Summary

Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory

Package variables

Inherit

Bio::Factory::SequenceFactoryI Bio::Root::Root

Synopsis

    use Bio::Seq::SeqFactory;
    my $factory = new Bio::Seq::SeqFactory;
    my $seq = $factory->create(-seq => 'WYRAVLC',
			       -id  => 'name');

    # If you want the factory to create Bio::Seq objects instead
    # of the default Bio::PrimarySeq objects, use the -type parameter:

    my $factory = new Bio::Seq::SeqFactory(-type => 'Bio::Seq');

Description

This object will build Bio::PrimarySeqI and Bio::SeqI objects
generically.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Seq::SeqFactory();
 Function: Builds a new Bio::Seq::SeqFactory object 
 Returns : Bio::Seq::SeqFactory
 Args    : -type => string, name of a PrimarySeqI derived class
                    This is optional. Default=Bio::PrimarySeq.

 Title   : create
 Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
 Function: Instantiates new Bio::SeqI (or one of its child classes)
           This object allows us to genericize the instantiation of sequence
           objects.
 Returns : Bio::PrimarySeq object (default)
           The return type is configurable using new(-type =>"...").
 Args    : initialization parameters specific to the type of sequence
           object we want.  Typically 
           -seq        => $str,
           -display_id => $name

 Title   : type
 Usage   : $obj->type($newval)
 Function: 
 Returns : value of type
 Args    : newvalue (optional)

Methods code

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my ($type) = $self->_rearrange([qw(TYPE)], @args);
  if( ! defined $type ) { 
      $type = 'Bio::PrimarySeq';
  }
  $self->type($type);
  return $self;

}

sub create {

   my ($self,@args) = @_;
   return $self->type->new(-verbose => $self->verbose, @args);

}

sub type {

   my ($self,$value) = @_;
   if( defined $value) {
       eval "require $value";
       if( $@ ) { $self->throw("$@: Unrecognized Sequence type for SeqFactory '$value'");}
       
       my $a = bless {},$value;
       unless( $a->isa('Bio::PrimarySeqI') ||
	       $a->isa('Bio::Seq::QualI') ) {
	   $self->throw("Must provide a valid Bio::PrimarySeqI or Bio::Seq::QualI or child class to SeqFactory Not $value");
       }
      $self->{'type'} = $value;
    }
    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/wiki/Mailing_lists  - 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 the
web:

  http://bugzilla.open-bio.org/

Email jason@bioperl.org

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