Summary

Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory

Package variables

Included modules

Inherit

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

Synopsis

    use Bio::Annotation::AnnotationFactory;
    # 
    my $factory = new Bio::Annotation::AnnotationFactory(-type => 'Bio::Annotation::SimpleValue');
    my $ann = $factory->create_object(-value => 'peroxisome',
                                      -tagname => 'cellular component');

Description

This object will build Bio::AnnotationI objects generically.

Methods

Methods description

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

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

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

 Returns : Bio::AnnotationI compliant object
           The return type is configurable using new(-type =>"...").
 Args    : initialization parameters specific to the type of annotation
           object we want.

 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)

 Title   : _guess_type
 Usage   :
 Function: Guesses the right type of Bio::AnnotationI implementation
           based on initialization parameters for the prospective
           object.
 Example :
 Returns : the type (a string, the module name)
 Args    : initialization parameters to be passed to the prospective
           cluster object

Methods code

sub new {

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

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

    $self->{'_loaded_types'} = {};
    $self->type($type) if $type;

    return $self;

}

sub create_object {

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

   my $type = $self->type(); 
   if(! $type) {
       # we need to guess this
       $type = $self->_guess_type(@args);
       if(! $type) {
	   $self->throw("No annotation type set and unable to guess.");
       }
       # load dynamically if it hasn't been loaded yet
       if(! $self->{'_loaded_types'}->{$type}) {
	   eval {
	       $self->_load_module($type);
	       $self->{'_loaded_types'}->{$type} = 1;
	   };
	   if($@) {
	       $self->throw("Bio::AnnotationI implementation $type ".
			    "failed to load: ".$@);
	   }
       }
   }
   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( $@ ) {
		$self->throw("Annotation class '$type' failed to load: ".
			     $@);
	    }
	    my $a = bless {},$type;
	    if( ! $a->isa('Bio::AnnotationI') ) {
		$self->throw("'$type' does not implement Bio::AnnotationI. ".
			     "Too bad.");
	    }
	    $self->{'_loaded_types'}->{$type} = 1;
	}
	return $self->{'type'} = $type;
    }
    return $self->{'type'};

}

sub _guess_type {

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

    # we can only guess from a certain number of arguments
    my ($val,$db,$text,$name,$authors) =
	$self->_rearrange([qw(VALUE
			      DATABASE
			      TEXT
			      NAME
			      AUTHORS
			      )], @args);
  SWITCH: {
      $val        && do { $type = "SimpleValue"; last SWITCH; };
      $authors    && do { $type = "Reference"; last SWITCH; };
      $db         && do { $type = "DBLink"; last SWITCH; };
      $text       && do { $type = "Comment"; last SWITCH; };
      $name       && do { $type = "OntologyTerm"; last SWITCH; };
      # what else could we look for?
  }
    $type = "Bio::Annotation::".$type;

    return $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 _