my $self = shift;


  $self->debug("DanioRerio Specific: building assembly table - chunk/clone");
  #this is easy, there is simply one entire chunk for a given clone

  my $source = $self->source();
  my $target = $self->target();
  my $dbh    = $self->dbh();

  $dbh->do
    ("INSERT INTO $target.assembly (asm_seq_region_id, cmp_seq_region_id, " .
     "                         asm_start, asm_end, cmp_start, cmp_end, ori) " .
     "SELECT tcm.new_id, tcm.old_id, 1, sr.length, 1, sr.length, 1 " .
     "FROM $target.tmp_cln_map tcm, $target.seq_region sr " .
     "WHERE sr.seq_region_id = tcm.new_id");
}



# we need to override the transfer of the genes since danio genes can be on
# supercontigs and on chromosomes

  my $self = shift;

  #chromosomes are made of chunks
  $self->assembly_contig_chromosome();

  #supercontigs are made of chunks
  $self->assembly_contig_supercontig();

  #clones are made of chunks
  $self->assembly_contig_clone();

  return;

  my $self = shift;

  $self->debug("DanioRerio Specific: creating chromosome, supercontig, clone "
               . " and chunk coordinate systems");

  my $target = $self->target();
  my $dbh    = $self->dbh();

  my $ass_def = $self->get_default_assembly();

  my @coords =
    (["chromosome" , $ass_def, "default_version", 1],
     ["supercontig", $ass_def, "default_version", 2],
     ["clone"      , undef, "default_version", 3],
     ["chunk"      , undef, "default_version,sequence_level", 4]);

  my @assembly_mappings =  ("chromosome:$ass_def|chunk",
                            "clone|chunk",
                            "supercontig:$ass_def|chunk",
                            "chromosome:$ass_def|chunk|clone",
                            "supercontig:$ass_def|chunk|clone",
                            "chromosome:$ass_def|chunk|supercontig");

  $self->debug("Building coord_system table");

  my $sth = $dbh->prepare
    ("INSERT INTO $target.coord_system (name, version, attrib, rank) " .
     "VALUES (?,?,?,?)");

  my %coord_system_ids;

  foreach my $cs (@coords) {
    $sth->execute(@$cs);
    $coord_system_ids{$cs->[0]} = $sth->{'mysql_insertid'};
  }
  $sth->finish();

  $self->debug("Adding assembly.mapping entries to meta table");

  $sth = $dbh->prepare("INSERT INTO $target.meta(meta_key, meta_value) " .
                       "VALUES ('assembly.mapping', ?)");

  foreach my $mapping (@assembly_mappings) {
    $sth->execute($mapping);
  }

  $sth->finish();


  return;

  my $self = shift;

  my $source = $self->source();
  my $target = $self->target();
  my $dbh    = $self->dbh();


  #
  # Turn all of the contents of the contig table into 'chunks' and 
  # give them arbitrary names like chunk1, chunk2. Keep old internal
  # ids for conveneience.
  #

  $self->debug("DanioRerio Specific: creating chunk seq_regions");

  my $sth = $dbh->prepare
    ("INSERT INTO $target.seq_region (seq_region_id, name, coord_system_id, " .
     "                                length) ".
     "SELECT ctg.contig_id, concat('chunk', ctg.contig_id), " .
     "       cs.coord_system_id, ctg.length " .
     "FROM   $source.contig ctg, $target.coord_system cs " .
     "WHERE  cs.name = 'chunk'");

  $sth->execute();

  $sth->finish();

  my $insert_sth = $dbh->prepare
    ("INSERT INTO $target.seq_region (name, coord_system_id, length) " .
     "VALUES (?,?,?)");

  my $tmp_chr_insert_sth = $dbh->prepare
    ("INSERT INTO $target.tmp_chr_map (old_id, new_id) VALUES (?, ?)");

  my $tmp_supercontig_insert_sth = $dbh->prepare
    ("INSERT INTO $target.tmp_superctg_map (name, new_id) VALUES (?,?)");

  my $tmp_clone_insert_sth = $dbh->prepare
    ("INSERT INTO $target.tmp_cln_map (old_id, new_id) VALUES (?,?)");


  #
  # create a temporary table to hold the ids of all 'toplevel'
  # seq_regions.  Keep the old chromosome_id, and the new seq_region_id
  #
  $dbh->do
    ("CREATE TEMPORARY TABLE $target.tmp_toplevel_map " .
     "(old_id INT, new_id INT, INDEX new_idx(new_id), INDEX old_idx(old_id))");

  my $tmp_toplevel_insert_sth = $dbh->prepare
    ("INSERT INTO $target.tmp_toplevel_map (old_id, new_id) VALUES (?,?)");


  #
  # Turn real clones into clones
  #
  $self->debug("DanioRerio Specific: creating clone seq_regions");

  my $select_sth = $dbh->prepare
    ("SELECT ctg.contig_id, ctg.name, ctg.length " .
     "FROM   $source.contig ctg " .
     "WHERE  ctg.name not like 'ctg%' and ctg.name not like 'NA%'");

  my $cs_id = $self->get_coord_system_id('clone');

  $select_sth->execute();

  my ($old_id, $name, $length);
  $select_sth->bind_columns(\$old_id,\$ name,\$ length);

  while ($select_sth->fetch()) {
    #insert into seq_region table
    $insert_sth->execute($name, $cs_id, $length);
    #copy old/new mapping into temporary table
    $tmp_clone_insert_sth->execute($old_id, $insert_sth->{'mysql_insertid'});
  }

  $select_sth->finish();

  #
  # Turn real chromosomes into chromosomes
  #
  $self->debug("DanioRerio Specific: creating chromosome seq_regions");

  $select_sth = $dbh->prepare
    ("SELECT chr.chromosome_id, chr.name, chr.length " .
     "FROM   $source.chromosome chr " .
     "WHERE  length(chr.name) <= 2");

  $cs_id = $self->get_coord_system_id('chromosome');

  $select_sth->execute();

  $select_sth->bind_columns(\$old_id,\$ name,\$ length);

  my %chr_id_added;

  while ($select_sth->fetch()) {
    #insert into seq_region table
    $insert_sth->execute($name, $cs_id, $length);
    #copy old/new mapping into temporary table
    my $new_id = $insert_sth->{'mysql_insertid'};
    $tmp_chr_insert_sth->execute($old_id, $new_id);
    $tmp_toplevel_insert_sth->execute($old_id, $new_id);
    $chr_id_added{$old_id} = 1;
  }

  $select_sth->finish();

  #
  # Turn supercontigs into supercontigs
  #
  $self->debug("DanioRerio Specific: creating supercontig seq_regions");

  $select_sth = $dbh->prepare
    ("SELECT a.chromosome_id, a.superctg_name, " .
     "       MAX(a.chr_end) - MIN(a.chr_start) + 1 " .
     "FROM   $source.assembly a, $target.coord_system cs " .
     "GROUP BY a.superctg_name");

  $select_sth->execute();
  $select_sth->bind_columns(\$old_id,\$ name,\$ length);

  $cs_id = $self->get_coord_system_id('supercontig');

  while ($select_sth->fetch()) {
    #insert into seq_region table
    $insert_sth->execute($name, $cs_id, $length);
    #copy old/new mapping into temporary table
    my $new_id = $insert_sth->{'mysql_insertid'};
    $tmp_supercontig_insert_sth->execute($name,$new_id);

    if(!$chr_id_added{$old_id}) {
      $chr_id_added{$old_id} = 1;
      $tmp_toplevel_insert_sth->execute($old_id, $new_id);
    }
  }

  $select_sth->finish();
  $tmp_chr_insert_sth->finish();
  $tmp_supercontig_insert_sth->finish();
  $tmp_clone_insert_sth->finish();
  $tmp_toplevel_insert_sth->finish();
  $insert_sth->finish();

  my $self = shift;

  my $target = $self->target();
  my $dbh = $self->dbh();

  my $attrib_type_id = $self->add_attrib_code();

  $self->debug("DanioRerio Specific: Setting toplevel attributes of " .
               "seq_regions");

  my $sth = $dbh->prepare("DELETE FROM $target.seq_region_attrib " .
                          "WHERE attrib_type_id = ?");
  $sth->execute($attrib_type_id);
  $sth->finish();

  $sth = $dbh->prepare("INSERT INTO $target.seq_region_attrib " .
                       '            (seq_region_id, attrib_type_id, value) ' .
                       "SELECT toplev.new_id, $attrib_type_id, 1 " .
                       "FROM   $target.tmp_toplevel_map toplev ");

  $sth->execute();
  $sth->finish();
}



1;

  my $self = shift;

  my $target = $self->target();
  my $source = $self->source();
  my $dbh    = $self->dbh();

  #
  # Transfer the gene table
  #

  $self->debug("DanioRerio Specific: Building gene table");

  # first transfer genes on chromosomes

  $dbh->do
    ("INSERT INTO $target.gene " .
     "SELECT g.gene_id, g.type, g.analysis_id, toplev.new_id, " .
     "MIN(IF (a.contig_ori=1,(e.contig_start+a.chr_start-a.contig_start)," .
     "       (a.chr_start+a.contig_end-e.contig_end ))) as start, " .
     "MAX(IF (a.contig_ori=1,(e.contig_end+a.chr_start-a.contig_start), " .
     "       (a.chr_start+a.contig_end-e.contig_start))) as end, " .
     "       a.contig_ori*e.contig_strand as strand, " .
     "       g.display_xref_id " .
     "FROM   $source.transcript t, $source.exon_transcript et, " .
     "       $source.exon e, $source.assembly a, $source.gene g, " .
     "       $target.tmp_toplevel_map toplev " .
     "WHERE  t.transcript_id = et.transcript_id " .
     "AND    et.exon_id = e.exon_id " .
     "AND    e.contig_id = a.contig_id " .
     "AND    g.gene_id = t.gene_id " .
     "AND    a.chromosome_id = toplev.old_id " .
     "GROUP BY g.gene_id");


  #
  # Transfer the transcript table
  #

  $self->debug("DanioRerio Specific: Building transcript table ");
  $dbh->do
    ("INSERT INTO $target.transcript " .
     "SELECT t.transcript_id, t.gene_id, toplev.new_id, " .
     "MIN(IF (a.contig_ori=1,(e.contig_start+a.chr_start-a.contig_start)," .
     "       (a.chr_start+a.contig_end-e.contig_end ))) as start, " .
     "MAX(IF (a.contig_ori=1,(e.contig_end+a.chr_start-a.contig_start), " .
     "       (a.chr_start+a.contig_end-e.contig_start))) as end, " .
     "       a.contig_ori*e.contig_strand as strand, " .
     "       t.display_xref_id " .
     "FROM   $source.transcript t, $source.exon_transcript et, " .
     "       $source.exon e, $source.assembly a, " .
     "       $target.tmp_toplevel_map toplev " .
     "WHERE  t.transcript_id = et.transcript_id " .
     "AND    et.exon_id = e.exon_id " .
     "AND    e.contig_id = a.contig_id " .
     "AND    a.chromosome_id = toplev.old_id " .
     "GROUP BY t.transcript_id");

  #
  # Transfer the exon table
  #

  $self->debug("DanioRerio Specific: Building exon table ");

  $dbh->do
    ("INSERT INTO $target.exon " .
     "SELECT e.exon_id, toplev.new_id, " .
     "MIN(IF (a.contig_ori=1,(e.contig_start+a.chr_start-a.contig_start)," .
     "       (a.chr_start+a.contig_end-e.contig_end ))) as start, " .
     "MAX(IF (a.contig_ori=1,(e.contig_end+a.chr_start-a.contig_start), " .
     "       (a.chr_start+a.contig_end-e.contig_start))) as end, " .
     "       a.contig_ori*e.contig_strand as strand, " .
     "       e.phase, e.end_phase " .
     "FROM   $source.transcript t, $source.exon_transcript et, " .
     "       $source.exon e, $source.assembly a, $source.gene g, " .
     "       $target.tmp_toplevel_map toplev " .
     "WHERE  t.transcript_id = et.transcript_id " .
     "AND    et.exon_id = e.exon_id " .
     "AND    e.contig_id = a.contig_id " .
     "AND    g.gene_id = t.gene_id " .
     "AND    a.chromosome_id = toplev.old_id " .
     "GROUP BY e.exon_id");

  #
  # Transfer translation table
  #

  $self->debug("Building translation table");

  $dbh->do
    ("INSERT INTO $target.translation " .
     "SELECT tl.translation_id, ts.transcript_id, tl.seq_start, " .
     "       tl.start_exon_id, tl.seq_end, tl.end_exon_id " .
     "FROM $source.transcript ts, $source.translation tl " .
     "WHERE ts.translation_id = tl.translation_id");

  return;