$db   = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
    $asma = $db->get_AssemblyMapperAdaptor();
    $csa  = $db->get_CoordSystemAdaptor();

    my $chr_cs = $cs_adaptor->fetch_by_name( 'chromosome', 'NCBI33' );
    my $cln_cs = $cs_adaptor->fetch_by_name('clone');

    $asm_mapper = $map_adaptor->fetch_by_CoordSystems( $cs1, $cs2 );

    # Map to contig coordinate system from chromosomal
    @cln_coords =
      $asm_mapper->map( 'X', 1_000_000, 2_000_000, 1, $chr_cs );

    # Map to chromosome coordinate system from contig
    @chr_coords =
      $asm_mapper->map( 'AL30421.1', 100, 10000, -1, $cln_cs );

    # List contig names for a region of chromsome
    @cln_ids = $asm_mapper->list_ids( '13', 1_000_000, 1, $chr_cs );

    # List chromosome names for a contig region
    @chr_ids =
      $asm_mapper->list_ids( 'AL30421.1', 1, 1000, -1, $cln_cs );

  chromosome <-> contig
  contig     <-> clone

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

  my $self = shift;
  return $self->{'first_cs'};

  my $self = shift;
  return $self->{'last_cs'};

  my ($self, $contig_id, $start, $end, $strand) = @_;

  deprecate('Use map() instead.');

  #not sure if contig_id is seq_region_id or name...
  return $self->map($contig_id, $start, $end, $strand,
                    $self->contig_CoordSystem());

  my $self = shift;
  return $self->map(@_,1);

  my $self = shift;
  return $self->{'first_cs'};

  my $self = shift;
  return $self->{'first_last_mapper'};

  my $self = shift;
  return $self->{'first_mid_mapper'};

  my $self = shift;
  return $self->{'first_registry'};

  my $self = shift;
  $self->{'first_registry'}->flush();
  $self->{'last_registry'}->flush();

  $self->{'first_mid_mapper'}->flush();
  $self->{'last_mid_mapper'}->flush();
  $self->{'first_last_mapper'}->flush();

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

  deprecate('Use map() or list_ids() instead.');

  my $csa = $self->db->get_CoordSystemAdaptor();

  my $top_level = $csa->fetch_top_level();

  my $asma = $self->adaptor->fetch_by_CoordSystems($object->coord_system(),
                                                   $top_level);

  my @list = $asma->list_ids($object->seq_region(), $object->start(),
                             $object->end(), $object->coord_system());

  return (@list > 0);

  my $self = shift;
  return $self->{'last_cs'};

  my $self = shift;
  return $self->{'last_mid_mapper'};

  my $self = shift;
  return $self->{'last_registry'};
}





#
# Methods supplied to maintain polymorphism with AssemblyMapper
# there is no real assembled or component in the chained mapper, since the
# ordering is arbitrary and both ends might actually be assembled, but these
# methods provide convenient synonyms
#

  my ($self, $chr_name, $start, $end) = @_;

  deprecate('Use list_ids() instead.');

  return $self->list_ids($chr_name, $start, $end, 
                         $self->assembled_CoordSystem());
}



1;

  throw('Incorrect number of arguments.') if(@_ != 5);
  my($self, $frm_seq_region_name, $frm_start, $frm_end, $frm_cs) = @_;

  my $is_insert = ($frm_start == $frm_end + 1);

  #the minimum area we want to register if registration is necessary is
  #about 1MB. Break requested ranges into chunks of 1MB and then register
  #this larger region if we have a registry miss.

  #use bitwise shift for fast and easy integer multiplication and division
  my ($min_start, $min_end);

  if($is_insert) {
    $min_start = (($frm_end >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_start >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1;
  } else {
    $min_start = (($frm_start >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_end >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1;
  }

  my @tmp;
  push @tmp, $frm_seq_region_name;
  my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs,\@ tmp)}[0];

  if($frm_cs->equals($self->{'first_cs'})) {
    my $registry = $self->{'first_registry'};

    my $ranges;


    if($is_insert) {
      $ranges = $registry->check_and_register
        ($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
    } else {
      $ranges = $registry->check_and_register
        ($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
    }

    if(defined($ranges)) {
      $self->adaptor->register_chained($self,$FIRST,$seq_region_id,$ranges);
    }

    return map {$_->to()->id()}
      $self->first_last_mapper()->list_pairs($seq_region_id, $frm_start,
				  $frm_end, $FIRST);

  } elsif($frm_cs->equals($self->{'last_cs'})) {
    my $registry = $self->{'last_registry'};

    my $ranges;
    if($is_insert) {
      $ranges = $registry->check_and_register
        ($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
    } else {
      $ranges = $registry->check_and_register
        ($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
    }

    if(defined($ranges)) {
      $self->adaptor->register_chained($self,$LAST,$seq_region_id,$ranges);
    }

    return map {$_->from()->id()}
      $self->first_last_mapper()->list_pairs($seq_region_id, $frm_start,
				  $frm_end, $LAST);
  } else {
    throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
          " is neither the first nor the last coordinate system " .
          " of this ChainedAssemblyMapper");
  }

  throw('Incorrect number of arguments.') if(@_ != 5);
  my($self, $frm_seq_region, $frm_start, $frm_end, $frm_cs) = @_;

  #retrieve the seq_region names
  my @seq_regs =
    $self->list_ids($frm_seq_region,$frm_start,$frm_end,$frm_cs);

  #The seq_regions are from the 'to' coordinate system not the
  #from coordinate system we used to obtain them
  my $to_cs;
  if($frm_cs->equals($self->first_CoordSystem())) {
    $to_cs = $self->last_CoordSystem();
  } else {
    $to_cs = $self->first_CoordSystem();
  }

  #convert them to names
  return @{$self->adaptor()->seq_ids_to_regions(\@seq_regs)};

  throw('Incorrect number of arguments.') if(@_ < 6);

  my ($self, $frm_seq_region_name, $frm_start,
      $frm_end, $frm_strand, $frm_cs, $fastmap, $to_slice) = @_;

  my $mapper  = $self->{'first_last_mapper'};
  my $first_cs  = $self->{'first_cs'};
  my $last_cs  = $self->{'last_cs'};

  my $is_insert = ($frm_end + 1 == $frm_start);

  my $frm;
  my $registry;




  my @tmp;
  push @tmp, $frm_seq_region_name;
  my $seq_region_id = @{$self->adaptor()->seq_regions_to_ids($frm_cs,\@ tmp)}[0];

  #speed critical section:
  #try to do simple pointer equality comparisons of the coord system objects
  #first since this is likely to work most of the time and is much faster
  #than a function call

  if($frm_cs == $first_cs ||
     ($frm_cs != $last_cs && $frm_cs->equals($first_cs))) {
    $frm = $FIRST;
    $registry = $self->{'first_registry'};
  } elsif($frm_cs == $last_cs || $frm_cs->equals($last_cs)) {
    $frm = $LAST;
    $registry = $self->{'last_registry'};
  } else {
    throw("Coordinate system " . $frm_cs->name . " " . $frm_cs->version .
          " is neither the first nor the last coordinate system " .
          " of this ChainedAssemblyMapper");
  }

  #the minimum area we want to register if registration is necessary is
  #about 1MB. Break requested ranges into chunks of 1MB and then register
  #this larger region if we have a registry miss.

  #use bitwise shift for fast and easy integer multiplication and division
  my ($min_start, $min_end);

  if($is_insert) {
    $min_start = (($frm_end >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_start >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1 ;
  } else {
    $min_start = (($frm_start >> $CHUNKFACTOR) << $CHUNKFACTOR);
    $min_end   = ((($frm_end >> $CHUNKFACTOR) + 1) << $CHUNKFACTOR) - 1 ;
  }

  #get a list of ranges in the requested region that have not been registered,
  #and register them at the same

  my $ranges;

  if($is_insert) {
    $ranges = $registry->check_and_register($seq_region_id, $frm_end,
                                            $frm_start, $min_start, $min_end);
  } else {
    $ranges = $registry->check_and_register($seq_region_id, $frm_start,
                                            $frm_end, $min_start, $min_end);
  }

  if(defined($ranges)) {
    if( $self->size() > $self->{'max_pair_count'} ) {
      $self->flush();

      if($is_insert) {
        $ranges = $registry->check_and_register
          ($seq_region_id, $frm_end, $frm_start, $min_start, $min_end);
      } else {
        $ranges = $registry->check_and_register
          ($seq_region_id, $frm_start, $frm_end, $min_start, $min_end);
      }
    }
    $self->adaptor->register_chained($self,$frm,$seq_region_id,$ranges,$to_slice);
  }

  if($fastmap) {
    return $mapper->fastmap($seq_region_id, $frm_start, $frm_end,
                            $frm_strand, $frm);
  }

  return $mapper->map_coordinates($seq_region_id, $frm_start, $frm_end,
                                  $frm_strand, $frm);

  my ($self, $contig_id, $start, $end, $strand) = @_;

  deprecate('Use map() instead.');

  #not sure if contig_id is seq_region_id or name...
  return $self->map($contig_id, $start, $end, $strand,
                   $self->contig_CoordSystem());

  my ($self, $chr_name, $start, $end, $strand) = @_;

  deprecate('Use map() instead.');

  return $self->map($chr_name, $start, $end, $strand,
                    $self->assembled_CoordSystem());

  my $self = shift;
  return $self->first_last_mapper();

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

  my $self = shift;
  return $self->{'mid_cs'};

  my ($caller,$adaptor,@coord_systems) = @_;

  my $class = ref($caller) || $caller;

  my $self = {};
  bless $self, $class;

  $self->adaptor($adaptor);

  if(@coord_systems != 3) {
    throw('ChainedMapper can only map between 3 coordinate systems. ' .
          scalar(@coord_systems) . ' were provided');
  }

  $adaptor->cache_seq_ids_with_mult_assemblys();

  # Set the component, intermediate and assembled coordinate systems
  $self->{'first_cs'}   = $coord_systems[0];
  $self->{'mid_cs'}   = $coord_systems[1];
  $self->{'last_cs'}   = $coord_systems[2];

  #maps between first and intermediate coord systems
  $self->{'first_mid_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $MIDDLE);

  #maps between last and intermediate
  $self->{'last_mid_mapper'} = Bio::EnsEMBL::Mapper->new($LAST, $MIDDLE);

  #mapper that is actually used and is loaded by the mappings generated
  #by the other two mappers
  $self->{'first_last_mapper'} = Bio::EnsEMBL::Mapper->new($FIRST, $LAST,
                                                           $coord_systems[0],
                                                           $coord_systems[2]);

  #need registries to keep track of what regions are registered in source
  #and destination coordinate systems
  $self->{'first_registry'} = Bio::EnsEMBL::Mapper::RangeRegistry->new();
  $self->{'last_registry'} = Bio::EnsEMBL::Mapper::RangeRegistry->new();

  $self->{'max_pair_count'} = $DEFAULT_MAX_PAIR_COUNT;

  return $self;

  my $self = shift;
  $self->adaptor->register_all_chained($self);
  return;

  my $self = shift;
  return ( $self->{'first_last_mapper'}->{'pair_count'} +
           $self->{'last_mid_mapper'}->{'pair_count'} +
           $self->{'first_mid_mapper'}->{'pair_count'} );

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

  Args       : none
  Example    : $coordsys = $cam->lsst_registry();
  Description: return the Registry.
  Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
  Exceptions : none
  Caller     : internal
  Status     : Stable