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lib/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm  view on Meta::CPAN

  if($have_dbIDs){
    $sql = "INSERT INTO ditag_feature ( ditag_feature_id, ditag_id, seq_region_id, seq_region_start, ".
           "seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
           "hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
    foreach my $ditag_feature (@good_ditag_features) {
      $sqladd = "";
      if($inserts){ $sqladd = ", " }
      $sqladd .= "(". $ditag_feature->ditag_feature_id.", ".$ditag_feature->ditag_id.", ".
	         ($ditag_feature->slice->get_seq_region_id).", ". $ditag_feature->start.", ".
		 $ditag_feature->end.", '".$ditag_feature->strand."', ".$ditag_feature->analysis->dbID.", ".
                 $ditag_feature->hit_start.", ".$ditag_feature->hit_end.", '".$ditag_feature->hit_strand.
		 "', '".$ditag_feature->cigar_line."', '".$ditag_feature->ditag_side."', ".
		 $ditag_feature->ditag_pair_id.")";
      $sql .= $sqladd;
      $inserts++;
    }
  }
  else{
    $sql = "INSERT INTO ditag_feature ( ditag_id, seq_region_id, seq_region_start, ".
           "seq_region_end, seq_region_strand, analysis_id, hit_start, hit_end, ".
           "hit_strand, cigar_line, ditag_side, ditag_pair_id ) VALUES ";
    foreach my $ditag_feature (@good_ditag_features) {
      $sqladd = "";
      if($inserts){ $sqladd = ", " }
      $sqladd .= "(". $ditag_feature->ditag_id.", ".($ditag_feature->slice->get_seq_region_id).", ".
	         $ditag_feature->start.", ".$ditag_feature->end.", '".$ditag_feature->strand."', ".
		 $ditag_feature->analysis->dbID.", ".$ditag_feature->hit_start.", ".$ditag_feature->hit_end.
		 ", '".$ditag_feature->hit_strand."', '".$ditag_feature->cigar_line."', '".
		 $ditag_feature->ditag_side."', ".$ditag_feature->ditag_pair_id.")";
      $sql .= $sqladd;
      $inserts++;
    }
  }

  #STORE
  if($inserts){
    print STDERR "\nHave $inserts Features.\n";
    eval{
      $db->dbc->do($sql);
    };
    if($@){
      warning("Problem inserting ditag feature batch!".$@."\n");
    }
  }
  else{
    warn "Nothing stored!";
  }

}


=head2 update

  Arg [1]    : ditagFeature to update
  Description: update an existing ditagFeature with new values
  Returntype : 1 on success
  Status     : At Risk

=cut

sub update {
  my ($self, $ditagFeature) = @_;

  my $sth = $self->prepare( "UPDATE ditag_feature
                             SET ditag_id=?, seq_region_id=?, seq_region_start=?, seq_region_end=?,
                             seq_region_strand=?, analysis_id=?, hit_start=?, hit_end=?, hit_strand=?,
                             cigar_line=?, ditag_side=?, ditag_pair_id=?
                             where ditag_feature_id=?;" );

  $sth->bind_param(1, $ditagFeature->ditag_id, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->seq_region_id, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->seq_region_start, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->seq_region_end, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->seq_region_strand, SQL_TINYINT);
  $sth->bind_param(1, $ditagFeature->hit_start, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->hit_end, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->hit_strand, SQL_TINYINT);
  $sth->bind_param(1, $ditagFeature->cigar_line, SQL_LONGVARCHAR);
  $sth->bind_param(1, $ditagFeature->ditag_side, SQL_VARCHAR);
  $sth->bind_param(1, $ditagFeature->ditag_pair_id, SQL_INTEGER);
  $sth->bind_param(1, $ditagFeature->dbID, SQL_INTEGER);

  my $result =$sth->execute();

  return $result;
}


=head2 list_dbIDs

  Args       : None
  Example    : my @feature_ids = @{$dfa->list_dbIDs()};
  Description: Gets an array of internal IDs for all DitagFeature objects in
               the current database.
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : List of ints
  Exceptions : None
  Status     : Stable

=cut

sub list_dbIDs {
  my ($self, $ordered) = @_;
	
  return $self->_list_dbIDs('ditag_feature', undef, $ordered);
}

1;