#!C:\Perl\bin\Perl.exe -w
#!/usr/bin/perl -w


package EBI::HtmlHelper;
require Exporter;

@ISA = qw(Exporter) ;
@EXPORT = qw(getServicesHelpMenuItems printTop printTopWithServicesHelpMenu top topWithMenu topWithServicesHelpMenu printTopWithMenu printBottom printBot bottom bot  getServicesHelpMenuItemsNew printTopNew printTopWithServicesHelpMenuNew topNew topWithMenuNew topWithServicesHelpMenuNew printTopWithMenuNew printBottomNew printBotNew bottomNew botNew buildicon) ;

#use strict;

my $Helper_firstWord = "EBI";
my $Helper_intTags =
[
  ["seqdb/introduction", "http://www3.ebi.ac.uk/internal/seqdb/introduction/", "INTRODUCTION"],
  ["seqdb/organisation", "http://www3.ebi.ac.uk/internal/seqdb/organisation/", "GROUP ORGANISATION"],
  ["seqdb/projects", "http://www3.ebi.ac.uk/internal/seqdb/projects/", "GROUP PROJECTS"],
  ["seqdb/curators", "http://www3.ebi.ac.uk/internal/seqdb/curators/", "CURATION &amp; SUBMISSION"],
  ["seqdb/computing", "http://www3.ebi.ac.uk/internal/seqdb/computing/", "COMPUTING PROCEDURES"],
  ["seqdb/release", "http://www3.ebi.ac.uk/internal/seqdb/release/", "RELEASE &amp; STATUS"]
];

my $Helper_leftMenuItems = [];
my $Helper_extTags =
[
  ["SHOULDNTMATCHTHISEVER!",  "/", "/Information/", "images/home.gif",  "images/home_o.gif", "EBI Home Page", "0"],
  ["aboutebi",  "/Information/",  "/Information/", "images/about.gif",     "images/about_o.gif", "About the EBI", "1"],
  ["groups",    "/Groups/",       "/Groups/",      "images/research.gif",  "images/research_o.gif", "Groups at the EBI", "2"],
  ["services",  "/services/",     "/services/",   "images/services.gif",   "images/services_o.gif", "EBI Services", "3"],
  ["tools",     "/Tools/",        "/services/",   "images/utilities.gif",  "images/utilities_o.gif", "EBI Toolbox", "4"],
  ["databases", "/Databases/",     "/services/",   "images/databases.gif",  "images/databases_o.gif", "EBI Databases", "5"],
  ["downloads", "/FTP/", "/services/", "images/downloads.gif", "images/downloads_o.gif", "EBI Downloads", "6"],
  ["submissions", "/Submissions/", "/services/",   "images/submissions.gif","images/submissions_o.gif", "EBI Submissions", "7"]
];

my $yes = "yes";
my $no = "no";
my $stretchy = $no;
# set to yes for nadeen/genomes - allows for huge page width

my $Helper_pageTitle = "EBI Servlet";
my $Helper_topMenuItem = "services";
my $Helper_headerScript = "";
my $Helper_unLoadMethods = "";
my $Helper_loadMethods = "";
my $Helper_lastWords = "Servlet";


my $rightContents="";

my $icon_title = "";
my $icon_image_url = "";
my $icon_image_path = "";
my $icon_subtitle = "";
my $icon_text = "";
my $icon = "";


my $Helper_intBot = "<td width=\"40%\" valign=\"top\"> <!-- TemplateBeginEditable name=\"rightnav\" --><!-- TemplateEndEditable --></td>\n"
. "</table>\n"
. "</body>\n"
. "<!-- InstanceEnd --></html>";



my $Helper_intBodyStart = "<body  bgcolor=\"#ffffff\" marginwidth=\"0\" marginheight=\"0\" leftmargin=\"0\" topmargin=\"0\" rightmargin=\"0\">\n"
. "<table width=\"100%\" border=\"0\" cellpadding=\"0\" cellspacing=\"0\" class=\"menubody\">\n"
. "  <form action=\"/cgi-bin/search/internal.cgi\" method=\"get\" name=\"search\">\n"
. "    <tr>\n"
. "      <td width=\"100%\" align=\"center\"><a href=\"http://www3.ebi.ac.uk/internal/seqdb/index.html\" class=\"headlink\">Home</a><span class=\"headtext\"> | </span><a href=\"http://www3.ebi.ac.uk/internal/seqdb/organisation/contact/index.html\" class=\"headlink\">Contact</a><span class=\"headtext\"> | </span><a href=\"http://www3.ebi.ac.uk/internal/seqdb/site/index.html\" class=\"headlink\">Site</a><span class=\"headtext\"> | <a href=\"#\" class=\"headlink\"></a></span><a href=\"http://www3.ebi.ac.uk/internal/seqdb/help/index.html\" class=\"headlink\">Help</a> </td>\n"
. "      <td valign=\"bottom\" rowspan=\"2\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"10\"></td>\n"
. "      <input type=\"hidden\" name=\"w\" value=\"1\" />\n"
. "      <input type=\"hidden\" name=\"sort\" value=\"Scores\" />\n"
. "      <input type=\"hidden\" name=\"display\" value=\"20\" />\n"
. "      <input type=\"hidden\" name=\"b\" value=\"1\" />\n"
. "      <input type=\"hidden\" name=\"t\" value=\"1\" />\n"
. "      <input type=\"hidden\" name=\"default\" value=\"1\" />\n"
. "      <input type=\"hidden\" name=\"d\" value=\"1\" />\n"
. "      <input type=\"hidden\" name=\"k\" value=\"1\" />\n"
. "      <input type=\"hidden\" name=\"showm\" value=\"5\" />\n"
. "      <td  align=\"center\" valign=\"middle\" nowrap=\"nowrap\" class=\"headtext\"><img alt=\"Image\" src=\"/services/images/trans.gif\" height=\"7\" width=\"4\"  border=\"0\" />Site search<img alt=\"Image\" src=\"/services/images/trans.gif\" height=\"7\" width=\"4\"  border=\"0\" /></td>\n"
. "      <td  align=\"center\" valign=\"middle\"><span class=\"small\"><input type=\"text\" name=\"terms\" value=\"\" onFocus=\"select(this);\"  maxlength=\"50\" size=\"15\" class=\"headtext\"></span></td>\n"
. "      <td  align=\"center\" valign=\"middle\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"10\"></td>\n"
. "      <td  align=\"center\" valign=\"middle\"><span class=\"small\"><input type=\"submit\" value=\"Go\" class=\"headtext\"></span></td>\n"
. "      <td  align=\"center\" valign=\"middle\" ><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"10\"></td>\n"
. "    </tr>\n"
. "  </form>\n"
. "</table>\n"
. "<table width=\"100%\" height=\"51\" border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n"
. " <tr>\n"
. "    <td width=\"129\" height=\"51\" align=\"left\"><a href=\"http://www3.ebi.ac.uk/internal/seqdb/index.html\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/bann_left.gif\" width=\"129\" height=\"51\" hspace=\"0\" vspace=\"0\" border=\"0\"></a></td>\n"
. "    <td width=\"100%\" height=\"51\" style='background-image: url(\"http://www3.ebi.ac.uk/internal/seqdb/images/bann_mid.gif\")'><img alt=\"Image\" src=\"/services/images/trans.gif\" height=\"7\" width=\"4\"  border=\"0\" /></td> \n"
. "    <td width=\"219\" height=\"51\" align=\"right\"><a href=\"/\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/bann_right.gif\" width=\"219\" height=\"51\" border=\"0\"></a></td>\n"
. "  </tr>\n"
. "</table>\n";

my $Helper_extForms = ''; # no longer static...



my $Helper_extBot = "		<!-- end contents here -->
		<!-- InstanceEndEditable -->
		<img src=\"/inc/images/spacer.gif\" class=\"spacer\" alt=\"spacer\" /></td><td class=\"rightmenucell\" id=\"rightmenucell\"><div class=\"rightmenu\" id=\"rightmenu\">";



my $Helper_extBot2 = "
 		<img src=\"/inc/images/spacer.gif\" class=\"spacer\" alt=\"spacer\" /></div></td></tr></table>
 		<table class=\"footerpane\" id=\"footerpane\" summary=\"The main footer pane of the page\"><tr><td colspan =\"4\" class=\"footerrow\"><div class=\"footerdiv\" id=\"footerdiv\"  style=\"z-index:2;\"><iframe src=\"/inc/foot.html\" name=\"foot\" frameborder=\"0\" marginwidth=\"0px\" marginheight=\"0px\" scrolling=\"no\"  height=\"22px\" width=\"100%\"  style=\"z-index:2;\"></iframe></div></td></tr></table><script  src=\"/inc/js/footer.js\" type=\"text/javascript\"></script></div>
 </body>
<!-- InstanceEnd --></html>";

my $Helper_title = "EBI Servlet";
my $Helper_pageUrl = 0;

my $Helper_extServicesHelpMenuItems =
[
  ["pop", "Help", "/help/help_frame.html"],
  ["pop", "General Help", "/help/general_frame.html"],
  ["pop", "Formats", "/help/formats_frame.html"],
  ["pop", "Gaps", "/help/gaps_frame.html"],
  ["pop", "Matrix", "/help/matrix_frame.html"],
  ["pop", "References", "/help/references_frame.html"]
];


sub bottom() {
	bottomNew("");
}




sub bottomNew($) {
	my ($rightContents) = @_;
	return $Helper_extBot . $rightContents . $Helper_extBot2;
}

sub bot($) {
	my ($topMenuItem) = @_;
	if ($topMenuItem=~ m|^internal/|) {
		return $Helper_intBot;
	}
	else {
		return $Helper_extBot . $Helper_extBot2;

	}
}




sub getLeftMenuItems() {
	return $Helper_leftMenuItems;
}


sub getTopMenuItem(){
	return $Helper_topMenuItem;
}


sub setLeftMenuItems($) {
  my ($menuItems) = @_;
  $Helper_leftMenuItems = $menuItems;

}


sub setTopMenuItem($){
	my ($menuItem) = @_;
	$Helper_topMenuItem = $menuItem;
}



#  add a custom last menu item to a copy of the services menu.<br />
sub setServicesHelpMenuItemName ($) {
	my ($name) = @_;
	if (! $Helper_leftMenuItems) {
		for (    my $i = 0; $i<@{$Helper_extServicesHelpMenuItems}; $i++) {
		  push @{$Helper_leftMenuItems}, @{$Helper_extServicesHelpMenuItems}[$i];
		}
		push @{$Helper_leftMenuItems}, ["pop", "", ""];
	}
	@{@{$Helper_leftMenuItems}[$#{$Helper_leftMenuItems}]}[2] = $name;
}



#  add a custom last menu item to a copy of the services menu.<br />
sub setServicesHelpMenuItemLink ($) {
	my ($link) = @_;
	if (! $Helper_leftMenuItems) {
		for (    my $i = 0; $i<@{$Helper_extServicesHelpMenuItems}; $i++) {
		  push @{$Helper_leftMenuItems}, @{$Helper_extServicesHelpMenuItems}[$i];
		}
		push @{$Helper_leftMenuItems}, ["pop", "", ""];
	}
	@{@{$Helper_leftMenuItems}[$#{$Helper_leftMenuItems}]}[2] = $link;
}


#  returns the bottom for an external page
sub getBottom() {
	return  bot($Helper_topMenuItem);
}




#  return the bottom of the page that matches the top generated by this library
sub getBot($) {
	my ($topMenuItem) = @_;
	return bot($topMenuItem);
};


#  In case you want to manipulate the serviceHelpMenuItems (i.e. to remove one of the items).<br />
# This returns a copy of the array you can play with and pass as the leftMenuItems.
sub getServicesHelpMenuItems () {
	return 0;
}



sub printBotNew($$$) {
	my ($out, $topMenuItem, $rightContents) = @_;
	if (! $out) {
		$out = \*STDOUT;
	}
	if ($topMenuItem=~ m|^internal/|) {
		print $out $Helper_intBot;
	}
	else {
		print $out $Helper_extBot;

		print $out $Helper_extBot2;
	}
}


sub printBottom ($) {
  my ($out) = @_;

	if (! $out) {
		$out = \*STDOUT;
	}
	print $out $Helper_extBot . $Helper_extBot2;;

}

sub printBot($$) {
	my ($out, $topMenuItem) = @_;
	my $tmp="";
	printBotNew($out, $topMenuItem, $tmp)
}




#  bean access to top of page. Call the set methods before this to alter the output.
sub getTop() {
	return top($Helper_topMenuItem, $Helper_title, $Helper_pageTitle, $Helper_pageUrl, $Helper_firstWord, $Helper_lastWords, $Helper_loadMethods, $Helper_unLoadMethods, $Helper_headerScript, $Helper_leftMenuItems);
}

sub getTopNew() {
	return top($Helper_topMenuItem, $Helper_title, $Helper_pageTitle, $Helper_pageUrl, $Helper_firstWord, $Helper_lastWords, $Helper_loadMethods, $Helper_unLoadMethods, $Helper_headerScript, $Helper_leftMenuItems, $rightContents, $stretchy);
}


#  Calls printTopWithMenu
sub printTop ($$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript) = @_;
	printTopWithMenu($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, 0);
}

sub printTopNew ($$$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $rightContents, $stretchy) = @_;
	printTopWithMenuNew($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, 0, $rightContents, $stretchy);
}

sub printTopWithServicesHelpMenu ($$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $lastitem) = @_;
	my @lmi = ();
	for (my $i = 0; $i < @{$Helper_extServicesHelpMenuItems}; $i++) {
		push @lmi, @{$Helper_extServicesHelpMenuItems}[$i];
	}
	push @lmi, $lastitem;
	printTopWithMenu($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, \@lmi);
}


sub printTopWithServicesHelpMenuNew ($$$$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $lastitem, $rightContents, $stretchy) = @_;
	my @lmi = ();
	for (my $i = 0; $i < @{$Helper_extServicesHelpMenuItems}; $i++) {
		push @lmi, @{$Helper_extServicesHelpMenuItems}[$i];
	}
	push @lmi, $lastitem;
	printTopWithMenuNew($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, \@lmi, $rightContents, $stretchy);
}

#  no menu required
sub top ($$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript) = @_;
	return topWithMenu ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, 0);
}

sub topNew ($$$$$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $rightContents, $stretchy) = @_;
	return topWithMenuNew ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, 0, $rightContents, $stretchy);
}

sub topWithMenu ($$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems) = @_;
	if ($topMenuItem  && $topMenuItem=~ m|^internal/(.*)|) {
		my $menuitem2  = $1;
		return internalTopWithMenu ($menuitem2, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems);
	}
	else {
		return externalTopWithMenu ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems);
	}
}

sub topWithMenuNew ($$$$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, $rightContents, $stretchy) = @_;
	if ($topMenuItem  && $topMenuItem=~ m|^internal/(.*)|) {
		my $menuitem2  = $1;
		return internalTopWithMenu ($menuitem2, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems);
	}
	else {
		return externalTopWithMenuNew ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, $rightContents, $stretchy);
	}
}

sub topWithServicesHelpMenu ($$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $lastitem) = @_;
	my @lmi = ();
	for (my $i = 0; $i<@{$Helper_extServicesHelpMenuItems}; $i++) {
		push @lmi, @{$Helper_extServicesHelpMenuItems}[$i];
	}
	push @lmi, $lastitem;
	return topWithMenu($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, \@lmi);
}

sub topWithServicesHelpMenuNew ($$$$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $lastitem, $rightContents, $stretchy) = @_;
	my @lmi = ();
	for (my $i = 0; $i<@{$Helper_extServicesHelpMenuItems}; $i++) {
		push @lmi, @{$Helper_extServicesHelpMenuItems}[$i];
	}
	push @lmi, $lastitem;
	return topWithMenuNew($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, \@lmi, $rightContents, $stretchy);
}

sub printTopWithMenu ($$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems) = @_;
	if ($topMenuItem  && $topMenuItem =~ m|^internal/(.*)|) {
		my $menuitem2  = $1;
		printInternalTopWithMenu ($out, $menuitem2, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems);
	}
	else {
		printExternalTopWithMenu($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems);
	}
}

sub printTopWithMenuNew ($$$$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, $rightContents, $stretchy) = @_;
	if ($topMenuItem  && $topMenuItem =~ m|^internal/(.*)|) {
		my $menuitem2  = $1;
		printInternalTopWithMenu ($out, $menuitem2, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems);
	}
	else {
		printExternalTopWithMenuNew($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, $rightContents, $stretchy);
	}
}


sub printExternalTopWithMenu ($$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems) = @_;
	printExternalTopWithMenuNew($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, "", "no")
}

sub externalTopWithMenu ($$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems) = @_;
	externalTopWithMenuNew ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, "", "");
}


sub buildicon($$$$$$){
my($icon_title, $icon_image_url, $icon_image_path, $icon_subtitle, $icon_text, $topMenuItem)=@_;

	my $topmenuindex  = 0;

	for (my $i = 0;  $i<@{$Helper_extTags}; $i++) {
		if(@{@{$Helper_extTags}[$i]}[0] eq $topMenuItem) {
			$topmenuindex = $i;
			last;
		}
	}




	$icon="<div class=\"boxleftplainheading\">
	    <a href=\"#\">" . $icon_title  . "</a>
	</div>
	<div class=\"boxleftplaincontents\">
	    <ul>
	       <li><b>" . $icon_subtitle . "</b>
	       <p>" . $icon_text . "</p> </li>
	    </ul>
	</div><br />";

      		return $icon;
}


########################adam.pl
#  #print ebi page top with menu
sub printExternalTopWithMenuNew ($$$$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, $rightContents, $stretchy) = @_;

	my $topmenuindex  = 0;
	my @menuItem = ("", "", "");
	my $contentWidth  = 0;
	if (! $out) {
		$out = \*STDOUT;
	}
	for (my $i = 0;  $i<@{$Helper_extTags}; $i++) {
		if(@{@{$Helper_extTags}[$i]}[0] eq $topMenuItem) {
			$topmenuindex = $i;
			last;
		}
	}
	print $out "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">
<html xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"eng\"><!-- InstanceBegin template=\"/Templates/new_template_leftmenu.dwt\" codeOutsideHTMLIsLocked=\"false\" -->
<head>
<meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\" />
<meta name=\"description\" content=\"The European Bioinformatics Institute\" />
<meta name=\"author\" content=\"EBI Web Team\" />
<meta http-equiv=\"Content-Language\" content=\"en-GB\" />
<meta http-equiv=\"Window-target\" content=\"_top\" />
<meta name=\"no-email-collection\" content=\"http://www.unspam.com/noemailcollection/\" />
<meta name=\"generator\" content=\"Dreamweaver 8\" />
";
	if (! $title) {
		print $out "<!-- InstanceBeginEditable name=\"doctitle\" --><title>EBI Servlet</title><!-- InstanceEndEditable -->\n";
	}
	else {
		print $out "<!-- InstanceBeginEditable name=\"doctitle\" --><title>"  . $title  . "</title><!-- InstanceEndEditable --><link rel=\"stylesheet\"  href=\"/inc/css/contents.css\"     type=\"text/css\" />
<link rel=\"stylesheet\"  href=\"/inc/css/userstyles.css\"   type=\"text/css\" />
<script src=\"/inc/js/contents.js\" type=\"text/javascript\"></script>
<script src=\"/inc/js/master.js\" type=\"text/javascript\"></script>
<link rel=\"stylesheet\"  href=\"/inc/css/sidebars.css\"   type=\"text/css\" />
<link rel=\"SHORTCUT ICON\" href=\"/bookmark.ico\" />\n";
	}
	if ($headerScript ) {
		print $out $headerScript;
	}
	print $out "<!-- InstanceBeginEditable name=\"head\" --><script language=\"javascript\" type=\"text/javascript\">\n<!--\n";
	print $out "function callLoadMethods()"  .  "{"  . "\n";
	if ($loadMethods ) {
		print $out $loadMethods;
	}
	print $out ";"  . "\n"  . "}"  . "\n";
	print $out "function callUnLoadMethods()"  .  "{"  . "\n";
	if ($unLoadMethods ) {
		print $out $unLoadMethods;
	}
	print $out ";"  . "\n"  . "}"  . "\n";
	print $out "\n// -->\n</script><!-- InstanceEndEditable -->";
	print $out "\n</head>\n";

	#  top of body is static...
	print $out "<body onunload=\"callUnLoadMethods()\" onload=\"callLoadMethods();if(navigator.userAgent.indexOf('MSIE') != -1) {document.getElementById('head').allowTransparency = true;}\">\n";
	print $out "	<div class=\"headerdiv\" id=\"headerdiv\" style=\"position:absolute; z-index: 1;\">
		<iframe src=\"/inc/head.html\" name=\"head\" id=\"head\" frameborder=\"0\" marginwidth=\"0px\" marginheight=\"0px\" scrolling=\"no\"  width=\"100%\" style=\"position:absolute; z-index: 1; height: 800px;\"></iframe>
	</div>
	<div class=\"contents\" id=\"contents\"><table class=\"contentspane\" id=\"contentspane\" summary=\"The main content pane of the page\"";



	if ($stretchy eq $yes){
		print $out " style=\"width: 100%\" ";
	}

	print $out "><tr><td class=\"leftmargin\"><img src=\"/inc/images/spacer.gif\" class=\"spacer\" alt=\"spacer\" /></td><td class=\"leftmenucell\" id=\"leftmenucell\">";

if ($leftMenuItems) {
	print $out "<div class=\"leftmenu\" id=\"leftmenu\" style=\"width: 145px; visibility: visible; display: block;\">";
}
else{
	print $out "<div class=\"leftmenu\" id=\"leftmenu\" style=\"width: 1px; visibility: visible; display: none;\">";
}


print $out "<!-- InstanceBeginEditable name=\"leftnav\" -->
		  <!-- start left menu here  -->";



	if ($leftMenuItems) {







		print $out "
<ul id=\"sidemenuid\" class=\"sidemenu\">\n";

		#  Now for the menu...


		for (my $i=0; @{$leftMenuItems}[$i]; $i++) {
			if ((ref @{$leftMenuItems}[$i])) {
				$menuItem[0] = @{@{$leftMenuItems}[$i]}[0];
				$menuItem[1] = @{@{$leftMenuItems}[$i]}[1];
				$menuItem[2] = @{@{$leftMenuItems}[$i]}[2];
			}
			else {
				if ($i+2 > @{$leftMenuItems}) {
					last;
				}
				$menuItem[0] = @{$leftMenuItems}[$i];
				$menuItem[1] = @{$leftMenuItems}[$i+1];
				$menuItem[2] = @{$leftMenuItems}[$i+2];
				$i += 2;
			}
			last if (! $menuItem[0]);

			if ("image" eq $menuItem[0]) {
				print $out "<li class=\"plainlist\"><a href=\"";
				print $out $menuItem[2]  . "\"><img alt=\"Image\" src=\"";
				print $out $menuItem[1]  . "\" border=\"0\" /></a></li>\n";
			}
			elsif ("link" eq $menuItem[0]) {
				print $out "<li><a href=\"";
				print $out $menuItem[2]  . "\">"  . $menuItem[1]  . "</a></li>\n";
			}
			elsif ("pop" eq $menuItem[0]) {
				print $out "<li><a href=\"#\"  onclick=\"openWindow(\'";
				print $out $menuItem[2]  . "\')\">"  . $menuItem[1]  . "</a></li>\n";
			}
			elsif ("text" eq $menuItem[0]) {
				print $out "<li class=\"plainlist\">";
				print $out  $menuItem[1]  . "</li>\n";
			}
			elsif ("free" eq $menuItem[0]) {
				print $out "<li class=\"plainlist\">" . $menuItem[1] . "</li>";
			}
			else {
				print $out "<!-- HelperWithMenu: ERROR WITH MENUITEM failed to recognise "  . $menuItem[0]  . " as a item type! -->\n";
			}
		}
		print $out "
</ul>
<!-- end left menu here -->";


	print $out "<br />" . $rightContents;

	}
	else {

	}
		print $out "
		  <!-- InstanceEndEditable -->";
		  if ($leftMenuItems) {
			print $out "<script type=\"text/javascript\" src=\"/inc/js/sidebars.js\"></script>";
			}
		print $out "<img src=\"/inc/images/spacer.gif\" class=\"spacer\" alt=\"spacer\" /></div></td><td class=\"contentsarea\" id=\"contentsarea\">
		<!-- InstanceBeginEditable name=\"contents\" --> ";

	#remove headings if dont specify firstWord

	if ($firstWord) {
		print $out     "<h1>";
		if ($firstWord ) {
		  print $out $firstWord;
		}

		#  $lastWords
		if ($lastWords ) {
			print $out $lastWords;
		}

		if ($firstWord ) {
		  print $out "</h1>";
		}
  	}
}


#########################ville.pl or index4b.pl
sub externalTopWithMenuNew ($$$$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems, $rightContents, $stretchy) = @_;
	my $top  = "";
	my $topmenuindex  = 0;
	my @menuItem = ("", "", "");
	my $contentWidth  = 0;
	for (    my $i = 0;  $i<@{$Helper_extTags}; $i++) {
		if(@{@{$Helper_extTags}[$i]}[0] eq $topMenuItem) {
			$topmenuindex = $i;
			last;
		}
	}



	$top = $top  . " <!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">
 <html xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"eng\"><!-- InstanceBegin template=\"/Templates/new_template_leftmenu_max.dwt\" codeOutsideHTMLIsLocked=\"false\" -->
 <head>
 <meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\" />
 <meta name=\"description\" content=\"The European Bioinformatics Institute\" />
 <meta name=\"author\" content=\"EBI Web Team\" />
 <meta http-equiv=\"Content-Language\" content=\"en-GB\" />
 <meta http-equiv=\"Window-target\" content=\"_top\" />
 <meta name=\"no-email-collection\" content=\"http://www.unspam.com/noemailcollection/\" />
 <meta name=\"generator\" content=\"Dreamweaver 8\" />
<!-- InstanceBeginEditable name=\"doctitle\" -->";
	if (! $title) {
		$top = $top  . "<!-- InstanceBeginEditable name=\"doctitle\" --><title>EBI Servlet</title><!-- InstanceEndEditable -->\n";
	}
	else {
		$top = $top  . "<!-- InstanceBeginEditable name=\"doctitle\" --><title>"  . $title  . "</title><!-- InstanceEndEditable -->\n";
	}
	if ($headerScript ) {
	  $top = $top  . $headerScript;
	}
	$top = $top  . "<!-- InstanceEndEditable -->
<link rel=\"stylesheet\"  href=\"/inc/css/contents.css\"     type=\"text/css\" />
<link rel=\"stylesheet\"  href=\"/inc/css/userstyles.css\"   type=\"text/css\" />
<script src=\"/inc/js/contents.js\" type=\"text/javascript\"></script>
<link rel=\"stylesheet\"  href=\"/inc/css/sidebars.css\"   type=\"text/css\" />
<link rel=\"SHORTCUT ICON\" href=\"/bookmark.ico\" />
<!-- InstanceBeginEditable name=\"head\" -->
<!--  start meta tags, css , javascript here   --><script  type=\"text/javascript\">\n<!--\n";
	$top = $top  . "function callLoadMethods()"  .  "{"  . "\n";
	if ($loadMethods ) {
		$top = $top  . $loadMethods;
	}
	$top = $top  . ";"  . "\n"  . "}"  . "\n";
	$top = $top  . "function callUnLoadMethods()"  .  "{"  . "\n";
	if ($unLoadMethods ) {
		$top = $top  . $unLoadMethods;
	}
	$top = $top  . ";"  . "\n"  . "}"  . "\n";
	$top = $top  . "\n// -->\n</script><!-- InstanceEndEditable -->";
	$top = $top  . "</head>\n";

	#  $top of body is static...
	$top = $top  . "<body onunload=\"callUnLoadMethods()\" onload=\"callLoadMethods();if(navigator.userAgent.indexOf('MSIE') != -1) {document.getElementById('head').allowTransparency = true;}\">\n";
	$top = $top  . "<!--  end meta tags, css , javascript here  -->
<!-- InstanceEndEditable -->
</head>
<body onload=\"if(navigator.userAgent.indexOf('MSIE') != -1) {document.getElementById('head').allowTransparency = true;}\">
	<div class=\"headerdiv\" id=\"headerdiv\" style=\"position:absolute; z-index: 1;\">
		<iframe src=\"/inc/head.html\" name=\"head\" id=\"head\" frameborder=\"0\" marginwidth=\"0px\" marginheight=\"0px\" scrolling=\"no\"  width=\"100%\" style=\"position:absolute; z-index: 1; height: 800px;\">[Your user agent does not support frames or is currently configured not to display iframes.</iframe>
	</div>
	<div class=\"contents\" id=\"contents\"><table class=\"contentspane\" id=\"contentspane\" summary=\"The main content pane of the page\"";


if ($stretchy eq $yes){
	$top = $top  . " style=\"width: 100%\" ";
}






	$top = $top  . "><tr><td class=\"leftmargin\"><img src=\"/inc/images/spacer.gif\" class=\"spacer\" alt=\"spacer\" /></td><td class=\"leftmenucell\" id=\"leftmenucell\">";
	if ($leftMenuItems ) {
		$top = $top  . "<div class=\"leftmenu\" id=\"leftmenu\" style=\"width: 145px; visibility: visible; display: block;\">";
	}
	else{
		$top = $top  . "<div class=\"leftmenu\" id=\"leftmenu\" style=\"width: 1px; visibility: visible; display: none;\">";
	}




		  $top = $top  . "<!-- InstanceBeginEditable name=\"leftnav\" -->
		  <!-- start left menu here  -->";

	if ($leftMenuItems ) {



		$top = $top  . "<ul id=\"sidemenuid\" class=\"sidemenu\">\n";

		#  Now for the menu...
		for (my $i = 0; @{$leftMenuItems}[$i]; $i++) {

			if ((ref @{$leftMenuItems}[$i])) {
				$menuItem[0] = @{@{$leftMenuItems}[$i]}[0];
				$menuItem[1] = @{@{$leftMenuItems}[$i]}[1];
				$menuItem[2] = @{@{$leftMenuItems}[$i]}[2];
			}
			else {
				if ($i+2 > @{$leftMenuItems}) {
					last;
				}
				$menuItem[0] = @{$leftMenuItems}[$i];
				$menuItem[1] = @{$leftMenuItems}[$i+1];
				$menuItem[2] = @{$leftMenuItems}[$i+2];
				$i += 2;
			}
			if ("image" eq $menuItem[0]) {
				$top = $top  . "<li><a href=\"";
				$top = $top  . $menuItem[2]  . "\"><img alt=\"Image\" src=\"";
				$top = $top  . $menuItem[1]  . "\" border=\"0\" /></a></li>\n";
			}
			elsif ("link" eq $menuItem[0]) {
				$top = $top  . "<li><a href=\"";
				$top = $top  . $menuItem[2]  . "\" >"  . $menuItem[1]  . "</a></li>\n";
			}
			elsif ("pop" eq $menuItem[0]) {
				$top = $top  . "<li><a href=\"#\"  onclick=\"openWindow(\'";
				$top = $top  . $menuItem[2]  . "\')\">"  . $menuItem[1]  . "</a></li>\n";
			}
			elsif ("text" eq $menuItem[0]) {
				$top = $top  . "<li>"  . $menuItem[1]  . "</li>\n";
			}
			elsif ("free" eq $menuItem[0]) {
				$top = $top  . "<li>"  . $menuItem[1]  . "</li>\n";
			}
			else {
				$top = $top  . "<!-- HelperWithMenu: ERROR WITH MENUITEM failed to recognise "  . $menuItem[0]  . " as a item type! -->\n";
			}
		}
		$top = $top  . "</ul>";

		$top = $top  . "<br />" . $rightContents;

	}
	else {

	}
	$top = $top  . "
		<!-- end left menu here -->
		<!-- InstanceEndEditable -->";
		if ($leftMenuItems ) {
	    	$top = $top  . "<script type=\"text/javascript\" src=\"/inc/js/sidebars.js\"></script>";
		}
		$top = $top  . "<img src=\"/inc/images/spacer.gif\" class=\"spacer\" alt=\"spacer\" /></div></td><td class=\"contentsarea\" id=\"contentsarea\">
		<!-- InstanceBeginEditable name=\"contents\" -->
		<!-- start contents here -->";


	if ($firstWord) {


		if ($firstWord ) {
			$top = $top  . "<h1>" . $firstWord;
		}
		if ($lastWords ) {
			$top = $top  . $lastWords;
		}
		if ($firstWord ) {
			$top = $top  . "</h1>";
		}
	}
	return $top;
}




































































#///////////////////THESE ARE NOT USUALLY USED //////////////////////////////////////////









sub printInternalTopWithMenu ($$$$$$$$$$$) {
	my ($out, $topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems) = @_;
	if (!$out) {
		$out = \*STDOUT;
	}
    my $topmenuindex = 0;
	my @menuItem = ();
    my $contentWidth = 0;
	for (my $i = 0; $i<@{$Helper_intTags}; $i++) {
		if (@{@{$Helper_intTags}[$i]}[0] eq $topMenuItem) {
			$topmenuindex = $i;
			last;
		}
	}
	print $out "<html lang=\"en\">\n<head>\n";
	print $out
	"<!-- InstanceBegin template=\"http://www3.ebi.ac.uk/Templates/organisation.dwt\" codeOutsideHTMLIsLocked=\"false\" -->\n"
	. "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\" />\n"
	. "<meta http-equiv=\"Owner\" CONTENT= \"EMBL Outstation - Hinxton, European Bioinformatics Institute\" />\n"
	. "<meta name=\"Author\" content=\"EBI External Services\" />\n"
	. "<script language=\"javascript\" src=\"/internal/seqdb/include/master.js\" type=\"text/javascript\"></script>\n";
	if ($headerScript ) {
		print $out $headerScript;
	}
	print $out "<!-- InstanceBeginEditable name=\"head\" --><script language=\"javascript\" type=\"text/javascript\">\n<!--\n";
	print $out "function callLoadMethods()"    . "{"  . "\n";
	if ($loadMethods ) {
		print $out $loadMethods;
	}
	print $out ";"  . "\n"  . "}"  . "\n";
	print $out "function callUnLoadMethods()"   . "{"  . "\n";
	if ($unLoadMethods ) {
		print $out $unLoadMethods;
	}
	print $out ";"  . "\n"  . "}"  . "\n";
	print $out "\n// -->\n</script><!-- InstanceEndEditable -->";
	print $out "<!-- InstanceBeginEditable name=\"doctitle\" -->\n";
	if (! $title) {
		print $out "<!-- InstanceBeginEditable name=\"doctitle\" --><title>EBI Servlet</title><!-- InstanceEndEditable -->\n";
	}
	else {
		print $out "<!-- InstanceBeginEditable name=\"doctitle\" --><title>"  . $title  . "</title><!-- InstanceEndEditable -->\n";
	}
	print $out
	"<!-- InstanceEndEditable -->\n"
	. "<link href=\"http://www3.ebi.ac.uk/internal/seqdb/include/stylesheet.css\" rel=\"stylesheet\" type=\"text/css\" />\n"
	. "</head>\n";
	print $out $Helper_intBodyStart;

	#  main navigation bar..
	print $out "<table width=\"100%\" border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n"
	. "  <tr align=\"center\">\n";

	for (my $i = 0; $i<@{$Helper_intTags}; $i++) {
		if ($i==$topmenuindex) {
			print $out "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menu_left.gif\" width=\"10\" height=\"16\"></td>\n";
			print $out "    <td nowrap=\"nowrap\" class=\"quickbody\"><a href=\""  . @{@{$Helper_intTags}[$i]}[1]  . "\" class=\"menulinkover\">"  . @{@{$Helper_intTags}[$i]}[2]  . "</a></td>\n";
		}
		else {
			if ($i==$topmenuindex . 1) {
			  print $out  "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menu_right.gif\" width=\"10\" height=\"16\"></td>\n";
			}
			else {
			  print $out "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menubar.gif\" width=\"10\" height=\"16\"></td>\n";
			}
			print $out "    <td nowrap=\"nowrap\"><a href=\""  . @{@{$Helper_intTags}[$i]}[1]  . "\" class=\"menulink\">"  . @{@{$Helper_intTags}[$i]}[2]  . "</a></td>\n";
		}
	}
	if ($topmenuindex==@{$Helper_intTags}) {
		print $out  "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menu_right.gif\" width=\"10\" height=\"16\" hspace=\"0\" vspace=\"0\" border=\"0\" align=\"left\"></td>\n";
	}
	else {
		print $out "      <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menubar.gif\" width=\"10\" height=\"16\" hspace=\"0\" vspace=\"0\" border=\"0\" align=\"left\"></td>\n";
	}
	print $out "<td  width=\"50%\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"2\" height=\"16\"></td>\n"
	. "</tr>\n" ;
	print $out " <tr  class=\"quickbody\">\n";
	for (my $i = 0;  $i<@{$Helper_intTags}; $i++) {
		print $out " <td  width=\"10\" height=\"3\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"3\"></td>\n"
		. " <td height=\"3\" width=\"" . ($i==@{$Helper_intTags} ? "100%" : "93") . "\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\""
		. ($i==@{$Helper_intTags} ? "1" : "93") . "\" height=\"3\"></td>\n";
	}
	print $out "<td  width=\"10\" height=\"3\" nowrap=\"nowrap\" ><img src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"3\" /></td>";
	print $out "<td height=\"3\" width=\"100%\"><img src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"3\" /></td>";
	print $out "<td  width=\"10\" height=\"3\" nowrap=\"nowrap\" ><img src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"3\" /></td>";
	print $out "<td height=\"3\" width=\"100%\"><img src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"3\" /></td>";
	print $out "</tr>\n</table>\n";
	print $out "<table width=\"100%\" height=\"80%\" border=\"0\" cellpadding=\"6\" cellspacing=\"0\">\n"
	. "  <tr>";

	#  left menu?
	if ($leftMenuItems ) {
		if (! $contentWidth) {
			$contentWidth = "560";
		}
		print $out "    <td width=\"175\" height=\"1\" align=\"center\" valign=\"top\" class=\"menubody\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"162\" height=\"1\"></td>\n"
		. "    <td height=\"1\" valign=\"top\"><!-- InstanceBeginEditable name=\"width\" --><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"560\" height=\"1\"><!-- InstanceEndEditable --></td>\n"
		. "    <td width=\"1\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"1\"></td>\n"
		. "  </tr>\n"
		. "  <tr>\n"
		. "    <td width=\"175\" align=\"center\" valign=\"top\" class=\"menubody\">\n"
		. "	  <table width=\"162\"  border=\"1\" align=\"center\" cellpadding=\"3\" cellspacing=\"0\" bordercolor=\"#29498C\">\n"
		. "	    <tr>\n"
		. "          <td width=\"175\">\n";

		for (my $i  = 0; $i< @{$leftMenuItems}; $i++) {
			if (ref (@{$leftMenuItems}[0])) {
				$menuItem[0] = @{@{$leftMenuItems}[$i]}[0];
				$menuItem[1] = @{@{$leftMenuItems}[$i]}[1];
				$menuItem[2] = @{@{$leftMenuItems}[$i]}[2];
			}
			else {
				if ($i+2 > @{$leftMenuItems}) {
					last;
				}
				$menuItem[0] = @{$leftMenuItems}[$i];
				$menuItem[1] = @{$leftMenuItems}[$i+1];
				$menuItem[2] = @{$leftMenuItems}[$i+2];
				$i+=2;
			}
			if ("$title" eq $menuItem[0]) {
				print $out "<li><span class=\"quicktext\">Quick Links</span></li>\n";
			}
			elsif ("link" eq $menuItem[0] || "text" eq $menuItem[0]) {
				print $out "<li class=\"quicklist\">";
				if ($menuItem[2] ) {
					print $out "<a class=\"quicklink\" href=\""  . $menuItem[2]  . "\">"  . $menuItem[1]  . "</a>";
				}
				else {
					print $out $menuItem[1];
				}
				print $out "</li>\n";
			}
			elsif ("image" eq $menuItem[0]) {
				if ($menuItem[2] ) {
					print $out "<img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"15\" height=\"15\"><a  class=\"quicklink\" href=\""  . $menuItem[2]  . "\"><img border=\"0\" alt=\"Image\" src=\""  . $menuItem[1]  . "\" /></a>";
				}
				else {
					print $out "<img border=\"0\" alt=\"Image\" src=\""  . $menuItem[1]  . "\" />";
				}
			}
			elsif ("pop" eq $menuItem[0]) {
				print $out "<li class=\"quicklist\">";
				if ($menuItem[2] ) {
					print $out "<a  class=\"quicklink\" href=\"#\" onclick=\"openWindow(\'"  . $menuItem[2]  . "\')\">"  . $menuItem[1]  . "</a>";
				}
				else {
					print $out $menuItem[1];
				}
				print $out "</li>\n";
			}
		}
		print $out "</td></tr></table>\n</td>";
	}
	else {
		if (!$contentWidth) {
			$contentWidth = "760";
		}
		print $out  "		    <td width=\"1\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"1\" /></td>\n"
		. "		    <td width=\"1\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"1\" /></td>\n"
		. "</td>";
	}
	print $out "<td width=\""  . $contentWidth  . "\" valign=\"top\">\n";
}


#  title that appears on the page immediately below the menuitem tabs<br />
# defaults to "EBI Servlet"
sub getTitle(){
	return $Helper_title;
}

sub setTitle($){
	my ($title) = @_;
	$Helper_title = $title;
}

sub getPageTitle(){
	return $Helper_pageTitle;
}

sub setPageTitle($){
	my ($title) = @_;
	$Helper_pageTitle = $title;
}

#  link to attach to title<br />
# defaults to 0 (no link generated)
sub getPageUrl(){
	return $Helper_pageUrl;
}

sub setPageUrl($){
	my ($pageUrl) = @_;
	$Helper_pageUrl = $pageUrl;
}

#  First word in main title of page<br />
# This word appears as white text on a green background<br />
# Defaults to "EBI"
sub getFirstWord (){
	return $Helper_firstWord;
}

sub setFirstWord($){
	my ($firstWord) = @_;
	$Helper_firstWord = $firstWord;
}

#  Remaining word(s) of page title<br />
# These word(s) appear as green text alongside firstWord<br />
# Defaults to "Servlet"
sub getLastWords(){
	return $Helper_lastWords;
}

sub setLastWords($){
	my ($lastWords) = @_;
	$Helper_lastWords = $lastWords;
}

#  javascript to call on loading the page<br />
# the surrounding html tags are generated - just javascript please!
sub getLoadMethods (){
	return $Helper_loadMethods;
}

sub setLoadMethods($){
	my ($loadMethods) = @_;
	$Helper_loadMethods = $loadMethods;
}

#  javascript to call on leaving the page<br />
# the surrounding html tags are generated - just javascript please!<br />
# Also note that it isn't good practice to annoy people with popups and such at this point!
sub getUnLoadMethods() {
	return $Helper_unLoadMethods;
}

sub setUnLoadMethods($){
	my ($unLoadMethods) = @_;
	$Helper_unLoadMethods = $unLoadMethods;
}

#  embedded in page &lt;head&gt;<br />
# You need the appropriate tags (i.e. &lt;script&gt;&lt/script&gt;) for this to work.
sub getHeaderScript() {
	return $Helper_headerScript;
}

sub setHeaderScript($){
	my ($headerScript) = @_;
	$Helper_headerScript = $headerScript;
}

sub internalTopWithMenu($$$$$$$$$$) {
	my ($topMenuItem, $title, $pageTitle, $pageUrl, $firstWord, $lastWords, $loadMethods, $unLoadMethods, $headerScript, $leftMenuItems) = @_;
	my $top  = "";
	my $topmenuindex  = 0;
	my @menuItem = ();
	my $contentWidth  = 0;
	for (my $i = 0; $i<@{$Helper_intTags}; $i++){
		if (@{@{$Helper_intTags}[$i]}[0] eq $topMenuItem) {
			$topmenuindex = $i;
			last;
		}
	}
	$top = $top  . "<html lang=\"en\">\n<head>\n";
	$top = $top  . "<!-- InstanceBegin template=\"http://www3.ebi.ac.uk/Templates/organisation.dwt\" codeOutsideHTMLIsLocked=\"false\" -->\n"
	. "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\" />\n"
	. "<meta http-equiv=\"Owner\" content= \"EMBL Outstation - Hinxton, European Bioinformatics Institute\" />\n"
	. "<meta name=\"Author\" content=\"EBI External Services\" />\n"
	. "<script language=\"javascript\" src=\"/internal/seqdb/include/master.js\" type=\"text/javascript\"></script>\n";
	if ($headerScript){
		$top = $top  . $headerScript;
	}
	$top = $top . "<!-- InstanceBeginEditable name=\"head\" --><script language=\"javascript\">\n<!--\n";
	$top = $top . "function callLoadMethods()" . "{"  . "\n";
	if ($loadMethods) {
		$top = $top  . $loadMethods;
	}
	$top = $top  . ";"  . "\n"  . "}"  . "\n";
	$top = $top  . "function callUnLoadMethods()" . "{"  . "\n";
	if ($unLoadMethods) {
		$top = $top . $unLoadMethods;
	}
	$top = $top  . ";"  . "\n"  . "}"  . "\n";
	$top = $top  . "\n// --></script><!-- InstanceEndEditable -->";
	$top = $top  . "<!-- InstanceBeginEditable name=\"doctitle\" -->\n";
	if (!$title){
		$top = $top  . "<!-- InstanceBeginEditable name=\"doctitle\" --><title>EBI Servlet</title><!-- InstanceEndEditable -->\n";
	}
	else {
		$top = $top  . "<!-- InstanceBeginEditable name=\"doctitle\" --><title>"  . $title  . "</title><!-- InstanceEndEditable -->\n";
	}
	$top = $top  . "<!-- InstanceEndEditable -->\n"
	. "<link href=\"http://www3.ebi.ac.uk/internal/seqdb/include/stylesheet.css\" rel=\"stylesheet\" type=\"text/css\" />\n"
	. "</head>\n";
	$top = $top  . $Helper_intBodyStart;

	#  main navigation bar..
	$top = $top  . "<table width=\"100%\" border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n"
	. "  <tr align=\"center\">\n";
	for (my $i = 0; $i<@{$Helper_intTags}; $i++){
		if ($i==$topmenuindex){
			$top = $top  . "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menu_left.gif\" width=\"10\" height=\"16\" /></td>\n";
			$top = $top  . "    <td nowrap=\"nowrap\" class=\"quickbody\"><a href=\""  . @{@{$Helper_intTags}[$i]}[1]  . "\" class=\"menulinkover\">"  . @{@{$Helper_intTags}[$i]}[2]  . "</a></td>\n";
		}
		else {
			if ($i==$topmenuindex . 1) {
				$top = $top  . "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menu_right.gif\" width=\"10\" height=\"16\" /></td>\n";
			}
			else {
				$top = $top  . "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menubar.gif\" width=\"10\" height=\"16\" /></td>\n";
			}
			$top = $top  . "    <td nowrap=\"nowrap\"><a href=\""  . @{@{$Helper_intTags}[$i]}[1]  . "\" class=\"menulink\">"  . @{@{$Helper_intTags}[$i]}[2]  . "</a></td>\n";
		}
	}
	if ($topmenuindex==@{$Helper_intTags}) {
		$top = $top  . "    <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menu_right.gif\" width=\"10\" height=\"16\" hspace=\"0\" vspace=\"0\" border=\"0\" align=\"left\"></td>\n";
	}
	else {
		$top = $top  . "      <td  width=\"10\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/menubar.gif\" width=\"10\" height=\"16\" hspace=\"0\" vspace=\"0\" border=\"0\" align=\"left\"></td>\n";
	}
	$top = $top  . "<td  width=\"50%\" height=\"16\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"2\" height=\"16\"></td>\n"
	. "</tr>\n" ;
	$top = $top  . " <tr  class=\"quickbody\">\n";
	for(my $i = 0; $i<@{$Helper_intTags} . 1; $i++){
		$top = $top  . " <td  width=\"10\" height=\"3\" nowrap=\"nowrap\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"10\" height=\"3\"></td>\n"
		. " <td height=\"3\" width=\"" + ($i==@{$Helper_intTags} ? "100%" : "93") + "\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\""
		+ ($i==@{$Helper_intTags} ? "1" : "93") + "\" height=\"3\"></td>\n";
	}
	$top = $top  . "</tr>\n</table>\n";
	$top = $top  . "<table width=\"100%\" height=\"80%\" border=\"0\" cellpadding=\"6\" cellspacing=\"0\">\n"
	. "  <tr>";
	if ($leftMenuItems){
		if (! $contentWidth){
			$contentWidth = "560";
		}
		$top = $top  . "    <td width=\"175\" height=\"1\" align=\"center\" valign=\"top\" class=\"menubody\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"162\" height=\"1\"></td>\n"
		. "    <td height=\"1\" valign=\"top\"><!-- InstanceBeginEditable name=\"width\" --><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"560\" height=\"1\"><!-- InstanceEndEditable --></td>\n"
		. "    <td width=\"1\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"1\"></td>\n"
		. "  </tr>\n"
		. "  <tr>\n"
		. "    <td width=\"175\" align=\"center\" valign=\"top\" class=\"menubody\">\n"
		. "	  <table width=\"162\"  border=\"1\" align=\"center\" cellpadding=\"3\" cellspacing=\"0\" bordercolor=\"#29498C\">\n"
		. "	    <tr>\n"
		. "          <td width=\"175\">";
		for(my $i = 0; $i< @{$leftMenuItems}[$i]; $i++){
			if ((ref @{$leftMenuItems}[$i])) {
				$menuItem[0] = @{@{$leftMenuItems}[$i]}[0];
				$menuItem[1] = @{@{$leftMenuItems}[$i]}[1];
				$menuItem[2] = @{@{$leftMenuItems}[$i]}[2];
			}
			else {
				if($i+2 > @{$leftMenuItems}) {
					last;
				}
				$menuItem[0] = @{$leftMenuItems}[$i];
				$menuItem[1] = @{$leftMenuItems}[$i+1];
				$menuItem[2] = @{$leftMenuItems}[$i+2];
				$i += 2;
			}
			if ("$title" eq $menuItem[0]) {
				$top = $top  . "<li><span class=\"quicktext\">Quick Links</span></li>\n";
			}
			elsif ("link" eq $menuItem[0] || "text" eq $menuItem[0]) {
				$top = $top  . "<li class=\"quicklist\">";
				if ($menuItem[2] ) {
					$top = $top  . "<a class=\"quicklink\" href=\""  . $menuItem[2]  . "\">"  . $menuItem[1]  . "</a>";
				}
				else {
					$top = $top  . $menuItem[1];
				}
				$top = $top  . "</li>\n";
			}
			elsif ("image" eq $menuItem[0]) {
				$top = $top  . "<li class=\"quicklist\">";
				if ($menuItem[2] ) {
					$top = $top  . "<a class=\"quicklink\" href=\""  . $menuItem[2]  . "\"><img alt=\"Image\" src=\""  . $menuItem[1]  . "\"></a>";
				}
				else {
					$top = $top  . "<img border=\"0\" alt=\"Image\" src=\""  . $menuItem[1]  . "\">";
				}
				$top = $top  . "</li>\n";
			}
			elsif ("pop" eq $menuItem[0]) {
				$top = $top  . "<li class=\"quicklist\">";
				if ($menuItem[2] ) {
				  $top = $top  . "<a class=\"quicklink\" href=\"#\" onclick=\"openWindow(\'"  . $menuItem[2]  . "\')\">"  . $menuItem[1]  . "</a>";
				}
				else {
				  $top = $top  . $menuItem[1];
				}
				$top = $top  . "</li>\n";
			}
			elsif ("free" eq $menuItem[0]) {
				$top = $top  . $menuItem[1];
			}
			else {
			  $top = $top  . "<!-- HelperWithMenu: ERROR WITH MENUITEM failed to recognise "  . $menuItem[0]  . " as a item type! -->\n";
			}
		}
		$top = $top  . "</td></tr></table>\n</td>";
	}
	else {
		if (!$contentWidth) {
			$contentWidth = "779";
		}
		$top = $top  . "		    <td width=\"1\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"1\"></td>\n"
		. "		    <td width=\"1\"><img alt=\"Image\" src=\"http://www3.ebi.ac.uk/internal/seqdb/images/spacer.gif\" width=\"1\" height=\"1\"></td>\n"
		. "</td>";
	}
	$top = $top  . "<td width=\""  . $contentWidth  . "\" valign=\"top\">";
	return $top;
}





#///////////////////THESE ARE NOT USED......//////////////////////////////////////////






















