<commit_before>=head1 NAME

NestedSet - DESCRIPTION of Object

=head1 SYNOPSIS

=head1 DESCRIPTION

Abstract superclass to encapsulate the process of storing and manipulating a
nested-set representation tree.  Also implements a 'reference count' system 
based on the ObjectiveC retain/release design. 
Designed to be used as the Root class for all Compara 'proxy' classes 
(Member, GenomeDB, DnaFrag, NCBITaxon) to allow them to be made into sets and trees.

=head1 CONTACT

  Contact <NAME> on implementation detail: <EMAIL>
  Contact <NAME> on implementation/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::NestedSet;

use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::Argument;

use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);

use Bio::TreeIO;
use Bio::EnsEMBL::Compara::Graph::Node;
use Bio::EnsEMBL::Compara::Member;
our @ISA = qw(Bio::EnsEMBL::Compara::Graph::Node);

#################################################
# Factory methods
#################################################

=head2 copy<commit_msg>No need of importing Bio::EnsEMBL::Compara::Member<commit_after>=head1 NAME

NestedSet - DESCRIPTION of Object

=head1 SYNOPSIS

=head1 DESCRIPTION

Abstract superclass to encapsulate the process of storing and manipulating a
nested-set representation tree.  Also implements a 'reference count' system 
based on the ObjectiveC retain/release design. 
Designed to be used as the Root class for all Compara 'proxy' classes 
(Member, GenomeDB, DnaFrag, NCBITaxon) to allow them to be made into sets and trees.

=head1 CONTACT

  Contact <NAME> on implementation detail: <EMAIL>
  Contact <NAME> on implementation/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::NestedSet;

use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::Argument;

use Bio::EnsEMBL::Utils::Exception qw(deprecate throw);

use Bio::TreeIO;
use Bio::EnsEMBL::Compara::Graph::Node;
our @ISA = qw(Bio::EnsEMBL::Compara::Graph::Node);

#################################################
# Factory methods
#################################################

=head2 copy
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