Bio::Seq SeqFastaSpeedFactory
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Summary
Bio::Seq::SeqFastaSpeedFactory - Rapid creation of Bio::Seq objects through a factory
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
Bio::Seq
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
newDescriptionCode
createDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Seq::SeqFastaSpeedFactory->new();
Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object
Returns : Bio::Seq::SeqFastaSpeedFactory
Args : None
createcodeprevnextTop
 Title   : create
Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
Function: Instantiates a new Bio::Seq object, correctly built but very
fast, knowing stuff about Bio::PrimarySeq and Bio::Seq
Returns : A Bio::Seq object
Args : Initialization parameters for the sequence object we want:
-id
-primary_id
-display_id
-desc
-seq
-alphabet
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  return $self;
}
createdescriptionprevnextTop
sub create {
    my ($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
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _