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Summary

Bio::Seq::SeqFastaSpeedFactory - Rapid creation of Bio::Seq objects through a factory

Package variables

Included modules

Inherit

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

Synopsis

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

Description

This factory was designed to build Bio::Seq objects as quickly as possible, but
is not as generic as Bio::Seq::SeqFactory. It can be used to create sequences
from non-rich file formats. The Bio::SeqIO::fasta sequence parser uses this
factory.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Seq::SeqFastaSpeedFactory->new();
 Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object 
 Returns : Bio::Seq::SeqFastaSpeedFactory
 Args    : None

 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 : A Bio::Seq object
 Args    : Initialization parameters for the sequence object we want:
              -id
              -primary_id
              -display_id
              -desc
              -seq
              -alphabet

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       = defined $param{'-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;
}

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/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

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:

  https://redmine.open-bio.org/projects/bioperl/

Email jason@bioperl.org

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