From d40155df398a48142e7630bda074cdf7941620ed Mon Sep 17 00:00:00 2001
From: Pujan Joshi <pujan@guavaworld.com>
Date: Wed, 3 Feb 2016 11:23:31 -0500
Subject: [PATCH 1/2] not needed anymore

---
 VQI_Observable1.js   |   57 -
 VQI_PathwayEditor.js | 2444 ------------------------------------------
 2 files changed, 2501 deletions(-)
 delete mode 100644 VQI_Observable1.js
 delete mode 100755 VQI_PathwayEditor.js

diff --git a/VQI_Observable1.js b/VQI_Observable1.js
deleted file mode 100644
index 9f1527d..0000000
--- a/VQI_Observable1.js
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Class VQIObservable
- * @author Pujan Joshi
- * @Date April 21, 2014
- * This is a generic Observable class
- * This class has basic methods to deal with observers
- * This class is also observer so it can subscribe to another obvervable class.
- * 
- */
-
-var VQI_Observable = function() {
-    this.subscribers = {
-        any: [] // event type: subscribers
-    };
-    this.subscribe = function(fn, type) {
-        type = type || 'any';
-        if (typeof this.subscribers[type] === "undefined") {
-            this.subscribers[type] = [];
-        }
-        this.subscribers[type].push(fn);
-    };
-    this.unsubscribe = function(fn, type) {
-        this.visitSubscribers('unsubscribe', fn, type);
-    };
-    this.publish = function(fn, type) {
-        this.visitSubscribers('publish', fn, type);
-    };
-    this.loading = function(fn, type) {
-        this.visitSubscribers('loading', fn, type);
-    };
-    this.visitSubscribers = function(action, fn, type) {
-        var pubtype = type || 'any';
-        var subscribers = this.subscribers[pubtype];
-        subscribers = subscribers || 0;
-        var i;
-        var max = subscribers.length;
-
-        for (i = 0; i < max; i += 1) {
-            if (action === 'publish') {
-//                console.log(this);
-                subscribers[i].update(fn, type);
-            } else if (action === 'loading') {
-
-                subscribers[i].loading();
-
-            } else {
-                if (subscribers[i] === fn) {
-                    subscribers.splice(i, 1);
-                }
-            }
-        }
-    };
-    
-    this.subscribeTo = function(observable, type){
-        observable.subscribe(this, type);
-    };
-};
\ No newline at end of file
diff --git a/VQI_PathwayEditor.js b/VQI_PathwayEditor.js
deleted file mode 100755
index 41f73fa..0000000
--- a/VQI_PathwayEditor.js
+++ /dev/null
@@ -1,2444 +0,0 @@
-var VQI_PathwayEditorGUI = function (parent) {
-
-    //Web services
-//	var serverURL = "http://cardinal3.engr.uconn.edu/pathwayVisual/";
-    var services = {};
-
-	/*Local Services*/
-	services["pathwayFinderUrl"] = "http://bibci.engr.uconn.edu/puj07001/pathway_services/find_path_and_score/find_path_and_score.php";
-	
-    /* 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 self = this;
-    var types = ["bundleOne", "bundleTwo", "gene", "geneProduct", "protein", "rna", "microRNA", "kinase", "ligand", "receptor", "biologicalProcess", "triangle", "rectangle", "circle", "ellipse", "pentagon", "hexagon", "heptagon", "octagon", "star", "diamond", "vee", "rhomboid", "label"];
-    var personId = "";
-	var pathName = "";
-	var states = [];
-    var stateRecycle = [];
-    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 id=\"" + parent + "-pathway-title\" 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 += "					<li><input id=\"" + parent + "-duplicate-nodes\" value=\"Duplicate Nodes\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
-    strVar += " 				<li role=\"separator\" class=\"divider\"></li>";
-	strVar += "					<li><input id=\"" + parent + "-config-pathway\" value=\"Configure\" 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-paths-all-drop\" value=\"Find All Pathways\" 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 += " 	<li style=\"margin: 2px\">";
-    strVar += "      	<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-search-node-name\" placeholder=\"Search\" class=\"form-control\" name=\"" + parent + "-search-node-name\">";
-    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 table-condensed\">";
-    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 += "			<\/tr>";
-    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-form-configure-pathway\" title=\"Configure Pathway\">";
-    strVar += " 		<form role=\"form\">";
-    strVar += "    			<div class =\"form-group\">";
-    strVar += "      			<label for=\"" + parent + "-configure-person-id\">person-id:<\/label>";
-    strVar += " 				<input type=\"text\" class=\"form-control\" name=\"" + parent + "-configure-person-id\" id=\"" + parent + "-configure-person-id\"><br>";
-	strVar += " 				<input id=\"" + parent + "-apply-configure-person-id\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    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 += "    			<div class =\"form-group\">";
-    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 id=\"" + parent + "-find-paths-all\" value=\"Find All\" type=\"button\" class=\"btn btn-link\"><\/input>";
-	strVar += " 				<input id=\"" + parent + "-find-paths-one\" value=\"Find\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += " 		<\/form>";
-    strVar += "	<\/div>";
-    strVar += "	<div id=\"" + parent + "-dialog-form-edge\" title=\"Edit edge(s)\">";
-    strVar += " 		<form>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += " 				<input id=\"" + parent + "-direction-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += " 				<input id=\"" + parent + "-arrow-type-edge-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += " 				<input id=\"" + parent + "-line-type-edge-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    strVar += "      			<label for=\"" + parent + "-segment-distances\">Segment Distances:(e.g. -20 20 -20)<\/label>";
-    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-segment-distances\" class=\"form-control\" name=\"" + parent + "-segment-distances\">";
-    strVar += "      			<label for=\"" + parent + "-segment-weights\">Segment Weights:(e.g. 0.25 0.5 0.75)<\/label>";
-    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-segment-weights\" class=\"form-control\" name=\"" + parent + "-segment-weights\">";
-    strVar += "      			<label for=\"" + parent + "-segment-enable-disable\">Enable Segmented<\/label>";
-    strVar += "      			<select style=\"width: 150px\" class=\"form-control\" id=\"" + parent + "-segmented-enable-disable\" name=\"" + parent + "-segmented-enable-disable\">";
-    strVar += "  					<option selected=\"\">enable<\/option>";
-    strVar += "  					<option\>disable<\/option>";
-    strVar += "					<\/select>";
-    strVar += " 				<input id=\"" + parent + "-apply-curve-changes\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += "    			</div>";
-    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(s)\">";
-    strVar += " 		<form>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += " 				<input id=\"" + parent + "-gene-name-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += " 				<input id=\"" + parent + "-height-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += " 				<input id=\"" + parent + "-width-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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-rectangle\">rectangle<\/option>";
-	strVar += "  					<option id=\"" + parent + "-select-circle\">circle<\/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 += " 				<input id=\"" + parent + "-type-node-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    strVar += "      			<label for=\"" + parent + "-rna\">RNA:<\/label>";
-    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-rna\" class=\"form-control\" name=\"" + parent + "-rna\">";
-    strVar += " 				<input id=\"" + parent + "-rna-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    strVar += "					<label for=\"" + parent + "-cnv\">CNV:<\/label>";
-    strVar += "      			<input type=\"text\" style=\"width: 150px\" id=\"" + parent + "-cnv\" class=\"form-control\" name=\"" + parent + "-cnv\">";
-    strVar += " 				<input id=\"" + parent + "-cnv-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 id=\"" + parent + "-mut-apply\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
-    strVar += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += "    			</div>";
-    strVar += "    			<div class =\"form-group\">";
-    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 += "    			</div>";
-    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);
-            var title = document.getElementById(parent + "-pathway-title");
-			pathName = name;
-            title.innerHTML = pathName+" <small>"+personId+"</small>";
-            removeHeroUnit();
-            setElements(obj);
-            save(obj, name);
-            dialogNewPathway.dialog("close");
-        }
-
-        function focus(name) {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            cy.elements("node[name *= \"" + name + "\"]").select();
-            cy.$('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);
-        }
-
-        function unFocus() {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            cy.$('node').unselect();
-            cy.$('node').removeStyle("opacity");
-            cy.$('edge').removeStyle("opacity");
-            cy.$('node:selected').removeStyle("opacity");
-            cy.$('edge:selected').removeStyle("opacity");
-        }
-
-        function search(event) {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            var name = document.getElementById(parent + "-search-node-name").value;
-            unFocus();
-            if (name != "") {
-                focus(name);
-            } else {
-                unFocus();
-            }
-        }
-
-        function exitSearch(event) {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            unFocus();
-        }
-
-        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;
-//			personId = event.target.files[0].name.substring(0,event.target.files[0].name.indexOf("."))
-			personId = event.target.files[0].name;
-			var title = document.getElementById(parent + "-pathway-title");
-            title.innerHTML = pathName+" <small>"+personId+"</small>";
-            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.$("node")[i].data("Type", "image");
-                }
-
-                if (typeof (cy.$("node")[i].data("zIndex")) != "undefined") {
-                    cy.$("node")[i].style("zIndex", cy.$("node")[i].data("zIndex"));
-                }
-            }
-
-            for (var i = 0; i < cy.$("edge").length; i++) {
-                if (typeof (cy.$("edge")[i].data("curveStyle")) != "undefined") {
-                    cy.$("edge")[i].style("curve-style", cy.$("edge")[i].data("curveStyle"));
-                }
-
-                if (typeof (cy.$("edge")[i].data("segmentDistances")) != "undefined") {
-                    cy.$("edge")[i].style("segment-distances", cy.$("edge")[i].data("segmentDistances"));
-                }
-
-                if (typeof (cy.$("edge")[i].data("segmentWeights")) != "undefined") {
-                    cy.$("edge")[i].style("segment-weights", cy.$("edge")[i].data("segmentWeights"));
-                }
-            }
-        }
-
-        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 (typeof (obj.elements.nodes[i].data.backgroundImage) == "undefined") {
-                    obj.elements.nodes[i].data.backgroundImage = "";
-                }
-
-                if (typeof (obj.elements.nodes[i].data.zIndex) == "undefined") {
-                    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;
-                }
-
-                if (obj.elements.nodes[i].data.Type == "gene") {
-                    obj.elements.nodes[i].data.Height = 20;
-                    obj.elements.nodes[i].data.Width = 50;
-                }
-//                else if (obj.elements.nodes[i].data.Type == "ellipse") {
-//                    obj.elements.nodes[i].data.Height = 20;
-//                    obj.elements.nodes[i].data.Width = 50;
-//                }
-            }
-
-            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 setElementsNoGUI(obj) {
-            preAddProcessing(obj);
-        }
-
-        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;
-                }
-
-                preAddProcessing(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);
-                var title = document.getElementById(parent + "-pathway-title");
-                pathName= obj.data.NAME;
-				title.innerHTML = pathName+" <small>"+personId+"</small>";
-                setElements(obj);
-            });
-        }
-
-        function onSelect(event) {
-            var id = event.target.value;
-            loadPathway(id);
-        }
-
-        function save(obj, name) {
-            obj.data.NAME = name;
-            $.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) {
-                        dialogPathwaySaveAs.dialog("close");
-                    });
-                } else {
-                    refreshPathwayList();
-                    dialogPathwaySaveAs.dialog("close");
-                }
-            });
-        }
-
-        function saveAsPathway(event) {
-            var obj = JSON.parse(states[states.length - 1]);
-            var name = document.getElementById(parent + "-pathway-name").value;
-            save(obj, name);
-        }
-
-        function savePathway(event) {
-            var obj = JSON.parse(states[states.length - 1]);
-            $.post(services['pathwaySaver'], {
-                updatePathway: JSON.stringify(obj)
-            }, function (data) {
-                dialogPathwaySaveAs.dialog("close");
-            });
-        }
-
-        function onPathwayReaderLoad(event) {
-            var obj = JSON.parse(event.target.result);
-            var title = document.getElementById(parent + "-pathway-title");
-			pathName = obj.data.NAME;
-            title.innerHTML = pathName+" <small>"+personId+"</small>";
-            setElements(obj);
-        }
-
-        function onColoringReaderLoad(event) {
-            var list = this.result.split('\n');
-            var lines = [];
-
-            for (var line = 0; line < list.length; line++) {
-                lines[line] = list[line].split('\t');
-            }
-            sprayColor(lines);
-        }
-
-        function sprayColorNoGUI(lines, obj) {
-            var lookup = {};
-            for (var i = 0, len = obj.elements.nodes.length; i < len; i++) {
-                if (typeof (lookup[obj.elements.nodes[i].data.name]) != "undefined")
-                    lookup[obj.elements.nodes[i].data.name].push(obj.elements.nodes[i].data);
-                else
-                    lookup[obj.elements.nodes[i].data.name] = [obj.elements.nodes[i].data];
-            }
-
-            var header = {};
-            for (var i = 0; i < lines[0].length; i++) {
-                var value = lines[0][i].toLowerCase().trim();
-                header[value] = i;
-            }
-
-            for (var line = 1; line < lines.length; line++) {
-                var target = lines[line][header["gene"]];
-                if (typeof (lookup[target]) != "undefined") {
-                    for (entry in lookup[target]) {
-                        if (typeof (header["mut"]) != "undefined") {
-                            mut = lines[line][header["mut"]];
-                            if (!isNaN(mut))
-                                lookup[target][entry].mut = mut;
-                            else
-                                lookup[target][entry].mut = "0";
-                        }
-                        if (typeof (header["cnv"]) != "undefined") {
-                            cnv = lines[line][header["cnv"]];
-                            if (!isNaN(cnv))
-                                lookup[target][entry].cnv = cnv;
-                            else
-                                lookup[target][entry].cnv = "0";
-                        }
-                        if (typeof (header["rna"]) != "undefined") {
-                            rna = lines[line][header["rna"]];
-                            if (!isNaN(rna))
-                                lookup[target][entry].rna = rna;
-                            else
-                                lookup[target][entry].rna = "0";
-                        }
-                    }
-                }
-            }
-        }
-
-        function sprayColor(lines) {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            var header = {};
-            for (var i = 0; i < lines[0].length; i++) {
-                var value = lines[0][i].toLowerCase().trim();
-                header[value] = i;
-            }
-
-            for (var line = 1; line < lines.length; line++) {
-                var target = cy.elements("node[name = \"" + lines[line][header["gene"]] + "\"]");
-                if (typeof (header["mut"]) != "undefined") {
-                    mut = lines[line][header["mut"]];
-                    if (!isNaN(mut))
-                        target.data('mut', mut);
-                    else
-                        target.data('mut', '0');
-                }
-                if (typeof (header["cnv"]) != "undefined") {
-                    cnv = lines[line][header["cnv"]];
-                    if (!isNaN(cnv))
-                        target.data('cnv', cnv);
-                    else
-                        target.data('cnv', '0');
-                }
-                if (typeof (header["rna"]) != "undefined") {
-                    rna = lines[line][header["rna"]];
-                    if (!isNaN(rna))
-                        target.data('rna', rna);
-                    else
-                        target.data('rna', '0');
-                }
-            }
-        }
-
-        function removeElements(event) {
-            if (selectedForEditNodes.length > 0)
-                selectedForEditNodes.remove();
-            if (selectedForEditEdges.length > 0)
-                selectedForEditEdges.remove();
-            saveState();
-        }
-
-        function addDuplicateNodes(event) {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            var node = [];
-            var edge = [];
-
-            var lookupDuplicatedNodes = [];
-            var lookupDuplicatedEdges = [];
-
-            for (var i = 0; i < selectedForEditNodes.length; i++) {
-                node.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: "dup" + selectedForEditNodes[i].data('id'),
-                        name: selectedForEditNodes[i].data('name'),
-                        selected: false,
-                        backgroundImage: selectedForEditNodes[i].data('backgroundImage'),
-                        zIndex: selectedForEditNodes[i].data('zIndex')
-                    },
-                    renderedPosition: {
-                        x: selectedForEditNodes[i].position('x') + 500,
-                        y: selectedForEditNodes[i].position('y')
-                    }
-                })
-                lookupDuplicatedNodes.push("dup" + selectedForEditNodes[i].data('id'));
-            }
-            for (var i = 0; i < selectedForEditNodes.length; i++) {
-                for (var j = 0; j < selectedForEditNodes[i].connectedEdges().length; j++) {
-                    if (lookupDuplicatedNodes.indexOf("dup" + selectedForEditNodes[i].connectedEdges()[j].data('source')) != -1 &&
-                            lookupDuplicatedNodes.indexOf("dup" + selectedForEditNodes[i].connectedEdges()[j].data('target')) != -1 &&
-                            lookupDuplicatedEdges.indexOf("dup" + selectedForEditNodes[i].connectedEdges()[j].data('id')) == -1
-                            ) {
-                        edge.push({
-                            group: "edges",
-                            data: {
-                                id: "dup" + 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: "dup" + selectedForEditNodes[i].connectedEdges()[j].data('source'),
-                                target: "dup" + selectedForEditNodes[i].connectedEdges()[j].data('target'),
-                                StartArrow: selectedForEditNodes[i].connectedEdges()[j].data('StartArrow'),
-                                curveStyle: selectedForEditNodes[i].connectedEdges()[j].data('curveStyle'),
-                                segmentDistances: selectedForEditNodes[i].connectedEdges()[j].data('segmentDistances'),
-                                segmentWeights: selectedForEditNodes[i].connectedEdges()[j].data('segmentWeights'),
-                                selected: selectedForEditNodes[i].connectedEdges()[j].data('selected')
-                            }
-                        })
-                        lookupDuplicatedEdges.push("dup" + selectedForEditNodes[i].connectedEdges()[j].data('id'));
-                    }
-                }
-            }
-
-            cy.add(node);
-            cy.add(edge);
-            postAddProcessing();
-            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();
-            }
-        }
-
-        //re-write
-        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'),
-                                curveStyle: node.children()[x].connectedEdges()[j].data('curveStyle'),
-                                segmentDistances: node.children()[x].connectedEdges()[j].data('segmentDistances'),
-                                segmentWeights: node.children()[x].connectedEdges()[j].data('segmentWeights'),
-                                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'),
-                                curveStyle: node.children()[x].connectedEdges()[j].data('curveStyle'),
-                                segmentDistances: node.children()[x].connectedEdges()[j].data('segmentDistances'),
-                                segmentWeights: node.children()[x].connectedEdges()[j].data('segmentWeights'),
-                                selected: node.children()[x].connectedEdges()[j].data('selected')
-                            }
-                        })
-                    }
-                    unbundleRecursive(node.children()[x], parents, edges, nodes, rCounter);
-                }
-            }
-        }
-
-        //re-write
-        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();
-        }
-
-        //re-write
-        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'),
-                        curveStyle: node.connectedEdges()[j].data('curveStyle'),
-                        segmentDistances: node.connectedEdges()[j].data('segmentDistances'),
-                        segmentWeights: node.connectedEdges()[j].data('segmentWeights'),
-                        selected: node.connectedEdges()[j].data('selected')
-                    }
-                })
-            }
-            for (var i = 0; i < node.children().size(); i++) {
-                recursiveBundle(node.children()[i], edges, nodes);
-            }
-        }
-
-        //re-write
-        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'),
-                                curveStyle: selectedForEditNodes[i].connectedEdges()[j].data('curveStyle'),
-                                segmentDistances: selectedForEditNodes[i].connectedEdges()[j].data('segmentDistances'),
-                                segmentWeights: selectedForEditNodes[i].connectedEdges()[j].data('segmentWeights'),
-                                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(sid,vid) {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            $.post(services['pathwayFinderUrl'], {
-				s: sid,
-				d: vid,
-				json: JSON.stringify(JSON.parse(states[states.length - 1])),
-				p: personId
-            }, function (yue_data) {
-                var result = JSON.parse(yue_data);
-                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);
-                }
-				table.deleteTHead();
-                
-				for (var n = 0; n <= result.length; n++) {
-                    var row = table.insertRow();
-
-                    var path = row.insertCell(0);
-                    var rScore = row.insertCell(1);
-					var genes = row.insertCell(2)
-					var source = row.insertCell(3);
-					var destination = row.insertCell(4);
-					var person = row.insertCell(5);
-					var consistent = row.insertCell(6);
-                    var mScore = row.insertCell(7);
-                    var mFdr = row.insertCell(8)
-                    var lowP = row.insertCell(9);
-                    var consistentLowP = row.insertCell(10);
-
-                    // Add some text to the new cells:
-
-                    if (n == 0) {
-                        path.innerHTML = "<i><h5><small>paths</small></h5></i>";
-                        rScore.innerHTML = "<i><h5><small>R-Score</small></h5></i>";
-                        genes.innerHTML = "<i><h5><small>Genes</small></h5></i>";
-						source.innerHTML = "<i><h5><small>Source</small></h5></i>";
-						destination.innerHTML = "<i><h5><small>Destination</small></h5></i>";
-						person.innerHTML = "<i><h5><small>Person</small></h5></i>";
-						consistent.innerHTML = "<i><h5><small>Consistent</small></h5></i>";
-						mScore.innerHTML = "<i><h5><small>M-Score</small></h5></i>";
-                        mFdr.innerHTML = "<i><h5><small>M-FDR</small></h5></i>";
-                        lowP.innerHTML = "<i><h5><small>LowP</small></h5></i>"
-                        consistentLowP.innerHTML = "<i><h5><small>Consistent Low P</small></h5></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.$('edge').unselect();
-							cy.$('node').style("opacity", 0.2);
-                            cy.$('edge').style("opacity", 0.2);
-                            for (var j = 0; j < result[k].edges.length; j++) {
-                                cy.elements("edge[id = \"" + result[k].edges[j] + "\"]").style("opacity", 1.0);
-                                var sourceNode = cy.elements("edge[id = \"" + result[k].edges[j] + "\"]").data('source');
-                                var targetNode = cy.elements("edge[id = \"" + result[k].edges[j] + "\"]").data('target');
-                                cy.elements("node[id = \"" + sourceNode + "\"]").style("opacity", 1.0);
-                                cy.elements("node[id = \"" + targetNode + "\"]").style("opacity", 1.0);
-                            }
-                        });
-                        path.appendChild(btn);
-                        rScore.innerHTML="<h5><small>"+result[n-1].rscore+"</small></h5>";
-                        genes.innerHTML="<h5><small>"+Object.keys(result[n-1].genes)+"</small></h5>";
-						source.innerHTML="<h5><small>"+result[n-1].source+"</small></h5>";
-						destination.innerHTML="<h5><small>"+result[n-1].destination+"</small></h5>";
-						person.innerHTML="<h5><small>"+result[n-1].person+"</small></h5>";
-						consistent.innerHTML="<h5><small>"+result[n-1].consistent+"</small></h5>";
-						mScore.innerHTML="<h5><small>"+result[n-1].mscore+"</small></h5>";
-						mFdr.innerHTML="<h5><small>"+result[n-1].mFDR+"</small></h5>";
-                        lowP.innerHTML="<h5><small>"+result[n-1].lowp+"</small></h5>";
-                        consistentLowP.innerHTML="<h5><small>"+result[n-1].consistent_lowp+"</small></h5>";
-                    }
-                }
-				sorttable.makeSortable(table);
-                dialogTable.dialog("open");
-                dialogPathfind.dialog("close");
-            });
-        }
-		
-		function findPathsAll(){
-			findPath(null,null);
-		}
-		
-		function findPathOne(){
-			var sid = orderedSelectedNodes[0]._private.data['id'];
-            var vid = orderedSelectedNodes[1]._private.data['id'];
-			findPath(sid,vid);
-		}
-
-        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 editEdgeArrowType() {
-            var arrowType = document.getElementById(parent + "-arrow-type-edge").value;
-            selectedForEditEdges.data('StartArrow', arrowType);
-            selectedForEditEdges.data('EndArrow', arrowType);
-            saveState();
-        }
-
-        function editEdgeLineType() {
-            var lineType = document.getElementById(parent + "-line-type-edge").value;
-            selectedForEditEdges.data('Type', lineType);
-            saveState();
-        }
-
-        function editEdgeDirection() {
-            var cy = $('#' + parent + '-cy').cytoscape('get');
-            if (document.getElementById(parent + '-direction').checked) {
-                var edges = [];
-                for (var i = 0; i < selectedForEditEdges.length; i++) {
-                    edges.push({
-                        group: "edges",
-                        data: {
-                            id: selectedForEditEdges[i].data('id'),
-                            Type: selectedForEditEdges[i].data('Type'),
-                            LineThickness: selectedForEditEdges[i].data('LineThickness'),
-                            EndArrow: selectedForEditEdges[i].data('EndArrow'),
-                            Coords: selectedForEditEdges[i].data('Coords'),
-                            ZOrder: selectedForEditEdges[i].data('ZOrder'),
-                            source: selectedForEditEdges[i].data('target'),
-                            target: selectedForEditEdges[i].data('source'),
-                            StartArrow: selectedForEditEdges[i].data('StartArrow'),
-                            selected: selectedForEditEdges[i].data('Selected')
-                        }
-                    })
-                }
-                selectedForEditEdges.remove();
-                cy.add(edges)
-                postAddProcessing();
-            }
-            dialogEdge.dialog("close");
-            saveState();
-        }
-
-        function toggleEdgeStyle() {
-            if (document.getElementById(parent + '-segmented-enable-disable').value == "enable")
-                edgeEnableSegmentedStyle();
-            else
-                edgeDisableSegmentedStyle();
-        }
-
-        function edgeEnableSegmentedStyle() {
-            var segmentDistances = document.getElementById(parent + "-segment-distances").value;
-            var segmentWeights = document.getElementById(parent + "-segment-weights").value;
-            selectedForEditEdges.style('curve-style', 'segments');
-            selectedForEditEdges.style('segment-distances', segmentDistances);
-            selectedForEditEdges.style('segment-weights', segmentWeights);
-            selectedForEditEdges.data('curveStyle', 'segments');
-            selectedForEditEdges.data('segmentDistances', segmentDistances);
-            selectedForEditEdges.data('segmentWeights', segmentWeights);
-            saveState();
-        }
-
-        function edgeDisableSegmentedStyle() {
-            selectedForEditEdges.style('curve-style', 'bezier');
-            selectedForEditEdges.data('curveStyle', 'bezier');
-            saveState();
-        }
-
-        function moveElementtoBackground(event) {
-            selectedForEditNodes.style("z-index", 0);
-            selectedForEditNodes.data("zIndex", 0);
-            selectedForEditEdges.style("z-index", 0);
-            selectedForEditEdges.data("zIndex", 0);
-            saveState();
-        }
-
-        function moveElementtoForeground(event) {
-            highestZOrder++;
-            selectedForEditNodes.style("z-index", highestZOrder);
-            selectedForEditNodes.data("zIndex", highestZOrder);
-            selectedForEditEdges.style("z-index", highestZOrder);
-            selectedForEditEdges.data("zIndex", highestZOrder);
-            saveState();
-        }
-
-        function removeBackgroundImageOnNode(event) {
-            selectedForEditNodes.removeStyle("background-image");
-            selectedForEditNodes.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;
-            selectedForEditNodes.data('Type', "image");
-            selectedForEditNodes.data("backgroundImage", img);
-            selectedForEditNodes.style("background-image", img);
-            saveState();
-        }
-
-        function editNodeWidth() {
-            var width = document.getElementById(parent + "-width").value;
-            selectedForEditNodes.data('Width', width);
-            saveState();
-        }
-
-        function editNodeHeight() {
-            var height = document.getElementById(parent + "-height").value;
-            selectedForEditNodes.data('Height', height);
-            saveState();
-        }
-
-        function editNodeType() {
-            var type = document.getElementById(parent + "-type-node").value;
-            selectedForEditNodes.data('Type', type);
-            saveState();
-        }
-
-        function editNodeName() {
-			var cy = $('#' + parent + '-cy').cytoscape('get');
-            var name = document.getElementById(parent + "-gene-name").value;
-			if(name.indexOf(',')==-1)
-				selectedForEditNodes.data('name', name);
-			else{
-				var node = [];
-				var names = name.split(',');
-				for(var i=0; selectedForEditNodes.length > i; i++){
-					selectedForEditNodes[i].data("Type","bundleOne");
-					var xGap=0;
-					var yGap=0;
-					for(var j=0; names.length > j; j++){
-						if(j%5 == 0){
-							xGap=0
-							yGap+=10
-						}else{
-							xGap+=10
-						}
-						var newPositionX = selectedForEditNodes[i].position("x")+xGap;
-						var newPositionY = selectedForEditNodes[i].position("y")+yGap;
-						node.push({
-							group: "nodes",
-							data: {
-								LabelSize: 10,
-								Type: "circle",
-								Valign: "Middle",
-								Width: 10,
-								Height: 10,
-								id: "n" + nodeCounter,
-								name: names[j],
-								selected: false,
-								backgroundImage: "",
-								zIndex: 0,
-								parent: selectedForEditNodes[i].data("id")
-								
-							},
-							position: {
-								x: newPositionX,
-								y: newPositionY
-							}	
-						})
-						nodeCounter++;
-					}
-					cy.add(node);
-					postAddProcessing();
-                    selectedForEditNodes[i].descendants().ungrabify();
-					saveState();
-				}
-			}	
-        }
-
-        function editNodeMUT() {
-            var mut = document.getElementById(parent + "-mut").value;
-            selectedForEditNodes.data('mut', mut);
-            saveState();
-        }
-
-        function editNodeCNV() {
-            var cnv = document.getElementById(parent + "-cnv").value;
-            selectedForEditNodes.data('cnv', cnv);
-            saveState();
-        }
-
-        function editNodeRNA() {
-            var rna = document.getElementById(parent + "-rna").value;
-            selectedForEditNodes.data('cnv', rna);
-            saveState();
-        }
-		
-		function editPersonId() {
-			id = document.getElementById(parent + "-configure-person-id").value;
-			setPersonId(id);
-        }
-		
-		function setPersonId(id) {
-			personId = id;
-			var title = document.getElementById(parent + "-pathway-title")
-			title.innerHTML = pathName+" <small>"+personId+"</small>";
-        }
-
-        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 dialogPathwayConfigureOpen(event) {
-            dialogPathwayConfigure.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="rectangle"]').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="circle"]').css({
-                    'shape': 'circle',
-                    '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 + '-collapse-informative').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');
-                    $('#' + parent + '-duplicate-nodes').removeClass('disabled');
-					$('#' + parent + '-config-pathway').removeClass('disabled');
-					$('#' + parent + '-find-paths-all-drop').removeClass('disabled');
-
-                    // Add processed nodes
-                    cy.add(obj.elements);
-                    cy.center();
-                    cy.fit();
-
-                    // Post-Add Process
-                    postAddProcessing();
-
-                    // add custom event
-                    var tappedBefore = null;
-                    cy.on('tap', function (event) {
-                        var tappedNow = event.cyTarget;
-                        setTimeout(function () {
-                            tappedBefore = null;
-                        }, 300);
-                        if (tappedBefore === tappedNow) {
-                            tappedNow.trigger('doubleTap');
-                            tappedBefore = null;
-                        } else {
-                            tappedBefore = tappedNow;
-                        }
-                    });
-
-                    // custom event handlers
-                    cy.on('click', 'node', function (event) {
-                        if (orderedSelectedNodes.length < 2)
-                            orderedSelectedNodes.push(event.cyTarget);
-                        else
-                            orderedSelectedNodes.shift();
-                        orderedSelectedNodes.push(event.cyTarget);
-                    });
-
-                    cy.on('cxttap', 'node', function (event) {
-                        target = event.cyTarget;
-                        target.select();
-                        selectedForEditNodes = cy.$('node:selected');
-                        dialogNode.dialog("open");
-                    });
-                    cy.on('cxttap', 'edge', function (event) {
-                        target = event.cyTarget;
-                        target.select();
-                        selectedForEditEdges = cy.$('edge:selected');
-                        dialogEdge.dialog("open");
-                    });
-
-                    cy.on('doubleTap', 'node', function (event) {
-                    });
-
-                    cy.on('doubleTap', 'edge', function (event) {
-                    });
-
-                    cy.on('select', 'node', function (event) {
-                        selectedForEditNodes = cy.$('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();
-                    if(typeof(self.sprayData) != "undefined")
-                        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-rectangle").disabled = false;
-					document.getElementById(parent + "-select-circle").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-rectangle").disabled = true;
-					document.getElementById(parent + "-select-circle").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: {
-                Cancel: function () {
-                    dialogNode.dialog("close");
-                }
-            },
-            close: function () {
-            }
-        });
-
-        dialogEdge = $("#" + parent + "-dialog-form-edge").dialog({
-            autoOpen: false,
-            height: 300,
-            width: 350,
-            buttons: {
-                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: {
-                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 () {
-            }
-        });
-		
-		dialogPathwayConfigure = $("#" + parent + "-dialog-form-configure-pathway").dialog({
-			open: function (event) {
-                document.getElementById(parent + "-configure-person-id").value = personId;
-            },
-            autoOpen: false,
-            height: 300,
-            width: 350,
-            buttons: {
-                Cancel: function () {
-                    dialogPathwayConfigure.dialog("close");
-                }
-            },
-            close: function () {
-            }
-        });
-
-        refreshPathwayList();
-
-        //load data local
-        document.getElementById(parent + '-file-pathway').addEventListener('change', onChangePathwayFile);
-        document.getElementById(parent + '-file-coloring').addEventListener('change', onChangeColoringFile);
-
-        //edit node(s)
-        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 + '-gene-name-apply').addEventListener('click', editNodeName);
-        document.getElementById(parent + '-height-apply').addEventListener('click', editNodeHeight);
-        document.getElementById(parent + '-width-apply').addEventListener('click', editNodeWidth);
-        document.getElementById(parent + '-type-node-apply').addEventListener('click', editNodeType);
-        document.getElementById(parent + '-rna-apply').addEventListener('click', editNodeRNA);
-        document.getElementById(parent + '-cnv-apply').addEventListener('click', editNodeCNV);
-        document.getElementById(parent + '-mut-apply').addEventListener('click', editNodeMUT);
-
-        //edit edge(s)
-        document.getElementById(parent + '-edge-move-to-background').addEventListener('click', moveElementtoBackground);
-        document.getElementById(parent + '-edge-move-to-foreground').addEventListener('click', moveElementtoForeground);
-        document.getElementById(parent + '-direction-apply').addEventListener('click', editEdgeDirection);
-        document.getElementById(parent + '-arrow-type-edge-apply').addEventListener('click', editEdgeArrowType);
-        document.getElementById(parent + '-line-type-edge-apply').addEventListener('click', editEdgeLineType);
-        document.getElementById(parent + '-apply-curve-changes').addEventListener('click', toggleEdgeStyle);
-		
-		//edit pathway settings
-		document.getElementById(parent + '-apply-configure-person-id').addEventListener('click', editPersonId);
-
-        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);
-        document.getElementById(parent + '-duplicate-nodes').addEventListener('click', addDuplicateNodes);
-		document.getElementById(parent + '-find-paths-all').addEventListener('click', findPathsAll);
-		document.getElementById(parent + '-find-paths-all-drop').addEventListener('click', findPathsAll);
-		document.getElementById(parent + '-find-paths-one').addEventListener('click', findPathOne);
-		document.getElementById(parent + '-config-pathway').addEventListener('click', dialogPathwayConfigureOpen);
-
-        //search
-        document.getElementById(parent + '-search-node-name').addEventListener('keyup', search);
-        document.getElementById(parent + '-search-node-name').addEventListener('focusout', exitSearch);
-
-        //external GUI functions
-
-        self.loadPathwayExternal = function (id) {
-            loadPathway(id);
-        }
-
-        self.sprayColorExternal = function (list) {
-            sprayColor(list);
-        }
-
-        self.setDataToSpray = function (data) {
-            this.sprayData = data;
-        };
-		
-		self.setPersonId = function (data) {
-            setPersonId(data);
-        };
-
-        //external No GUI functions
-
-        self.printGraphExternalNoGUI = function () {
-            console.log(self.json);
-        }
-
-        self.produceJSONExternalNoGUI = function () {
-            download(JSON.stringify(self.json), "data.txt", "text/plain");
-        }
-
-        self.sprayColorExternalNoGUI = function (list) {
-            sprayColorNoGUI(list, self.json);
-        }
-
-        self.loadPathwayExternalNoGUI = function (id) {
-            $.post(services['pathwayFinder'], {
-                pid: id
-            }, function (data) {
-                self.json = JSON.parse(data);
-                setElementsNoGUI(self.json);
-            });
-        }
-
-        self.findPathAndScoreExternalYueNoGUI = function (sid, did, f) {
-            var paths = findPath(self.json, sid, did);
-            var nodes = convertEdgePathtoNodePathNoGUI(paths, self.json);
-            $.post(services['pathwayScorer'], {
-                data_json: JSON.stringify(self.json)
-            }, function (yue_data) {
-                var result = []
-                var scoreJSON = JSON.parse(yue_data);
-                for (var n = 0; n < paths.length; n++) {
-                    var score = getPathScore(paths[n], scoreJSON).toString();
-                    result.push({"path": n, "edges": paths[n], "nodes": nodes[n], "score": score});
-                }
-                f(result);
-            });
-        }
-
-        self.findPathAndScoreExternalThamNoGUI = function (sid, did, f) {
-            var paths = findPath(self.json, sid, did);
-            var nodes = convertEdgePathtoNodePathNoGUI(paths, self.json);
-            $.post(services['pathwayWeightedScorer'], {
-                data_paths: JSON.stringify(nodes)
-            }, function (tham_data) {
-                var result = [];
-                var score = JSON.parse(tham_data);
-                for (var n = 0; n < paths.length; n++) {
-                    result.push({"path": n, "edges": paths[n], "nodes": nodes[n], "score": score[n]});
-                }
-                f(result);
-            });
-        }
-    });
-};

From e8ef0d199a51b0cbf039c95053277d973469ab20 Mon Sep 17 00:00:00 2001
From: Pujan Joshi <pujan@guavaworld.com>
Date: Wed, 3 Feb 2016 13:34:51 -0500
Subject: [PATCH 2/2] minor fixes in NoGUI to make it work

---
 VQI_PathwayEditorNoGUI.js | 38 +++++++++++++++++++++++++-------------
 change.php                |  0
 2 files changed, 25 insertions(+), 13 deletions(-)
 delete mode 100644 change.php

diff --git a/VQI_PathwayEditorNoGUI.js b/VQI_PathwayEditorNoGUI.js
index 2581a07..a923c00 100644
--- a/VQI_PathwayEditorNoGUI.js
+++ b/VQI_PathwayEditorNoGUI.js
@@ -1,7 +1,11 @@
 var VQI_PathwayEditorNoGUI = function () {
-	self = this;
-	
-	function preAddProcessing(obj) {
+    self = this;
+    var nodeTypes = ["bundleone", "bundletwo", "gene", "geneproduct", "protein", "rna", "microrna", "kinase", "ligand", "receptor", "biologicalprocess", "triangle", "rectangle", "circle", "ellipse", "pentagon", "hexagon", "heptagon", "octagon", "star", "diamond", "vee", "rhomboid", "label"];
+    var services = {};
+    services['pathwayFinder'] = 'http://bibci.engr.uconn.edu/yuz12012/pathwayVisual//PathwayParser/ajaxJSON.php';
+    var nodeCounter = 0;
+    var edgeCounter = 0;
+    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));
@@ -17,7 +21,7 @@ var VQI_PathwayEditorNoGUI = function () {
                 obj.elements.nodes[i].data.zIndex = 0;
             }
 
-            if (types.indexOf(obj.elements.nodes[i].data.Type) == -1) {
+            if (nodeTypes.indexOf(obj.elements.nodes[i].data.Type) == -1) {
                 obj.elements.nodes[i].data.Type = "label";
             }
 
@@ -47,8 +51,8 @@ var VQI_PathwayEditorNoGUI = function () {
             }
         }
     }
-		
-	function sprayColorNoGUI(lines, obj) {
+
+    function sprayColorNoGUI(lines, obj) {
         var lookup = {};
         for (var i = 0, len = obj.elements.nodes.length; i < len; i++) {
             if (typeof (lookup[obj.elements.nodes[i].data.name]) != "undefined")
@@ -80,7 +84,7 @@ var VQI_PathwayEditorNoGUI = function () {
                             lookup[target][entry].cnv = cnv;
                         else
                             lookup[target][entry].cnv = "0";
-                        }
+                    }
                     if (typeof (header["rna"]) != "undefined") {
                         rna = lines[line][header["rna"]];
                         if (!isNaN(rna))
@@ -92,12 +96,12 @@ var VQI_PathwayEditorNoGUI = function () {
             }
         }
     }
-	
-	function setElementsNoGUI(obj) {
+
+    function setElementsNoGUI(obj) {
         preAddProcessing(obj);
     }
-		
-	self.printGraphExternalNoGUI = function () {
+
+    self.printGraphExternalNoGUI = function () {
         console.log(self.json);
     }
 
@@ -108,13 +112,21 @@ var VQI_PathwayEditorNoGUI = function () {
     self.sprayColorExternalNoGUI = function (list) {
         sprayColorNoGUI(list, self.json);
     }
-
-    self.loadPathwayExternalNoGUI = function (id) {
+    
+    self.getJSON = function () {
+        return JSON.stringify(self.json);
+    }
+    
+    self.loadPathwayExternalNoGUI = function (id, person, f) {
+        var callback = f || null;
         $.post(services['pathwayFinder'], {
             pid: id
         }, function (data) {
             self.json = JSON.parse(data);
             setElementsNoGUI(self.json);
+            if (callback !== null) {
+                callback(id, person);
+            }
         });
     }
 }
\ No newline at end of file
diff --git a/change.php b/change.php
deleted file mode 100644
index e69de29..0000000