SitewiseOmegaAdaptor documentation.

sub fetch_all_by_ProteinTreeId {
    my ($self, $protein_tree_id) = @_;
    my $sitewise_dnds_values = [];

    my $sql = qq{
  	SELECT
	    sitewise_id,
	    aln_position,
	    node_id,
	    tree_node_id,
	    omega,
	    omega_lower,
	    omega_upper,
	    optimal,
	    threshold_on_branch_ds,
	    type
	FROM
	    sitewise_aln
	WHERE
	    node_id = ?
	};

    my $sth = $self->prepare($sql);
    $sth->execute($protein_tree_id);

    my $sitewise_dnds;
    while (my ($sitewise_id,$aln_position,$node_id,$tree_node_id,
               $omega,$omega_lower,$omega_upper,$optimal,
               $threshold_on_branch_ds,$type) = $sth->fetchrow_array()) {
	$sitewise_dnds = Bio::EnsEMBL::Compara::SitewiseOmega->new_fast(
				       {'adaptor' => $self,
					'_dbID' => $sitewise_id,
					'aln_position' => $aln_position,
					'node_id' => $node_id,
					'tree_node_id' => $tree_node_id,
					'omega' => $omega,
					'omega_lower' => $omega_lower,
					'omega_upper' => $omega_upper,
					'optimal' => $optimal,
					'threshold_on_branch_ds' => $threshold_on_branch_ds,
					'type' => $type});
	push(@$sitewise_dnds_values, $sitewise_dnds);
    }

    #sort into numerical order based on aln_position
    my @sorted_values = sort {$a->{aln_position} <=> $b->{aln_position}} @$sitewise_dnds_values;
    return\@ sorted_values;
}


1;
}