Summary

Bio::Seq::SeqFactory - 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::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::Seq 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 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,%param) = @_;

    my $sequence = $param{'-seq'}  || $param{'-SEQ'};
    my $fulldesc = $param{'-desc'} || $param{'-DESC'};
    my $id       = $param{'-id'}   || $param{'-ID'} ||
	           $param{'-primary_id'}   || $param{'-PRIMARY_ID'};

    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 ) {
	$t_pseq->_guess_alphabet();
    }

    return $seq;

}

General documentation

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  bioperl-bugs@bioperl.org
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Additional contributors names and emails here

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