## This is an insert for GBrowse gbrowse.conf for viewing
## annotations on the same Dros. species assembly from different
## GBrowse sources.  You need to have your own GBrowse with
## one of the genomes below.  Edit for each species gbrowse.conf
## -- Don Gilbert, Dec. 2005

html4 = sub {
  my $segment  = shift;
  my $settings = shift;
  return unless($segment);
  ##my @showgroup= qw(dg es pt); # drop/add as desired to show
  my @showgroup= qw(pt); # es
  my(%orgs,%baseurl,%label,%homepage);
  # key: pt = ponting group, es = eisen group, dg = drospege group
  # CHANGE EACH SPECIES gbrowse.conf :(
  # @orgs{qw(dg es pt)}= ("dana", "ananassae", "Dananassae");
  @orgs{qw(dg es pt)}= ("dere", "erecta", "Derecta");
  # @orgs{qw(dg es pt)}= ("dgri", "grimshawi", "Dgrimshawi");
  # @orgs{qw(dg es pt)}= ("dmel", "melanogaster", "Dmelanogaster");
  # @orgs{qw(dg es pt)}= ("dmoj", "mojavensis", "Dmojavensis");
  # @orgs{qw(dg es pt)}= ("dper", "persimilis", "Dpersimilis");
  # @orgs{qw(dg es pt)}= ("dpse", "pseudoobscura", "Dpseudoobscura");
  # @orgs{qw(dg es pt)}= ("dsec", "sechellia", "Dsechellia");
  # @orgs{qw(dg es pt)}= ("dsim", "simulans", "Dsimulans");
  # @orgs{qw(dg es pt)}= ("dvir", "virilis", "Dvirilis");
  # @orgs{qw(dg es pt)}= ("dwil", "willistoni", "Dwillistoni");
  # @orgs{qw(dg es pt)}= ("dyak", "yakuba", "Dyakuba");
  @baseurl{qw(dg es pt)}= (
    "http://insects.eugenes.org/species/cgi-bin/gbrowse_img/",
    "http://rana.lbl.gov/cgi-bin/gbrowse_img/",
    "http://wwwfgu.anat.ox.ac.uk:8080/cgi-bin/gbrowse_img/");
  @label{qw(dg es pt)}= (
    "DroSpeGe Annotations",
    "Eisen Annotations",
    "Ponting Annotations");
  @homepage{qw(dg es pt)}= (
    "<a href='http://insects.eugenes.org/species/'>DroSpeGe at Indiana</a>\n",
    "<a href='http://rana.lbl.gov/'>Eisen Group at LBL</a>\n",
    "<a href='http://www.mrcfgu.ox.ac.uk/ponting.htm'>Ponting Group at Oxford</a>\n");
  my $html= "<hr>";
  my $itop= "<table width=\"95%\" align=\"center\" border=0 ><tr><td><center>\n";
  my $ibot= "</center></td></tr></table><br/>\n";
  foreach my $group (@showgroup) {
    my $org = $orgs{$group};
    my $tog = CGI::Toggle::toggle_section( "<b>$label{$group}</b>", "INSERT_HERE" );
    my $imgcell= " &nbsp; &nbsp; use <b>Update Image</b> to view map ";
    my $width = $settings->{'width'} || 800;
    my $wid1  = $width+75;
       ## $width = $width+50 if ($group eq "es"); #? why; older gbrowse? ; no longer
    unless($tog =~ m/el_hidden/) {
      my $loc= $segment->seq_id() .":".$segment->start()."..".$segment->end();
      if($org =~ m/(dper|persimilis|dsec|sechellia)/i) {
        if ($group eq "dg") { $loc =~ s/super/scaffold/; } # dg preferred common name
        else { $loc =~ s/scaffold/super/; } # pt, es use broads scaffold name
      elsif($org =~ m/(pse)/i) {
        if ($group eq "pt") { $loc =~ s/^(.)/chr$1/; } # pt; add 'chr' to ID
        else {  $loc =~ s/^chr//;} # dg, es use flybase chr name
        }
      $org .= "/"; ## unless($group eq "es"); # for newer gbrowse/paths/
      my $url= $baseurl{$group}."$org\?name=$loc;e=1;width=$width";
         $url.=";t=Transcripts+OrthologyDmelanogaster" if ($group eq "pt");
         $url.=";t=tblastDM+blastndmel" if ($group eq "dg");
      my $imgs = "<iframe frameborder='0' width='$wid1' height='120'\n src='$url'></iframe>\n";
      $imgcell = $homepage{$group} . $itop . $imgs . $ibot;
      }
    $tog =~ s/INSERT_HERE/$imgcell/;
    $html .= $tog;
    }
  return $html;
  }