Bio::SeqIO abi
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SeqIO::abi - abi 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 abi 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::SeqWithQuality 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(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq'));      
  }
  unless ($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, 'abi');

    # 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, 'abi');
    }

    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 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/MailList.shtml - About the mailing lists
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 email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
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 _