<commit_before>=head1 NAME

NestedSetAdaptor - DESCRIPTION of Object

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 CONTACT

  Contact <NAME> on implemetation/design detail: <EMAIL>
  Contact <NAME> on EnsEMBL in general: <EMAIL>

=head1 APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

=cut

package Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor;

use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Compara::NestedSet;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;

our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);


###########################
# FETCH methods
###########################

sub fetch_node_by_node_id {
  my ($self, $node_id) = @_;

  my $table= $self->tables->[0]->[1];
  my $constraint = "WHERE $table.node_id = $node_id";
  my ($node) = @{$self->_generic_fetch($constraint)};
  return $node;
}

sub fetch_node_by_node_id_with_super {
  my ($self, $node_id, $super) = @_;

  my $table= $self->tables->[0]->[1];
  if ($super eq 'super') {
    $table = 'super_' . $table;
  }
  my $constraint = "WHERE $table.node_id = $node_id";
  my ($node) = @{$self->_generic_fetch($constraint)};
  return $node;
}


sub fetch_parent_for_node {
  my ($self, $node) = @_;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $table= $self->tables->[0]->[1];
  my $constraint = "WHERE $table.node_id = " . $node->_parent_id;
  my ($parent) = @{$self->_generic_fetch($constraint)};
  return $parent;
}


sub fetch_all_children_for_node {
  my ($self, $node) = @_;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $constraint = "WHERE parent_id = " . $node->node_id;
  my $kids = $self->_generic_fetch($constraint);
  foreach my $child (@{$kids}) { $node->add_child($child); }

  return $node;
}

sub fetch_all_leaves_indexed {
  my ($self, $node) = @_;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $table= $self->tables->[0]->[1];
  my $left_index = $node->left_index;
  my $right_index = $node->right_index;
  my $constraint = "WHERE ($table.right_index - $table.left_index) = 1 AND $table.left_index > $left_index AND $table.right_index < $right_index";
  my @leaves = @{$self->_generic_fetch($constraint)};

  return \@leaves;
}


sub fetch_subtree_under_node {
  my $self = shift;
  my $node = shift;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  unless ($node->left_index && $node->right_index) {
    warning("fetch_tree_at_node_id subroutine assumes that left and right index has been built and store in the database.\n This does not seem to be the case for node_id=".$node->node_id.". Returning node.\n");
    return $node;
  }

  my $table = $self->tables->[0]->[0];
  my $alias = $self->tables->[0]->[1];

  my $constraint = ", $table AS root_node WHERE $alias.left_index 
                         BETWEEN root_node.left_index AND root_node.right_index
                    AND root_node.node_id=". $node->node_id;

  my $all_nodes = $self->_generic_fetch($constraint);
  push @{$all_nodes}, $node;
  $self->_build_tree_from_nodes($all_nodes);
  return $node;
}


sub fetch_tree_at_node_id {
  my $self = shift;
  my $node_id = shift;

  my $node = $self->fetch_node_by_node_id($node_id);

  unless ($node->left_index && $node->right_index) {
    warning("fetch_tree_at_node_id subroutine assumes that left and right index has been built and store in the database.\n This does not seem to be the case for node_id=$node_id. Using fetch_node_by_node_id instead, and returning node.\n");
    return $node;
  }

  my $table = $self->tables->[0]->[0];
  my $alias = $self->tables->[0]->[1];

  my $constraint = ", $table AS root_node WHERE $alias.left_index 
                         BETWEEN root_node.left_index AND root_node.right_index
                    AND root_node.node_id=". $node_id;

  my $all_nodes = $self->_generic_fetch($constraint);
  my $root = $self->_build_tree_from_nodes($all_nodes);
  return $root;
}


sub fetch_all_roots {
  my $self = shift;

  my $constraint = "WHERE root_id = 0";
  return $self->_generic_fetch($constraint);
}


sub fetch_subroot_by_left_right_index {
  my ($self,$node) = @_;

  unless ($node->left_index && $node->right_index) {
    warning("fetch_subroot_by_left_right_index subroutine assumes that left and right index has been built and store in the database.\n This does not seem to be the case.\n");
  }
  my $left_index = $node->left_index;
  my $right_index = $node->right_index;

  my $constraint = "WHERE parent_id = root_id";
  $constraint .= " AND left_index<=$left_index";
  $constraint .= " AND right_index>=$right_index";
  return $self->_generic_fetch($constraint)->[0];
}


=head2 fetch_root_by_node

  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $node
  Example    : $root = $nested_set_adaptor->fetch_root_by_node($node);
  Description: Returns the root of the tree for this node
               with links to all the intermediate nodes. Sister nodes
               are not included in the result. Use fetch_node_by_node_id()
               method to get the whole tree (loaded on demand)
  Returntype : Bio::EnsEMBL::Compara::NestedSet
  Exceptions : thrown if $node is not defined
  Status     : At-risk
  Caller     : $nested_set->root

=cut

sub fetch_root_by_node {
  my ($self, $node) = @_;

  unless(UNIVERSAL::isa($node, 'Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $alias = $self->tables->[0]->[1];

  my $left_index = $node->left_index;
  my $right_index = $node->right_index;

  my $constraint = "WHERE $alias.left_index <= $left_index AND $alias.right_index >= $right_index";
  my $nodes = $self->_generic_fetch($constraint);
  my $root = $self->_build_tree_from_nodes($nodes);

  return $root;
}



###########################
# STORE methods
###########################

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

  unless(UNIVERSAL::isa($node, 'Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $parent_id = 0;
  if($node->parent) {
    $parent_id = $node->parent->node_id ;
  }
  my $root_id = $node->root->node_id;

 my $table= $self->tables->[0]->[0];
  my $sql = "UPDATE $table SET ".
               "parent_id=$parent_id".
               ",root_id=$root_id".
               ",left_index=" . $node->left_index .
               ",right_index=" . $node->right_index .
               ",distance_to_parent=" . $node->distance_to_parent .
             " WHERE $table.node_id=". $node->node_id;

  $self->dbc->do($sql);
}


sub update_subtree {
  my $self = shift;
  my $node = shift;

  $self->update($node);

  foreach my $child (@{$node->children}) {
    $self->update_subtree($child);
  }
}

=head2 store

  Arg [1]    :
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :

=cut

sub store {
  my ($self, $node) = @_;

  throw("must subclass and provide correct table names");

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $sth = $self->prepare("INSERT INTO tree_node (parent_id, name) VALUES (?,?)");
  if(defined($node->parent_node)) {
    $sth->execute($node->parent_node->dbID, $node->name);
  } else {
    $sth->execute(0, $node->name);
  }
  $node->dbID( $sth->{'mysql_insertid'} );
  $node->adaptor($self);
  $sth->finish;

  #
  #now recursively do all the children
  #
  my $children = $node->children_nodes;
  foreach my $child_node (@$children) {  
    $self->store($child_node);
  }

  return $node->dbID;
}


sub sync_tree_leftright_index {
  my $self= shift;
  my $tree_root = shift;

  my $table = $self->tables->[0]->[0];
  
  my $dc = $self->dbc->disconnect_when_inactive;
  $self->dbc->disconnect_when_inactive(0);

  $self->dbc->do("LOCK TABLES $table WRITE");

  my $sql = "SELECT max(right_index) FROM $table;";
  my $sth = $self->dbc->prepare($sql);
  $sth->execute();
  my ($max_counter) = $sth->fetchrow_array();
  $sth->finish;
  
  $tree_root->build_leftright_indexing($max_counter+1);

  $sql = "UPDATE $table SET ".
            "left_index=" . $tree_root->left_index .
            ",right_index=" . $tree_root->right_index .
         " WHERE $table.node_id=". $tree_root->node_id;
  $self->dbc->do($sql);

  $self->dbc->do("UNLOCK TABLES");
  $self->dbc->disconnect_when_inactive($dc);

  return undef;
}


##################################
#
# Database related methods, sublcass overrides/inherits
#
##################################

sub tables {
  my $self = shift;
  throw("must subclass and provide correct table names");
}

sub columns {
  my $self = shift;
  throw("must subclass and provide correct column names");
}

sub left_join_clause {
  return "";
}

sub default_where_clause {
  my $self = shift;
  return '';
}

sub final_clause {
  my $self = shift;
  $self->{'final_clause'} = shift if(@_);
  return $self->{'final_clause'};
}


sub create_instance_from_rowhash {
  my $self = shift;
  my $rowhash = shift;

  #my $node = $self->cache_fetch_by_id($rowhash->{'node_id'});
  #return $node if($node);
  
  my $node = new Bio::EnsEMBL::Compara::NestedSet;
  $self->init_instance_from_rowhash($node, $rowhash);
  
  #$self->cache_add_object($node);

  return $node;
}


sub init_instance_from_rowhash {
  my $self = shift;
  my $node = shift;
  my $rowhash = shift;

  $node->adaptor($self);
  $node->node_id               ($rowhash->{'node_id'});
  $node->_parent_id            ($rowhash->{'parent_id'});
  $node->_root_id              ($rowhash->{'root_id'});
  $node->left_index            ($rowhash->{'left_index'});
  $node->right_index           ($rowhash->{'right_index'});
  $node->distance_to_parent    ($rowhash->{'distance_to_parent'});
  
  return $node;
}


##################################
#
# INTERNAL METHODS
#
##################################

sub new {
  my $class = shift;

  my $self = $class->SUPER::new(@_);
  
  $self->{'_node_cache'} = [];
  return $self;
}

sub DESTROY {
  my $self = shift;
  $self->clear_cache;
  $self->SUPER::DESTROY if $self->can("SUPER::DESTROY");
}

sub cache_fetch_by_id {
  my $self = shift;
  my $node_id = shift;
  
  for(my $index=0; $index<scalar(@{$self->{'_node_cache'}}); $index++) {
    my $node = $self->{'_node_cache'}->[$index];
    if($node->node_id == $node_id) {
      splice(@{$self->{'_node_cache'}}, $index, 1); #removes from list
      unshift @{$self->{'_node_cache'}}, $node; #put at front of list 
      return $node;
    }
  }
  return undef;
}


sub cache_add_object
{
  my $self = shift;
  my $node = shift;

  unshift @{$self->{'_node_cache'}}, $node; #put at front of list 
  while(scalar(@{$self->{'_node_cache'}}) > 3000) {
    my $old = pop @{$self->{'_node_cache'}};
    #print("shrinking cache : "); $old->print_node;
  }
  return undef;
}

sub clear_cache {
  my $self = shift;
  
  $self->{'_node_cache'} = [];
  return undef;
}

sub _build_tree_from_nodes {
  my $self = shift;
  my $node_list = shift;

  #first hash all the nodes by id for fast access
  my %node_hash;
  foreach my $node (@{$node_list}) {
    $node->no_autoload_children;
    $node_hash{$node->node_id} = $node;
  }
  
  #next add children to their parents
  my $root = undef;
  foreach my $node (@{$node_list}) {
    my $parent = $node_hash{$node->_parent_id};
    if($parent) { $parent->add_child($node); } 
    else { $root = $node; }
  }
  return $root;
}


###################################
#
# _generic_fetch system
#
#####################################

=head2 _generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('WHERE contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch

=cut
  
sub _generic_fetch {
  my ($self, $constraint, $join, $final_clause) = @_;

  my $sql = $self->_construct_sql_query($constraint, $join, $final_clause);

  #print STDERR $sql,"\n";
  my $node_list = [];

  my $sth = $self->prepare($sql);
  $sth->execute;
  $node_list = $self->_objs_from_sth($sth);
  $sth->finish;

  return $node_list;
}

sub _construct_sql_query {
  my ($self, $constraint, $join, $final_clause) = @_;

  my @tables = @{$self->tables};
  my $columns = join(', ', @{$self->columns()});
  
  my $default_where = $self->default_where_clause;
  if($default_where) {
    if($constraint) { 
      $constraint .= " AND $default_where ";
    } else {
      $constraint = " WHERE $default_where ";
    }
  }

  if ($join) {
    foreach my $single_join (@{$join}) {
      my ($tablename, $condition, $extracolumns) = @{$single_join};
      if ($tablename && $condition) {
        push @tables, $tablename;
        
        if($constraint) {
          $constraint .= " AND $condition";
        } else {
          $constraint = " WHERE $condition";
        }
      } 
      if ($extracolumns) {
        $columns .= ", " . join(', ', @{$extracolumns});
      }
    }
  }
      
  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql = "SELECT $columns FROM $tablenames";
  $sql .= " ". $self->left_join_clause;
  $sql .= " $constraint" if($constraint);

  #append additional clauses which may have been defined
  if (!$final_clause) {
    $final_clause = $self->final_clause;
  }
  $sql .= " $final_clause" if($final_clause);

  return $sql;
}


1;
<commit_msg>t.root_id needed in fetch_all_roots method<commit_after>=head1 NAME

NestedSetAdaptor - DESCRIPTION of Object

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 CONTACT

  Contact <NAME> on implemetation/design detail: <EMAIL>
  Contact <NAME> on EnsEMBL in general: <EMAIL>

=head1 APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

=cut

package Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor;

use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
use Bio::EnsEMBL::Compara::NestedSet;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;

our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);


###########################
# FETCH methods
###########################

sub fetch_node_by_node_id {
  my ($self, $node_id) = @_;

  my $table= $self->tables->[0]->[1];
  my $constraint = "WHERE $table.node_id = $node_id";
  my ($node) = @{$self->_generic_fetch($constraint)};
  return $node;
}

sub fetch_node_by_node_id_with_super {
  my ($self, $node_id, $super) = @_;

  my $table= $self->tables->[0]->[1];
  if ($super eq 'super') {
    $table = 'super_' . $table;
  }
  my $constraint = "WHERE $table.node_id = $node_id";
  my ($node) = @{$self->_generic_fetch($constraint)};
  return $node;
}


sub fetch_parent_for_node {
  my ($self, $node) = @_;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $table= $self->tables->[0]->[1];
  my $constraint = "WHERE $table.node_id = " . $node->_parent_id;
  my ($parent) = @{$self->_generic_fetch($constraint)};
  return $parent;
}


sub fetch_all_children_for_node {
  my ($self, $node) = @_;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $constraint = "WHERE parent_id = " . $node->node_id;
  my $kids = $self->_generic_fetch($constraint);
  foreach my $child (@{$kids}) { $node->add_child($child); }

  return $node;
}

sub fetch_all_leaves_indexed {
  my ($self, $node) = @_;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $table= $self->tables->[0]->[1];
  my $left_index = $node->left_index;
  my $right_index = $node->right_index;
  my $constraint = "WHERE ($table.right_index - $table.left_index) = 1 AND $table.left_index > $left_index AND $table.right_index < $right_index";
  my @leaves = @{$self->_generic_fetch($constraint)};

  return \@leaves;
}


sub fetch_subtree_under_node {
  my $self = shift;
  my $node = shift;

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  unless ($node->left_index && $node->right_index) {
    warning("fetch_tree_at_node_id subroutine assumes that left and right index has been built and store in the database.\n This does not seem to be the case for node_id=".$node->node_id.". Returning node.\n");
    return $node;
  }

  my $table = $self->tables->[0]->[0];
  my $alias = $self->tables->[0]->[1];

  my $constraint = ", $table AS root_node WHERE $alias.left_index 
                         BETWEEN root_node.left_index AND root_node.right_index
                    AND root_node.node_id=". $node->node_id;

  my $all_nodes = $self->_generic_fetch($constraint);
  push @{$all_nodes}, $node;
  $self->_build_tree_from_nodes($all_nodes);
  return $node;
}


sub fetch_tree_at_node_id {
  my $self = shift;
  my $node_id = shift;

  my $node = $self->fetch_node_by_node_id($node_id);

  unless ($node->left_index && $node->right_index) {
    warning("fetch_tree_at_node_id subroutine assumes that left and right index has been built and store in the database.\n This does not seem to be the case for node_id=$node_id. Using fetch_node_by_node_id instead, and returning node.\n");
    return $node;
  }

  my $table = $self->tables->[0]->[0];
  my $alias = $self->tables->[0]->[1];

  my $constraint = ", $table AS root_node WHERE $alias.left_index 
                         BETWEEN root_node.left_index AND root_node.right_index
                    AND root_node.node_id=". $node_id;

  my $all_nodes = $self->_generic_fetch($constraint);
  my $root = $self->_build_tree_from_nodes($all_nodes);
  return $root;
}


sub fetch_all_roots {
  my $self = shift;

  my $constraint = "t.WHERE root_id = 0";
  return $self->_generic_fetch($constraint);
}


sub fetch_subroot_by_left_right_index {
  my ($self,$node) = @_;

  unless ($node->left_index && $node->right_index) {
    warning("fetch_subroot_by_left_right_index subroutine assumes that left and right index has been built and store in the database.\n This does not seem to be the case.\n");
  }
  my $left_index = $node->left_index;
  my $right_index = $node->right_index;

  my $constraint = "WHERE parent_id = root_id";
  $constraint .= " AND left_index<=$left_index";
  $constraint .= " AND right_index>=$right_index";
  return $self->_generic_fetch($constraint)->[0];
}


=head2 fetch_root_by_node

  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $node
  Example    : $root = $nested_set_adaptor->fetch_root_by_node($node);
  Description: Returns the root of the tree for this node
               with links to all the intermediate nodes. Sister nodes
               are not included in the result. Use fetch_node_by_node_id()
               method to get the whole tree (loaded on demand)
  Returntype : Bio::EnsEMBL::Compara::NestedSet
  Exceptions : thrown if $node is not defined
  Status     : At-risk
  Caller     : $nested_set->root

=cut

sub fetch_root_by_node {
  my ($self, $node) = @_;

  unless(UNIVERSAL::isa($node, 'Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $alias = $self->tables->[0]->[1];

  my $left_index = $node->left_index;
  my $right_index = $node->right_index;

  my $constraint = "WHERE $alias.left_index <= $left_index AND $alias.right_index >= $right_index";
  my $nodes = $self->_generic_fetch($constraint);
  my $root = $self->_build_tree_from_nodes($nodes);

  return $root;
}



###########################
# STORE methods
###########################

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

  unless(UNIVERSAL::isa($node, 'Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $parent_id = 0;
  if($node->parent) {
    $parent_id = $node->parent->node_id ;
  }
  my $root_id = $node->root->node_id;

 my $table= $self->tables->[0]->[0];
  my $sql = "UPDATE $table SET ".
               "parent_id=$parent_id".
               ",root_id=$root_id".
               ",left_index=" . $node->left_index .
               ",right_index=" . $node->right_index .
               ",distance_to_parent=" . $node->distance_to_parent .
             " WHERE $table.node_id=". $node->node_id;

  $self->dbc->do($sql);
}


sub update_subtree {
  my $self = shift;
  my $node = shift;

  $self->update($node);

  foreach my $child (@{$node->children}) {
    $self->update_subtree($child);
  }
}

=head2 store

  Arg [1]    :
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :

=cut

sub store {
  my ($self, $node) = @_;

  throw("must subclass and provide correct table names");

  unless($node->isa('Bio::EnsEMBL::Compara::NestedSet')) {
    throw("set arg must be a [Bio::EnsEMBL::Compara::NestedSet] not a $node");
  }

  my $sth = $self->prepare("INSERT INTO tree_node (parent_id, name) VALUES (?,?)");
  if(defined($node->parent_node)) {
    $sth->execute($node->parent_node->dbID, $node->name);
  } else {
    $sth->execute(0, $node->name);
  }
  $node->dbID( $sth->{'mysql_insertid'} );
  $node->adaptor($self);
  $sth->finish;

  #
  #now recursively do all the children
  #
  my $children = $node->children_nodes;
  foreach my $child_node (@$children) {  
    $self->store($child_node);
  }

  return $node->dbID;
}


sub sync_tree_leftright_index {
  my $self= shift;
  my $tree_root = shift;

  my $table = $self->tables->[0]->[0];
  
  my $dc = $self->dbc->disconnect_when_inactive;
  $self->dbc->disconnect_when_inactive(0);

  $self->dbc->do("LOCK TABLES $table WRITE");

  my $sql = "SELECT max(right_index) FROM $table;";
  my $sth = $self->dbc->prepare($sql);
  $sth->execute();
  my ($max_counter) = $sth->fetchrow_array();
  $sth->finish;
  
  $tree_root->build_leftright_indexing($max_counter+1);

  $sql = "UPDATE $table SET ".
            "left_index=" . $tree_root->left_index .
            ",right_index=" . $tree_root->right_index .
         " WHERE $table.node_id=". $tree_root->node_id;
  $self->dbc->do($sql);

  $self->dbc->do("UNLOCK TABLES");
  $self->dbc->disconnect_when_inactive($dc);

  return undef;
}


##################################
#
# Database related methods, sublcass overrides/inherits
#
##################################

sub tables {
  my $self = shift;
  throw("must subclass and provide correct table names");
}

sub columns {
  my $self = shift;
  throw("must subclass and provide correct column names");
}

sub left_join_clause {
  return "";
}

sub default_where_clause {
  my $self = shift;
  return '';
}

sub final_clause {
  my $self = shift;
  $self->{'final_clause'} = shift if(@_);
  return $self->{'final_clause'};
}


sub create_instance_from_rowhash {
  my $self = shift;
  my $rowhash = shift;

  #my $node = $self->cache_fetch_by_id($rowhash->{'node_id'});
  #return $node if($node);
  
  my $node = new Bio::EnsEMBL::Compara::NestedSet;
  $self->init_instance_from_rowhash($node, $rowhash);
  
  #$self->cache_add_object($node);

  return $node;
}


sub init_instance_from_rowhash {
  my $self = shift;
  my $node = shift;
  my $rowhash = shift;

  $node->adaptor($self);
  $node->node_id               ($rowhash->{'node_id'});
  $node->_parent_id            ($rowhash->{'parent_id'});
  $node->_root_id              ($rowhash->{'root_id'});
  $node->left_index            ($rowhash->{'left_index'});
  $node->right_index           ($rowhash->{'right_index'});
  $node->distance_to_parent    ($rowhash->{'distance_to_parent'});
  
  return $node;
}


##################################
#
# INTERNAL METHODS
#
##################################

sub new {
  my $class = shift;

  my $self = $class->SUPER::new(@_);
  
  $self->{'_node_cache'} = [];
  return $self;
}

sub DESTROY {
  my $self = shift;
  $self->clear_cache;
  $self->SUPER::DESTROY if $self->can("SUPER::DESTROY");
}

sub cache_fetch_by_id {
  my $self = shift;
  my $node_id = shift;
  
  for(my $index=0; $index<scalar(@{$self->{'_node_cache'}}); $index++) {
    my $node = $self->{'_node_cache'}->[$index];
    if($node->node_id == $node_id) {
      splice(@{$self->{'_node_cache'}}, $index, 1); #removes from list
      unshift @{$self->{'_node_cache'}}, $node; #put at front of list 
      return $node;
    }
  }
  return undef;
}


sub cache_add_object
{
  my $self = shift;
  my $node = shift;

  unshift @{$self->{'_node_cache'}}, $node; #put at front of list 
  while(scalar(@{$self->{'_node_cache'}}) > 3000) {
    my $old = pop @{$self->{'_node_cache'}};
    #print("shrinking cache : "); $old->print_node;
  }
  return undef;
}

sub clear_cache {
  my $self = shift;
  
  $self->{'_node_cache'} = [];
  return undef;
}

sub _build_tree_from_nodes {
  my $self = shift;
  my $node_list = shift;

  #first hash all the nodes by id for fast access
  my %node_hash;
  foreach my $node (@{$node_list}) {
    $node->no_autoload_children;
    $node_hash{$node->node_id} = $node;
  }
  
  #next add children to their parents
  my $root = undef;
  foreach my $node (@{$node_list}) {
    my $parent = $node_hash{$node->_parent_id};
    if($parent) { $parent->add_child($node); } 
    else { $root = $node; }
  }
  return $root;
}


###################################
#
# _generic_fetch system
#
#####################################

=head2 _generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('WHERE contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch

=cut
  
sub _generic_fetch {
  my ($self, $constraint, $join, $final_clause) = @_;

  my $sql = $self->_construct_sql_query($constraint, $join, $final_clause);

  #print STDERR $sql,"\n";
  my $node_list = [];

  my $sth = $self->prepare($sql);
  $sth->execute;
  $node_list = $self->_objs_from_sth($sth);
  $sth->finish;

  return $node_list;
}

sub _construct_sql_query {
  my ($self, $constraint, $join, $final_clause) = @_;

  my @tables = @{$self->tables};
  my $columns = join(', ', @{$self->columns()});
  
  my $default_where = $self->default_where_clause;
  if($default_where) {
    if($constraint) { 
      $constraint .= " AND $default_where ";
    } else {
      $constraint = " WHERE $default_where ";
    }
  }

  if ($join) {
    foreach my $single_join (@{$join}) {
      my ($tablename, $condition, $extracolumns) = @{$single_join};
      if ($tablename && $condition) {
        push @tables, $tablename;
        
        if($constraint) {
          $constraint .= " AND $condition";
        } else {
          $constraint = " WHERE $condition";
        }
      } 
      if ($extracolumns) {
        $columns .= ", " . join(', ', @{$extracolumns});
      }
    }
  }
      
  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql = "SELECT $columns FROM $tablenames";
  $sql .= " ". $self->left_join_clause;
  $sql .= " $constraint" if($constraint);

  #append additional clauses which may have been defined
  if (!$final_clause) {
    $final_clause = $self->final_clause;
  }
  $sql .= " $final_clause" if($final_clause);

  return $sql;
}


1;

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