my $self = shift;

  if(@_) {
    $self->{'cigar_line'} = shift;
  }

  return $self->{'cigar_line'};

  my $self = shift;

  if(@_) {
    $self->{'dbID'} = shift;
  }

  return $self->{'dbID'};

  my $self = shift;

  if(@_) {
    $self->{'ditag'} = shift;
  } elsif(!$self->{'ditag'}) {
    if($self->{'ditag_id'}) {
      #lazy load the ditag
      my $ditag_adaptor = $self->analysis->adaptor->db->get_DitagAdaptor;
      $self->{'ditag'}  = $ditag_adaptor->fetch_by_dbID($self->ditag_id);
    }
    else{
      throw "Could not get Ditag for DitagFeature ".$self->dbID;
    }
  }

  return($self->{'ditag'});

  my $self = shift;

  if(@_) {
    $self->{'ditag_id'} = shift;
  }

  return $self->{'ditag_id'};

  my $self = shift;

  if(@_) {
    $self->{'ditag_pair_id'} = shift;
  }

  return $self->{'ditag_pair_id'};

  my $self = shift;

  if(@_) {
    $self->{'ditag_side'} = shift;
  }

  return $self->{'ditag_side'};

  my $self = shift;

  if(@_) {
    $self->{'end'} = shift;
  }

  return $self->{'end'};

  throw("Deprecated method, please use ditag() instead.\n")

  my $self = shift;

  my ($start, $end, $strand);
  if($self->ditag_side eq "F"){
    $start = $self->start;
    $end   = $self->end;
  }
  else{
    my ($ditag_a, $ditag_b, $more);
    eval{
     ($ditag_a, $ditag_b, $more) = @{$self->adaptor->fetch_all_by_ditagID($self->ditag_id,
									  $self->ditag_pair_id,
									  $self->analysis->dbID)};
    };
    if($@ or !defined($ditag_a) or !defined($ditag_b)){
      throw("Cannot find 2nd tag of pair (".$self->dbID.", ".$self->ditag_id.", ".
	    $self->ditag_pair_id.", ".$self->analysis->dbID.")\n".$@);
    }
    else{
#      if(defined $more){
#	throw("More than two DitagFeatures were returned for ".$self->dbID.", ".$self->ditag_id
#	      .", ".$self->ditag_pair_id);
#      }

      ($ditag_a->start < $ditag_b->start) ? ($start = $ditag_a->start) : ($start = $ditag_b->start);
      ($ditag_a->end   > $ditag_b->end)   ? ($end   = $ditag_a->end)   : ($end   = $ditag_b->end);
      if($ditag_a->strand != $ditag_b->strand){
	throw('the strands of the two ditagFeatures are different! '.$ditag_a->strand.'/'.$ditag_b->strand);
      }
    }
  }

  return($start, $end, $self->strand);

  my $self = shift;

  if(@_) {
    $self->{'hit_end'} = shift;
  }

  return $self->{'hit_end'};

  my $self = shift;

  if(@_) {
    $self->{'hit_start'} = shift;
  }

  return $self->{'hit_start'};

  my $self = shift;

  if(@_) {
    $self->{'hit_strand'} = shift;
  }

  return $self->{'hit_strand'};

  my ($caller, @args) = @_;
  my ( $dbID, $adaptor, $start, $end, $strand, $slice, $analysis, $hit_start, $hit_end, 
       $hit_strand, $ditag_id, $ditag_side, $cigar_line, $ditag_pair_id, $tag_count, $ditag  ) =
	 rearrange( [ 'dbid', 'adaptor' ,'start', 'end', 'strand', 'slice', 'analysis', 'hit_start',
	'hit_end', 'hit_strand', 'ditag_id', 'ditag_side', 'cigar_line', 'ditag_pair_id' ,'tag_count', 'ditag'],
       @args );
  my $class = ref($caller) || $caller;

  if($analysis) {
    if(!ref($analysis) || !$analysis->isa('Bio::EnsEMBL::Analysis')) {
      throw('-ANALYSIS argument must be a Bio::EnsEMBL::Analysis not '.
            $analysis);
    }
  }
  if(defined($strand)) {
    if(!($strand =~ /^-?\d$/) or !($strand == 1) && !($strand == -1) && !($strand == 0)) {
      throw('-STRAND argument must be 1, -1, or 0');
    }
  }
  if(defined($hit_strand)) {
    if(!($hit_strand == 1) && !($hit_strand == -1) && !($hit_strand == 0)) {
      throw('-HIT_STRAND argument must be 1, -1, or 0 not '.$hit_strand);
    }
  }
  if(defined($start) && defined($end)) {
    if($end+1 < $start) {
      throw('Start must be less than or equal to end+1.');
    }
  }
  else{
    throw('Need start and end location.');
  }
  if(!(defined($hit_start) && defined($hit_end))) {
    throw('Need hit start and hit end location.');
  }
  if(!defined($tag_count) or (!$tag_count =~ /^[\d]+$/)){
    $tag_count = 1;
  }

  my $self = bless( {'dbID'          => $dbID,
                     'analysis'      => $analysis,
                     'adaptor'       => $adaptor,
                     'slice'         => $slice,
                     'start'         => $start,
                     'end'           => $end,
		     'strand'        => $strand,
		     'hit_start'     => $hit_start,
		     'hit_end'       => $hit_end,
		     'hit_strand'    => $hit_strand,
                     'ditag_id'      => $ditag_id,
		     'ditag_pair_id' => $ditag_pair_id,
                     'ditag_side'    => $ditag_side,
                     'cigar_line'    => $cigar_line,
		     'tag_count'     => $tag_count,
		     'ditag'         => $ditag,
                    }, $class);

  return $self;

  my $self = shift;

  $self->{'sequence'} = $self->adaptor->sequence($self->dbID());

  return $self->{'sequence'};

  my $self = shift;

  if(@_) {
    $self->{'slice'} = shift;
  }

  return $self->{'slice'};

  my $self = shift;

  if(@_) {
    $self->{'start'} = shift;
  }

  return $self->{'start'};

  my $self = shift;

  if(@_) {
    $self->{'strand'} = shift;
  }

  return $self->{'strand'};

  my $self = shift;

  if(@_) {
    $self->{'tag_count'} = shift;
  }

  return $self->{'tag_count'};
}

1;

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.