my $msa = $registry->get_adaptor( 'Human', 'Core', 'MiscSet' );

  my $misc_set = $msa->fetch_by_dbID(1234);

  $misc_set = $msa->fetch_by_code('clone');

  my $self = shift;

  my $sth = $self->prepare
    ('SELECT misc_set_id, code, name, description, max_length FROM misc_set');

  $sth->execute();

  my ($dbID, $code, $name, $desc, $max_len);
  $sth->bind_columns(\$dbID,\$ code,\$ name,\$ desc,\$ max_len);

  my @all;

  while($sth->fetch()) {
    my $ms = Bio::EnsEMBL::MiscSet->new
      (-DBID     => $dbID,
       -ADAPTOR  => $self,
       -CODE     => $code,
       -NAME     =>  $name,
       -DESCRIPTION => $desc,
       -LONGEST_FEATURE => $max_len);

    $self->{'_id_cache'}->{$dbID} = $ms;
    $self->{'_code_cache'}->{lc($code)} = $ms;
    push @all, $ms;
  }

  $sth->finish();

  return\@ all;

  my $self = shift;
  my $code = shift;

  if(!$self->{'_code_cache'}->{lc($code)}) {
    # on cache miss, reread whole table and reload cache
    $self->fetch_all();
  }

  return $self->{'_code_cache'}->{lc($code)};

  my $self = shift;
  my $dbID = shift;

  if(!$self->{'_id_cache'}->{$dbID}) {
    # on a cache miss reread the whole table and reload the cache
    $self->fetch_all();
  }

  return $self->{'_id_cache'}->{$dbID};

  my $class = shift;

  my $self = $class->SUPER::new(@_);

  $self->{'_id_cache'} = {};
  $self->{'_code_cache'} = {};

  # cache the entire contents of the misc set table
  # the table is small and it removes the need to repeatedly query the
  # table or join to the table

  $self->fetch_all();

  return $self;

  my $self = shift;
  my @misc_sets = @_;

  # we use 'insert ignore' so that inserts can occur safely on the farm
  # otherwise 2 processes could try to insert at the same time and one
  # would fail

  my $sth = $self->prepare
    ("INSERT IGNORE INTO misc_set " .
     "SET code = ?, " .
     "    name = ?, " .
     "    description = ?, " .
     "    max_length  = ?");

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

 SET:
  foreach my $ms (@misc_sets) {
    if(!ref($ms) || !$ms->isa('Bio::EnsEMBL::MiscSet')) {
      throw("List of MiscSet arguments expected.");
    }

    if($ms->is_stored($db)) {
      warning("MiscSet [".$ms->dbID."] is already stored in this database.");
      next SET;
    }

    $sth->bind_param(1,$ms->code,SQL_VARCHAR);
    $sth->bind_param(2,$ms->name,SQL_VARCHAR);
    $sth->bind_param(3,$ms->description,SQL_LONGVARCHAR);
    $sth->bind_param(4,$ms->longest_feature,SQL_INTEGER);

    my $num_inserted = $sth->execute();

    my $dbID;

    if($num_inserted == 0) {
      # insert failed because set with this code already exists
      my $sth2 = $self->prepare("SELECT misc_set_id from misc_set " .
                                "WHERE code = ?");
      $sth2->bind_param(1,$ms->code,SQL_VARCHAR);
      $sth2->execute();

      if($sth2->rows() != 1) {
        throw("Could not retrieve or store MiscSet, code=[".$ms->code."]\n".
              "Wrong database user/permissions?");
      }

      ($dbID) = $sth2->fetchrow_array();
    } else {
      $dbID = $sth->{'mysql_insertid'};
    }

    $ms->dbID($dbID);
    $ms->adaptor($self);

    # update the internal caches
    $self->{'_id_cache'}->{$dbID} = $ms;
    $self->{'_code_cache'}->{lc($ms->code())} = $ms;
  }

  return;
}



1;

  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>.