throw("'$type' does not implement Bio::Ontology::TermI. ".
			     "Too bad.");
	    }
	    $self->{'_loaded_types'}->{$type} = 1;
	}
	return $self->{'type'} = $type;
    }
    return $self->{'type'};

}

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/MailList.shtml  - About the mailing lists

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/

Email hlapp at gmx.net

This is mostly copy-and-paste with subsequent adaptation from
Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
to him.

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