Bio::Factory
ObjectFactory
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Summary
Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory
Package variables
No package variables defined.
Inherit
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
Methods
Methods description
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. |
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. |
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) |
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) |
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
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 $self;} | sub create_object
{ my ($self,@args) = @_;
my $type = $self->type();
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( $@ ) {
$self->throw("module for '$type' failed to load: ".
$@);
}
my $o = bless {},$type;
if(!$self->_validate_type($o)) {
$self->throw("'$type' is not valid for factory ".ref($self));
}
$self->{'_loaded_types'}->{$type} = 1;
}
return $self->{'type'} = $type;
}
return $self->{'type'};} | sub interface
{ my $self = shift;
my $interface = shift;
if($interface) {
return $self->{'interface'} = $interface;
}
return $self->{'interface'};} | sub _validate_type
{ my ($self,$obj) = @_;
if(! $obj->isa($self->interface())) {
$self->throw("invalid type: '".ref($obj).
"' does not implement '".$self->interface()."'");
}
return 1;
}
*create =\& create_object;
1;} | 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
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 _