Toolbar

Summary

Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects

Package variables

Included modules

Inherit

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

Synopsis

    use Bio::Search::HSP::HSPFactory;
    my $factory = new Bio::Search::HSP::HSPFactory();
    my $resultobj = $factory->create(@args);

Description

This is a general way of hiding the object creation process so that we
can dynamically change the objects that are created by the SearchIO
parser depending on what format report we are parsing.
This object is for creating new HSPs.

Methods

Methods description

 Title   : create
 Usage   : $factory->create(%args)
 Function: Create a new Bio::Search::HSP::HSPI object  
 Returns : Bio::Search::HSP::HSPI
 Args    : hash of initialization parameters

 Title   : new
 Usage   : my $obj = new Bio::Search::HSP::HSPFactory();
 Function: Builds a new Bio::Search::HSP::HSPFactory object 
 Returns : Bio::Search::HSP::HSPFactory
 Args    :

 Title   : type
 Usage   : $factory->type('Bio::Search::HSP::GenericHSP');
 Function: Get/Set the HSP creation type
 Returns : string
 Args    : [optional] string to set

Methods code

BEGIN {

     $DEFAULT_TYPE = 'Bio::Search::HSP::GenericHSP';

}

sub create {

   my ($self,@args) = @_;
   my $type = $self->type;
   eval { $self->_load_module($type) };
   if( $@ ) { $self->throw("Unable to load module $type"); }
   return $type->new(@args);

}

sub new {

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

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

}

sub type {

    my ($self,$type) = @_;
   if( defined $type ) { 
       # redundancy with the create method which also calls _load_module
       # I know - but this is not a highly called object so I am going 
       # to leave it in
       eval {$self->_load_module($type) };
       if( $@ ){ $self->warn("Cannot find module $type, unable to set type") } 
       else { $self->{'_type'} = $type; }
   }
    return $self->{'_type'} || $DEFAULT_TYPE;
}

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/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 jason@bioperl.org
Describe contact details here

Additional contributors names and emails here

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