#used when getting constrained elements by slice or dnafrag	my ($self) = shift;
	my ($sql, $constrained_elements, $mlss_id, $dnafrag_id, $start, $end, $lower_bound, $slice) = @_;
	$sql = qq{
       		SELECT
       		constrained_element_id,
       		dnafrag_start,
       		dnafrag_end,
      		score,
      		p_value,
       		taxonomic_level
       		FROM
       		constrained_element} . $sql;

	my $sth = $self->prepare($sql);
	$sth->execute($mlss_id, $dnafrag_id, $start, $end, $lower_bound);
	my ($dbID, $ce_start, $ce_end, $score, $p_value, $tax_level);
	$sth->bind_columns(\$dbID,\$ ce_start,\$ ce_end,\$ score,\$ p_value,\$ tax_level);
	while ($sth->fetch()) {
		my $constrained_element = Bio::EnsEMBL::Compara::ConstrainedElement->new_fast (
			{
				'adaptor' => $self,
				'dbID' => $dbID,
				'slice' => $slice,
				'start' =>  ($ce_start - $start + 1), 
				'end' => ($ce_end - $start + 1),
				'method_link_species_set_id' => $mlss_id,
				'score' => $score,
				'p_value' => $p_value,
				'taxonomic_level' => $tax_level,
				'reference_dnafrag_id' => $dnafrag_id,
			}
		);
		push(@$constrained_elements, $constrained_element);
	}

#used when getting constrained elements by constrained_element_id	my ($self) = shift;
	my ($sql, $constrained_elements, $dbIDs) = @_;
        
	$sql = qq{
       		SELECT
       		ce.constrained_element_id,
       		ce.dnafrag_id,
       		ce.dnafrag_start,
       		ce.dnafrag_end,
       		ce.method_link_species_set_id,
      		ce.score,
      		ce.p_value,
       		ce.taxonomic_level,
		gdb.name,
		df.name
       		FROM
       		constrained_element ce
		INNER JOIN 
		dnafrag df 
		ON
		df.dnafrag_id = ce.dnafrag_id
		INNER JOIN 
		genome_db gdb
		ON 
		gdb.genome_db_id = df.genome_db_id} . $sql;

	my $sth = $self->prepare($sql);
	foreach my $constrained_element_id (@{ $dbIDs }) {
		my (%general_attributes, @alignment_segments);
		$sth->execute( $constrained_element_id );
		my ($dbID, $dnafrag_id, $ce_start, $ce_end, $mlssid, $score, $p_value, $tax_level, $species_name, $dnafrag_name);
	 	$sth->bind_columns(\$dbID,\$ dnafrag_id,\$ ce_start,\$ ce_end,\$ mlssid,\$ 
					score,\$ p_value,\$ tax_level,\$ species_name,\$ dnafrag_name);	
		while ($sth->fetch()) {
			$general_attributes{dbID} = $dbID;
			$general_attributes{mlssid} = $mlssid;
			$general_attributes{score} = $score;
			$general_attributes{p_value} = $p_value;
			$general_attributes{taxonomic_level} = $tax_level;
			push(@alignment_segments, [ $dnafrag_id, $ce_start, $ce_end, $species_name, $dnafrag_name ]);
		}
		my $constrained_element = Bio::EnsEMBL::Compara::ConstrainedElement->new_fast (
			{
				'adaptor' => $self,
				'dbID' => $general_attributes{dbID},
				'alignment_segments' =>\@ alignment_segments,
				'method_link_species_set_id' => $general_attributes{mlssid},
				'score' => $general_attributes{score},
				'p_value' => $general_attributes{p_value},
				'taxonomic_level' => $general_attributes{taxonomic_level},
			}
		);
		push(@$constrained_elements, $constrained_element);
	}
}

1;

  my ($self, $mlss_obj) = @_;

  if (defined($mlss_obj)) {
    throw("$mlss_obj is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object")	
      unless ($mlss_obj->isa("Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
  } else {
    throw("undefined Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
  }

  my $cons_ele_sql =
        qq{DELETE FROM constrained_element WHERE method_link_species_set_id = ?};
  
# Delete constrtained element entries by mlss_id
  my $sth = $self->prepare($cons_ele_sql);
  $sth->execute($mlss_obj->dbID);

	my ($self, $mlss_obj, $dnafrag_obj, $dnafrag_start, $dnafrag_end) = @_;
	if (defined($mlss_obj)) {
		throw("$mlss_obj is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object")	
		unless ($mlss_obj->isa("Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
	} else {
		throw("undefined Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
	} 
	if(defined($dnafrag_obj)) {
		throw("$dnafrag_obj is not a Bio::EnsEMBL::Compara::DnaFrag object")
		unless ($dnafrag_obj->isa("Bio::EnsEMBL::Compara::DnaFrag"));
	} else {
		throw("undefined Bio::EnsEMBL::Compara::DnaFrag object");
	}

	my (@constrained_elements, $lower_bound);
	my $sql = qq{
		WHERE
		method_link_species_set_id = ?
		AND
		dnafrag_id = ?
	};
 
	if (defined($dnafrag_start) && defined($dnafrag_end) && ($dnafrag_start <= $dnafrag_end)) {
		my $max_alignment_length = $mlss_obj->max_alignment_length;
		$lower_bound = $dnafrag_start - $max_alignment_length;
	} else {
		$dnafrag_start = 1;
		$dnafrag_end = $dnafrag_obj->length;
		$lower_bound = $dnafrag_start;
	}
	$sql .= qq{
		AND
		dnafrag_end >= ?
		AND
		dnafrag_start <= ?
		AND
		dnafrag_start >= ?
	};
	$self->_fetch_all_ConstrainedElements($sql,\@ constrained_elements, 
			$mlss_obj->dbID, $dnafrag_obj->dbID, $dnafrag_start, $dnafrag_end, $lower_bound);
	return\@ constrained_elements;

	my ($self, $mlss_obj, $slice_obj) = @_;
	if (defined($mlss_obj)) {
		throw("$mlss_obj is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object")	
		unless ($mlss_obj->isa("Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
	} else {
		throw("undefined Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
	}
	if (defined($slice_obj)) {
		throw("$slice_obj is not a Bio::EnsEMBL::Slice object")	
		unless ($slice_obj->isa("Bio::EnsEMBL::Slice"));
	} else {
		throw("undefined Bio::EnsEMBL::Slice object");
	}

	my $dnafrag_adp = $self->db->get_DnaFragAdaptor;
	my $dnafrag = $dnafrag_adp->fetch_by_Slice($slice_obj);
	my $sql = qq{
		WHERE
		method_link_species_set_id = ?
		AND
		dnafrag_id = ? 
	};
	my (@constrained_elements, $lower_bound);

	if(defined($slice_obj->start) && defined($slice_obj->end) && 
		($slice_obj->start <= $slice_obj->end)) {
			my $max_alignment_length = $mlss_obj->max_alignment_length;
			$lower_bound = $slice_obj->start - $max_alignment_length;
			$sql .= qq{
				AND
				dnafrag_end >= ?
				AND
				dnafrag_start <= ?
				AND
				dnafrag_start >= ?
			};
	}
	
	$self->_fetch_all_ConstrainedElements($sql,\@ constrained_elements,
		$mlss_obj->dbID, $dnafrag->dbID, $slice_obj->start, $slice_obj->end, $lower_bound, $slice_obj);
	return\@ constrained_elements;

	my ($self, $constrained_element_ids) = @_;
	if(defined($constrained_element_ids)) {
		throw("Arg-1 needs to be a listref of dbIDs") unless (
			ref($constrained_element_ids) eq "ARRAY");
	}
	my @constrained_elements;
	my $sql = qq{
		WHERE
		ce.constrained_element_id = ?
	};
	$self->_fetch_all_ConstrainedElements_by_dbID($sql,\@ constrained_elements, $constrained_element_ids);
	return\@ constrained_elements;

  my ($self, $constrained_element_id) = @_;
  return ($self->fetch_all_by_dbID([$constrained_element_id]))->[0];

  my $class = shift;
  my $self = $class->SUPER::new(@_);
  $self->{_use_autoincrement} = 0;
  return $self;

	my ( $self, $mlss_obj, $constrained_elements ) = @_;
	if (defined($mlss_obj)) {
		throw("$mlss_obj is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object")	
		unless ($mlss_obj->isa("Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
	} else {
		throw("undefined Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object");
	}

	my $mlssid = $mlss_obj->dbID;
	my $mlssid_sql =
	"SELECT MAX(constrained_element_id) FROM constrained_element WHERE" .
	" constrained_element_id > " . $mlssid .
	"0000000000 AND constrained_element_id < " .
	($mlssid + 1) . "0000000000";

	my $mlssid_sth = $self->prepare($mlssid_sql);

	my $constrained_element_sql = qq{INSERT INTO constrained_element (
		constrained_element_id,
		dnafrag_id,
		dnafrag_start, 
		dnafrag_end,
		score,
		method_link_species_set_id,
		p_value,
		taxonomic_level
	) VALUES (?,?,?,?,?,?,?,?)};

	my $constrained_element_sth = $self->prepare($constrained_element_sql) or die;

	##lock table 
	$self->dbc->do(qq{ LOCK TABLES constrained_element WRITE });

	foreach my $constrained_element_group (@$constrained_elements) {
		$mlssid_sth->execute();
		my $constrained_element_id = ($mlssid_sth->fetchrow_array() or
		($mlssid * 10000000000)) + 1;
		foreach my $constrained_element (@{$constrained_element_group}) {
			throw("$constrained_element is not a Bio::EnsEMBL::Compara::ConstrainedElement object")
			unless ($constrained_element->isa("Bio::EnsEMBL::Compara::ConstrainedElement"));
			$constrained_element_sth->execute(
				$constrained_element_id,
				$constrained_element->reference_dnafrag_id,
				$constrained_element->start,
				$constrained_element->end,
				$constrained_element->score,
				$mlssid,
				($constrained_element->p_value or undef),
				($constrained_element->taxonomic_level or undef)
			);
		}
	}
	## Unlock tables
	$self->dbc->do("UNLOCK TABLES");