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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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

DESCRIPTION

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This object will build Bio::Seq objects generically.

FEEDBACK

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Mailing Lists

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

Support

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.

Reporting Bugs

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/

AUTHOR - Jason Stajich

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Email jason@bioperl.org

APPENDIX

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

new

 Title   : new
 Usage   : my $obj = Bio::Seq::SeqFastaSpeedFactory->new();
 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.

create

 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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Seq::SeqFastaSpeedFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Seq::SeqFastaSpeedFactory;
use strict;

use Bio::Seq;
use Bio::PrimarySeq;

use base qw(Bio::Root::Root Bio::Factory::SequenceFactoryI);


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;