4fc853e7da49682627c5dcaf82ce7b76d923ea2b
max
  Tue Oct 13 18:59:56 2015 -0700
Revert "Revert "adding menu entries under genomes and genome browser, refs #16022""

This reverts commit 006f356d9ec06729b2693cfeda849e5a6c67c4dd.

diff --git src/hg/js/jquery.plugins.js src/hg/js/jquery.plugins.js
index 01f5828..54f683b 100644
--- src/hg/js/jquery.plugins.js
+++ src/hg/js/jquery.plugins.js
@@ -1,492 +1,492 @@
 /* JQuery Plugins + some code required for drop down menus
  * Must be loaded after jquery.js
  *
  * CONTENTS:
  * drupal.js (Jabico used this for the dropdown menus)
  * bgiframe v2.1
  * hoverIntent r5
  * Superfish v1.4.8 - jQuery menu widget
  * Superfish initialization (Add Superfish to all Nice menus with some basic options.)
  
  */
 
 
 
 /* This first one is not actually a JQuery plugin, 
 but drupal.js required for nicemenus.js to work */
 
 var Drupal = Drupal || { 'settings': {}, 'behaviors': {}, 'themes': {}, 'locale': {} };
 
 /**
  * Set the variable that indicates if JavaScript behaviors should be applied
  */
 Drupal.jsEnabled = document.getElementsByTagName && document.createElement && document.createTextNode && document.documentElement && document.getElementById;
 
 /**
  * Attach all registered behaviors to a page element.
  *
  * Behaviors are event-triggered actions that attach to page elements, enhancing
  * default non-Javascript UIs. Behaviors are registered in the Drupal.behaviors
  * object as follows:
  * @code
  *    Drupal.behaviors.behaviorName = function () {
  *      ...
  *    };
  * @endcode
  *
  * Drupal.attachBehaviors is added below to the jQuery ready event and so
  * runs on initial page load. Developers implementing AHAH/AJAX in their
  * solutions should also call this function after new page content has been
  * loaded, feeding in an element to be processed, in order to attach all
  * behaviors to the new content.
  *
  * Behaviors should use a class in the form behaviorName-processed to ensure
  * the behavior is attached only once to a given element. (Doing so enables
  * the reprocessing of given elements, which may be needed on occasion despite
  * the ability to limit behavior attachment to a particular element.)
  *
  * @param context
  *   An element to attach behaviors to. If none is given, the document element
  *   is used.
  */
 Drupal.attachBehaviors = function(context) {
   context = context || document;
   if (Drupal.jsEnabled) {
     // Execute all of them.
     jQuery.each(Drupal.behaviors, function() {
       this(context);
     });
   }
 };
 
 /**
  * Encode special characters in a plain-text string for display as HTML.
  */
 Drupal.checkPlain = function(str) {
   str = String(str);
   var replace = { '&': '&amp;', '"': '&quot;', '<': '&lt;', '>': '&gt;' };
   for (var character in replace) {
     var regex = new RegExp(character, 'g');
     str = str.replace(regex, replace[character]);
   }
   return str;
 };
 
 /**
  * Translate strings to the page language or a given language.
  *
  * See the documentation of the server-side t() function for further details.
  *
  * @param str
  *   A string containing the English string to translate.
  * @param args
  *   An object of replacements pairs to make after translation. Incidences
  *   of any key in this array are replaced with the corresponding value.
  *   Based on the first character of the key, the value is escaped and/or themed:
  *    - !variable: inserted as is
  *    - @variable: escape plain text to HTML (Drupal.checkPlain)
  *    - %variable: escape text and theme as a placeholder for user-submitted
  *      content (checkPlain + Drupal.theme('placeholder'))
  * @return
  *   The translated string.
  */
 Drupal.t = function(str, args) {
   // Fetch the localized version of the string.
   if (Drupal.locale.strings && Drupal.locale.strings[str]) {
     str = Drupal.locale.strings[str];
   }
 
   if (args) {
     // Transform arguments before inserting them
     for (var key in args) {
       switch (key.charAt(0)) {
         // Escaped only
         case '@':
           args[key] = Drupal.checkPlain(args[key]);
         break;
         // Pass-through
         case '!':
           break;
         // Escaped and placeholder
         case '%':
         default:
           args[key] = Drupal.theme('placeholder', args[key]);
           break;
       }
       str = str.replace(key, args[key]);
     }
   }
   return str;
 };
 
 /**
  * Format a string containing a count of items.
  *
  * This function ensures that the string is pluralized correctly. Since Drupal.t() is
  * called by this function, make sure not to pass already-localized strings to it.
  *
  * See the documentation of the server-side format_plural() function for further details.
  *
  * @param count
  *   The item count to display.
  * @param singular
  *   The string for the singular case. Please make sure it is clear this is
  *   singular, to ease translation (e.g. use "1 new comment" instead of "1 new").
  *   Do not use @count in the singular string.
  * @param plural
  *   The string for the plural case. Please make sure it is clear this is plural,
  *   to ease translation. Use @count in place of the item count, as in "@count
  *   new comments".
  * @param args
  *   An object of replacements pairs to make after translation. Incidences
  *   of any key in this array are replaced with the corresponding value.
  *   Based on the first character of the key, the value is escaped and/or themed:
  *    - !variable: inserted as is
  *    - @variable: escape plain text to HTML (Drupal.checkPlain)
  *    - %variable: escape text and theme as a placeholder for user-submitted
  *      content (checkPlain + Drupal.theme('placeholder'))
  *   Note that you do not need to include @count in this array.
  *   This replacement is done automatically for the plural case.
  * @return
  *   A translated string.
  */
 Drupal.formatPlural = function(count, singular, plural, args) {
   var args = args || {};
   args['@count'] = count;
   // Determine the index of the plural form.
   var index = Drupal.locale.pluralFormula ? Drupal.locale.pluralFormula(args['@count']) : ((args['@count'] == 1) ? 0 : 1);
 
   if (index == 0) {
     return Drupal.t(singular, args);
   }
   else if (index == 1) {
     return Drupal.t(plural, args);
   }
   else {
     args['@count['+ index +']'] = args['@count'];
     delete args['@count'];
     return Drupal.t(plural.replace('@count', '@count['+ index +']'));
   }
 };
 
 /**
  * Generate the themed representation of a Drupal object.
  *
  * All requests for themed output must go through this function. It examines
  * the request and routes it to the appropriate theme function. If the current
  * theme does not provide an override function, the generic theme function is
  * called.
  *
  * For example, to retrieve the HTML that is output by theme_placeholder(text),
  * call Drupal.theme('placeholder', text).
  *
  * @param func
  *   The name of the theme function to call.
  * @param ...
  *   Additional arguments to pass along to the theme function.
  * @return
  *   Any data the theme function returns. This could be a plain HTML string,
  *   but also a complex object.
  */
 Drupal.theme = function(func) {
   for (var i = 1, args = []; i < arguments.length; i++) {
     args.push(arguments[i]);
   }
 
   return (Drupal.theme[func] || Drupal.theme.prototype[func]).apply(this, args);
 };
 
 /**
  * Parse a JSON response.
  *
  * The result is either the JSON object, or an object with 'status' 0 and 'data' an error message.
  */
 Drupal.parseJson = function (data) {
   if ((data.substring(0, 1) != '{') && (data.substring(0, 1) != '[')) {
     return { status: 0, data: data.length ? data : Drupal.t('Unspecified error') };
   }
   return eval('(' + data + ');');
 };
 
 /**
  * Freeze the current body height (as minimum height). Used to prevent
  * unnecessary upwards scrolling when doing DOM manipulations.
  */
 Drupal.freezeHeight = function () {
   Drupal.unfreezeHeight();
   var div = document.createElement('div');
   $(div).css({
     position: 'absolute',
     top: '0px',
     left: '0px',
     width: '1px',
     height: $('body').css('height')
   }).attr('id', 'freeze-height');
   $('body').append(div);
 };
 
 /**
  * Unfreeze the body height
  */
 Drupal.unfreezeHeight = function () {
   $('#freeze-height').remove();
 };
 
 /**
  * Wrapper around encodeURIComponent() which avoids Apache quirks (equivalent of
  * drupal_urlencode() in PHP). This function should only be used on paths, not
  * on query string arguments.
  */
 Drupal.encodeURIComponent = function (item, uri) {
   uri = uri || location.href;
   item = encodeURIComponent(item).replace(/%2F/g, '/');
   return (uri.indexOf('?q=') != -1) ? item : item.replace(/%26/g, '%2526').replace(/%23/g, '%2523').replace(/\/\//g, '/%252F');
 };
 
 /**
  * Get the text selection in a textarea.
  */
 Drupal.getSelection = function (element) {
   if (typeof(element.selectionStart) != 'number' && document.selection) {
     // The current selection
     var range1 = document.selection.createRange();
     var range2 = range1.duplicate();
     // Select all text.
     range2.moveToElementText(element);
     // Now move 'dummy' end point to end point of original range.
     range2.setEndPoint('EndToEnd', range1);
     // Now we can calculate start and end points.
     var start = range2.text.length - range1.text.length;
     var end = start + range1.text.length;
     return { 'start': start, 'end': end };
   }
   return { 'start': element.selectionStart, 'end': element.selectionEnd };
 };
 
 /**
  * Build an error message from ahah response.
  */
 Drupal.ahahError = function(xmlhttp, uri) {
   if (xmlhttp.status == 200) {
     if (jQuery.trim($(xmlhttp.responseText).text())) {
       var message = Drupal.t("An error occurred. \n@uri\n@text", {'@uri': uri, '@text': xmlhttp.responseText });
     }
     else {
       var message = Drupal.t("An error occurred. \n@uri\n(no information available).", {'@uri': uri, '@text': xmlhttp.responseText });
     }
   }
   else {
     var message = Drupal.t("An HTTP error @status occurred. \n@uri", {'@uri': uri, '@status': xmlhttp.status });
   }
   return message;
 }
 
 // Global Killswitch on the <html> element
 if (Drupal.jsEnabled) {
   // Global Killswitch on the <html> element
   $(document.documentElement).addClass('js');
   // 'js enabled' cookie
   document.cookie = 'has_js=1; path=/';
   // Attach all behaviors.
   $(document).ready(function() {
     Drupal.attachBehaviors(this);
   });
 }
 
 /**
  * The default themes.
  */
 Drupal.theme.prototype = {
 
   /**
    * Formats text for emphasized display in a placeholder inside a sentence.
    *
    * @param str
    *   The text to format (plain-text).
    * @return
    *   The formatted text (html).
    */
   placeholder: function(str) {
     return '<em>' + Drupal.checkPlain(str) + '</em>';
   }
 };
 
 
 
 
 /* bgiframe v2.1
  * Copyright (c) 2006 Brandon Aaron (http://brandonaaron.net)
  * Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) 
  * and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
  *
  * $LastChangedDate: 2007-06-19 20:25:28 -0500 (Tue, 19 Jun 2007) $
  * $Rev: 2111 $
  *
  * Version 2.1
  */
 (function($){$.fn.bgIframe=$.fn.bgiframe=function(s){if($.browser.msie&&parseInt($.browser.version)<=6){s=$.extend({top:'auto',left:'auto',width:'auto',height:'auto',opacity:true,src:'javascript:false;'},s||{});var prop=function(n){return n&&n.constructor==Number?n+'px':n;},html='<iframe class="bgiframe"frameborder="0"tabindex="-1"src="'+s.src+'"'+'style="display:block;position:absolute;z-index:-1;'+(s.opacity!==false?'filter:Alpha(Opacity=\'0\');':'')+'top:'+(s.top=='auto'?'expression(((parseInt(this.parentNode.currentStyle.borderTopWidth)||0)*-1)+\'px\')':prop(s.top))+';'+'left:'+(s.left=='auto'?'expression(((parseInt(this.parentNode.currentStyle.borderLeftWidth)||0)*-1)+\'px\')':prop(s.left))+';'+'width:'+(s.width=='auto'?'expression(this.parentNode.offsetWidth+\'px\')':prop(s.width))+';'+'height:'+(s.height=='auto'?'expression(this.parentNode.offsetHeight+\'px\')':prop(s.height))+';'+'"/>';return this.each(function(){if($('> iframe.bgiframe',this).length==0)this.insertBefore(document.createElement(html),this.firstChild);});}return this;};if(!$.browser.version)$.browser.version=navigator.userAgent.toLowerCase().match(/.+(?:rv|it|ra|ie)[\/: ]([\d.]+)/)[1];})(jQuery);
 
 
 
 /**
 * hoverIntent r5 // 2007.03.27 // jQuery 1.1.2+
 * <http://cherne.net/brian/resources/jquery.hoverIntent.html>
 * 
 * @param  f  onMouseOver function || An object with configuration options
 * @param  g  onMouseOut function  || Nothing (use configuration options object)
 * @author    Brian Cherne <brian@cherne.net>
 */
 (function($){$.fn.hoverIntent=function(f,g){var cfg={sensitivity:7,interval:100,timeout:0};cfg=$.extend(cfg,g?{over:f,out:g}:f);var cX,cY,pX,pY;var track=function(ev){cX=ev.pageX;cY=ev.pageY;};var compare=function(ev,ob){ob.hoverIntent_t=clearTimeout(ob.hoverIntent_t);if((Math.abs(pX-cX)+Math.abs(pY-cY))<cfg.sensitivity){$(ob).unbind("mousemove",track);ob.hoverIntent_s=1;return cfg.over.apply(ob,[ev]);}else{pX=cX;pY=cY;ob.hoverIntent_t=setTimeout(function(){compare(ev,ob);},cfg.interval);}};var delay=function(ev,ob){ob.hoverIntent_t=clearTimeout(ob.hoverIntent_t);ob.hoverIntent_s=0;return cfg.out.apply(ob,[ev]);};var handleHover=function(e){var p=(e.type=="mouseover"?e.fromElement:e.toElement)||e.relatedTarget;while(p&&p!=this){try{p=p.parentNode;}catch(e){p=this;}}if(p==this){return false;}var ev=jQuery.extend({},e);var ob=this;if(ob.hoverIntent_t){ob.hoverIntent_t=clearTimeout(ob.hoverIntent_t);}if(e.type=="mouseover"){pX=ev.pageX;pY=ev.pageY;$(ob).bind("mousemove",track);if(ob.hoverIntent_s!=1){ob.hoverIntent_t=setTimeout(function(){compare(ev,ob);},cfg.interval);}}else{$(ob).unbind("mousemove",track);if(ob.hoverIntent_s==1){ob.hoverIntent_t=setTimeout(function(){delay(ev,ob);},cfg.timeout);}}};return this.mouseover(handleHover).mouseout(handleHover);};})(jQuery);
 
 
 
 
 
 /*
  * Superfish v1.4.8 - jQuery menu widget
  * Copyright (c) 2008 Joel Birch
  *
  * Dual licensed under the MIT and GPL licenses:
  * 	http://www.opensource.org/licenses/mit-license.php
  * 	http://www.gnu.org/licenses/gpl.html
  *
  * CHANGELOG: http://users.tpg.com.au/j_birch/plugins/superfish/changelog.txt
  */
 
 ;(function($){
 	$.fn.superfish = function(op){
 
 		var sf = $.fn.superfish,
 			c = sf.c,
 			$arrow = $(['<span class="',c.arrowClass,'"> &#187;</span>'].join('')),
 			over = function(){
 				var $$ = $(this), menu = getMenu($$);
 				clearTimeout(menu.sfTimer);
 				$$.showSuperfishUl().siblings().hideSuperfishUl();
 			},
 			out = function(){
 				var $$ = $(this), menu = getMenu($$), o = sf.op;
 				clearTimeout(menu.sfTimer);
 				menu.sfTimer=setTimeout(function(){
 					o.retainPath=($.inArray($$[0],o.$path)>-1);
 					$$.hideSuperfishUl();
 					if (o.$path.length && $$.parents(['li.',o.hoverClass].join('')).length<1){over.call(o.$path);}
 				},o.delay);	
 			},
 			getMenu = function($menu){
 				var menu = $menu.parents(['ul.',c.menuClass,':first'].join(''))[0];
 				sf.op = sf.o[menu.serial];
 				return menu;
 			},
 			addArrow = function($a){ $a.addClass(c.anchorClass).append($arrow.clone()); };
 			
 		return this.each(function() {
 			var s = this.serial = sf.o.length;
 			var o = $.extend({},sf.defaults,op);
 			o.$path = $('li.'+o.pathClass,this).slice(0,o.pathLevels).each(function(){
 				$(this).addClass([o.hoverClass,c.bcClass].join(' '))
 					.filter('li:has(ul)').removeClass(o.pathClass);
 			});
 			sf.o[s] = sf.op = o;
 			
 			$('li:has(ul)',this)[($.fn.hoverIntent && !o.disableHI) ? 'hoverIntent' : 'hover'](over,out).each(function() {
 				if (o.autoArrows) addArrow( $('>a:first-child',this) );
 			})
 			.not('.'+c.bcClass)
 				.hideSuperfishUl();
 			
 			var $a = $('a',this);
 			$a.each(function(i){
 				var $li = $a.eq(i).parents('li');
 				$a.eq(i).focus(function(){over.call($li);}).blur(function(){out.call($li);});
 			});
 			o.onInit.call(this);
 			
 		}).each(function() {
 			var menuClasses = [c.menuClass];
 			if (sf.op.dropShadows  && !($.browser.msie && $.browser.version < 7)) menuClasses.push(c.shadowClass);
 			$(this).addClass(menuClasses.join(' '));
 		});
 	};
 
 	var sf = $.fn.superfish;
 	sf.o = [];
 	sf.op = {};
 	sf.IE7fix = function(){
 		var o = sf.op;
 		if ($.browser.msie && $.browser.version > 6 && o.dropShadows && o.animation.opacity!=undefined)
 			this.toggleClass(sf.c.shadowClass+'-off');
 		};
 	sf.c = {
 		bcClass     : 'sf-breadcrumb',
 		menuClass   : 'sf-js-enabled',
 		anchorClass : 'sf-with-ul',
 		arrowClass  : 'sf-sub-indicator',
 		shadowClass : 'sf-shadow'
 	};
 	sf.defaults = {
 		hoverClass	: 'sfHover',
 		pathClass	: 'overideThisToUse',
 		pathLevels	: 1,
 		delay		: 800,
 		animation	: {opacity:'show'},
 		speed		: 'normal',
 		autoArrows	: true,
 		dropShadows : true,
 		disableHI	: false,		// true disables hoverIntent detection
 		onInit		: function(){}, // callback functions
 		onBeforeShow: function(){},
 		onShow		: function(){},
 		onHide		: function(){}
 	};
 	$.fn.extend({
 		hideSuperfishUl : function(){
 			var o = sf.op,
 				not = (o.retainPath===true) ? o.$path : '';
 			o.retainPath = false;
 			var $ul = $(['li.',o.hoverClass].join(''),this).add(this).not(not).removeClass(o.hoverClass)
 					.find('>ul').hide().css('visibility','hidden');
 			o.onHide.call($ul);
 			return this;
 		},
 		showSuperfishUl : function(){
 			var o = sf.op,
 				sh = sf.c.shadowClass+'-off',
 				$ul = this.addClass(o.hoverClass)
 					.find('>ul:hidden').css('visibility','visible');
 			sf.IE7fix.call($ul);
 			o.onBeforeShow.call($ul);
 			$ul.animate(o.animation,o.speed,function(){ sf.IE7fix.call($ul); o.onShow.call($ul); });
 			return this;
 		}
 	});
 
 })(jQuery);
 
 
 
 
 
 
 // This uses Superfish 1.4.8
 // (http://users.tpg.com.au/j_birch/plugins/superfish)
 // Add Superfish to all Nice menus with some basic options.
 (function ($) {
   $(document).ready(function() {
     $('ul.nice-menu').superfish({
       // Apply a generic hover class.
       hoverClass: 'over',
       // Disable generation of arrow mark-up.
-      autoArrows: true,
+      autoArrows: false,
       // Disable drop shadows.
       dropShadows: false,
       // Mouse delay.
       delay: Drupal.settings.nice_menus_options.delay,
       // Animation speed.
       speed: Drupal.settings.nice_menus_options.speed
     // Add in Brandon Aaron’s bgIframe plugin for IE select issues.
     // http://plugins.jquery.com/node/46/release
     }).find('ul').bgIframe({opacity:false});
     $('ul.nice-menu ul').css('display', 'none');
   });
 })(jQuery);