Bio::Factory ObjectFactory
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory
Package variables
No package variables defined.
Inherit
Bio::Factory::ObjectFactoryI Bio::Root::Root
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.
Methods
newDescriptionCode
create_objectDescriptionCode
typeDescriptionCode
interfaceDescriptionCode
_validate_typeDescriptionCode
Methods description
newcode    nextTop
 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 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_objectcodeprevnextTop
 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.
typecodeprevnextTop
 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)
interfacecodeprevnextTop
 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_typecodeprevnextTop
 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().
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

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

    $self->{'_loaded_types'} = {};
    $self->interface($interface || "Bio::Root::RootI");
    $self->type($type) if $type;

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

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

    if(@_) {
	my $type = shift;
	if($type && (! $self->{'_loaded_types'}->{$type})) {
	    eval {
		$self->_load_module($type);
	    };
	    if( $@ ) {
		$self->throw("module for '$type' failed to load: ".
			     $@);
	    }
	    my $o = bless {},$type;
	    if(!$self->_validate_type($o)) { # this may throw an exception
$self->throw("'$type' is not valid for factory ".ref($self)); } $self->{'_loaded_types'}->{$type} = 1; } return $self->{'type'} = $type; } return $self->{'type'};
}
interfacedescriptionprevnextTop
sub interface {
    my $self = shift;
    my $interface = shift;

    if($interface) {
	return $self->{'interface'} = $interface;
    }
    return $self->{'interface'};
}
_validate_typedescriptionprevnextTop
sub _validate_type {
    my ($self,$obj) = @_;

    if(! $obj->isa($self->interface())) {
	$self->throw("invalid type: '".ref($obj).
		     "' does not implement '".$self->interface()."'");
    }
    return 1;
}

#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*create =\& create_object; 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LappTop
Email hlapp at gmx.net
CONTRIBUTORSTop
This is mostly copy-and-paste with subsequent adaptation from
Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
to him.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _