diff --git a/VQI_PathwayEditor.js b/VQI_PathwayEditor.js
index 7fe7b3f..2ac818b 100755
--- a/VQI_PathwayEditor.js
+++ b/VQI_PathwayEditor.js
@@ -1,2069 +1,2082 @@
-var VQI_PathwayEditor = function(parent) {
-
-	var self = this;
-
-	//Web services
-	var serverURL = "http://cardinal3.engr.uconn.edu/pathwayVisual/";
-	var services = {};
-
-	services['pathwayFinder'] = serverURL + 'PathwayParser/ajaxJSON.php';
-	services['pathwaySaver'] = serverURL + 'PathwayParser/updateDB_json.php';
-        services['pathwayScorer'] = 'http://137.99.11.36/pathwayVisual/ScoreSystem/getScore.php';
-        services['pathwayWeightedScorer'] = 'http://137.99.11.122/pathway2/pathwayweightedscorer.php';
-	services['objectFinder'] = 'http://137.99.11.122/pathway2/qsys_json.php';
-
-	// Globals
-	var states = [];
-	var types = ["bundleOne", "bundleTwo", "gene", "geneProduct", "protein", "rna", "microRNA", "kinase", "ligand", "receptor", "biologicalProcess", "triangle","ellipse","pentagon","hexagon","heptagon","octagon","star","diamond","vee","rhomboid","label"];
-	var stateRecycle = [];
-	var lastEvent = 0;
-	var selectedForQueryNodes = [];
-	var selectedForEditNodes = [];
-	var selectedForEditEdges = [];
-	var orderedSelectedNodes = [];
-	var grabbedCollapsedForEditNodes = [];
-	var coloredNodes = [];
-	var edgeCounter = 0;
-	var nodeCounter = 0;
-	var loadCounts = 0;
-	var target = 0;
-	var header = "";
-	var counts = {};
-	var strInfo;
-	var highestZOrder = 999;
-
-	var strVar = "";
-	strVar += " <nav class=\"navbar navbar-default\">";
-	strVar += " <div class=\"container-fluid\">";
-	strVar += " <div class=\"navbar-header\">";
-	strVar += " 	<a class=\"navbar-brand\" href=\"#\">Pathway name</a>";
-	strVar += " <\/div>";
-	strVar += " <ul class=\"nav navbar-nav\">";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += " 		<label for=\"" + parent + "-file-pathway\">Local Pathway File:<\/label>";
-	strVar += "			<input id=\"" + parent + "-file-pathway\" value=\"Pick Pathway File\" type=\"file\"><\/input>";
-	strVar += " 	<\/li>";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += " 		<label for=\"" + parent + "-file-coloring\">Local Pathway Coloring:<\/label>";
-	strVar += "			<input id=\"" + parent + "-file-coloring\" value=\"Pick Spray File\" type=\"file\"><\/input>";
-	strVar += " 	<\/li>";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += " 		<label for=\"" + parent + "-pathway-selector\">Pathway:<\/label>";
-	strVar += " 		<select style=\"width: 150px\" id=\"" + parent + "-pathway-selector\" name=\"" + parent + "-pathway-selector\">";
-	strVar += "  			<option selected=\"\">Please Select<\/option>";
-	strVar += "			<\/select>";
-	strVar += " 	<\/li>";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += "			<div class=\"dropdown\">";
-	strVar += "  			<button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Edit<span class=\"caret\"><\/span><\/button>";
-	strVar += "				<ul class=\"dropdown-menu\">";
-	strVar += "					<li><input id=\"" + parent + "-add-node\" value=\"Add Node\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "					<li><input id=\"" + parent + "-add-edge\" value=\"Add Edge\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += " 				<li><input id=\"" + parent + "-delete-elements\" value=\"Delete Selected Element(s)\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += " 				<li role=\"separator\" class=\"divider\"></li>";
-	strVar += "					<li><input id=\"" + parent + "-bundle\" value=\"Bundle\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "					<li><input id=\"" + parent + "-unbundle\" value=\"Unbundle\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "					<li><input id=\"" + parent + "-collapse\" value=\"Collapse\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "					<li><input id=\"" + parent + "-expand\" value=\"Expand\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "				<\/ul>";
-	strVar += "			</div>";
-	strVar += " 	<\/li>";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += "			<div class=\"dropdown\">";
-	strVar += "  			<button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Process<span class=\"caret\"><\/span><\/button>";
-	strVar += "				<ul class=\"dropdown-menu\">";
-	strVar += "					<li><input id=\"" + parent + "-findpath\" value=\"Find Pathway\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "					<li><input id=\"" + parent + "-find-object\" value=\"Find Object\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "				<\/ul>";
-	strVar += "			</div>";
-	strVar += " 	<\/li>";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += "			<div class=\"dropdown\">";
-	strVar += "  			<button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Archive<span class=\"caret\"><\/span><\/button>";
-	strVar += "				<ul class=\"dropdown-menu\">";
-	strVar += "					<li><input id=\"" + parent + "-pathway-save\" value=\"Save\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-	strVar += "					<li><input id=\"" + parent + "-pathway-saveAs\" value=\"SaveAs\" type=\"button\" class=\"btn btn-link disabled\"><\/li>";
-	strVar += " 				<li><input id=\"" + parent + "-produce-JSON\" value=\"Export JSON\" type=\"button\" class=\"btn btn-link disabled\"><\/li>";
-	strVar += "				<\/ul>";
-	strVar += "			<\/div>";
-	strVar += " 	<li\">";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += "			<input id=\"" + parent + "-undo\" value=\"Undo\" type=\"button\" class=\"btn btn-primary disabled\"><\/input>";
-	strVar += " 	<\/li>";
-	strVar += " 	<li style=\"margin: 2px\">";
-	strVar += "			<input id=\"" + parent + "-redo\" value=\"Redo\" type=\"button\" class=\"btn btn-primary disabled\"><\/input>";
-	strVar += " 	<\/li>";
-	strVar += " <\/ul>";
-	strVar += " <\/div>";
-	strVar += " <\/nav>";
-	strVar += " <div id=\"" + parent + "-dialog-table\" title=\"Result\">";
-	strVar += "	<table id=\"" + parent + "-inner-table\" class=\"table table-hover\">";
-	strVar += "		<tr>";
-	strVar += "         <td>name</td>";
-	strVar += "			<td>percentage</td>";
-	strVar += "			<td>rna distance</td>";
-	strVar += "			<td>cnv distance</td>";
-	strVar += "			<td>mut distance</td>";
-	strVar += "	</table>";
-	strVar += "	<\/div>";
-	strVar += " <div id=\"" + parent + "-dialog-form-save-as-pathway\" title=\"SaveAs\">";
-	strVar += " 		<form role=\"form\">";
-	strVar += "    		<fieldset>";
-	strVar += "      			<label for=\"" + parent + "-pathway-name\">pathway-name:<\/label>";
-	strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-pathway-name\" id=\"" + parent + "-pathway-name\"><br>";
-	strVar += " 				<input type=\"submit\" class=\"btn btn-default\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
-	strVar += "    		<\/fieldset>";
-	strVar += " 		<\/form>";
-	strVar += "	<\/div>";
-	strVar += " <div id=\"" + parent + "-dialog-form-new-pathway\" title=\"New Pathway\">";
-	strVar += " 		<form role=\"form\">";
-	strVar += "    		<fieldset>";
-	strVar += "      			<label for=\"" + parent + "-new-pathway-name\">pathway-name:<\/label>";
-	strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-new-pathway-name\" id=\"" + parent + "-new-pathway-name\"><br>";
-	strVar += " 				<input type=\"submit\" class=\"btn btn-default\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
-	strVar += "    		<\/fieldset>";
-	strVar += " 		<\/form>";
-	strVar += "	<\/div>";
-	strVar += " <div id=\"" + parent + "-dialog-bundle\" title=\"Bundle\">";
-	strVar += " 		<form role=\"form\">";
-	strVar += "    		<fieldset>";
-	strVar += "      			<label for=\"" + parent + "-type-bundle\">type:<\/label>";
-	strVar += "      			<select style=\"width: 150px\" id=\"" + parent + "-type-bundle\" name=\"" + parent + "-type-bundle\">";
-	strVar += "  					<option selected=\"\">bundleOne<\/option>";
-	strVar += "  					<option>bundleTwo<\/option>";
-	strVar += "				<\/select>";
-	strVar += "    		<\/fieldset>";
-	strVar += " 		<\/form>";
-	strVar += "	<\/div>";
-	strVar += " <div id=\"" + parent + "-dialog-form-find-path\" title=\"Find path\">";
-	strVar += " 		<form role=\"form\">";
-	strVar += "    		<fieldset>";
-	strVar += "      			<label for=\"" + parent + "-sid\">sid:<\/label>";
-	strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-sid\" id=\"" + parent + "-sid\"><br>";
-	strVar += "      			<label for=\"" + parent + "-vid\">vid:<\/label>";
-	strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-vid\" id=\"" + parent + "-vid\"><br>";
-	strVar += " 				<input type=\"submit\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
-	strVar += "    		<\/fieldset>";
-	strVar += " 		<\/form>";
-	strVar += "	<\/div>";
-	strVar += "	<div id=\"" + parent + "-dialog-form-edge\" title=\"Edit edge\">";
-	strVar += " 		<form role=\"form\">";
-	strVar += "    		<fieldset>";
-	strVar += "      			<label for=\"" + parent + "-direction\">change direction:<\/label>";
-	strVar += "      			<input type=\"checkbox\" class=\"form-control\" name=\"" + parent + "-direction\" id=\"" + parent + "-direction\" value=\"Yes\"><\/input>";
-	strVar += "      			<label for=\"" + parent + "-arrow-type-edge\">arrow type:<\/label>";
-	strVar += "      			<select style=\"width: 150px\" class=\"form-control\" id=\"" + parent + "-arrow-type-edge\" name=\"" + parent + "-arrow-type-edge\">";
-	strVar += "  					<option selected=\"\">TBar<\/option>";
-	strVar += "  					<option>Arrow<\/option>";
-	strVar += "  					<option>Line<\/option>";
-	strVar += "					<\/select>";
-	strVar += "      			<label for=\"" + parent + "-line-type-edge\">line type:<\/label>";
-	strVar += "      			<select style=\"width: 150px\" class=\"form-control\" id=\"" + parent + "-line-type-edge\" name=\"" + parent + "-line-type-edge\">";
-	strVar += "  					<option selected=\"\">Solid<\/option>";
-	strVar += "  					<option>Dotted<\/option>";
-	strVar += "  					<option>Dashed<\/option>";
-	strVar += "					<\/select>";
-	strVar += "    				<label for=\"" + parent + "-edge-move-to-background\">Move to Background:<\/label>";
-	strVar += "    				<input id=\"" + parent + "-edge-move-to-background\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
-	strVar += "    				<label for=\"" + parent + "-edge-move-to-foreground\">Move to Foreground:<\/label>";
-	strVar += "    				<input id=\"" + parent + "-edge-move-to-foreground\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
-	strVar += " 			<input type=\"submit\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
-	strVar += "    		<\/fieldset>";
-	strVar += "  		<\/form>";
-	strVar += "	<\/div>";
-	strVar += "<div id=\"" + parent + "-intro-hero-unit\" class=\"container\"style=\"margin-top: 100px\">";
-	strVar += "		<div class=\"jumbotron\">";
-	strVar += "			<h1>Pathway Editor</h1>";
-	strVar += "			<p><i>Pre-alpha version of the pathway editor. You can either start a new pathway or load an existing one...</i></p>";
-	strVar += " 		<input id=\"" + parent + "-new-pathway\" value=\"New Pathway\" type=\"button\" class=\"btn btn-success\"><\/input>";
-	strVar += " 		<a id=\"" + parent + "-link-github\" type=\"button\" class=\"btn btn-success\" href=\"https://github.uconn.edu/ivp08001/pathway\">Github Source<\/a>";
-	strVar += "     </div>";
-	strVar += " </div>";
-	strVar += "	<div id=\"" + parent + "-dialog-form-node\" title=\"Edit node\">";
-	strVar += " 		<form role=\"form\">";
-	strVar += "    		<fieldset>";
-	strVar += "      			<label for=\"" + parent + "-gene-name\">gene-name:<\/label>";
-	strVar += "      			<input type=\"text\" name=\"" + parent + "-gene-name\" class=\"form-control\" id=\"" + parent + "-gene-name\" value=\"\" class=\"text ui-widget-content ui-corner-all\"><\/input>";
-	strVar += "      			<label for=\"" + parent + "-height\">height:<\/label>";
-	strVar += "      			<input type=\"text\" name=\"" + parent + "-height\" id=\"" + parent + "-height\" class=\"form-control\" value=\"\" class=\"text ui-widget-content ui-corner-all\"><\/input>";
-	strVar += "      			<label for=\"" + parent + "-width\">width:<\/label>";
-	strVar += "      			<input type=\"text\" name=\"" + parent + "-width\" id=\"" + parent + "-width\" class=\"form-control\" value=\"\" class=\"text ui-widget-content ui-corner-all\"><\/input>";
-	strVar += "      			<label for=\"" + parent + "-type-node\">type:<\/label>";
-	strVar += "      			<select style=\"width: 150px\" id=\"" + parent + "-type-node\" class=\"form-control\" name=\"" + parent + "-type-node\">";
-	strVar += "  					<option id=\"" + parent + "-select-bundleOne\" selected=\"\">bundleOne<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-bundleTwo\">bundleTwo<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-gene\">gene<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-geneProduct\">geneProduct<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-protein\">protein<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-rna\">rna<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-mircoRNA\">microRNA<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-kinase\">kinase<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-ligand\">ligand<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-receptor\">receptor<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-biologicalProcess\">biologicalProcess<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-triangle\">triangle<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-ellipse\">ellipse<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-pentagon\">pentagon<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-hexagon\">hexagon<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-heptagon\">heptagon<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-octagon\">octagon<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-star\">star<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-diamond\">diamond<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-vee\">vee<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-rhomboid\">rhomboid<\/option>";	
-	strVar += "  					<option id=\"" + parent + "-select-label\">label<\/option>";
-	strVar += "					<\/select>";
-	strVar += "      			<label for=\"" + parent + "-rna\">RNA:<\/label>";
-	strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-rna\" class=\"form-control\" name=\"" + parent + "-rna\">";
-	strVar += "					<label for=\"" + parent + "-cnv\">CNV:<\/label>";
-	strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-cnv\" class=\"form-control\" name=\"" + parent + "-cnv\">";
-	strVar += "					<label for=\"" + parent + "-mut\">MUT:<\/label>";
-	strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-mut\" class=\"form-control\" name=\"" + parent + "-mut\">";
-	strVar += " 			    <input type=\"submit\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
-	strVar += "    				<label for=\"" + parent + "-background-image\">Local Image File:<\/label>";
-	strVar += "					<input id=\"" + parent + "-background-image\" value=\"Pick an Image File\" type=\"file\"><\/input>";
-	strVar += "    				<label for=\"" + parent + "-background-image-remove\">Remove Background image:<\/label>";
-	strVar += "					<input id=\"" + parent + "-background-image-remove\" value=\"Remove\" type=\"button\" class=\"btn btn-link\"><\/input>";
-	strVar += "    				<label for=\"" + parent + "-node-move-to-background\">Move to Background:<\/label>";
-	strVar += "    				<input id=\"" + parent + "-node-move-to-background\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
-	strVar += "    				<label for=\"" + parent + "-node-move-to-foreground\">Move to Foreground:<\/label>";
-	strVar += "    				<input id=\"" + parent + "-node-move-to-foreground\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
-	strVar += "				<\/fieldset>";
-	strVar += "  		<\/form>";
-	strVar += "	<\/div>";
-	strVar += "	<div id=\"" + parent + "-cy\" style=\"height: 100%;width: 100%;position: absolute; left: 0;\"><\/div>";
-
-	document.getElementById(parent).innerHTML = strVar;
-
-	$(function() {// on dom ready
-
-		function removeHeroUnit() {
-			var heroUnit = document.getElementById(parent + "-intro-hero-unit");
-			if (heroUnit != null)
-				heroUnit.parentNode.removeChild(heroUnit);
-		}
-
-		function newPathway(event) {
-			var name = document.getElementById(parent + "-new-pathway-name").value;
-			var data = '{"format_version" : "1.0","generated_by" : "cytoscape-3.2.1","target_cytoscapejs_version" : "~2.1","data" :{"shared_name":"","ID":"","BOARDWIDTH":"","BOARDHEIGHT":"","LICENSE":"CC BY 2.0","ORGANISM":"","NAME":"","INSTRUCTION":"","AUTHOR":"","VERSION":"","PATHWAY_TYPE":"original","SUID":205,"__Annotations":[],"selected":true},"elements" : {"nodes" :[],"edges" :[]}}'
-			var obj = JSON.parse(data);
-			removeHeroUnit();
-			setElements(obj);
-			dialogNewPathway.dialog("close");
-		}
-
-		function onChangePathwayFile(event) {
-			var reader = new FileReader();
-			reader.onload = onPathwayReaderLoad;
-			reader.readAsText(event.target.files[0]);
-			removeHeroUnit();
-		}
-
-		function collapseBundle(event) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			for (var i = 0; i < selectedForEditNodes.size(); i++) {
-				if (selectedForEditNodes[i].isParent()) {
-					selectedForEditNodes[i].descendants().addClass('collapsed');
-					selectedForEditNodes[i].descendants().unselectify();
-					selectedForEditNodes[i].descendants().ungrabify();
-					selectedForEditNodes[i].descendants().positions({
-						x : selectedForEditNodes[i].position('x') + selectedForEditNodes[i].width() / 2,
-						y : selectedForEditNodes[i].position('y') + selectedForEditNodes[i].height() / 2
-					});
-				}
-			}
-			saveState();
-		}
-
-		function expandBundle(event) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			for (var i = 0; i < selectedForEditNodes.size(); i++) {
-				if (selectedForEditNodes[i].isParent()) {
-					selectedForEditNodes[i].descendants().removeClass('collapsed');
-					selectedForEditNodes[i].descendants().selectify();
-					selectedForEditNodes[i].descendants().grabify();
-				}
-			}
-			saveState();
-		}
-
-		function onChangeColoringFile(event) {
-			var reader = new FileReader();
-			reader.onload = onColoringReaderLoad;
-			reader.readAsText(event.target.files[0]);
-			saveState();
-		}
-
-		function postAddProcessing() {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			
-			//Post-Add Process
-			for (var i = 0; i < cy.$("node").length; i++) {
-				if ( typeof (cy.$("node")[i].data("backgroundImage")) != "undefined" && cy.$("node")[i].data("backgroundImage") != "") {
-					cy.$("node")[i].style("backgroundImage", cy.$("node")[i].data("backgroundImage"));
-					cy.$("node")[i].data("Type", "image");
-				}
-			}
-
-			for (var i = 0; i < cy.$("node").length; i++) {
-				if ( typeof (cy.$("node")[i].data("zIndex")) != "undefined") {
-					cy.$("node")[i].style("zIndex", cy.$("node")[i].data("zIndex"));
-				}
-			}
-		}
-		
-		function preAddProcessing(obj) {
-			for (var i = 0; i < obj.elements.nodes.length; i++) {
-				if (obj.elements.nodes[i].data.id.substring(0, 1) == "n") {
-					var number = parseInt(obj.elements.nodes[i].data.id.substring(1, obj.elements.nodes.length - 1));
-					if (number > nodeCounter)
-						nodeCounter = number + 1;
-				}
-					
-				if (types.indexOf(obj.elements.nodes[i].data.backgroundImage) == -1) {
-					obj.elements.nodes[i].data.backgroundImage = "";
-				}
-					
-				if (types.indexOf(obj.elements.nodes[i].data.zIndex) == -1) {
-					obj.elements.nodes[i].data.zIndex = 0;
-				}
-					
-				if (types.indexOf(obj.elements.nodes[i].data.Type) == -1) {
-					obj.elements.nodes[i].data.Type = "label";
-				}
-					
-				if (typeof (obj.elements.nodes[i].data.rna) == "undefined") {
-					obj.elements.nodes[i].data.rna = 0;
-				}
-				
-				if (typeof (obj.elements.nodes[i].data.cnv) == "undefined") {
-					obj.elements.nodes[i].data.cnv = 0;
-				}
-					
-				if (typeof (obj.elements.nodes[i].data.mut) == "undefined") {
-					obj.elements.nodes[i].data.mut = 0;
-				}
-			}
-			
-			for (var i = 0; i < obj.elements.edges.length; i++) {
-				if (obj.elements.edges[i].data.id.substring(0, 1) == "e") {
-					var number = parseInt(obj.elements.edges[i].data.id.substring(1, obj.elements.edges.length - 1));
-					if (number > edgeCounter)
-						edgeCounter = number + 1;
-				}
-			}
-		}
-
-		function setElements(obj) {
-			if (loadCounts == 0) {
-				header = obj.data;
-				visualPathway(obj);
-			} else {
-
-				// Pre-Add process
-
-				var cy = $('#' + parent + '-cy').cytoscape('get');
-				for (var i = 0; i < obj.elements.nodes.length; i++) {
-					obj.elements.nodes[i].position.x = obj.elements.nodes[i].position.x + 1000 * loadCounts;
-				}
-
-				preProcessingAdd(obj);
-
-				// Add nodes
-				cy.add(obj.elements);
-				cy.center();
-				cy.fit();
-
-				//Post-Add Process
-				postAddProcessing();
-
-			}
-			loadCounts++;
-			saveState();
-		}
-
-		function loadPathway(id) {
-			$.post(services['pathwayFinder'], {
-				pid : id
-			}, function(data) {
-				removeHeroUnit();
-				var obj = JSON.parse(data);
-				setElements(obj);
-			});
-		}
-
-		function onSelect(event) {
-			var id = event.target.value;
-			loadPathway(id);
-		}
-
-		function saveAsPathway(event) {
-			var obj = JSON.parse(states[states.length - 1]);
-			obj.data.NAME = document.getElementById(parent + "-pathway-name").value;
-			$.post(services['pathwaySaver'], {
-				insertPathway : JSON.stringify(obj)
-			}, function(data) {
-				if (data != "Success!") {
-					obj.data.ID = data;
-					$.post(services['pathwaySaver'], {
-						updatePathway : JSON.stringify(obj)
-					}, function(data) {
-						console.log(data)
-						dialogPathwaySaveAs.dialog("close");
-					});
-				} else {
-					refreshPathwayList();
-					dialogPathwaySaveAs.dialog("close");
-				}
-			});
-		}
-
-		function savePathway(event) {
-			var obj = JSON.parse(states[states.length - 1]);
-			$.post(services['pathwaySaver'], {
-				updatePathway : JSON.stringify(obj)
-			}, function(data) {
-				console.log(data);
-				dialogPathwaySaveAs.dialog("close");
-			});
-		}
-
-		function onPathwayReaderLoad(event) {
-			var obj = JSON.parse(event.target.result);
-			setElements(obj);
-		}
-
-		function onColoringReaderLoad(event) {
-			var list = this.result.split('\n');
-			var lines = [];
-
-			for (var line = 1; line < list.length; line++) {
-				lines[line] = list[line].split('\t');
-			}
-
-			sprayColor(lines);
-		}
-
-		function sprayColor(lines) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			for (var line = 1; line < lines.length; line++) {
-				var target = cy.elements("node[name = \"" + lines[line][0] + "\"]");
-				var mut = lines[line][1];
-				var cnv = lines[line][2];
-				var rna = lines[line][3];
-				target.data('rna', rna);
-				target.data('cnv', cnv);
-				target.data('mut', mut);
-
-				if (rna > 0) {
-					setNodeStyle(target, 'red_bg', '', '');
-				} else if (rna < 0) {
-					setNodeStyle(target, 'green_bg', '', '');
-				} else {
-					setNodeStyle(target, '', '', '');
-				}
-
-				if (cnv > 0) {
-					setNodeStyle(target, '', 'red_border', '');
-				} else if (cnv < 0) {
-					setNodeStyle(target, '', 'purple_border', '');
-				} else {
-					setNodeStyle(target, '', '', '');
-				}
-
-				if (mut > 0) {
-					setNodeStyle(target, '', '', 'red_shadow');
-				} else if (mut <= 0) {
-					setNodeStyle(target, '', '', 'no_shadow');
-				} else {
-					setNodeStyle(target, '', '', '');
-				}
-			}
-		}
-
-		function removeElements(event) {
-			if(selectedForEditNodes.length > 0)
-				selectedForEditNodes.remove();
-			if(selectedForEditEdges.length > 0)
-				selectedForEditEdges.remove();
-			saveState();
-		}
-
-		function addNode(event) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var name = "n" + nodeCounter;
-			var node = [];
-
-			// Screen Dimensions
-			var dualScreenLeft = window.screenLeft != undefined ? window.screenLeft : screen.left;
-			var dualScreenTop = window.screenTop != undefined ? window.screenTop : screen.top;
-			var width = window.innerWidth ? window.innerWidth : document.documentElement.clientWidth ? document.documentElement.clientWidth : screen.width;
-			var height = window.innerHeight ? window.innerHeight : document.documentElement.clientHeight ? document.documentElement.clientHeight : screen.height;
-			var left = ((width / 2) - (100 / 2)) + dualScreenLeft;
-			var top = ((height / 2) - (25 / 2)) + dualScreenTop;
-
-			node.push({
-				group : "nodes",
-				data : {
-					LabelSize : 10,
-					Type : "gene",
-					Valign : "Middle",
-					Width : 100,
-					Height : 25,
-					id : "n" + nodeCounter,
-					name : name,
-					selected : false,
-					backgroundImage: "",
-					zIndex: 0
-				},
-				renderedPosition : {
-					x : left,
-					y : top
-				}
-			})
-
-			nodeCounter++;
-			cy.add(node);
-			postAddProcessing();
-			saveState();
-		}
-
-		function addEdge(event) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			for (var i = 0; i < selectedForEditNodes.length - 1; i++) {
-				var sourceE = selectedForEditNodes[i].data('id');
-				var targetE = selectedForEditNodes[i + 1].data('id');
-
-				var edge = [];
-
-				edge.push({
-					group : "edges",
-					data : {
-						id : "e" + edgeCounter,
-						Type : "Solid",
-						LineThickness : 1.0,
-						EndArrow : "Line",
-						Coords : [{
-							"x" : 0,
-							"y" : 0
-						}, {
-							"x" : 0,
-							"y" : 0
-						}],
-						ZOrder : "12288",
-						source : sourceE,
-						target : targetE,
-						StartArrow : "Line",
-						selected : false
-					}
-				})
-
-				edgeCounter++;
-				cy.add(edge);
-				postAddProcessing();
-				saveState();
-			}
-		}
-
-		function unbundleRecursive(node, parents, edges, nodes, rCounter) {
-			rCounter++;
-			if (rCounter == 1 && node.isParent()) {
-				parents.push(node);
-				for (var x = 0; x < node.children().size(); x++) {
-					if (node.parent().length != 0) {
-						nodes.push({
-							group : "nodes",
-							data : {
-								LabelSize : node.children()[x].data('LabelSize'),
-								Type : node.children()[x].data('Type'),
-								Valign : node.children()[x].data('Valign'),
-								Width : node.children()[x].data('Width'),
-								Height : node.children()[x].data('Height'),
-								id : node.children()[x].data('id'),
-								name : node.children()[x].data('name'),
-								selected : node.children()[x].data('selected'),
-								cnv : node.children()[x].data('cnv'),
-								rna : node.children()[x].data('rna'),
-								mut : node.children()[x].data('mut'),
-								parent : node.parent().data('id'),
-								backgroundImage: node.children()[x].data('backgroundImage'),
-								zIndex: node.children()[x].data('zIndex')
-							},
-							position : {
-								x : node.children()[x].position('x'),
-								y : node.children()[x].position('y')
-							}
-						});
-					} else {
-						nodes.push({
-							group : "nodes",
-							data : {
-								LabelSize : node.children()[x].data('LabelSize'),
-								Type : node.children()[x].data('Type'),
-								Valign : node.children()[x].data('Valign'),
-								Width : node.children()[x].data('Width'),
-								Height : node.children()[x].data('Height'),
-								id : node.children()[x].data('id'),
-								name : node.children()[x].data('name'),
-								selected : node.children()[x].data('selected'),
-								cnv : node.children()[x].data('cnv'),
-								rna : node.children()[x].data('rna'),
-								mut : node.children()[x].data('mut'),
-								backgroundImage: node.children()[x].data('backgroundImage'),
-								zIndex: node.children()[x].data('zIndex')
-							},
-							position : {
-								x : node.children()[x].position('x'),
-								y : node.children()[x].position('y')
-							}
-						});
-					}
-					for (var j = 0; j < node.children()[x].connectedEdges().size(); j++) {
-						edges.push({
-							group : "edges",
-							data : {
-								id : node.children()[x].connectedEdges()[j].data('id'),
-								Type : node.children()[x].connectedEdges()[j].data('Type'),
-								LineThickness : node.children()[x].connectedEdges()[j].data('LineThickness'),
-								EndArrow : node.children()[x].connectedEdges()[j].data('EndArrow'),
-								Coords : node.children()[x].connectedEdges()[j].data('Coords'),
-								ZOrder : node.children()[x].connectedEdges()[j].data('ZOrder'),
-								source : node.children()[x].connectedEdges()[j].data('source'),
-								target : node.children()[x].connectedEdges()[j].data('target'),
-								StartArrow : node.children()[x].connectedEdges()[j].data('StartArrow'),
-								selected : node.children()[x].connectedEdges()[j].data('selected')
-							}
-						})
-					}
-					unbundleRecursive(node.children()[x], parents, edges, nodes, rCounter);
-				}
-			} else if (rCounter > 1 && node.isParent()) {
-				for (var x = 0; x < node.children().size(); x++) {
-					if (node.length != 0) {
-						nodes.push({
-							group : "nodes",
-							data : {
-								LabelSize : node.children()[x].data('LabelSize'),
-								Type : node.children()[x].data('Type'),
-								Valign : node.children()[x].data('Valign'),
-								Width : node.children()[x].data('Width'),
-								Height : node.children()[x].data('Height'),
-								id : node.children()[x].data('id'),
-								name : node.children()[x].data('name'),
-								selected : node.children()[x].data('selected'),
-								cnv : node.children()[x].data('cnv'),
-								rna : node.children()[x].data('rna'),
-								mut : node.children()[x].data('mut'),
-								parent : node.data('id'),
-								backgroundImage: node.children()[x].data('backgroundImage'),
-								zIndex: node.children()[x].data('zIndex')
-							},
-							position : {
-								x : node.children()[x].position('x'),
-								y : node.children()[x].position('y')
-							}
-						});
-					} else {
-						nodes.push({
-							group : "nodes",
-							data : {
-								LabelSize : node.children()[x].data('LabelSize'),
-								Type : node.children()[x].data('Type'),
-								Valign : node.children()[x].data('Valign'),
-								Width : node.children()[x].data('Width'),
-								Height : node.children()[x].data('Height'),
-								id : node.children()[x].data('id'),
-								name : node.children()[x].data('name'),
-								selected : node.children()[x].data('selected'),
-								cnv : node.children()[x].data('cnv'),
-								rna : node.children()[x].data('rna'),
-								mut : node.children()[x].data('mut'),
-								backgroundImage: node.children()[x].data('backgroundImage'),
-								zIndex: node.children()[x].data('zIndex')
-							},
-							position : {
-								x : node.children()[x].position('x'),
-								y : node.children()[x].position('y')
-							}
-						});
-					}
-
-					for (var j = 0; j < node.children()[x].connectedEdges().size(); j++) {
-						edges.push({
-							group : "edges",
-							data : {
-								id : node.children()[x].connectedEdges()[j].data('id'),
-								Type : node.children()[x].connectedEdges()[j].data('Type'),
-								LineThickness : node.children()[x].connectedEdges()[j].data('LineThickness'),
-								EndArrow : node.children()[x].connectedEdges()[j].data('EndArrow'),
-								Coords : node.children()[x].connectedEdges()[j].data('Coords'),
-								ZOrder : node.children()[x].connectedEdges()[j].data('ZOrder'),
-								source : node.children()[x].connectedEdges()[j].data('source'),
-								target : node.children()[x].connectedEdges()[j].data('target'),
-								StartArrow : node.children()[x].connectedEdges()[j].data('StartArrow'),
-								selected : node.children()[x].connectedEdges()[j].data('selected')
-							}
-						})
-					}
-					unbundleRecursive(node.children()[x], parents, edges, nodes, rCounter);
-				}
-			}
-		}
-
-		function unbundle(event) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var parents = [];
-			var nodes = [];
-			var edges = [];
-			var rCounter = 0;
-
-			for (var i = 0; i < selectedForEditNodes.size(); i++) {
-				unbundleRecursive(selectedForEditNodes[i], parents, edges, nodes, rCounter);
-			}
-
-			// Remove parents (in the instance that they haven't been removed!)
-			for (var i = 0; i < parents.length; i++) {
-				parents[i].remove();
-			}
-
-			// Add new nodes
-			cy.add(nodes.concat(edges));
-			postAddProcessing();
-			saveState();
-		}
-
-		function recursiveBundle(node, edges, nodes) {
-			nodes.push({
-				group : "nodes",
-				data : {
-					LabelSize : node.data('LabelSize'),
-					Type : node.data('Type'),
-					Valign : node.data('Valign'),
-					Width : node.data('Width'),
-					Height : node.data('Height'),
-					id : node.data('id'),
-					name : node.data('name'),
-					selected : node.data('selected'),
-					cnv : node.data('cnv'),
-					rna : node.data('rna'),
-					mut : node.data('mut'),
-					parent : node.data('parent'),
-					backgroundImage: node.data('backgroundImage'),
-					zIndex: node.data('zIndex')
-				},
-				position : {
-					x : node.position('x'),
-					y : node.position('y')
-				}
-			});
-			for (var j = 0; j < node.connectedEdges().size(); j++) {
-				edges.push({
-					group : "edges",
-					data : {
-						id : node.connectedEdges()[j].data('id'),
-						Type : node.connectedEdges()[j].data('Type'),
-						LineThickness : node.connectedEdges()[j].data('LineThickness'),
-						EndArrow : node.connectedEdges()[j].data('EndArrow'),
-						Coords : node.connectedEdges()[j].data('Coords'),
-						ZOrder : node.connectedEdges()[j].data('ZOrder'),
-						source : node.connectedEdges()[j].data('source'),
-						target : node.connectedEdges()[j].data('target'),
-						StartArrow : node.connectedEdges()[j].data('StartArrow'),
-						selected : node.connectedEdges()[j].data('selected')
-					}
-				})
-			}
-			for (var i = 0; i < node.children().size(); i++) {
-				recursiveBundle(node.children()[i], edges, nodes);
-			}
-		}
-
-		function bundle(event) {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var type = document.getElementById(parent + "-type-bundle").value;
-			var nodes = [];
-			var edges = [];
-			// Create new parent
-			nodes.push({
-				group : "nodes",
-				data : {
-					LabelSize : 10,
-					Type : type,
-					Valign : "Middle",
-					Width : 80.75,
-					Height : 100,
-					id : "n" + nodeCounter,
-					name : "n" + nodeCounter,
-					selected : false,
-					backgroundImage: "",
-					zIndex: 0
-				},
-				position : {
-					x : 500,
-					y : 500
-				}
-			})
-
-			// Create copies of old nodes
-			for (var i = 0; i < selectedForEditNodes.size(); i++) {
-				if (!selectedForEditNodes[i].isChild()) {
-					nodes.push({
-						group : "nodes",
-						data : {
-							LabelSize : selectedForEditNodes[i].data('LabelSize'),
-							Type : selectedForEditNodes[i].data('Type'),
-							Valign : selectedForEditNodes[i].data('Valign'),
-							Width : selectedForEditNodes[i].data('Width'),
-							Height : selectedForEditNodes[i].data('Height'),
-							id : selectedForEditNodes[i].data('id'),
-							name : selectedForEditNodes[i].data('name'),
-							selected : selectedForEditNodes[i].data('selected'),
-							cnv : selectedForEditNodes[i].data('cnv'),
-							rna : selectedForEditNodes[i].data('rna'),
-							mut : selectedForEditNodes[i].data('mut'),
-							parent : "n" + nodeCounter,
-							backgroundImage: selectedForEditNodes[i].data('backgroundImage'),
-							zIndex: selectedForEditNodes[i].data('zIndex')
-							
-						},
-						position : {
-							x : selectedForEditNodes[i].position('x'),
-							y : selectedForEditNodes[i].position('y')
-						}
-					});
-					for (var j = 0; j < selectedForEditNodes[i].connectedEdges().size(); j++) {
-						edges.push({
-							group : "edges",
-							data : {
-								id : selectedForEditNodes[i].connectedEdges()[j].data('id'),
-								Type : selectedForEditNodes[i].connectedEdges()[j].data('Type'),
-								LineThickness : selectedForEditNodes[i].connectedEdges()[j].data('LineThickness'),
-								EndArrow : selectedForEditNodes[i].connectedEdges()[j].data('EndArrow'),
-								Coords : selectedForEditNodes[i].connectedEdges()[j].data('Coords'),
-								ZOrder : selectedForEditNodes[i].connectedEdges()[j].data('ZOrder'),
-								source : selectedForEditNodes[i].connectedEdges()[j].data('source'),
-								target : selectedForEditNodes[i].connectedEdges()[j].data('target'),
-								StartArrow : selectedForEditNodes[i].connectedEdges()[j].data('StartArrow'),
-								selected : selectedForEditNodes[i].connectedEdges()[j].data('selected')
-							}
-						})
-					}
-				}
-				if (selectedForEditNodes[i].isParent() || selectedForEditNodes[i].isChild()) {
-					recursiveBundle(selectedForEditNodes[i], edges, nodes);
-				}
-			}
-
-			// Remove old nodes
-			selectedForEditNodes.remove();
-
-			// Add new nodes
-			cy.add(nodes.concat(edges));
-			postAddProcessing();
-
-			if (!cy.elements("node[id = \"n" + nodeCounter + "\"]").isParent())
-				cy.elements("node[id = \"n" + nodeCounter + "\"]").remove();
-
-			// increment nodeCounter to insure unique id
-			nodeCounter++;
-
-			// Remove dialog box
-			dialogBundle.dialog("close");
-			saveState();
-		}
-
-		function produceJSON(event) {
-			download(states[states.length - 1], "data.txt", "text/plain");
-		}
-
-		function refreshPathwayList() {
-			var select = document.getElementById(parent + "-pathway-selector");
-
-			while (select.firstChild) {
-				select.removeChild(select.firstChild);
-			}
-
-			$.get(services['pathwayFinder'], {
-				pathwayList : '1'
-			}, function(data) {
-				var obj = JSON.parse(data);
-				var el = document.createElement("option");
-				el.textContent = "Select pathway";
-				select.appendChild(el);
-				for (var i = 0; i < obj.length; i++) {
-					var opt = obj[i].NAME;
-					var val = obj[i].ID;
-					var el = document.createElement("option");
-					el.textContent = opt;
-					el.value = val;
-					select.appendChild(el);
-				}
-			});
-
-		}
-
-		function findPath(Json, sid, vid) {
-			var nodes = Json['elements']['nodes'];
-			nodes = nodes.filter(function(item) {
-				if (item['data']['NODE_TYPE'] !== 'GROUP') {
-					return true;
-				}
-
-			});
-			//console.log(nodes);
-			var edges = Json['elements']['edges'];
-			var result = [];
-			//array of arrays containing the graphids for edges in the path
-			var path = [];
-			var nodeTrack = [];
-
-			function mapLocation(x, y) {
-				var deta = 1;
-
-				for (var j = 0; j < nodes.length; j++) {
-					var x0 = nodes[j]['position']['x'];
-					var y0 = nodes[j]['position']['y'];
-					var w = nodes[j]['data']['Width'];
-					var h = nodes[j]['data']['Height'];
-
-					if (x > x0 - w / 2 - deta & x < x0 + w / 2 + deta & y > y0 - h / 2 - deta & y < y0 + h / 2 + deta) {
-						return nodes[j]['data']['SUID'];
-
-					}
-				}
-			}
-
-			function findEdgeBySource(gid) {
-				if (gid == undefined | gid == '0') {
-					return;
-				}
-
-				var end = true;
-				for (var i = 0; i < edges.length; i++) {
-					var eid = edges[i]['data']['id'];
-					var s = (!('source' in edges[i]['data']) ? mapLocation(edges[i]['data']['Coords'][0]['x'], edges[i]['data']['Coords'][0]['y']) : edges[i]['data']['source']);
-
-					if (s == gid) {
-
-						var cl = edges[i]['data']['Coords'].length;
-						var t = (!('target' in edges[i]['data']) ? mapLocation(edges[i]['data']['Coords'][cl - 1]['x'], edges[i]['data']['Coords'][cl - 1]['y']) : edges[i]['data']['target']);
-
-						if (t == vid) {
-							var p = path.slice();
-							p.push(eid);
-							result.push(p);
-
-							continue;
-
-						} else if (nodeTrack.indexOf(eid) == -1 & t !== undefined & t !== '0') {
-							path.push(eid);
-							nodeTrack.push(eid);
-
-							findEdgeBySource(t);
-						} else {
-							continue;
-						}
-					}
-				}
-				if (end == true) {
-					path.pop();
-					nodeTrack.pop();
-
-				}
-				return true;
-			}
-
-			findEdgeBySource(sid);
-			return result;
-
-		}
-
-		function getPathScore(edgeArray, scoreJSON) {
-			var sum = 0;
-			var max = 0;
-			for (var i = 0; i < edgeArray.length; i++) {
-				sum = sum + (i + 1) * scoreJSON[edgeArray[i]] / edgeArray.length;
-				max = max + (i + 1) / edgeArray.length;
-			}
-			return parseFloat((sum / max).toFixed(5));
-		}
-		
-		function convertEdgePathtoNodePath(selectedPaths){
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var nodePath = [];
-			for (var n = 0; n < selectedPaths.length; n++) {
-				nodePath.push([])
-				for (var j = 0; j < selectedPaths[n].length; j++) {
-					if(j < selectedPaths[n].length-1){
-						var sourceNodeId = cy.elements("edge[id = \"" + selectedPaths[n][j] + "\"]").data('source');
+var VQI_PathwayEditor = function (parent) {
+
+    var self = this;
+
+    //Web services
+//	var serverURL = "http://cardinal3.engr.uconn.edu/pathwayVisual/";
+    var services = {};
+
+    /* Yue's Local Server*/
+    services['pathwayFinder'] = 'http://cardinal3.engr.uconn.edu/pathwayVisual/PathwayParser/ajaxJSON.php';
+    services['pathwaySaver'] = 'http://cardinal3.engr.uconn.edu/pathwayVisual/PathwayParser/updateDB_json.php';
+    services['pathwayScorer'] = 'http://cardinal3.engr.uconn.edu/pathwayVisual/ScoreSystem/getScore.php';
+    /* Yue's local server URLs end here */
+
+    /* Tham's local server */
+    services['pathwayWeightedScorer'] = 'http://137.99.11.122/pathway2/pathwayweightedscorer.php';
+    services['objectFinder'] = 'http://137.99.11.122/pathway2/qsys_json.php';
+    /* Tham's local server URL end here */
+
+    /* BIBCI Server */
+//    services['pathwayFinder'] = 'http://bibci.engr.uconn.edu/yuz12012/pathwayVisual//PathwayParser/ajaxJSON.php';
+//    services['pathwaySaver'] = 'http://bibci.engr.uconn.edu/yuz12012/pathwayVisual//PathwayParser/updateDB_json.php';
+//    services['pathwayScorer'] = 'http://bibci.engr.uconn.edu/yuz12012/pathwayVisual/ScoreSystem/getScore.php';
+//    services['pathwayWeightedScorer'] = 'http://bibci.engr.uconn.edu/thh13003/pathway2/pathwayweightedscorer.php';
+//    services['objectFinder'] = 'http://bibci.engr.uconn.edu/thh13003/pathway2/qsys_json.php';
+
+
+    // Globals
+    var states = [];
+    var types = ["bundleOne", "bundleTwo", "gene", "geneProduct", "protein", "rna", "microRNA", "kinase", "ligand", "receptor", "biologicalProcess", "triangle", "ellipse", "pentagon", "hexagon", "heptagon", "octagon", "star", "diamond", "vee", "rhomboid", "label"];
+    var stateRecycle = [];
+    var lastEvent = 0;
+    var selectedForQueryNodes = [];
+    var selectedForEditNodes = [];
+    var selectedForEditEdges = [];
+    var orderedSelectedNodes = [];
+    var grabbedCollapsedForEditNodes = [];
+    var coloredNodes = [];
+    var edgeCounter = 0;
+    var nodeCounter = 0;
+    var loadCounts = 0;
+    var target = 0;
+    var header = "";
+    var counts = {};
+    var strInfo;
+    var highestZOrder = 999;
+
+    var strVar = "";
+    strVar += " <nav class=\"navbar navbar-default\">";
+    strVar += " <div class=\"container-fluid\">";
+    strVar += " <div class=\"navbar-header\">";
+    strVar += " 	<a class=\"navbar-brand\" href=\"#\">Pathway name</a>";
+    strVar += " <\/div>";
+    strVar += " <ul class=\"nav navbar-nav\">";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += " 		<label for=\"" + parent + "-file-pathway\">Local Pathway File:<\/label>";
+    strVar += "			<input id=\"" + parent + "-file-pathway\" value=\"Pick Pathway File\" type=\"file\"><\/input>";
+    strVar += " 	<\/li>";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += " 		<label for=\"" + parent + "-file-coloring\">Local Pathway Coloring:<\/label>";
+    strVar += "			<input id=\"" + parent + "-file-coloring\" value=\"Pick Spray File\" type=\"file\"><\/input>";
+    strVar += " 	<\/li>";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += " 		<label for=\"" + parent + "-pathway-selector\">Pathway:<\/label>";
+    strVar += " 		<select style=\"width: 150px\" id=\"" + parent + "-pathway-selector\" name=\"" + parent + "-pathway-selector\">";
+    strVar += "  			<option selected=\"\">Please Select<\/option>";
+    strVar += "			<\/select>";
+    strVar += " 	<\/li>";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += "			<div class=\"dropdown\">";
+    strVar += "  			<button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Edit<span class=\"caret\"><\/span><\/button>";
+    strVar += "				<ul class=\"dropdown-menu\">";
+    strVar += "					<li><input id=\"" + parent + "-add-node\" value=\"Add Node\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "					<li><input id=\"" + parent + "-add-edge\" value=\"Add Edge\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += " 				<li><input id=\"" + parent + "-delete-elements\" value=\"Delete Selected Element(s)\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += " 				<li role=\"separator\" class=\"divider\"></li>";
+    strVar += "					<li><input id=\"" + parent + "-bundle\" value=\"Bundle\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "					<li><input id=\"" + parent + "-unbundle\" value=\"Unbundle\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "					<li><input id=\"" + parent + "-collapse\" value=\"Collapse\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "					<li><input id=\"" + parent + "-expand\" value=\"Expand\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "				<\/ul>";
+    strVar += "			</div>";
+    strVar += " 	<\/li>";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += "			<div class=\"dropdown\">";
+    strVar += "  			<button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Process<span class=\"caret\"><\/span><\/button>";
+    strVar += "				<ul class=\"dropdown-menu\">";
+    strVar += "					<li><input id=\"" + parent + "-findpath\" value=\"Find Pathway\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "					<li><input id=\"" + parent + "-find-object\" value=\"Find Object\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "				<\/ul>";
+    strVar += "			</div>";
+    strVar += " 	<\/li>";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += "			<div class=\"dropdown\">";
+    strVar += "  			<button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Archive<span class=\"caret\"><\/span><\/button>";
+    strVar += "				<ul class=\"dropdown-menu\">";
+    strVar += "					<li><input id=\"" + parent + "-pathway-save\" value=\"Save\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
+    strVar += "					<li><input id=\"" + parent + "-pathway-saveAs\" value=\"SaveAs\" type=\"button\" class=\"btn btn-link disabled\"><\/li>";
+    strVar += " 				<li><input id=\"" + parent + "-produce-JSON\" value=\"Export JSON\" type=\"button\" class=\"btn btn-link disabled\"><\/li>";
+    strVar += "				<\/ul>";
+    strVar += "			<\/div>";
+    strVar += " 	<li\">";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += "			<input id=\"" + parent + "-undo\" value=\"Undo\" type=\"button\" class=\"btn btn-primary disabled\"><\/input>";
+    strVar += " 	<\/li>";
+    strVar += " 	<li style=\"margin: 2px\">";
+    strVar += "			<input id=\"" + parent + "-redo\" value=\"Redo\" type=\"button\" class=\"btn btn-primary disabled\"><\/input>";
+    strVar += " 	<\/li>";
+    strVar += " <\/ul>";
+    strVar += " <\/div>";
+    strVar += " <\/nav>";
+    strVar += " <div id=\"" + parent + "-dialog-table\" title=\"Result\">";
+    strVar += "	<table id=\"" + parent + "-inner-table\" class=\"table table-hover\">";
+    strVar += "		<tr>";
+    strVar += "         <td>name</td>";
+    strVar += "			<td>percentage</td>";
+    strVar += "			<td>rna distance</td>";
+    strVar += "			<td>cnv distance</td>";
+    strVar += "			<td>mut distance</td>";
+    strVar += "	</table>";
+    strVar += "	<\/div>";
+    strVar += " <div id=\"" + parent + "-dialog-form-save-as-pathway\" title=\"SaveAs\">";
+    strVar += " 		<form role=\"form\">";
+    strVar += "    		<fieldset>";
+    strVar += "      			<label for=\"" + parent + "-pathway-name\">pathway-name:<\/label>";
+    strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-pathway-name\" id=\"" + parent + "-pathway-name\"><br>";
+    strVar += " 				<input type=\"submit\" class=\"btn btn-default\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
+    strVar += "    		<\/fieldset>";
+    strVar += " 		<\/form>";
+    strVar += "	<\/div>";
+    strVar += " <div id=\"" + parent + "-dialog-form-new-pathway\" title=\"New Pathway\">";
+    strVar += " 		<form role=\"form\">";
+    strVar += "    		<fieldset>";
+    strVar += "      			<label for=\"" + parent + "-new-pathway-name\">pathway-name:<\/label>";
+    strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-new-pathway-name\" id=\"" + parent + "-new-pathway-name\"><br>";
+    strVar += " 				<input type=\"submit\" class=\"btn btn-default\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
+    strVar += "    		<\/fieldset>";
+    strVar += " 		<\/form>";
+    strVar += "	<\/div>";
+    strVar += " <div id=\"" + parent + "-dialog-bundle\" title=\"Bundle\">";
+    strVar += " 		<form role=\"form\">";
+    strVar += "    		<fieldset>";
+    strVar += "      			<label for=\"" + parent + "-type-bundle\">type:<\/label>";
+    strVar += "      			<select style=\"width: 150px\" id=\"" + parent + "-type-bundle\" name=\"" + parent + "-type-bundle\">";
+    strVar += "  					<option selected=\"\">bundleOne<\/option>";
+    strVar += "  					<option>bundleTwo<\/option>";
+    strVar += "				<\/select>";
+    strVar += "    		<\/fieldset>";
+    strVar += " 		<\/form>";
+    strVar += "	<\/div>";
+    strVar += " <div id=\"" + parent + "-dialog-form-find-path\" title=\"Find path\">";
+    strVar += " 		<form role=\"form\">";
+    strVar += "    		<fieldset>";
+    strVar += "      			<label for=\"" + parent + "-sid\">sid:<\/label>";
+    strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-sid\" id=\"" + parent + "-sid\"><br>";
+    strVar += "      			<label for=\"" + parent + "-vid\">vid:<\/label>";
+    strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-vid\" id=\"" + parent + "-vid\"><br>";
+    strVar += " 				<input type=\"submit\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
+    strVar += "    		<\/fieldset>";
+    strVar += " 		<\/form>";
+    strVar += "	<\/div>";
+    strVar += "	<div id=\"" + parent + "-dialog-form-edge\" title=\"Edit edge\">";
+    strVar += " 		<form role=\"form\">";
+    strVar += "    		<fieldset>";
+    strVar += "      			<label for=\"" + parent + "-direction\">change direction:<\/label>";
+    strVar += "      			<input type=\"checkbox\" class=\"form-control\" name=\"" + parent + "-direction\" id=\"" + parent + "-direction\" value=\"Yes\"><\/input>";
+    strVar += "      			<label for=\"" + parent + "-arrow-type-edge\">arrow type:<\/label>";
+    strVar += "      			<select style=\"width: 150px\" class=\"form-control\" id=\"" + parent + "-arrow-type-edge\" name=\"" + parent + "-arrow-type-edge\">";
+    strVar += "  					<option selected=\"\">TBar<\/option>";
+    strVar += "  					<option>Arrow<\/option>";
+    strVar += "  					<option>Line<\/option>";
+    strVar += "					<\/select>";
+    strVar += "      			<label for=\"" + parent + "-line-type-edge\">line type:<\/label>";
+    strVar += "      			<select style=\"width: 150px\" class=\"form-control\" id=\"" + parent + "-line-type-edge\" name=\"" + parent + "-line-type-edge\">";
+    strVar += "  					<option selected=\"\">Solid<\/option>";
+    strVar += "  					<option>Dotted<\/option>";
+    strVar += "  					<option>Dashed<\/option>";
+    strVar += "					<\/select>";
+    strVar += "    				<label for=\"" + parent + "-edge-move-to-background\">Move to Background:<\/label>";
+    strVar += "    				<input id=\"" + parent + "-edge-move-to-background\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
+    strVar += "    				<label for=\"" + parent + "-edge-move-to-foreground\">Move to Foreground:<\/label>";
+    strVar += "    				<input id=\"" + parent + "-edge-move-to-foreground\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
+    strVar += " 			<input type=\"submit\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
+    strVar += "    		<\/fieldset>";
+    strVar += "  		<\/form>";
+    strVar += "	<\/div>";
+    strVar += "<div id=\"" + parent + "-intro-hero-unit\" class=\"container\"style=\"margin-top: 100px\">";
+    strVar += "		<div class=\"jumbotron\">";
+    strVar += "			<h1>Pathway Editor</h1>";
+    strVar += "			<p><i>Pre-alpha version of the pathway editor. You can either start a new pathway or load an existing one...</i></p>";
+    strVar += " 		<input id=\"" + parent + "-new-pathway\" value=\"New Pathway\" type=\"button\" class=\"btn btn-success\"><\/input>";
+    strVar += " 		<a id=\"" + parent + "-link-github\" type=\"button\" class=\"btn btn-success\" href=\"https://github.uconn.edu/ivp08001/pathway\">Github Source<\/a>";
+    strVar += "     </div>";
+    strVar += " </div>";
+    strVar += "	<div id=\"" + parent + "-dialog-form-node\" title=\"Edit node\">";
+    strVar += " 		<form role=\"form\">";
+    strVar += "    		<fieldset>";
+    strVar += "      			<label for=\"" + parent + "-gene-name\">gene-name:<\/label>";
+    strVar += "      			<input type=\"text\" name=\"" + parent + "-gene-name\" class=\"form-control\" id=\"" + parent + "-gene-name\" value=\"\" class=\"text ui-widget-content ui-corner-all\"><\/input>";
+    strVar += "      			<label for=\"" + parent + "-height\">height:<\/label>";
+    strVar += "      			<input type=\"text\" name=\"" + parent + "-height\" id=\"" + parent + "-height\" class=\"form-control\" value=\"\" class=\"text ui-widget-content ui-corner-all\"><\/input>";
+    strVar += "      			<label for=\"" + parent + "-width\">width:<\/label>";
+    strVar += "      			<input type=\"text\" name=\"" + parent + "-width\" id=\"" + parent + "-width\" class=\"form-control\" value=\"\" class=\"text ui-widget-content ui-corner-all\"><\/input>";
+    strVar += "      			<label for=\"" + parent + "-type-node\">type:<\/label>";
+    strVar += "      			<select style=\"width: 150px\" id=\"" + parent + "-type-node\" class=\"form-control\" name=\"" + parent + "-type-node\">";
+    strVar += "  					<option id=\"" + parent + "-select-bundleOne\" selected=\"\">bundleOne<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-bundleTwo\">bundleTwo<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-gene\">gene<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-geneProduct\">geneProduct<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-protein\">protein<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-rna\">rna<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-mircoRNA\">microRNA<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-kinase\">kinase<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-ligand\">ligand<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-receptor\">receptor<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-biologicalProcess\">biologicalProcess<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-triangle\">triangle<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-ellipse\">ellipse<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-pentagon\">pentagon<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-hexagon\">hexagon<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-heptagon\">heptagon<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-octagon\">octagon<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-star\">star<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-diamond\">diamond<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-vee\">vee<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-rhomboid\">rhomboid<\/option>";
+    strVar += "  					<option id=\"" + parent + "-select-label\">label<\/option>";
+    strVar += "					<\/select>";
+    strVar += "      			<label for=\"" + parent + "-rna\">RNA:<\/label>";
+    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-rna\" class=\"form-control\" name=\"" + parent + "-rna\">";
+    strVar += "					<label for=\"" + parent + "-cnv\">CNV:<\/label>";
+    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-cnv\" class=\"form-control\" name=\"" + parent + "-cnv\">";
+    strVar += "					<label for=\"" + parent + "-mut\">MUT:<\/label>";
+    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-mut\" class=\"form-control\" name=\"" + parent + "-mut\">";
+    strVar += " 			    <input type=\"submit\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
+    strVar += "    				<label for=\"" + parent + "-background-image\">Local Image File:<\/label>";
+    strVar += "					<input id=\"" + parent + "-background-image\" value=\"Pick an Image File\" type=\"file\"><\/input>";
+    strVar += "    				<label for=\"" + parent + "-background-image-remove\">Remove Background image:<\/label>";
+    strVar += "					<input id=\"" + parent + "-background-image-remove\" value=\"Remove\" type=\"button\" class=\"btn btn-link\"><\/input>";
+    strVar += "    				<label for=\"" + parent + "-node-move-to-background\">Move to Background:<\/label>";
+    strVar += "    				<input id=\"" + parent + "-node-move-to-background\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
+    strVar += "    				<label for=\"" + parent + "-node-move-to-foreground\">Move to Foreground:<\/label>";
+    strVar += "    				<input id=\"" + parent + "-node-move-to-foreground\" value=\"Move\" type=\"button\" class=\"btn btn-link\"><\/input>";
+    strVar += "				<\/fieldset>";
+    strVar += "  		<\/form>";
+    strVar += "	<\/div>";
+    strVar += "	<div id=\"" + parent + "-cy\" style=\"height: 100%;width: 100%;position: absolute; left: 0;\"><\/div>";
+
+    document.getElementById(parent).innerHTML = strVar;
+
+    $(function () {// on dom ready
+
+        function removeHeroUnit() {
+            var heroUnit = document.getElementById(parent + "-intro-hero-unit");
+            if (heroUnit != null)
+                heroUnit.parentNode.removeChild(heroUnit);
+        }
+
+        function newPathway(event) {
+            var name = document.getElementById(parent + "-new-pathway-name").value;
+            var data = '{"format_version" : "1.0","generated_by" : "cytoscape-3.2.1","target_cytoscapejs_version" : "~2.1","data" :{"shared_name":"","ID":"","BOARDWIDTH":"","BOARDHEIGHT":"","LICENSE":"CC BY 2.0","ORGANISM":"","NAME":"","INSTRUCTION":"","AUTHOR":"","VERSION":"","PATHWAY_TYPE":"original","SUID":205,"__Annotations":[],"selected":true},"elements" : {"nodes" :[],"edges" :[]}}'
+            var obj = JSON.parse(data);
+            removeHeroUnit();
+            setElements(obj);
+            dialogNewPathway.dialog("close");
+        }
+
+        function onChangePathwayFile(event) {
+            var reader = new FileReader();
+            reader.onload = onPathwayReaderLoad;
+            reader.readAsText(event.target.files[0]);
+            removeHeroUnit();
+        }
+
+        function collapseBundle(event) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            for (var i = 0; i < selectedForEditNodes.size(); i++) {
+                if (selectedForEditNodes[i].isParent()) {
+                    selectedForEditNodes[i].descendants().addClass('collapsed');
+                    selectedForEditNodes[i].descendants().unselectify();
+                    selectedForEditNodes[i].descendants().ungrabify();
+                    selectedForEditNodes[i].descendants().positions({
+                        x: selectedForEditNodes[i].position('x') + selectedForEditNodes[i].width() / 2,
+                        y: selectedForEditNodes[i].position('y') + selectedForEditNodes[i].height() / 2
+                    });
+                }
+            }
+            saveState();
+        }
+
+        function expandBundle(event) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            for (var i = 0; i < selectedForEditNodes.size(); i++) {
+                if (selectedForEditNodes[i].isParent()) {
+                    selectedForEditNodes[i].descendants().removeClass('collapsed');
+                    selectedForEditNodes[i].descendants().selectify();
+                    selectedForEditNodes[i].descendants().grabify();
+                }
+            }
+            saveState();
+        }
+
+        function onChangeColoringFile(event) {
+            var reader = new FileReader();
+            reader.onload = onColoringReaderLoad;
+            reader.readAsText(event.target.files[0]);
+            saveState();
+        }
+
+        function postAddProcessing() {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+
+            //Post-Add Process
+            for (var i = 0; i < cy.$("node").length; i++) {
+                if (typeof (cy.$("node")[i].data("backgroundImage")) != "undefined" && cy.$("node")[i].data("backgroundImage") != "") {
+                    cy.$("node")[i].style("backgroundImage", cy.$("node")[i].data("backgroundImage"));
+                    cy.$("node")[i].data("Type", "image");
+                }
+            }
+
+            for (var i = 0; i < cy.$("node").length; i++) {
+                if (typeof (cy.$("node")[i].data("zIndex")) != "undefined") {
+                    cy.$("node")[i].style("zIndex", cy.$("node")[i].data("zIndex"));
+                }
+            }
+        }
+
+        function preAddProcessing(obj) {
+            for (var i = 0; i < obj.elements.nodes.length; i++) {
+                if (obj.elements.nodes[i].data.id.substring(0, 1) == "n") {
+                    var number = parseInt(obj.elements.nodes[i].data.id.substring(1, obj.elements.nodes.length - 1));
+                    if (number > nodeCounter)
+                        nodeCounter = number + 1;
+                }
+
+                if (types.indexOf(obj.elements.nodes[i].data.backgroundImage) == -1) {
+                    obj.elements.nodes[i].data.backgroundImage = "";
+                }
+
+                if (types.indexOf(obj.elements.nodes[i].data.zIndex) == -1) {
+                    obj.elements.nodes[i].data.zIndex = 0;
+                }
+
+                if (types.indexOf(obj.elements.nodes[i].data.Type) == -1) {
+                    obj.elements.nodes[i].data.Type = "label";
+                }
+
+                if (typeof (obj.elements.nodes[i].data.rna) == "undefined") {
+                    obj.elements.nodes[i].data.rna = 0;
+                }
+
+                if (typeof (obj.elements.nodes[i].data.cnv) == "undefined") {
+                    obj.elements.nodes[i].data.cnv = 0;
+                }
+
+                if (typeof (obj.elements.nodes[i].data.mut) == "undefined") {
+                    obj.elements.nodes[i].data.mut = 0;
+                }
+            }
+
+            for (var i = 0; i < obj.elements.edges.length; i++) {
+                if (obj.elements.edges[i].data.id.substring(0, 1) == "e") {
+                    var number = parseInt(obj.elements.edges[i].data.id.substring(1, obj.elements.edges.length - 1));
+                    if (number > edgeCounter)
+                        edgeCounter = number + 1;
+                }
+            }
+        }
+
+        function setElements(obj) {
+            if (loadCounts == 0) {
+                header = obj.data;
+                visualPathway(obj);
+            } else {
+
+                // Pre-Add process
+
+                var cy = $('#' + parent + '-cy').cytoscape('get');
+                for (var i = 0; i < obj.elements.nodes.length; i++) {
+                    obj.elements.nodes[i].position.x = obj.elements.nodes[i].position.x + 1000 * loadCounts;
+                }
+
+                preProcessingAdd(obj);
+
+                // Add nodes
+                cy.add(obj.elements);
+                cy.center();
+                cy.fit();
+
+                //Post-Add Process
+                postAddProcessing();
+
+            }
+            loadCounts++;
+            saveState();
+        }
+
+        function loadPathway(id) {
+            $.post(services['pathwayFinder'], {
+                pid: id
+            }, function (data) {
+                removeHeroUnit();
+                var obj = JSON.parse(data);
+                setElements(obj);
+            });
+        }
+
+        function onSelect(event) {
+            var id = event.target.value;
+            loadPathway(id);
+        }
+
+        function saveAsPathway(event) {
+            var obj = JSON.parse(states[states.length - 1]);
+            obj.data.NAME = document.getElementById(parent + "-pathway-name").value;
+            $.post(services['pathwaySaver'], {
+                insertPathway: JSON.stringify(obj)
+            }, function (data) {
+                if (data != "Success!") {
+                    obj.data.ID = data;
+                    $.post(services['pathwaySaver'], {
+                        updatePathway: JSON.stringify(obj)
+                    }, function (data) {
+                        console.log(data)
+                        dialogPathwaySaveAs.dialog("close");
+                    });
+                } else {
+                    refreshPathwayList();
+                    dialogPathwaySaveAs.dialog("close");
+                }
+            });
+        }
+
+        function savePathway(event) {
+            var obj = JSON.parse(states[states.length - 1]);
+            $.post(services['pathwaySaver'], {
+                updatePathway: JSON.stringify(obj)
+            }, function (data) {
+                console.log(data);
+                dialogPathwaySaveAs.dialog("close");
+            });
+        }
+
+        function onPathwayReaderLoad(event) {
+            var obj = JSON.parse(event.target.result);
+            setElements(obj);
+        }
+
+        function onColoringReaderLoad(event) {
+            var list = this.result.split('\n');
+            var lines = [];
+
+            for (var line = 1; line < list.length; line++) {
+                lines[line] = list[line].split('\t');
+            }
+
+            sprayColor(lines);
+        }
+
+        function sprayColor(lines) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            for (var line = 1; line < lines.length; line++) {
+                var target = cy.elements("node[name = \"" + lines[line][0] + "\"]");
+                var mut = lines[line][1];
+                var cnv = lines[line][2];
+                var rna = lines[line][3];
+                target.data('rna', rna);
+                target.data('cnv', cnv);
+                target.data('mut', mut);
+
+                if (rna > 0) {
+                    setNodeStyle(target, 'red_bg', '', '');
+                } else if (rna < 0) {
+                    setNodeStyle(target, 'green_bg', '', '');
+                } else {
+                    setNodeStyle(target, '', '', '');
+                }
+
+                if (cnv > 0) {
+                    setNodeStyle(target, '', 'red_border', '');
+                } else if (cnv < 0) {
+                    setNodeStyle(target, '', 'purple_border', '');
+                } else {
+                    setNodeStyle(target, '', '', '');
+                }
+
+                if (mut > 0) {
+                    setNodeStyle(target, '', '', 'red_shadow');
+                } else if (mut <= 0) {
+                    setNodeStyle(target, '', '', 'no_shadow');
+                } else {
+                    setNodeStyle(target, '', '', '');
+                }
+            }
+        }
+
+        function removeElements(event) {
+            if (selectedForEditNodes.length > 0)
+                selectedForEditNodes.remove();
+            if (selectedForEditEdges.length > 0)
+                selectedForEditEdges.remove();
+            saveState();
+        }
+
+        function addNode(event) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var name = "n" + nodeCounter;
+            var node = [];
+
+            // Screen Dimensions
+            var dualScreenLeft = window.screenLeft != undefined ? window.screenLeft : screen.left;
+            var dualScreenTop = window.screenTop != undefined ? window.screenTop : screen.top;
+            var width = window.innerWidth ? window.innerWidth : document.documentElement.clientWidth ? document.documentElement.clientWidth : screen.width;
+            var height = window.innerHeight ? window.innerHeight : document.documentElement.clientHeight ? document.documentElement.clientHeight : screen.height;
+            var left = ((width / 2) - (100 / 2)) + dualScreenLeft;
+            var top = ((height / 2) - (25 / 2)) + dualScreenTop;
+
+            node.push({
+                group: "nodes",
+                data: {
+                    LabelSize: 10,
+                    Type: "gene",
+                    Valign: "Middle",
+                    Width: 100,
+                    Height: 25,
+                    id: "n" + nodeCounter,
+                    name: name,
+                    selected: false,
+                    backgroundImage: "",
+                    zIndex: 0
+                },
+                renderedPosition: {
+                    x: left,
+                    y: top
+                }
+            })
+
+            nodeCounter++;
+            cy.add(node);
+            postAddProcessing();
+            saveState();
+        }
+
+        function addEdge(event) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            for (var i = 0; i < selectedForEditNodes.length - 1; i++) {
+                var sourceE = selectedForEditNodes[i].data('id');
+                var targetE = selectedForEditNodes[i + 1].data('id');
+
+                var edge = [];
+
+                edge.push({
+                    group: "edges",
+                    data: {
+                        id: "e" + edgeCounter,
+                        Type: "Solid",
+                        LineThickness: 1.0,
+                        EndArrow: "Line",
+                        Coords: [{
+                                "x": 0,
+                                "y": 0
+                            }, {
+                                "x": 0,
+                                "y": 0
+                            }],
+                        ZOrder: "12288",
+                        source: sourceE,
+                        target: targetE,
+                        StartArrow: "Line",
+                        selected: false
+                    }
+                })
+
+                edgeCounter++;
+                cy.add(edge);
+                postAddProcessing();
+                saveState();
+            }
+        }
+
+        function unbundleRecursive(node, parents, edges, nodes, rCounter) {
+            rCounter++;
+            if (rCounter == 1 && node.isParent()) {
+                parents.push(node);
+                for (var x = 0; x < node.children().size(); x++) {
+                    if (node.parent().length != 0) {
+                        nodes.push({
+                            group: "nodes",
+                            data: {
+                                LabelSize: node.children()[x].data('LabelSize'),
+                                Type: node.children()[x].data('Type'),
+                                Valign: node.children()[x].data('Valign'),
+                                Width: node.children()[x].data('Width'),
+                                Height: node.children()[x].data('Height'),
+                                id: node.children()[x].data('id'),
+                                name: node.children()[x].data('name'),
+                                selected: node.children()[x].data('selected'),
+                                cnv: node.children()[x].data('cnv'),
+                                rna: node.children()[x].data('rna'),
+                                mut: node.children()[x].data('mut'),
+                                parent: node.parent().data('id'),
+                                backgroundImage: node.children()[x].data('backgroundImage'),
+                                zIndex: node.children()[x].data('zIndex')
+                            },
+                            position: {
+                                x: node.children()[x].position('x'),
+                                y: node.children()[x].position('y')
+                            }
+                        });
+                    } else {
+                        nodes.push({
+                            group: "nodes",
+                            data: {
+                                LabelSize: node.children()[x].data('LabelSize'),
+                                Type: node.children()[x].data('Type'),
+                                Valign: node.children()[x].data('Valign'),
+                                Width: node.children()[x].data('Width'),
+                                Height: node.children()[x].data('Height'),
+                                id: node.children()[x].data('id'),
+                                name: node.children()[x].data('name'),
+                                selected: node.children()[x].data('selected'),
+                                cnv: node.children()[x].data('cnv'),
+                                rna: node.children()[x].data('rna'),
+                                mut: node.children()[x].data('mut'),
+                                backgroundImage: node.children()[x].data('backgroundImage'),
+                                zIndex: node.children()[x].data('zIndex')
+                            },
+                            position: {
+                                x: node.children()[x].position('x'),
+                                y: node.children()[x].position('y')
+                            }
+                        });
+                    }
+                    for (var j = 0; j < node.children()[x].connectedEdges().size(); j++) {
+                        edges.push({
+                            group: "edges",
+                            data: {
+                                id: node.children()[x].connectedEdges()[j].data('id'),
+                                Type: node.children()[x].connectedEdges()[j].data('Type'),
+                                LineThickness: node.children()[x].connectedEdges()[j].data('LineThickness'),
+                                EndArrow: node.children()[x].connectedEdges()[j].data('EndArrow'),
+                                Coords: node.children()[x].connectedEdges()[j].data('Coords'),
+                                ZOrder: node.children()[x].connectedEdges()[j].data('ZOrder'),
+                                source: node.children()[x].connectedEdges()[j].data('source'),
+                                target: node.children()[x].connectedEdges()[j].data('target'),
+                                StartArrow: node.children()[x].connectedEdges()[j].data('StartArrow'),
+                                selected: node.children()[x].connectedEdges()[j].data('selected')
+                            }
+                        })
+                    }
+                    unbundleRecursive(node.children()[x], parents, edges, nodes, rCounter);
+                }
+            } else if (rCounter > 1 && node.isParent()) {
+                for (var x = 0; x < node.children().size(); x++) {
+                    if (node.length != 0) {
+                        nodes.push({
+                            group: "nodes",
+                            data: {
+                                LabelSize: node.children()[x].data('LabelSize'),
+                                Type: node.children()[x].data('Type'),
+                                Valign: node.children()[x].data('Valign'),
+                                Width: node.children()[x].data('Width'),
+                                Height: node.children()[x].data('Height'),
+                                id: node.children()[x].data('id'),
+                                name: node.children()[x].data('name'),
+                                selected: node.children()[x].data('selected'),
+                                cnv: node.children()[x].data('cnv'),
+                                rna: node.children()[x].data('rna'),
+                                mut: node.children()[x].data('mut'),
+                                parent: node.data('id'),
+                                backgroundImage: node.children()[x].data('backgroundImage'),
+                                zIndex: node.children()[x].data('zIndex')
+                            },
+                            position: {
+                                x: node.children()[x].position('x'),
+                                y: node.children()[x].position('y')
+                            }
+                        });
+                    } else {
+                        nodes.push({
+                            group: "nodes",
+                            data: {
+                                LabelSize: node.children()[x].data('LabelSize'),
+                                Type: node.children()[x].data('Type'),
+                                Valign: node.children()[x].data('Valign'),
+                                Width: node.children()[x].data('Width'),
+                                Height: node.children()[x].data('Height'),
+                                id: node.children()[x].data('id'),
+                                name: node.children()[x].data('name'),
+                                selected: node.children()[x].data('selected'),
+                                cnv: node.children()[x].data('cnv'),
+                                rna: node.children()[x].data('rna'),
+                                mut: node.children()[x].data('mut'),
+                                backgroundImage: node.children()[x].data('backgroundImage'),
+                                zIndex: node.children()[x].data('zIndex')
+                            },
+                            position: {
+                                x: node.children()[x].position('x'),
+                                y: node.children()[x].position('y')
+                            }
+                        });
+                    }
+
+                    for (var j = 0; j < node.children()[x].connectedEdges().size(); j++) {
+                        edges.push({
+                            group: "edges",
+                            data: {
+                                id: node.children()[x].connectedEdges()[j].data('id'),
+                                Type: node.children()[x].connectedEdges()[j].data('Type'),
+                                LineThickness: node.children()[x].connectedEdges()[j].data('LineThickness'),
+                                EndArrow: node.children()[x].connectedEdges()[j].data('EndArrow'),
+                                Coords: node.children()[x].connectedEdges()[j].data('Coords'),
+                                ZOrder: node.children()[x].connectedEdges()[j].data('ZOrder'),
+                                source: node.children()[x].connectedEdges()[j].data('source'),
+                                target: node.children()[x].connectedEdges()[j].data('target'),
+                                StartArrow: node.children()[x].connectedEdges()[j].data('StartArrow'),
+                                selected: node.children()[x].connectedEdges()[j].data('selected')
+                            }
+                        })
+                    }
+                    unbundleRecursive(node.children()[x], parents, edges, nodes, rCounter);
+                }
+            }
+        }
+
+        function unbundle(event) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var parents = [];
+            var nodes = [];
+            var edges = [];
+            var rCounter = 0;
+
+            for (var i = 0; i < selectedForEditNodes.size(); i++) {
+                unbundleRecursive(selectedForEditNodes[i], parents, edges, nodes, rCounter);
+            }
+
+            // Remove parents (in the instance that they haven't been removed!)
+            for (var i = 0; i < parents.length; i++) {
+                parents[i].remove();
+            }
+
+            // Add new nodes
+            cy.add(nodes.concat(edges));
+            postAddProcessing();
+            saveState();
+        }
+
+        function recursiveBundle(node, edges, nodes) {
+            nodes.push({
+                group: "nodes",
+                data: {
+                    LabelSize: node.data('LabelSize'),
+                    Type: node.data('Type'),
+                    Valign: node.data('Valign'),
+                    Width: node.data('Width'),
+                    Height: node.data('Height'),
+                    id: node.data('id'),
+                    name: node.data('name'),
+                    selected: node.data('selected'),
+                    cnv: node.data('cnv'),
+                    rna: node.data('rna'),
+                    mut: node.data('mut'),
+                    parent: node.data('parent'),
+                    backgroundImage: node.data('backgroundImage'),
+                    zIndex: node.data('zIndex')
+                },
+                position: {
+                    x: node.position('x'),
+                    y: node.position('y')
+                }
+            });
+            for (var j = 0; j < node.connectedEdges().size(); j++) {
+                edges.push({
+                    group: "edges",
+                    data: {
+                        id: node.connectedEdges()[j].data('id'),
+                        Type: node.connectedEdges()[j].data('Type'),
+                        LineThickness: node.connectedEdges()[j].data('LineThickness'),
+                        EndArrow: node.connectedEdges()[j].data('EndArrow'),
+                        Coords: node.connectedEdges()[j].data('Coords'),
+                        ZOrder: node.connectedEdges()[j].data('ZOrder'),
+                        source: node.connectedEdges()[j].data('source'),
+                        target: node.connectedEdges()[j].data('target'),
+                        StartArrow: node.connectedEdges()[j].data('StartArrow'),
+                        selected: node.connectedEdges()[j].data('selected')
+                    }
+                })
+            }
+            for (var i = 0; i < node.children().size(); i++) {
+                recursiveBundle(node.children()[i], edges, nodes);
+            }
+        }
+
+        function bundle(event) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var type = document.getElementById(parent + "-type-bundle").value;
+            var nodes = [];
+            var edges = [];
+            // Create new parent
+            nodes.push({
+                group: "nodes",
+                data: {
+                    LabelSize: 10,
+                    Type: type,
+                    Valign: "Middle",
+                    Width: 80.75,
+                    Height: 100,
+                    id: "n" + nodeCounter,
+                    name: "n" + nodeCounter,
+                    selected: false,
+                    backgroundImage: "",
+                    zIndex: 0
+                },
+                position: {
+                    x: 500,
+                    y: 500
+                }
+            })
+
+            // Create copies of old nodes
+            for (var i = 0; i < selectedForEditNodes.size(); i++) {
+                if (!selectedForEditNodes[i].isChild()) {
+                    nodes.push({
+                        group: "nodes",
+                        data: {
+                            LabelSize: selectedForEditNodes[i].data('LabelSize'),
+                            Type: selectedForEditNodes[i].data('Type'),
+                            Valign: selectedForEditNodes[i].data('Valign'),
+                            Width: selectedForEditNodes[i].data('Width'),
+                            Height: selectedForEditNodes[i].data('Height'),
+                            id: selectedForEditNodes[i].data('id'),
+                            name: selectedForEditNodes[i].data('name'),
+                            selected: selectedForEditNodes[i].data('selected'),
+                            cnv: selectedForEditNodes[i].data('cnv'),
+                            rna: selectedForEditNodes[i].data('rna'),
+                            mut: selectedForEditNodes[i].data('mut'),
+                            parent: "n" + nodeCounter,
+                            backgroundImage: selectedForEditNodes[i].data('backgroundImage'),
+                            zIndex: selectedForEditNodes[i].data('zIndex')
+
+                        },
+                        position: {
+                            x: selectedForEditNodes[i].position('x'),
+                            y: selectedForEditNodes[i].position('y')
+                        }
+                    });
+                    for (var j = 0; j < selectedForEditNodes[i].connectedEdges().size(); j++) {
+                        edges.push({
+                            group: "edges",
+                            data: {
+                                id: selectedForEditNodes[i].connectedEdges()[j].data('id'),
+                                Type: selectedForEditNodes[i].connectedEdges()[j].data('Type'),
+                                LineThickness: selectedForEditNodes[i].connectedEdges()[j].data('LineThickness'),
+                                EndArrow: selectedForEditNodes[i].connectedEdges()[j].data('EndArrow'),
+                                Coords: selectedForEditNodes[i].connectedEdges()[j].data('Coords'),
+                                ZOrder: selectedForEditNodes[i].connectedEdges()[j].data('ZOrder'),
+                                source: selectedForEditNodes[i].connectedEdges()[j].data('source'),
+                                target: selectedForEditNodes[i].connectedEdges()[j].data('target'),
+                                StartArrow: selectedForEditNodes[i].connectedEdges()[j].data('StartArrow'),
+                                selected: selectedForEditNodes[i].connectedEdges()[j].data('selected')
+                            }
+                        })
+                    }
+                }
+                if (selectedForEditNodes[i].isParent() || selectedForEditNodes[i].isChild()) {
+                    recursiveBundle(selectedForEditNodes[i], edges, nodes);
+                }
+            }
+
+            // Remove old nodes
+            selectedForEditNodes.remove();
+
+            // Add new nodes
+            cy.add(nodes.concat(edges));
+            postAddProcessing();
+
+            if (!cy.elements("node[id = \"n" + nodeCounter + "\"]").isParent())
+                cy.elements("node[id = \"n" + nodeCounter + "\"]").remove();
+
+            // increment nodeCounter to insure unique id
+            nodeCounter++;
+
+            // Remove dialog box
+            dialogBundle.dialog("close");
+            saveState();
+        }
+
+        function produceJSON(event) {
+            download(states[states.length - 1], "data.txt", "text/plain");
+        }
+
+        function refreshPathwayList() {
+            var select = document.getElementById(parent + "-pathway-selector");
+
+            while (select.firstChild) {
+                select.removeChild(select.firstChild);
+            }
+
+            $.get(services['pathwayFinder'], {
+                pathwayList: '1'
+            }, function (data) {
+                var obj = JSON.parse(data);
+                var el = document.createElement("option");
+                el.textContent = "Select pathway";
+                select.appendChild(el);
+                for (var i = 0; i < obj.length; i++) {
+                    var opt = obj[i].NAME;
+                    var val = obj[i].ID;
+                    var el = document.createElement("option");
+                    el.textContent = opt;
+                    el.value = val;
+                    select.appendChild(el);
+                }
+            });
+
+        }
+
+        function findPath(Json, sid, vid) {
+            var nodes = Json['elements']['nodes'];
+            nodes = nodes.filter(function (item) {
+                if (item['data']['NODE_TYPE'] !== 'GROUP') {
+                    return true;
+                }
+
+            });
+            //console.log(nodes);
+            var edges = Json['elements']['edges'];
+            var result = [];
+            //array of arrays containing the graphids for edges in the path
+            var path = [];
+            var nodeTrack = [];
+
+            function mapLocation(x, y) {
+                var deta = 1;
+
+                for (var j = 0; j < nodes.length; j++) {
+                    var x0 = nodes[j]['position']['x'];
+                    var y0 = nodes[j]['position']['y'];
+                    var w = nodes[j]['data']['Width'];
+                    var h = nodes[j]['data']['Height'];
+
+                    if (x > x0 - w / 2 - deta & x < x0 + w / 2 + deta & y > y0 - h / 2 - deta & y < y0 + h / 2 + deta) {
+                        return nodes[j]['data']['SUID'];
+
+                    }
+                }
+            }
+
+            function findEdgeBySource(gid) {
+                if (gid == undefined | gid == '0') {
+                    return;
+                }
+
+                var end = true;
+                for (var i = 0; i < edges.length; i++) {
+                    var eid = edges[i]['data']['id'];
+                    var s = (!('source' in edges[i]['data']) ? mapLocation(edges[i]['data']['Coords'][0]['x'], edges[i]['data']['Coords'][0]['y']) : edges[i]['data']['source']);
+
+                    if (s == gid) {
+
+                        var cl = edges[i]['data']['Coords'].length;
+                        var t = (!('target' in edges[i]['data']) ? mapLocation(edges[i]['data']['Coords'][cl - 1]['x'], edges[i]['data']['Coords'][cl - 1]['y']) : edges[i]['data']['target']);
+
+                        if (t == vid) {
+                            var p = path.slice();
+                            p.push(eid);
+                            result.push(p);
+
+                            continue;
+
+                        } else if (nodeTrack.indexOf(eid) == -1 & t !== undefined & t !== '0') {
+                            path.push(eid);
+                            nodeTrack.push(eid);
+
+                            findEdgeBySource(t);
+                        } else {
+                            continue;
+                        }
+                    }
+                }
+                if (end == true) {
+                    path.pop();
+                    nodeTrack.pop();
+
+                }
+                return true;
+            }
+
+            findEdgeBySource(sid);
+            return result;
+
+        }
+
+        function getPathScore(edgeArray, scoreJSON) {
+            var sum = 0;
+            var max = 0;
+            for (var i = 0; i < edgeArray.length; i++) {
+                sum = sum + (i + 1) * scoreJSON[edgeArray[i]] / edgeArray.length;
+                max = max + (i + 1) / edgeArray.length;
+            }
+            return parseFloat((sum / max).toFixed(5));
+        }
+
+        function convertEdgePathtoNodePath(selectedPaths) {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var nodePath = [];
+            for (var n = 0; n < selectedPaths.length; n++) {
+                nodePath.push([])
+                for (var j = 0; j < selectedPaths[n].length; j++) {
+                    if (j < selectedPaths[n].length - 1) {
+                        var sourceNodeId = cy.elements("edge[id = \"" + selectedPaths[n][j] + "\"]").data('source');
                         var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('name');
-						var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('cnv');
-						var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('rna');
-						var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('mut');
-						if(cy.elements("node[id = \"" + sourceNodeId + "\"]").isParent()){
-							nodePath[n].push([]);
-							for(var k = 0; k < cy.elements("node[id = \"" + sourceNodeId + "\"]").children().length; k++){
-								var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.name
-								var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.cnv
-								var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.rna
-								var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.mut
-								nodePath[n][j].push({"name": sourceNodeName,"cnv":sourceNodeCnv,"rna":sourceNodeRna,"mut":sourceNodeMut});
-							}
-						} else {
-							nodePath[n].push([{"name": sourceNodeName,"cnv":sourceNodeCnv,"rna":sourceNodeRna,"mut":sourceNodeMut}]);
-							
-						}
-					} else {
-						var sourceNodeId = cy.elements("edge[id = \"" + selectedPaths[n][j] + "\"]").data('source');
-						var targetNodeId = cy.elements("edge[id = \"" + selectedPaths[n][j] + "\"]").data('target');
-                        
-						var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('name');
-						var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('cnv');
-						var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('rna');
-						var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('mut');
-                        
-						var targetNodeName = cy.elements("node[id = \"" + targetNodeId + "\"]").data('name');
-						var targetNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('cnv');
-						var targetNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('rna');
-						var targetNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('mut');
-						
-						if(cy.elements("node[id = \"" + sourceNodeId + "\"]").isParent()){
-							nodePath[n].push([]);
-							for(var k = 0; k < cy.elements("node[id = \"" + sourceNodeId + "\"]").children().length; k++){
-								var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.name
-								var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.cnv
-								var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.rna
-								var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.mut
-								nodePath[n][j].push({"name": sourceNodeName,"cnv":sourceNodeCnv,"rna":sourceNodeRna,"mut":sourceNodeMut});
-							}
-						} else {
-							nodePath[n].push([{"name": sourceNodeName,"cnv":sourceNodeCnv,"rna":sourceNodeRna,"mut":sourceNodeMut}]);
-						}
-						if(cy.elements("node[id = \"" + targetNodeId + "\"]").isParent()){
-							nodePath[n].push([]);
-							for(var k = 0; k < cy.elements("node[id = \"" + targetNodeId + "\"]").children().length; k++){
-								var targetNodeName = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.name
-								var targetNodeCnv = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.cnv
-								var targetNodeRna = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.rna
-								var targetNodeMut = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.mut
-								nodePath[n][j].push({"name": targetNodeName,"cnv":targetNodeCnv,"rna":targetNodeRna,"mut":targetNodeMut});
-							}
-						} else {
-							nodePath[n].push([{"name": targetNodeName,"cnv":targetNodeCnv,"rna":targetNodeRna,"mut":targetNodeMut}]);
-						}
-					}
-				}
-			}
-			return nodePath;
-		}
-
-		function wrapperFindPath() {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var sid = orderedSelectedNodes[0]._private.data['id'];
-			var vid = orderedSelectedNodes[1]._private.data['id'];
-			$.post(services['pathwayScorer'], {
-				data_json : JSON.stringify(JSON.parse(states[states.length - 1]))
-			}, function(yue_data) {
-				var selectedPaths = findPath(JSON.parse(states[states.length - 1]), sid, vid);
-				var nodePaths = convertEdgePathtoNodePath(selectedPaths);
-				console.log(JSON.stringify(nodePaths));
-				$.post(services['pathwayWeightedScorer'], {
-					data_paths : JSON.stringify(nodePaths)
-				}, function(tham_data) {
-					console.log(tham_data)
-					var scoreJSON = JSON.parse(yue_data);
-					var fdrJSON = JSON.parse(tham_data);
-					console.log(fdrJSON);
-					var table = document.getElementById(parent + "-inner-table");
-					var length = document.getElementById(parent + "-inner-table").rows.length;
-
-					if ( typeof (selectedPaths) == "undefined") {
-						dialogPathfind.dialog("close");
-					}
-
-					for (var n = 0; n < length; n++) {
-						table.deleteRow(0);
-					}
-					for (var n = 0; n <= selectedPaths.length; n++) {
-						var row = table.insertRow();
-
-						var path = row.insertCell(0);
-						var score = row.insertCell(1);
-						var fdr = row.insertCell(2);
-
-						// Add some text to the new cells:
-
-						if (n == 0) {
-							path.innerHTML = "<i><h3>paths</h3></i>";
-							score.innerHTML = "<i><h3>scores</h3></i>"
-							fdr.innerHTML = "<i><h3>fdr</h3></i>"
-						} else {
-							var btn = document.createElement("button");
-							var t = document.createTextNode((n - 1).toString());
-							btn.className = "btn btn-link";
-							btn.appendChild(t);
-							btn.addEventListener('click', function(event) {
-							var k = parseInt(event.currentTarget.innerHTML);
-							cy.$('node').unselect();
-							cy.$('edge').unselect();
-							for (var j = 0; j < selectedPaths[k].length; j++) {
-								cy.elements("edge[id = \"" + selectedPaths[k][j] + "\"]").select();
-								var sourceNode = cy.elements("edge[id = \"" + selectedPaths[k][j] + "\"]").data('source');
-								var targetNode = cy.elements("edge[id = \"" + selectedPaths[k][j] + "\"]").data('target');
-								cy.elements("node[id = \"" + targetNode + "\"]").select();
-								cy.elements("node[id = \"" + sourceNode + "\"]").select();
-								cy.$('node').style("opacity", 0.2);
-								cy.$('edge').style("opacity", 0.2);
-								cy.$('node:selected').style("opacity", 1.0);
-								cy.$('edge:selected').style("opacity", 1.0);
-								}
-							});
-							path.appendChild(btn);
-							score.appendChild(document.createTextNode(getPathScore(selectedPaths[n - 1], scoreJSON).toString()));
-							fdr.appendChild(document.createTextNode(fdrJSON[n-1]));
-						}
-					}
-					dialogTable.dialog("open");
-					dialogPathfind.dialog("close");			
-				});
-			})
-		}
-
-		function saveState() {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var nodes = cy.$('node');
-			var edges = cy.$('edge');
-			var data = '{"format_version" : "1.0","generated_by" : "cytoscape-3.2.1","target_cytoscapejs_version" : "~2.1","data" :' + JSON.stringify(header) + ',"elements" : {"nodes" :' + JSON.stringify(nodes.jsons()) + ',"edges" :' + JSON.stringify(edges.jsons()) + '}}';
-			states.push(data);
-		}
-
-		function undo() {
-			if (states.length > 1) {
-				var cy = $('#' + parent + '-cy').cytoscape('get');
-				cy.$('node').remove();
-				cy.$('edge').remove();
-				stateRecycle.push(states.pop());
-				var obj = JSON.parse(states[states.length - 1]);
-				cy.add(obj.elements);
-				postAddProcessing();
-			}
-		}
-
-		function redo() {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			if (stateRecycle.length > 1) {
-				cy.$('node').remove();
-				cy.$('edge').remove();
-				states.push(stateRecycle.pop());
-				var obj = JSON.parse(states[states.length - 1]);
-				cy.add(obj.elements)
-				postAddProcessing();
-			}
-		}
-
-		function clone(obj) {
-			if (null == obj || "object" != typeof obj)
-				return obj;
-			var copy = obj.constructor();
-			for (var attr in obj) {
-				if (obj.hasOwnProperty(attr))
-					copy[attr] = obj[attr];
-			}
-			return copy;
-		}
-
-		function setNodeStyle(target, background, border, shadow) {
-			if (background != '') {
-				target.removeClass('green_bg');
-				target.removeClass('red_bg');
-				target.removeClass('white_bg');
-				target.addClass(background);
-			}
-			if (border != '') {
-				target.removeClass('purple_border');
-				target.removeClass('red_border');
-				target.removeClass('black_border');
-				target.addClass(border);
-			}
-			if (shadow != '') {
-				target.removeClass('red_shadow');
-				target.removeClass('no_shadow');
-				target.addClass(shadow);
-			}
-
-			if (background == '' && border == '' && shadow == '') {
-				target.removeClass('green_bg');
-				target.removeClass('red_bg');
-				target.removeClass('white_bg');
-				target.removeClass('purple_border');
-				target.removeClass('red_border');
-				target.removeClass('black_border');
-				target.removeClass('red_shadow');
-				target.removeClass('no_shadow');
-			}
-		}
-
-		function editEdge() {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-			var direction = document.getElementById(parent + "-direction").value;
-			var arrowType = document.getElementById(parent + "-arrow-type-edge").value;
-			var lineType = document.getElementById(parent + "-line-type-edge").value;
-			target.data('StartArrow', arrowType);
-			target.data('EndArrow', arrowType);
-			target.data('Type', lineType);
-			if (document.getElementById(parent + '-direction').checked) {
-				var edge = [];
-
-				edge.push({
-					group : "edges",
-					data : {
-						id : target.data('id'),
-						Type : target.data('Type'),
-						LineThickness : target.data('LineThickness'),
-						EndArrow : target.data('EndArrow'),
-						Coords : target.data('Coords'),
-						ZOrder : target.data('ZOrder'),
-						source : target.data('target'),
-						target : target.data('source'),
-						StartArrow : target.data('StartArrow'),
-						selected : target.data('Selected')
-					}
-				})
-				target.remove();
-				cy.add(edge);
-				postAddProcessing();
-			}
-			dialogEdge.dialog("close");
-			saveState();
-		}
-
-		function moveElementtoBackground(event) {
-			target.style("z-index", 0);
-			target.data("zIndex", 0);
-			saveState();
-		}
-
-		function moveElementtoForeground(event) {
-			highestZOrder++;
-			target.style("z-index", highestZOrder);
-			target.data("zIndex", highestZOrder);
-			saveState();
-		}
-
-		function removeBackgroundImageOnNode(event) {
-			target.removeStyle("background-image");
-			target.data("backgroundImage", "");
-			saveState();
-		}
-
-		function onChangeBackgroundImageOnNode(event) {
-			var reader = new FileReader();
-			reader.onload = onBackgroundImageReaderLoad;
-			reader.readAsDataURL(event.target.files[0]);
-			saveState();
-		}
-
-		function onBackgroundImageReaderLoad() {
-			var img = event.target.result;
-			target.data('Type', "image");
-			target.data("backgroundImage", img);
-			target.style("background-image", img);
-			saveState();
-		}
-
-		function editNode() {
-			var name = document.getElementById(parent + "-gene-name").value;
-			var width = document.getElementById(parent + "-width").value;
-			var height = document.getElementById(parent + "-height").value;
-			var type = document.getElementById(parent + "-type-node").value;
-			target.data('name', name);
-			target.data('Width', width);
-			target.data('Height', height);
-			target.data('Type', type);
-
-			var node_name = target.data("name");
-			selectedForQueryNodes.push(node_name);
-			var rna = document.getElementById(parent + "-rna").value;
-			var cnv = document.getElementById(parent + "-cnv").value;
-			var mut = document.getElementById(parent + "-mut").value;
-			target.data('rna', rna);
-			target.data('cnv', cnv);
-			target.data('mut', mut);
-
-			coloredNodes.push({
-				"gene_name" : node_name,
-				"rna" : rna,
-				"cnv" : cnv,
-				"mut" : mut
-			});
-			$('#' + parent + '-variable').val($('#' + parent + '-variable').val() + coloredNodes);
-			dialogNode.dialog("close");
-			saveState();
-		}
-
-		function dialogNewPathwayOpen(event) {
-			dialogNewPathway.dialog("open");
-		}
-
-		function dialogBundleOpen(event) {
-			dialogBundle.dialog("open");
-		}
-
-		function dialogPathfindOpen(event) {
-			dialogPathfind.dialog("open");
-		}
-
-		function dialogPathwaySaveAsOpen(event) {
-			dialogPathwaySaveAs.dialog("open");
-		}
-
-		function findObject(event) {
-			var val = event.target.value;
-			$.post(services['objectFinder'], {
-				pattern : JSON.stringify(coloredNodes)
-			}, function(data) {
-				if (data == "[]")
-					data = '{"X1":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X2":{"percentage":0.33333,"rna_distance":30.44444,"cnv_distance":0,"mut_distance":0},"X9":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X29":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X24":{"percentage":0.33333,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X34":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X38":{"percentage":0.33333,"rna_distance":30.44444,"cnv_distance":0,"mut_distance":0},"X40":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X45":{"percentage":0.66667,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X46":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X48":{"percentage":1,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X53":{"percentage":1,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X59":{"percentage":0.66667,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X156":{"percentage":0.33333,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X15":{"percentage":0.33333,"rna_distance":0,"cnv_distance":0,"mut_distance":2},"X22":{"percentage":0.33333,"rna_distance":0,"cnv_distance":0,"mut_distance":0}}'
-				var array = data.split("},");
-				for (var i = 0; i < array.length; i++) {
-					array[i] = array[i].split(":{");
-					array[i][1] = array[i][1].split(",");
-					array[i][0] = array[i][0].replace(/\W/g, '');
-					for (var j = 0; j < array[i][1].length; j++) {
-						array[i][1][j] = array[i][1][j].replace(/[^\d.-]/g, '');
-					}
-				}
-
-				var table = document.getElementById(parent + "-inner-table");
-				var length = document.getElementById(parent + "-inner-table").rows.length;
-				for (var n = 0; n < length; n++) {
-					table.deleteRow(0);
-				}
-				for (var n = 0; n <= array.length; n++) {
-					var row = table.insertRow();
-
-					var name = row.insertCell(0)
-					var percentage = row.insertCell(1);
-					var rnaDistance = row.insertCell(2);
-					var cnvDistance = row.insertCell(3);
-					var mutDistance = row.insertCell(4);
-
-					// Add some text to the new cells:
-
-					if (n == 0) {
-						name.innerHTML = "<i><h3>name</h3></i>";
-						percentage.innerHTML = "<i><h3>percentage</h3></i>";
-						rnaDistance.innerHTML = "<i><h3>rna</h3></i>";
-						cnvDistance.innerHTML = "<i><h3>cnv</h3></i>";
-						mutDistance.innerHTML = "<i><h3>mut</h3></i>";
-					} else {
-						name.innerHTML = array[n-1][0];
-						percentage.innerHTML = array[n-1][1][0];
-						rnaDistance.innerHTML = array[n-1][1][1];
-						cnvDistance.innerHTML = array[n-1][1][2];
-						mutDistance.innerHTML = array[n-1][1][3];
-					}
-				}
-				//document.getElementById(parent + "-dialog-table").innerHTML = data;
-				dialogTable.dialog("open")
-			});
-		}
-
-		function visualPathway(obj) {
-			$('#' + parent + '-cy').cytoscape({
-				style : cytoscape.stylesheet()
-
-				// node elements default css (unselected state)
-				.selector('node').css({
-					'content' : 'data(name)',
-					'padding-left' : 2,
-					'padding-right' : 2,
-					'font-family' : 'data(LabelSize)',
-					'background-image-opacity' : .75,
-					'opacity' : 0.75,
-					'text-opacity' : 0.75
-				}).selector('node[Type="bundleOne"]').css({
-					'shape' : 'roundrectangle',
-					'background-color' : 'lightgray',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="bundleTwo"]').css({
-					'shape' : 'roundrectangle',
-					'background-color' : 'gray',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="gene"]').css({
-					'shape' : 'ellipse',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="geneProduct"]').css({
-					'shape' : 'circle',
-					'radius' : 5,
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="protein"]').css({
-					'shape' : 'rectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="rna"]').css({
-					'shape' : 'circle',
-					'radius' : 5,
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'dotted',
-					'border-width' : 1
-				}).selector('node[Type="microRNA"]').css({
-					'shape' : 'circle',
-					'radius' : 5,
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'dashed',
-					'border-width' : 1
-				}).selector('node[Type="kinase"]').css({
-					'shape' : 'rectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'dashed',
-					'border-width' : 1
-				}).selector('node[Type="ligand"]').css({
-					'shape' : 'rectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'dotted',
-					'border-width' : 1
-				}).selector('node[Type="receptor"]').css({
-					'shape' : 'rectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'double',
-					'border-width' : 1
-				}).selector('node[Type="biologicalProcess"]').css({
-					'shape' : 'roundrectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="triangle"]').css({
-					'shape' : 'triangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="ellipse"]').css({
-					'shape' : 'ellipse',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="pentagon"]').css({
-					'shape' : 'pentagon',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="hexagon"]').css({
-					'shape' : 'hexagon',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="heptagon"]').css({
-					'shape' : 'heptagon',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="octagon"]').css({
-					'shape' : 'octagon',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="star"]').css({
-					'shape' : 'star',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="diamond"]').css({
-					'shape' : 'diamond',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="vee"]').css({
-					'shape' : 'vee',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="rhomboid"]').css({
-					'shape' : 'rhomboid',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="label"]').css({
-					'shape' : 'rectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-color' : 'white',
-					'border-color' : 'white',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[Type="image"]').css({
-					'shape' : 'rectangle',
-					'width' : 'data(Width)',
-					'height' : 'data(Height)',
-					'color' : 'black',
-					'text-valign' : 'center',
-					'background-opacity' : 0,
-					'border-color' : 'white',
-					'border-style' : 'solid',
-					'border-width' : 1,
-					'background-fit' : 'contain'
-				}).selector('node[Shape="Brace"]').css({
-					'shape' : 'rectangle',
-					'width' : '1',
-					'height' : 'data(Width)',
-					'background-color' : 'black',
-					'color' : 'black',
-					'border-color' : 'black',
-					'border-style' : 'solid',
-					'border-width' : 1
-				}).selector('node[rna < 0]').css({
-					'background-color' : 'lightgreen',
-					'color' : 'black'
-				}).selector('node[rna > 0]').css({
-					'background-color' : 'lightsalmon',
-					'color' : 'black'
-				}).selector('node[cnv < 0]').css({
-					'border-color' : 'mediumpurple',
-					'border-width' : 3
-				}).selector('node[cnv > 0]').css({
-					'border-color' : 'red',
-					'border-width' : 3
-				}).selector('node[mut > 0]').css({
-					'shadow-opacity' : 1,
-					'shadow-color' : 'red',
-					'border-width' : 1
-				})
-
-				// edge elements default css (unselected)
-				.selector('edge').css({
-					'line-color' : 'black',
-					'line-style' : 'solid',
-					'opacity' : 0.75,
-					'text-opacity' : 0.75,
-					'width' : 1
-				}).selector('edge[EndArrow="Line"]').css({
-					'target-arrow-shape' : 'line',
-					'target-arrow-color' : 'black',
-					'target-arrow-fill' : 'filled'
-				}).selector('edge[EndArrow="Arrow"]').css({
-					'target-arrow-shape' : 'triangle',
-					'target-arrow-color' : 'black',
-					'target-arrow-fill' : 'filled'
-				}).selector('edge[EndArrow="TBar"]').css({
-					'target-arrow-shape' : 'tee',
-					'target-arrow-color' : 'black',
-					'target-arrow-fill' : 'filled'
-				}).selector('edge[Type="Solid"]').css({
-					'line-style' : 'solid'
-				}).selector('edge[Type="Dashed"]').css({
-					'line-style' : 'dashed'
-				}).selector('edge[Type="Dotted"]').css({
-					'line-style' : 'dotted'
-				})
-
-
-				// node & edge elements (selected state)
-				.selector('edge:selected').css({
-					'background-color' : 'green',
-					'line-color' : 'green',
-					'target-arrow-color' : 'green',
-					'source-arrow-color' : 'green',
-					'opacity' : 1.0,
-					'text-opacity' : 1.0
-				}).selector('node:selected').css({
-					'background-color' : 'green',
-					'opacity' : 1.0,
-					'text-opacity' : 1.0
-				})
-
-				// query purpose
-				.selector('.green_bg').css({
-					'background-color' : 'lightgreen',
-					'color' : 'black'
-				}).selector('.red_bg').css({
-					'background-color' : 'lightsalmon',
-					'color' : 'black'
-				}).selector('.white_bg').css({
-					'background-color' : 'white',
-					'color' : 'black'
-				}).selector('.purple_border').css({
-					'border-color' : 'mediumpurple',
-					'border-width' : 3
-				}).selector('.red_border').css({
-					'border-color' : 'red',
-					'border-width' : 3
-				}).selector('.black_border').css({
-					'border-color' : 'black',
-					'border-width' : 3
-				}).selector('.red_shadow').css({
-					'shadow-opacity' : 1,
-					'shadow-color' : 'red',
-					'border-width' : 1
-				}).selector('.no_shadow').css({
-					'shadow-opacity' : 0,
-					'shadow-color' : 'red',
-					'border-width' : 1
-				})
-
-				// collapse
-				.selector('.collapsed').css({
-					'opacity' : 0.01
-				}),
-				layout : {
-					name : 'preset',
-					padding : 10
-				},
-				ready : function() {
-					var cy = $('#' + parent + '-cy').cytoscape('get');
-
-					preAddProcessing(obj);
-
-					//un-disable options
-					$('#' + parent + '-select-bundleOne').removeClass('disabled');
-					$('#' + parent + '-add-node').removeClass('disabled');
-					$('#' + parent + '-add-edge').removeClass('disabled');
-					$('#' + parent + '-delete-elements').removeClass('disabled');
-					$('#' + parent + '-bundle').removeClass('disabled');
-					$('#' + parent + '-unbundle').removeClass('disabled');
-					$('#' + parent + '-collapse').removeClass('disabled');
-					$('#' + parent + '-expand').removeClass('disabled');
-					$('#' + parent + '-findpath').removeClass('disabled');
-					$('#' + parent + '-find-object').removeClass('disabled');
-					$('#' + parent + '-pathway-save').removeClass('disabled');
-					$('#' + parent + '-pathway-saveAs').removeClass('disabled');
-					$('#' + parent + '-produce-JSON').removeClass('disabled');
-					$('#' + parent + '-undo').removeClass('disabled');
-					$('#' + parent + '-redo').removeClass('disabled');
-
-					// Add processed nodes
-					cy.add(obj.elements);
-					cy.center();
-					cy.fit();
-
-					// Post-Add Process
-					postAddProcessing();
-
-					// add custom event
-					var tappedBefore = null;
-					cy.on('tap', function(event) {
-						var tappedNow = event.cyTarget;
-						setTimeout(function() {
-							tappedBefore = null;
-						}, 300);
-						if (tappedBefore === tappedNow) {
-							tappedNow.trigger('doubleTap');
-							tappedBefore = null;
-						} else {
-							tappedBefore = tappedNow;
-						}
-					});
-
-					// custom event handlers
-					cy.on('click', 'node', function(event) {
-						if (orderedSelectedNodes.length < 2)
-							orderedSelectedNodes.push(event.cyTarget);
-						else
-							orderedSelectedNodes.shift();
-						orderedSelectedNodes.push(event.cyTarget);
-					});
-
-					cy.on('doubleTap', 'node', function(event) {
-						target = event.cyTarget;
-						dialogNode.dialog("open");
-					});
-
-					cy.on('doubleTap', 'edge', function(event) {
-						target = event.cyTarget;
-						dialogEdge.dialog("open");
-					});
-
-					cy.on('select', 'node', function(event) {
-						selectedForEditNodes = cy.$('node:selected');
-						//			    	saveState();
-					});
-
-					cy.on('unselect', 'node', function(event) {
-						selectedForEditNodes = cy.$('node:selected');
-						//			    	saveState();
-					});
-
-					cy.on('select', 'edge', function(event) {
-						selectedForEditEdges = cy.$('edge:selected');
-						//			    	saveState();
-					});
-
-					cy.on('unselect', 'edge', function(event) {
-						selectedForEditEdges = cy.$('edge:selected');
-						//			    	saveState();
-					});
-
-					cy.on('grab', 'node', function(event) {
-						if (cy.$('node:grabbed').isParent() && !cy.$('node:grabbed').descendants()[0].grabbable()) {
-							grabbedCollapsedForEditNodes = cy.$('node:grabbed');
-							grabbedCollapsedForEditNodes.descendants().grabify();
-						}
-						saveState();
-					});
-
-					cy.on('free', 'node', function(event) {
-						//			    	saveState();
-						if (grabbedCollapsedForEditNodes.constructor !== Array)
-							grabbedCollapsedForEditNodes.descendants().ungrabify();
-						grabbedCollapsedForEditNodes = [];
-					});
-
-					cy.on('data', 'node', function(event) {
-						//					saveState();
-					});
-
-					cy.on('style', 'node', function(event) {
-						//					saveState();
-					});
-
-					saveState();
-					sprayColor(self.sprayData);
-				},
-				// initial viewport state:
-				zoom : 1,
-				pan : {
-					x : 0,
-					y : 0
-				},
-				// interaction options:
-				minZoom : 1e-50,
-				maxZoom : 1e50,
-				zoomingEnabled : true,
-				userZoomingEnabled : true,
-				panningEnabled : true,
-				userPanningEnabled : true,
-				boxSelectionEnabled : true,
-				selectionType : 'additive',
-				touchTapThreshold : 8,
-				desktopTapThreshold : 4,
-				autolock : false,
-				autoungrabify : false,
-				autounselectify : false,
-				// rendering options:
-				headless : false,
-				styleEnabled : true,
-				hideEdgesOnViewport : false,
-				hideLabelsOnViewport : false,
-				textureOnViewport : false,
-				motionBlur : false,
-				motionBlurOpacity : 0.2,
-				wheelSensitivity : 0.2,
-				pixelRatio : 1,
-				initrender : function(evt) {/* ... */
-				},
-				renderer : {/* ... */}
-			});
-		}
-
-		dialogTable = $("#" + parent + "-dialog-table").dialog({
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				Cancel : function() {
-					dialogTable.dialog("close");
-					var cy = $('#' + parent + '-cy').cytoscape('get');
-					cy.$('node').removeStyle("opacity");
-					cy.$('edge').removeStyle("opacity");
-					cy.$('node:selected').removeStyle("opacity");
-					cy.$('edge:selected').removeStyle("opacity");
-				}
-			},
-			close : function() {
-				var cy = $('#' + parent + '-cy').cytoscape('get');
-				cy.$('node').removeStyle("opacity");
-				cy.$('edge').removeStyle("opacity");
-				cy.$('node:selected').removeStyle("opacity");
-				cy.$('edge:selected').removeStyle("opacity");
-			}
-		});
-
-		dialogNode = $("#" + parent + "-dialog-form-node").dialog({
-			open : function(event) {
-				if (!target.isParent()) {
-					document.getElementById(parent + '-select-bundleOne').disabled = true;
-					document.getElementById(parent + '-select-bundleTwo').disabled = true;
-					document.getElementById(parent + "-select-gene").disabled = false;
-					document.getElementById(parent + "-select-geneProduct").disabled = false;
-					document.getElementById(parent + "-select-protein").disabled = false;
-					document.getElementById(parent + "-select-rna").disabled = false;
-					document.getElementById(parent + "-select-mircoRNA").disabled = false;
-					document.getElementById(parent + "-select-kinase").disabled = false;
-					document.getElementById(parent + "-select-ligand").disabled = false;
-					document.getElementById(parent + "-select-receptor").disabled = false;
-					document.getElementById(parent + "-select-biologicalProcess").disabled = false;
-					document.getElementById(parent + "-select-triangle").disabled = false;
-					document.getElementById(parent + "-select-ellipse").disabled = false;
-					document.getElementById(parent + "-select-pentagon").disabled = false;
-					document.getElementById(parent + "-select-hexagon").disabled = false;
-					document.getElementById(parent + "-select-heptagon").disabled = false;
-					document.getElementById(parent + "-select-octagon").disabled = false;
-					document.getElementById(parent + "-select-star").disabled = false;
-					document.getElementById(parent + "-select-diamond").disabled = false;
-					document.getElementById(parent + "-select-vee").disabled = false;
-					document.getElementById(parent + "-select-rhomboid").disabled = false;
-					document.getElementById(parent + "-select-label").disabled = false;
-				} else {
-					document.getElementById(parent + '-select-bundleOne').disabled = false;
-					document.getElementById(parent + '-select-bundleTwo').disabled = false;
-					document.getElementById(parent + "-select-gene").disabled = true;
-					document.getElementById(parent + "-select-geneProduct").disabled = true;
-					document.getElementById(parent + "-select-protein").disabled = true;
-					document.getElementById(parent + "-select-rna").disabled = true;
-					document.getElementById(parent + "-select-mircoRNA").disabled = true;
-					document.getElementById(parent + "-select-kinase").disabled = true;
-					document.getElementById(parent + "-select-ligand").disabled = true;
-					document.getElementById(parent + "-select-receptor").disabled = true;
-					document.getElementById(parent + "-select-biologicalProcess").disabled = true;
-					document.getElementById(parent + "-select-triangle").disabled = true;
-					document.getElementById(parent + "-select-ellipse").disabled = true;
-					document.getElementById(parent + "-select-pentagon").disabled = true;
-					document.getElementById(parent + "-select-hexagon").disabled = true;
-					document.getElementById(parent + "-select-heptagon").disabled = true;
-					document.getElementById(parent + "-select-octagon").disabled = true;
-					document.getElementById(parent + "-select-star").disabled = true;
-					document.getElementById(parent + "-select-diamond").disabled = true;
-					document.getElementById(parent + "-select-vee").disabled = true;
-					document.getElementById(parent + "-select-rhomboid").disabled = true;
-					document.getElementById(parent + "-select-label").disabled = true;
-				}
-				document.getElementById(parent + "-gene-name").value = target.data('name');
-				document.getElementById(parent + "-width").value = target.data('Width');
-				document.getElementById(parent + "-height").value = target.data('Height');
-				document.getElementById(parent + "-type-node").value = target.data('Type');
-				if ( typeof (target.data('rna')) != "undefined")
-					document.getElementById(parent + "-rna").value = target.data('rna');
-				else
-					document.getElementById(parent + "-rna").value = '0';
-
-				if ( typeof (target.data('cnv')) != "undefined")
-					document.getElementById(parent + "-cnv").value = target.data('cnv');
-				else
-					document.getElementById(parent + "-cnv").value = '0';
-
-				if ( typeof (target.data('mut')) != "undefined")
-					document.getElementById(parent + "-mut").value = target.data('mut');
-				else
-					document.getElementById(parent + "-mut").value = '0';
-			},
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				"submit" : editNode,
-				Cancel : function() {
-					dialogNode.dialog("close");
-				}
-			},
-			close : function() {
-			}
-		});
-
-		dialogEdge = $("#" + parent + "-dialog-form-edge").dialog({
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				"submit" : editEdge,
-				Cancel : function() {
-					dialogEdge.dialog("close");
-				}
-			},
-			close : function() {
-			}
-		});
-
-		dialogPathfind = $("#" + parent + "-dialog-form-find-path").dialog({
-			open : function(event) {
-				document.getElementById(parent + "-sid").value = orderedSelectedNodes[0]._private.data['name'];
-				document.getElementById(parent + "-vid").value = orderedSelectedNodes[1]._private.data['name'];
-			},
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				"submit" : wrapperFindPath,
-				Cancel : function() {
-					dialogPathfind.dialog("close");
-				}
-			},
-			close : function() {
-			}
-		});
-
-		dialogPathwaySaveAs = $("#" + parent + "-dialog-form-save-as-pathway").dialog({
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				"submit" : saveAsPathway,
-				Cancel : function() {
-					dialogPathwaySaveAs.dialog("close");
-				}
-			},
-			close : function() {
-			}
-		});
-
-		dialogNewPathway = $("#" + parent + "-dialog-form-new-pathway").dialog({
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				"submit" : newPathway,
-				Cancel : function() {
-					dialogNewPathway.dialog("close");
-				}
-			},
-			close : function() {
-			}
-		});
-
-		dialogBundle = $("#" + parent + "-dialog-bundle").dialog({
-			autoOpen : false,
-			height : 300,
-			width : 350,
-			buttons : {
-				"submit" : bundle,
-				Cancel : function() {
-					dialogBundle.dialog("close");
-				}
-			},
-			close : function() {
-			}
-		});
-
-		refreshPathwayList();
-		document.getElementById(parent + '-new-pathway').addEventListener('click', dialogNewPathwayOpen);
-		document.getElementById(parent + '-file-pathway').addEventListener('change', onChangePathwayFile);
-		document.getElementById(parent + '-file-coloring').addEventListener('change', onChangeColoringFile);
-		document.getElementById(parent + '-background-image').addEventListener('change', onChangeBackgroundImageOnNode);
-		document.getElementById(parent + '-background-image-remove').addEventListener('click', removeBackgroundImageOnNode);
-		document.getElementById(parent + '-node-move-to-background').addEventListener('click', moveElementtoBackground);
-		document.getElementById(parent + '-node-move-to-foreground').addEventListener('click', moveElementtoForeground);
-		document.getElementById(parent + '-edge-move-to-background').addEventListener('click', moveElementtoBackground);
-		document.getElementById(parent + '-edge-move-to-foreground').addEventListener('click', moveElementtoForeground);
-		document.getElementById(parent + '-new-pathway').addEventListener('click', dialogNewPathwayOpen);
-		document.getElementById(parent + '-findpath').addEventListener('click', dialogPathfindOpen);
-		document.getElementById(parent + '-find-object').addEventListener('click', findObject);
-		document.getElementById(parent + '-pathway-selector').addEventListener('change', onSelect);
-		document.getElementById(parent + '-pathway-saveAs').addEventListener('click', dialogPathwaySaveAsOpen);
-		document.getElementById(parent + '-pathway-save').addEventListener('click', savePathway);
-		document.getElementById(parent + '-delete-elements').addEventListener('click', removeElements);
-		document.getElementById(parent + '-add-node').addEventListener('click', addNode);
-		document.getElementById(parent + '-add-edge').addEventListener('click', addEdge);
-		document.getElementById(parent + '-expand').addEventListener('click', expandBundle);
-		document.getElementById(parent + '-collapse').addEventListener('click', collapseBundle);
-		document.getElementById(parent + '-bundle').addEventListener('click', dialogBundleOpen);
-		document.getElementById(parent + '-unbundle').addEventListener('click', unbundle);
-		document.getElementById(parent + '-produce-JSON').addEventListener('click', produceJSON);
-		document.getElementById(parent + '-undo').addEventListener('click', undo);
-		document.getElementById(parent + '-redo').addEventListener('click', redo);
-
-       //external functions
+                        var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('cnv');
+                        var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('rna');
+                        var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('mut');
+                        if (cy.elements("node[id = \"" + sourceNodeId + "\"]").isParent()) {
+                            nodePath[n].push([]);
+                            for (var k = 0; k < cy.elements("node[id = \"" + sourceNodeId + "\"]").children().length; k++) {
+                                var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.name
+                                var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.cnv
+                                var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.rna
+                                var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.mut
+                                nodePath[n][j].push({"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut});
+                            }
+                        } else {
+                            nodePath[n].push([{"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut}]);
+
+                        }
+                    } else {
+                        var sourceNodeId = cy.elements("edge[id = \"" + selectedPaths[n][j] + "\"]").data('source');
+                        var targetNodeId = cy.elements("edge[id = \"" + selectedPaths[n][j] + "\"]").data('target');
+
+                        var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('name');
+                        var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('cnv');
+                        var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('rna');
+                        var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('mut');
+
+                        var targetNodeName = cy.elements("node[id = \"" + targetNodeId + "\"]").data('name');
+                        var targetNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('cnv');
+                        var targetNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('rna');
+                        var targetNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").data('mut');
+
+                        if (cy.elements("node[id = \"" + sourceNodeId + "\"]").isParent()) {
+                            nodePath[n].push([]);
+                            for (var k = 0; k < cy.elements("node[id = \"" + sourceNodeId + "\"]").children().length; k++) {
+                                var sourceNodeName = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.name
+                                var sourceNodeCnv = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.cnv
+                                var sourceNodeRna = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.rna
+                                var sourceNodeMut = cy.elements("node[id = \"" + sourceNodeId + "\"]").children()[k]._private.data.mut
+                                nodePath[n][j].push({"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut});
+                            }
+                        } else {
+                            nodePath[n].push([{"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut}]);
+                        }
+                        if (cy.elements("node[id = \"" + targetNodeId + "\"]").isParent()) {
+                            nodePath[n].push([]);
+                            for (var k = 0; k < cy.elements("node[id = \"" + targetNodeId + "\"]").children().length; k++) {
+                                var targetNodeName = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.name
+                                var targetNodeCnv = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.cnv
+                                var targetNodeRna = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.rna
+                                var targetNodeMut = cy.elements("node[id = \"" + targetNodeId + "\"]").children()[k]._private.data.mut
+                                nodePath[n][j].push({"name": targetNodeName, "cnv": targetNodeCnv, "rna": targetNodeRna, "mut": targetNodeMut});
+                            }
+                        } else {
+                            nodePath[n].push([{"name": targetNodeName, "cnv": targetNodeCnv, "rna": targetNodeRna, "mut": targetNodeMut}]);
+                        }
+                    }
+                }
+            }
+            return nodePath;
+        }
+
+        function wrapperFindPath() {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var sid = orderedSelectedNodes[0]._private.data['id'];
+            var vid = orderedSelectedNodes[1]._private.data['id'];
+            $.post(services['pathwayScorer'], {
+                data_json: JSON.stringify(JSON.parse(states[states.length - 1]))
+            }, function (yue_data) {
+                var selectedPaths = findPath(JSON.parse(states[states.length - 1]), sid, vid);
+                var nodePaths = convertEdgePathtoNodePath(selectedPaths);
+                console.log(JSON.stringify(nodePaths));
+                $.post(services['pathwayWeightedScorer'], {
+                    data_paths: JSON.stringify(nodePaths)
+                }, function (tham_data) {
+                    console.log(tham_data)
+                    var scoreJSON = JSON.parse(yue_data);
+                    var fdrJSON = JSON.parse(tham_data);
+                    console.log(fdrJSON);
+                    var table = document.getElementById(parent + "-inner-table");
+                    var length = document.getElementById(parent + "-inner-table").rows.length;
+
+                    if (typeof (selectedPaths) == "undefined") {
+                        dialogPathfind.dialog("close");
+                    }
+
+                    for (var n = 0; n < length; n++) {
+                        table.deleteRow(0);
+                    }
+                    for (var n = 0; n <= selectedPaths.length; n++) {
+                        var row = table.insertRow();
+
+                        var path = row.insertCell(0);
+                        var score = row.insertCell(1);
+                        var fdr = row.insertCell(2);
+
+                        // Add some text to the new cells:
+
+                        if (n == 0) {
+                            path.innerHTML = "<i><h3>paths</h3></i>";
+                            score.innerHTML = "<i><h3>scores</h3></i>"
+                            fdr.innerHTML = "<i><h3>fdr</h3></i>"
+                        } else {
+                            var btn = document.createElement("button");
+                            var t = document.createTextNode((n - 1).toString());
+                            btn.className = "btn btn-link";
+                            btn.appendChild(t);
+                            btn.addEventListener('click', function (event) {
+                                var k = parseInt(event.currentTarget.innerHTML);
+                                cy.$('node').unselect();
+                                cy.$('edge').unselect();
+                                for (var j = 0; j < selectedPaths[k].length; j++) {
+                                    cy.elements("edge[id = \"" + selectedPaths[k][j] + "\"]").select();
+                                    var sourceNode = cy.elements("edge[id = \"" + selectedPaths[k][j] + "\"]").data('source');
+                                    var targetNode = cy.elements("edge[id = \"" + selectedPaths[k][j] + "\"]").data('target');
+                                    cy.elements("node[id = \"" + targetNode + "\"]").select();
+                                    cy.elements("node[id = \"" + sourceNode + "\"]").select();
+                                    cy.$('node').style("opacity", 0.2);
+                                    cy.$('edge').style("opacity", 0.2);
+                                    cy.$('node:selected').style("opacity", 1.0);
+                                    cy.$('edge:selected').style("opacity", 1.0);
+                                }
+                            });
+                            path.appendChild(btn);
+                            score.appendChild(document.createTextNode(getPathScore(selectedPaths[n - 1], scoreJSON).toString()));
+                            fdr.appendChild(document.createTextNode(fdrJSON[n - 1]));
+                        }
+                    }
+                    dialogTable.dialog("open");
+                    dialogPathfind.dialog("close");
+                });
+            })
+        }
+
+        function saveState() {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var nodes = cy.$('node');
+            var edges = cy.$('edge');
+            var data = '{"format_version" : "1.0","generated_by" : "cytoscape-3.2.1","target_cytoscapejs_version" : "~2.1","data" :' + JSON.stringify(header) + ',"elements" : {"nodes" :' + JSON.stringify(nodes.jsons()) + ',"edges" :' + JSON.stringify(edges.jsons()) + '}}';
+            states.push(data);
+        }
+
+        function undo() {
+            if (states.length > 1) {
+                var cy = $('#' + parent + '-cy').cytoscape('get');
+                cy.$('node').remove();
+                cy.$('edge').remove();
+                stateRecycle.push(states.pop());
+                var obj = JSON.parse(states[states.length - 1]);
+                cy.add(obj.elements);
+                postAddProcessing();
+            }
+        }
+
+        function redo() {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            if (stateRecycle.length > 1) {
+                cy.$('node').remove();
+                cy.$('edge').remove();
+                states.push(stateRecycle.pop());
+                var obj = JSON.parse(states[states.length - 1]);
+                cy.add(obj.elements)
+                postAddProcessing();
+            }
+        }
+
+        function clone(obj) {
+            if (null == obj || "object" != typeof obj)
+                return obj;
+            var copy = obj.constructor();
+            for (var attr in obj) {
+                if (obj.hasOwnProperty(attr))
+                    copy[attr] = obj[attr];
+            }
+            return copy;
+        }
+
+        function setNodeStyle(target, background, border, shadow) {
+            if (background != '') {
+                target.removeClass('green_bg');
+                target.removeClass('red_bg');
+                target.removeClass('white_bg');
+                target.addClass(background);
+            }
+            if (border != '') {
+                target.removeClass('purple_border');
+                target.removeClass('red_border');
+                target.removeClass('black_border');
+                target.addClass(border);
+            }
+            if (shadow != '') {
+                target.removeClass('red_shadow');
+                target.removeClass('no_shadow');
+                target.addClass(shadow);
+            }
+
+            if (background == '' && border == '' && shadow == '') {
+                target.removeClass('green_bg');
+                target.removeClass('red_bg');
+                target.removeClass('white_bg');
+                target.removeClass('purple_border');
+                target.removeClass('red_border');
+                target.removeClass('black_border');
+                target.removeClass('red_shadow');
+                target.removeClass('no_shadow');
+            }
+        }
+
+        function editEdge() {
+            var cy = $('#' + parent + '-cy').cytoscape('get');
+            var direction = document.getElementById(parent + "-direction").value;
+            var arrowType = document.getElementById(parent + "-arrow-type-edge").value;
+            var lineType = document.getElementById(parent + "-line-type-edge").value;
+            target.data('StartArrow', arrowType);
+            target.data('EndArrow', arrowType);
+            target.data('Type', lineType);
+            if (document.getElementById(parent + '-direction').checked) {
+                var edge = [];
+
+                edge.push({
+                    group: "edges",
+                    data: {
+                        id: target.data('id'),
+                        Type: target.data('Type'),
+                        LineThickness: target.data('LineThickness'),
+                        EndArrow: target.data('EndArrow'),
+                        Coords: target.data('Coords'),
+                        ZOrder: target.data('ZOrder'),
+                        source: target.data('target'),
+                        target: target.data('source'),
+                        StartArrow: target.data('StartArrow'),
+                        selected: target.data('Selected')
+                    }
+                })
+                target.remove();
+                cy.add(edge);
+                postAddProcessing();
+            }
+            dialogEdge.dialog("close");
+            saveState();
+        }
+
+        function moveElementtoBackground(event) {
+            target.style("z-index", 0);
+            target.data("zIndex", 0);
+            saveState();
+        }
+
+        function moveElementtoForeground(event) {
+            highestZOrder++;
+            target.style("z-index", highestZOrder);
+            target.data("zIndex", highestZOrder);
+            saveState();
+        }
+
+        function removeBackgroundImageOnNode(event) {
+            target.removeStyle("background-image");
+            target.data("backgroundImage", "");
+            saveState();
+        }
+
+        function onChangeBackgroundImageOnNode(event) {
+            var reader = new FileReader();
+            reader.onload = onBackgroundImageReaderLoad;
+            reader.readAsDataURL(event.target.files[0]);
+            saveState();
+        }
+
+        function onBackgroundImageReaderLoad() {
+            var img = event.target.result;
+            target.data('Type', "image");
+            target.data("backgroundImage", img);
+            target.style("background-image", img);
+            saveState();
+        }
+
+        function editNode() {
+            var name = document.getElementById(parent + "-gene-name").value;
+            var width = document.getElementById(parent + "-width").value;
+            var height = document.getElementById(parent + "-height").value;
+            var type = document.getElementById(parent + "-type-node").value;
+            target.data('name', name);
+            target.data('Width', width);
+            target.data('Height', height);
+            target.data('Type', type);
+
+            var node_name = target.data("name");
+            selectedForQueryNodes.push(node_name);
+            var rna = document.getElementById(parent + "-rna").value;
+            var cnv = document.getElementById(parent + "-cnv").value;
+            var mut = document.getElementById(parent + "-mut").value;
+            target.data('rna', rna);
+            target.data('cnv', cnv);
+            target.data('mut', mut);
+
+            coloredNodes.push({
+                "gene_name": node_name,
+                "rna": rna,
+                "cnv": cnv,
+                "mut": mut
+            });
+            $('#' + parent + '-variable').val($('#' + parent + '-variable').val() + coloredNodes);
+            dialogNode.dialog("close");
+            saveState();
+        }
+
+        function dialogNewPathwayOpen(event) {
+            dialogNewPathway.dialog("open");
+        }
+
+        function dialogBundleOpen(event) {
+            dialogBundle.dialog("open");
+        }
+
+        function dialogPathfindOpen(event) {
+            dialogPathfind.dialog("open");
+        }
+
+        function dialogPathwaySaveAsOpen(event) {
+            dialogPathwaySaveAs.dialog("open");
+        }
+
+        function findObject(event) {
+            var val = event.target.value;
+            $.post(services['objectFinder'], {
+                pattern: JSON.stringify(coloredNodes)
+            }, function (data) {
+                if (data == "[]")
+                    data = '{"X1":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X2":{"percentage":0.33333,"rna_distance":30.44444,"cnv_distance":0,"mut_distance":0},"X9":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X29":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X24":{"percentage":0.33333,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X34":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X38":{"percentage":0.33333,"rna_distance":30.44444,"cnv_distance":0,"mut_distance":0},"X40":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X45":{"percentage":0.66667,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X46":{"percentage":0.66667,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X48":{"percentage":1,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X53":{"percentage":1,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X59":{"percentage":0.66667,"rna_distance":36,"cnv_distance":0,"mut_distance":0},"X156":{"percentage":0.33333,"rna_distance":0,"cnv_distance":0,"mut_distance":0},"X15":{"percentage":0.33333,"rna_distance":0,"cnv_distance":0,"mut_distance":2},"X22":{"percentage":0.33333,"rna_distance":0,"cnv_distance":0,"mut_distance":0}}'
+                var array = data.split("},");
+                for (var i = 0; i < array.length; i++) {
+                    array[i] = array[i].split(":{");
+                    array[i][1] = array[i][1].split(",");
+                    array[i][0] = array[i][0].replace(/\W/g, '');
+                    for (var j = 0; j < array[i][1].length; j++) {
+                        array[i][1][j] = array[i][1][j].replace(/[^\d.-]/g, '');
+                    }
+                }
+
+                var table = document.getElementById(parent + "-inner-table");
+                var length = document.getElementById(parent + "-inner-table").rows.length;
+                for (var n = 0; n < length; n++) {
+                    table.deleteRow(0);
+                }
+                for (var n = 0; n <= array.length; n++) {
+                    var row = table.insertRow();
+
+                    var name = row.insertCell(0)
+                    var percentage = row.insertCell(1);
+                    var rnaDistance = row.insertCell(2);
+                    var cnvDistance = row.insertCell(3);
+                    var mutDistance = row.insertCell(4);
+
+                    // Add some text to the new cells:
+
+                    if (n == 0) {
+                        name.innerHTML = "<i><h3>name</h3></i>";
+                        percentage.innerHTML = "<i><h3>percentage</h3></i>";
+                        rnaDistance.innerHTML = "<i><h3>rna</h3></i>";
+                        cnvDistance.innerHTML = "<i><h3>cnv</h3></i>";
+                        mutDistance.innerHTML = "<i><h3>mut</h3></i>";
+                    } else {
+                        name.innerHTML = array[n - 1][0];
+                        percentage.innerHTML = array[n - 1][1][0];
+                        rnaDistance.innerHTML = array[n - 1][1][1];
+                        cnvDistance.innerHTML = array[n - 1][1][2];
+                        mutDistance.innerHTML = array[n - 1][1][3];
+                    }
+                }
+                //document.getElementById(parent + "-dialog-table").innerHTML = data;
+                dialogTable.dialog("open")
+            });
+        }
+
+        function visualPathway(obj) {
+            $('#' + parent + '-cy').cytoscape({
+                style: cytoscape.stylesheet()
+
+                        // node elements default css (unselected state)
+                        .selector('node').css({
+                    'content': 'data(name)',
+                    'padding-left': 2,
+                    'padding-right': 2,
+                    'font-family': 'data(LabelSize)',
+                    'background-image-opacity': .75,
+                    'opacity': 0.75,
+                    'text-opacity': 0.75
+                }).selector('node[Type="bundleOne"]').css({
+                    'shape': 'roundrectangle',
+                    'background-color': 'lightgray',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="bundleTwo"]').css({
+                    'shape': 'roundrectangle',
+                    'background-color': 'gray',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="gene"]').css({
+                    'shape': 'ellipse',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="geneProduct"]').css({
+                    'shape': 'circle',
+                    'radius': 5,
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="protein"]').css({
+                    'shape': 'rectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="rna"]').css({
+                    'shape': 'circle',
+                    'radius': 5,
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'dotted',
+                    'border-width': 1
+                }).selector('node[Type="microRNA"]').css({
+                    'shape': 'circle',
+                    'radius': 5,
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'dashed',
+                    'border-width': 1
+                }).selector('node[Type="kinase"]').css({
+                    'shape': 'rectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'dashed',
+                    'border-width': 1
+                }).selector('node[Type="ligand"]').css({
+                    'shape': 'rectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'dotted',
+                    'border-width': 1
+                }).selector('node[Type="receptor"]').css({
+                    'shape': 'rectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'double',
+                    'border-width': 1
+                }).selector('node[Type="biologicalProcess"]').css({
+                    'shape': 'roundrectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="triangle"]').css({
+                    'shape': 'triangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="ellipse"]').css({
+                    'shape': 'ellipse',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="pentagon"]').css({
+                    'shape': 'pentagon',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="hexagon"]').css({
+                    'shape': 'hexagon',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="heptagon"]').css({
+                    'shape': 'heptagon',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="octagon"]').css({
+                    'shape': 'octagon',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="star"]').css({
+                    'shape': 'star',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="diamond"]').css({
+                    'shape': 'diamond',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="vee"]').css({
+                    'shape': 'vee',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="rhomboid"]').css({
+                    'shape': 'rhomboid',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="label"]').css({
+                    'shape': 'rectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-color': 'white',
+                    'border-color': 'white',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[Type="image"]').css({
+                    'shape': 'rectangle',
+                    'width': 'data(Width)',
+                    'height': 'data(Height)',
+                    'color': 'black',
+                    'text-valign': 'center',
+                    'background-opacity': 0,
+                    'border-color': 'white',
+                    'border-style': 'solid',
+                    'border-width': 1,
+                    'background-fit': 'contain'
+                }).selector('node[Shape="Brace"]').css({
+                    'shape': 'rectangle',
+                    'width': '1',
+                    'height': 'data(Width)',
+                    'background-color': 'black',
+                    'color': 'black',
+                    'border-color': 'black',
+                    'border-style': 'solid',
+                    'border-width': 1
+                }).selector('node[rna < 0]').css({
+                    'background-color': 'lightgreen',
+                    'color': 'black'
+                }).selector('node[rna > 0]').css({
+                    'background-color': 'lightsalmon',
+                    'color': 'black'
+                }).selector('node[cnv < 0]').css({
+                    'border-color': 'mediumpurple',
+                    'border-width': 3
+                }).selector('node[cnv > 0]').css({
+                    'border-color': 'red',
+                    'border-width': 3
+                }).selector('node[mut > 0]').css({
+                    'shadow-opacity': 1,
+                    'shadow-color': 'red',
+                    'border-width': 1
+                })
+
+                        // edge elements default css (unselected)
+                        .selector('edge').css({
+                    'line-color': 'black',
+                    'line-style': 'solid',
+                    'opacity': 0.75,
+                    'text-opacity': 0.75,
+                    'width': 1
+                }).selector('edge[EndArrow="Line"]').css({
+                    'target-arrow-shape': 'line',
+                    'target-arrow-color': 'black',
+                    'target-arrow-fill': 'filled'
+                }).selector('edge[EndArrow="Arrow"]').css({
+                    'target-arrow-shape': 'triangle',
+                    'target-arrow-color': 'black',
+                    'target-arrow-fill': 'filled'
+                }).selector('edge[EndArrow="TBar"]').css({
+                    'target-arrow-shape': 'tee',
+                    'target-arrow-color': 'black',
+                    'target-arrow-fill': 'filled'
+                }).selector('edge[Type="Solid"]').css({
+                    'line-style': 'solid'
+                }).selector('edge[Type="Dashed"]').css({
+                    'line-style': 'dashed'
+                }).selector('edge[Type="Dotted"]').css({
+                    'line-style': 'dotted'
+                })
+
+
+                        // node & edge elements (selected state)
+                        .selector('edge:selected').css({
+                    'background-color': 'green',
+                    'line-color': 'green',
+                    'target-arrow-color': 'green',
+                    'source-arrow-color': 'green',
+                    'opacity': 1.0,
+                    'text-opacity': 1.0
+                }).selector('node:selected').css({
+                    'background-color': 'green',
+                    'opacity': 1.0,
+                    'text-opacity': 1.0
+                })
+
+                        // query purpose
+                        .selector('.green_bg').css({
+                    'background-color': 'lightgreen',
+                    'color': 'black'
+                }).selector('.red_bg').css({
+                    'background-color': 'lightsalmon',
+                    'color': 'black'
+                }).selector('.white_bg').css({
+                    'background-color': 'white',
+                    'color': 'black'
+                }).selector('.purple_border').css({
+                    'border-color': 'mediumpurple',
+                    'border-width': 3
+                }).selector('.red_border').css({
+                    'border-color': 'red',
+                    'border-width': 3
+                }).selector('.black_border').css({
+                    'border-color': 'black',
+                    'border-width': 3
+                }).selector('.red_shadow').css({
+                    'shadow-opacity': 1,
+                    'shadow-color': 'red',
+                    'border-width': 1
+                }).selector('.no_shadow').css({
+                    'shadow-opacity': 0,
+                    'shadow-color': 'red',
+                    'border-width': 1
+                })
+
+                        // collapse
+                        .selector('.collapsed').css({
+                    'opacity': 0.01
+                }),
+                layout: {
+                    name: 'preset',
+                    padding: 10
+                },
+                ready: function () {
+                    var cy = $('#' + parent + '-cy').cytoscape('get');
+
+                    preAddProcessing(obj);
+
+                    //un-disable options
+                    $('#' + parent + '-select-bundleOne').removeClass('disabled');
+                    $('#' + parent + '-add-node').removeClass('disabled');
+                    $('#' + parent + '-add-edge').removeClass('disabled');
+                    $('#' + parent + '-delete-elements').removeClass('disabled');
+                    $('#' + parent + '-bundle').removeClass('disabled');
+                    $('#' + parent + '-unbundle').removeClass('disabled');
+                    $('#' + parent + '-collapse').removeClass('disabled');
+                    $('#' + parent + '-expand').removeClass('disabled');
+                    $('#' + parent + '-findpath').removeClass('disabled');
+                    $('#' + parent + '-find-object').removeClass('disabled');
+                    $('#' + parent + '-pathway-save').removeClass('disabled');
+                    $('#' + parent + '-pathway-saveAs').removeClass('disabled');
+                    $('#' + parent + '-produce-JSON').removeClass('disabled');
+                    $('#' + parent + '-undo').removeClass('disabled');
+                    $('#' + parent + '-redo').removeClass('disabled');
+
+                    // Add processed nodes
+                    cy.add(obj.elements);
+                    cy.center();
+                    cy.fit();
+
+                    // Post-Add Process
+                    postAddProcessing();
+
+                    // add custom event
+                    var tappedBefore = null;
+                    cy.on('tap', function (event) {
+                        var tappedNow = event.cyTarget;
+                        setTimeout(function () {
+                            tappedBefore = null;
+                        }, 300);
+                        if (tappedBefore === tappedNow) {
+                            tappedNow.trigger('doubleTap');
+                            tappedBefore = null;
+                        } else {
+                            tappedBefore = tappedNow;
+                        }
+                    });
+
+                    // custom event handlers
+                    cy.on('click', 'node', function (event) {
+                        if (orderedSelectedNodes.length < 2)
+                            orderedSelectedNodes.push(event.cyTarget);
+                        else
+                            orderedSelectedNodes.shift();
+                        orderedSelectedNodes.push(event.cyTarget);
+                    });
+
+                    cy.on('doubleTap', 'node', function (event) {
+                        target = event.cyTarget;
+                        dialogNode.dialog("open");
+                    });
+
+                    cy.on('doubleTap', 'edge', function (event) {
+                        target = event.cyTarget;
+                        dialogEdge.dialog("open");
+                    });
+
+                    cy.on('select', 'node', function (event) {
+                        selectedForEditNodes = cy.$('node:selected');
+                        //			    	saveState();
+                    });
+
+                    cy.on('unselect', 'node', function (event) {
+                        selectedForEditNodes = cy.$('node:selected');
+                        //			    	saveState();
+                    });
+
+                    cy.on('select', 'edge', function (event) {
+                        selectedForEditEdges = cy.$('edge:selected');
+                        //			    	saveState();
+                    });
+
+                    cy.on('unselect', 'edge', function (event) {
+                        selectedForEditEdges = cy.$('edge:selected');
+                        //			    	saveState();
+                    });
+
+                    cy.on('grab', 'node', function (event) {
+                        if (cy.$('node:grabbed').isParent() && !cy.$('node:grabbed').descendants()[0].grabbable()) {
+                            grabbedCollapsedForEditNodes = cy.$('node:grabbed');
+                            grabbedCollapsedForEditNodes.descendants().grabify();
+                        }
+                        saveState();
+                    });
+
+                    cy.on('free', 'node', function (event) {
+                        //			    	saveState();
+                        if (grabbedCollapsedForEditNodes.constructor !== Array)
+                            grabbedCollapsedForEditNodes.descendants().ungrabify();
+                        grabbedCollapsedForEditNodes = [];
+                    });
+
+                    cy.on('data', 'node', function (event) {
+                        //					saveState();
+                    });
+
+                    cy.on('style', 'node', function (event) {
+                        //					saveState();
+                    });
+
+                    saveState();
+                    sprayColor(self.sprayData);
+                },
+                // initial viewport state:
+                zoom: 1,
+                pan: {
+                    x: 0,
+                    y: 0
+                },
+                // interaction options:
+                minZoom: 1e-50,
+                maxZoom: 1e50,
+                zoomingEnabled: true,
+                userZoomingEnabled: true,
+                panningEnabled: true,
+                userPanningEnabled: true,
+                boxSelectionEnabled: true,
+                selectionType: 'additive',
+                touchTapThreshold: 8,
+                desktopTapThreshold: 4,
+                autolock: false,
+                autoungrabify: false,
+                autounselectify: false,
+                // rendering options:
+                headless: false,
+                styleEnabled: true,
+                hideEdgesOnViewport: false,
+                hideLabelsOnViewport: false,
+                textureOnViewport: false,
+                motionBlur: false,
+                motionBlurOpacity: 0.2,
+                wheelSensitivity: 0.2,
+                pixelRatio: 1,
+                initrender: function (evt) {/* ... */
+                },
+                renderer: {/* ... */}
+            });
+        }
+
+        dialogTable = $("#" + parent + "-dialog-table").dialog({
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                Cancel: function () {
+                    dialogTable.dialog("close");
+                    var cy = $('#' + parent + '-cy').cytoscape('get');
+                    cy.$('node').removeStyle("opacity");
+                    cy.$('edge').removeStyle("opacity");
+                    cy.$('node:selected').removeStyle("opacity");
+                    cy.$('edge:selected').removeStyle("opacity");
+                }
+            },
+            close: function () {
+                var cy = $('#' + parent + '-cy').cytoscape('get');
+                cy.$('node').removeStyle("opacity");
+                cy.$('edge').removeStyle("opacity");
+                cy.$('node:selected').removeStyle("opacity");
+                cy.$('edge:selected').removeStyle("opacity");
+            }
+        });
+
+        dialogNode = $("#" + parent + "-dialog-form-node").dialog({
+            open: function (event) {
+                if (!target.isParent()) {
+                    document.getElementById(parent + '-select-bundleOne').disabled = true;
+                    document.getElementById(parent + '-select-bundleTwo').disabled = true;
+                    document.getElementById(parent + "-select-gene").disabled = false;
+                    document.getElementById(parent + "-select-geneProduct").disabled = false;
+                    document.getElementById(parent + "-select-protein").disabled = false;
+                    document.getElementById(parent + "-select-rna").disabled = false;
+                    document.getElementById(parent + "-select-mircoRNA").disabled = false;
+                    document.getElementById(parent + "-select-kinase").disabled = false;
+                    document.getElementById(parent + "-select-ligand").disabled = false;
+                    document.getElementById(parent + "-select-receptor").disabled = false;
+                    document.getElementById(parent + "-select-biologicalProcess").disabled = false;
+                    document.getElementById(parent + "-select-triangle").disabled = false;
+                    document.getElementById(parent + "-select-ellipse").disabled = false;
+                    document.getElementById(parent + "-select-pentagon").disabled = false;
+                    document.getElementById(parent + "-select-hexagon").disabled = false;
+                    document.getElementById(parent + "-select-heptagon").disabled = false;
+                    document.getElementById(parent + "-select-octagon").disabled = false;
+                    document.getElementById(parent + "-select-star").disabled = false;
+                    document.getElementById(parent + "-select-diamond").disabled = false;
+                    document.getElementById(parent + "-select-vee").disabled = false;
+                    document.getElementById(parent + "-select-rhomboid").disabled = false;
+                    document.getElementById(parent + "-select-label").disabled = false;
+                } else {
+                    document.getElementById(parent + '-select-bundleOne').disabled = false;
+                    document.getElementById(parent + '-select-bundleTwo').disabled = false;
+                    document.getElementById(parent + "-select-gene").disabled = true;
+                    document.getElementById(parent + "-select-geneProduct").disabled = true;
+                    document.getElementById(parent + "-select-protein").disabled = true;
+                    document.getElementById(parent + "-select-rna").disabled = true;
+                    document.getElementById(parent + "-select-mircoRNA").disabled = true;
+                    document.getElementById(parent + "-select-kinase").disabled = true;
+                    document.getElementById(parent + "-select-ligand").disabled = true;
+                    document.getElementById(parent + "-select-receptor").disabled = true;
+                    document.getElementById(parent + "-select-biologicalProcess").disabled = true;
+                    document.getElementById(parent + "-select-triangle").disabled = true;
+                    document.getElementById(parent + "-select-ellipse").disabled = true;
+                    document.getElementById(parent + "-select-pentagon").disabled = true;
+                    document.getElementById(parent + "-select-hexagon").disabled = true;
+                    document.getElementById(parent + "-select-heptagon").disabled = true;
+                    document.getElementById(parent + "-select-octagon").disabled = true;
+                    document.getElementById(parent + "-select-star").disabled = true;
+                    document.getElementById(parent + "-select-diamond").disabled = true;
+                    document.getElementById(parent + "-select-vee").disabled = true;
+                    document.getElementById(parent + "-select-rhomboid").disabled = true;
+                    document.getElementById(parent + "-select-label").disabled = true;
+                }
+                document.getElementById(parent + "-gene-name").value = target.data('name');
+                document.getElementById(parent + "-width").value = target.data('Width');
+                document.getElementById(parent + "-height").value = target.data('Height');
+                document.getElementById(parent + "-type-node").value = target.data('Type');
+                if (typeof (target.data('rna')) != "undefined")
+                    document.getElementById(parent + "-rna").value = target.data('rna');
+                else
+                    document.getElementById(parent + "-rna").value = '0';
+
+                if (typeof (target.data('cnv')) != "undefined")
+                    document.getElementById(parent + "-cnv").value = target.data('cnv');
+                else
+                    document.getElementById(parent + "-cnv").value = '0';
+
+                if (typeof (target.data('mut')) != "undefined")
+                    document.getElementById(parent + "-mut").value = target.data('mut');
+                else
+                    document.getElementById(parent + "-mut").value = '0';
+            },
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                "submit": editNode,
+                Cancel: function () {
+                    dialogNode.dialog("close");
+                }
+            },
+            close: function () {
+            }
+        });
+
+        dialogEdge = $("#" + parent + "-dialog-form-edge").dialog({
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                "submit": editEdge,
+                Cancel: function () {
+                    dialogEdge.dialog("close");
+                }
+            },
+            close: function () {
+            }
+        });
+
+        dialogPathfind = $("#" + parent + "-dialog-form-find-path").dialog({
+            open: function (event) {
+                document.getElementById(parent + "-sid").value = orderedSelectedNodes[0]._private.data['name'];
+                document.getElementById(parent + "-vid").value = orderedSelectedNodes[1]._private.data['name'];
+            },
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                "submit": wrapperFindPath,
+                Cancel: function () {
+                    dialogPathfind.dialog("close");
+                }
+            },
+            close: function () {
+            }
+        });
+
+        dialogPathwaySaveAs = $("#" + parent + "-dialog-form-save-as-pathway").dialog({
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                "submit": saveAsPathway,
+                Cancel: function () {
+                    dialogPathwaySaveAs.dialog("close");
+                }
+            },
+            close: function () {
+            }
+        });
+
+        dialogNewPathway = $("#" + parent + "-dialog-form-new-pathway").dialog({
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                "submit": newPathway,
+                Cancel: function () {
+                    dialogNewPathway.dialog("close");
+                }
+            },
+            close: function () {
+            }
+        });
+
+        dialogBundle = $("#" + parent + "-dialog-bundle").dialog({
+            autoOpen: false,
+            height: 300,
+            width: 350,
+            buttons: {
+                "submit": bundle,
+                Cancel: function () {
+                    dialogBundle.dialog("close");
+                }
+            },
+            close: function () {
+            }
+        });
+
+        refreshPathwayList();
+        document.getElementById(parent + '-new-pathway').addEventListener('click', dialogNewPathwayOpen);
+        document.getElementById(parent + '-file-pathway').addEventListener('change', onChangePathwayFile);
+        document.getElementById(parent + '-file-coloring').addEventListener('change', onChangeColoringFile);
+        document.getElementById(parent + '-background-image').addEventListener('change', onChangeBackgroundImageOnNode);
+        document.getElementById(parent + '-background-image-remove').addEventListener('click', removeBackgroundImageOnNode);
+        document.getElementById(parent + '-node-move-to-background').addEventListener('click', moveElementtoBackground);
+        document.getElementById(parent + '-node-move-to-foreground').addEventListener('click', moveElementtoForeground);
+        document.getElementById(parent + '-edge-move-to-background').addEventListener('click', moveElementtoBackground);
+        document.getElementById(parent + '-edge-move-to-foreground').addEventListener('click', moveElementtoForeground);
+        document.getElementById(parent + '-new-pathway').addEventListener('click', dialogNewPathwayOpen);
+        document.getElementById(parent + '-findpath').addEventListener('click', dialogPathfindOpen);
+        document.getElementById(parent + '-find-object').addEventListener('click', findObject);
+        document.getElementById(parent + '-pathway-selector').addEventListener('change', onSelect);
+        document.getElementById(parent + '-pathway-saveAs').addEventListener('click', dialogPathwaySaveAsOpen);
+        document.getElementById(parent + '-pathway-save').addEventListener('click', savePathway);
+        document.getElementById(parent + '-delete-elements').addEventListener('click', removeElements);
+        document.getElementById(parent + '-add-node').addEventListener('click', addNode);
+        document.getElementById(parent + '-add-edge').addEventListener('click', addEdge);
+        document.getElementById(parent + '-expand').addEventListener('click', expandBundle);
+        document.getElementById(parent + '-collapse').addEventListener('click', collapseBundle);
+        document.getElementById(parent + '-bundle').addEventListener('click', dialogBundleOpen);
+        document.getElementById(parent + '-unbundle').addEventListener('click', unbundle);
+        document.getElementById(parent + '-produce-JSON').addEventListener('click', produceJSON);
+        document.getElementById(parent + '-undo').addEventListener('click', undo);
+        document.getElementById(parent + '-redo').addEventListener('click', redo);
+
+        //external functions
 
         self.loadPathwayExternal = function (id) {
             loadPathway(id);