Bio::SeqIO pln
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Summary
Bio::SeqIO::pln - pln trace sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::Seq::SeqFactory
Bio::SeqIO
Synopsis
Do not use this module directly. Use it via the Bio::SeqIO class.
Description
This object can transform Bio::Seq objects to and from pln trace
files.
Methods
BEGIN
No description
Code
_initialize
No description
Code
next_seqDescriptionCode
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq::Quality object
Args : NONE
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
Methods code
BEGINdescriptionprevnextTop
sub BEGIN {
    eval { require Bio::SeqIO::staden::read; };
    if ($@) {
	$READ_AVAIL = 0;
    } else {
	push @ISA, "Bio::SeqIO::staden::read";
	$READ_AVAIL = 1;
    }
}
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);  
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality'));      
  }
  unless ($READ_AVAIL) {
      Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
			      -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
			    );
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($self) = @_;

    my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'pln');

    # create the seq object
$seq = $self->sequence_factory->create(-seq => $seq, -id => $id, -primary_id => $id, -desc => $desc, -alphabet => 'DNA', -qual => $qual ); return $seq;
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self,@seq) = @_;

    my $fh = $self->_fh;
    foreach my $seq (@seq) {
	$self->write_trace($fh, $seq, 'pln');
    }

    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;
}

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 one
of the Bioperl mailing lists. 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
the bugs and their resolution.
Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Aaron MackeyTop
Email: amackey@virginia.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _