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.
Included modules
Inherit
Synopsis
use Bio::Factory::ObjectFactory;
my $factory = new Bio::Factory::ObjectFactory(-type => 'Bio::Ontology::GOterm');
my $term = $factory->create_object(-name => 'peroxisome',
-ontology => 'Gene Factory',
-identifier => 'GO:0005777');
Description
Methods
Methods description
Title : _validate_type
Usage :
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.
Args : A hash reference blessed into the specified type, allowing
queries like isa(). |
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 : 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 : new
Usage : my $obj = new Bio::Factory::ObjectFactory();
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 : 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) |
Methods code
sub _validate_type
{ my ($self,$obj) = @_;
if(! $obj->isa($self->interface())) {
$self->throw("invalid type: '".ref($obj).
"' does not implement '".$self->interface()."'");
}
return 1;
}
*create =\& create_object;
1;} | sub create_object
{ my ($self,@args) = @_;
my $type = $self->type();
return $type->new(-verbose => $self->verbose, @args); } | sub interface
{ my $self = shift;
my $interface = shift;
if($interface) {
return $self->{'interface'} = $interface;
}
return $self->{'interface'};} | sub new
{ my($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 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'};} | 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 _