//YAHOO.widget.Logger.enableBrowserConsole();

var intranet = false;
if (location.protocol == "https:") {
	intranet = true;
}


YAHOO.util.Event.onAvailable("navmenu", function () {

var infoMenu = new YAHOO.widget.Menu("infomenu");
infoMenu.addItem(new YAHOO.widget.MenuItem("Goals of the Project", {url: "/goals.html"}));
infoMenu.addItem(new YAHOO.widget.MenuItem("People", {url: "/people.html"}));
infoMenu.addItem(new YAHOO.widget.MenuItem("Participating Institutions", {url: "/institutions.html"}));
infoMenu.addItem(new YAHOO.widget.MenuItem("Publications", {url: "/publications.html"}));
infoMenu.addItem(new YAHOO.widget.MenuItem("Resequencing Populations", {url: "/populations.html"}));
infoMenu.addItem(new YAHOO.widget.MenuItem("Training Programs", {url: "/training.html"}));
if (intranet) { infoMenu.addItem(new YAHOO.widget.MenuItem("Meetings", {url: "/intranet/meetings/index.html"})); }
infoMenu.addItem(new YAHOO.widget.MenuItem("Bioinformatics Tools", {url: "/bioinformaticstools.html"}));
infoMenu.addItem(new YAHOO.widget.MenuItem("Links", {url: "/links.html"}));
var infoMenuBarItem = new YAHOO.widget.MenuBarItem("Information", {url: "/cgi-bin/menu.py?menu=info", submenu: infoMenu});
var dataMenu = new YAHOO.widget.Menu("datamenu");
dataMenu.addItem(new YAHOO.widget.MenuItem("Transporter List", {url: "/cgi-bin/Study.py"}));
dataMenu.addItem(new YAHOO.widget.MenuItem("MicroArray Data", {url: "/microview/index.html"}));
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Conserved Region", {url: "/intranet/genomic_alignments/index.html"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Population Genetics Statistics", {url: "/cgi-bin/intranet/PopGen.py"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Clinical Studies", {url: "/cgi-bin/intranet/clinical/clinical-status.py"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Cellular Phenotype Studies", {url: "/intranet/cellular/index.html"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Subject Set View", {url: "/cgi-bin/intranet/SubjectSet.py?uid=SOPHIE"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Data Status", {url: "/cgi-bin/intranet/datastatus/datastatus.py"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Data Processing", {url: "/cgi-bin/intranet/dataprocess.py"})); }
if (intranet) { dataMenu.addItem(new YAHOO.widget.MenuItem("Data Problems", {url: "/cgi-bin/intranet/dataproblems.py"})); }
var dataMenuBarItem = new YAHOO.widget.MenuBarItem("Data Access", {url: "/cgi-bin/menu.py?menu=data", submenu: dataMenu});
var toolsMenu = new YAHOO.widget.Menu("toolsmenu");
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Share Documents", {url: "/cgi-bin/intranet/sharefile.py?category=forms"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Link Publications to SNPs", {url: "/cgi-bin/intranet/pubmed/pubmedEdit.py"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Validate Data", {url: "/cgi-bin/intranet/datavalidate.py"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Transfer Data", {url: "/cgi-bin/intranet/datatransfer/datatransfer.py"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Color Haplotype Figures", {url: "/cgi-bin/intranet/colorhaplo2.py"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Haploview File Download", {url: "/cgi-bin/intranet/HaploView.py"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Protocols/Db Schema", {url: "/intranet/datatransfer/protocols.html"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Deprecated Protocols", {url: "/intranet/datatransfer/deprecated.html"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Browse IDs", {url: "/cgi-bin/intranet/databrowser/databrowser.py"})); }
if (intranet) { toolsMenu.addItem(new YAHOO.widget.MenuItem("Edit Transmembrane Domains", {url: "/cgi-bin/intranet/tmdedit/tmdedit.py"})); }
var toolsMenuBarItem = new YAHOO.widget.MenuBarItem("Tools", {url: "/cgi-bin/menu.py?menu=tools", submenu: toolsMenu});
var policiesMenu = new YAHOO.widget.Menu("policiesmenu");
policiesMenu.addItem(new YAHOO.widget.MenuItem("Data Usage Policies", {url: "/datapolicies.html"}));
if (intranet) { policiesMenu.addItem(new YAHOO.widget.MenuItem("Collaboration Policy", {url: "/intranet/collaboration_policy.html"})); }
if (intranet) { policiesMenu.addItem(new YAHOO.widget.MenuItem("Community Issues", {url: "/intranet/community_issues.html"})); }
policiesMenu.addItem(new YAHOO.widget.MenuItem("Bioethics Resources", {url: "http://www.nih.gov/sigs/bioethics/named_populations.html"}));
policiesMenu.addItem(new YAHOO.widget.MenuItem("UCSF Committee on Human Research (HRR'policies')", {url: "http://www.research.ucsf.edu/chr/"}));
policiesMenu.addItem(new YAHOO.widget.MenuItem("UCSF CHR Guidelines", {url: "http://www.research.ucsf.edu/chr/Guide/chr10_ConsentGuides.asp"}));
var policiesMenuBarItem = new YAHOO.widget.MenuBarItem("Policies", {url: "/cgi-bin/menu.py?menu=policies", submenu: policiesMenu});
var statsMenu = new YAHOO.widget.Menu("statsmenu");
if (intranet) { statsMenu.addItem(new YAHOO.widget.MenuItem("Hardy-Weinberg Equilibrium", {url: "/cgi-bin/intranet/hwe.py"})); }
if (intranet) { statsMenu.addItem(new YAHOO.widget.MenuItem("Web Statistics", {url: "http://www.cgl.ucsf.edu/reports/webstats/pharmacogenetics.ucsf.edu.html"})); }
var statsMenuBarItem = new YAHOO.widget.MenuBarItem("Statistics", {url: "/cgi-bin/menu.py?menu=stats", submenu: statsMenu});
var oldsiteMenu = new YAHOO.widget.Menu("oldsitemenu");
var oldsiteMenuBarItem = new YAHOO.widget.MenuBarItem("Old Site", {url: "/intranet/oldsite/index.html"});
var publicsiteMenu = new YAHOO.widget.Menu("publicsitemenu");
var publicsiteMenuBarItem = new YAHOO.widget.MenuBarItem("Public Site", {url: "http://pharmacogenetics.ucsf.edu/"});

	// SET UP MENU BAR
	var navMenuBar = new YAHOO.widget.MenuBar("navmenubar", {
		autosubmenudisplay: true,
		hidedelay: 750,
		lazyload: true });
	YAHOO.util.Dom.addClass(navMenuBar.element, "yuimenubarnav"); // adds triangle arrows

navMenuBar.addItem(infoMenuBarItem);
navMenuBar.addItem(dataMenuBarItem);
if (intranet) { navMenuBar.addItem(toolsMenuBarItem); }
navMenuBar.addItem(policiesMenuBarItem);
if (intranet) { navMenuBar.addItem(statsMenuBarItem); }
if (intranet) { navMenuBar.addItem(oldsiteMenuBarItem); }
if (intranet) { navMenuBar.addItem(publicsiteMenuBarItem); }

	// for public site only
	if (! intranet) { 
		navMenuBar.addItem(new YAHOO.widget.MenuBarItem("Intranet", {
			url: "https://pharmacogenetics.ucsf.edu:8001/"
		}));
	};

	navMenuBar.render("navmenu");
	// Display different color on intranet template to help orient users.
	// Must occur after rendering of menus.
	if (intranet) {
		$('.yui-skin-sam .yuimenubar')
			.css('background', '#669933')
			.css('border', '1px solid #669933');
		$('.yui-skin-sam .yuimenubarnav .yuimenubaritem')
			.css('border', '1px solid #669933');
		$('.yui-skin-sam .yuimenuitemlabel-selected')
			.css('color', '#669933');
		$('#pmtnav').css('background-color', '#669933');
	}
	navMenuBar.show();

	// CONTACT "MENU"
	var contactMenuBarItem = new YAHOO.widget.MenuBarItem("CONTACT US",
		{ url: "/contact.html" });
	var contactMenuBar = new YAHOO.widget.MenuBar("contactmenubar", {
		autosubmenudisplay: true,
		hidedelay: 750,
		lazyload: true });
	contactMenuBar.addItem(contactMenuBarItem);
	contactMenuBar.render("contactmenu");
	contactMenuBar.show();
});