Summary

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

Package variables

Included modules

Inherit

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

Synopsis

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

Description

This object will build Bio::Seq objects generically.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Seq::SeqFastaSpeedFactory();
 Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object 
 Returns : Bio::Seq::SeqFastaSpeedFactory
 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 a new Bio::Seq object, correctly built but very
           fast, knowing stuff about Bio::PrimarySeq and Bio::Seq
 Returns : Bio::Seq

 Args    : initialization parameters specific to the type of sequence
           object we want.  Typically 
           -seq        => $str,
           -id         => $name

Methods code

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  return $self;

}

sub create {

    my ($self,@args) = @_;
    
    my %param = @args;
    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
    
    my $sequence = $param{'-seq'};
    my $fulldesc = $param{'-desc'};
    my $id       = $param{'-id'} || $param{'-primary_id'};
    my $alphabet = $param{'-alphabet'};

    my $seq = bless {}, "Bio::Seq";
    my $t_pseq = $seq->{'primary_seq'} = bless {}, "Bio::PrimarySeq";
    $t_pseq->{'seq'}  = $sequence;
    $t_pseq->{'desc'} = $fulldesc;
    $t_pseq->{'display_id'} = $id;
    $t_pseq->{'primary_id'} = $id;
    $seq->{'primary_id'} = $id; # currently Bio::Seq does not delegate this
    if( $sequence and !$alphabet ) {
	$t_pseq->_guess_alphabet();
    } elsif ( $sequence and $alphabet ) {
        $t_pseq->{'alphabet'} = $alphabet;
    }

    return $seq;

}

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 _