From 3559188f2898f011cb93053c0c1a1e824e9fe86a Mon Sep 17 00:00:00 2001
From: ivanPozdnyakov <ivan.pozdnyakov@uconn.edu>
Date: Sun, 24 Jan 2016 13:14:08 -0500
Subject: [PATCH] set default value for old position values in pre-processing
 (might not actually be necessary). Also now valid types are identified with
 lowercase identifying names, making any type of casing in the json valid. The
 name in the json is converted to lower and then compared.

---
 VQI_PathwayEditorGUI.js | 50 ++++++++++++++++++++++-------------------
 index.php               |  5 +++--
 2 files changed, 30 insertions(+), 25 deletions(-)

diff --git a/VQI_PathwayEditorGUI.js b/VQI_PathwayEditorGUI.js
index 7b579f6..a7dc8f4 100644
--- a/VQI_PathwayEditorGUI.js
+++ b/VQI_PathwayEditorGUI.js
@@ -18,7 +18,7 @@ var VQI_PathwayEditorGUI = function (parent) {
 
     // 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 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 = [];
@@ -155,8 +155,8 @@ var VQI_PathwayEditorGUI = function (parent) {
     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 += "  					<option selected=\"\">bundleone<\/option>";
+    strVar += "  					<option>bundletwo<\/option>";
     strVar += "					<\/select>";
     strVar += "    			<\/fieldset>";
     strVar += " 		<\/form>";
@@ -248,17 +248,17 @@ var VQI_PathwayEditorGUI = function (parent) {
     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-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-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-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-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>";
@@ -510,9 +510,11 @@ var VQI_PathwayEditorGUI = function (parent) {
                     obj.elements.nodes[i].data.zIndex = 0;
                 }
 				
-                if (types.indexOf(obj.elements.nodes[i].data.Type) == -1) {
+                if (types.indexOf(obj.elements.nodes[i].data.Type.toLowerCase()) == -1) {
                     obj.elements.nodes[i].data.Type = "label";
-                }
+                } else {
+					obj.elements.nodes[i].data.Type = obj.elements.nodes[i].data.Type.toLowerCase();
+				}
 
                 if (typeof (obj.elements.nodes[i].data.rna) == "undefined") {
                     obj.elements.nodes[i].data.rna = 0;
@@ -525,10 +527,13 @@ var VQI_PathwayEditorGUI = function (parent) {
                 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;
+				
+				if (typeof (obj.elements.nodes[i].data.oldPositionX) == "undefined") {
+                    obj.elements.nodes[i].data.oldPositionX = 0;
+                }
+				
+				if (typeof (obj.elements.nodes[i].data.oldPositionY) == "undefined") {
+                    obj.elements.nodes[i].data.oldPositionY = 0;
                 }
             }
 
@@ -738,8 +743,7 @@ var VQI_PathwayEditorGUI = function (parent) {
                 }
             }
 			dupCounter++;
-            cy.add(node);
-            cy.add(edge);
+            cy.add(node.concat(edge));
             postAddProcessing();
             saveState();
         }
@@ -1590,7 +1594,7 @@ var VQI_PathwayEditorGUI = function (parent) {
                     'background-image-opacity': .75,
                     'opacity': 0.75,
                     'text-opacity': 0.75
-                }).selector('node[Type="bundleOne"]').css({
+                }).selector('node[Type="bundleone"]').css({
                     'shape': 'roundrectangle',
                     'background-color': 'lightgray',
                     'color': 'black',
@@ -1598,7 +1602,7 @@ var VQI_PathwayEditorGUI = function (parent) {
                     'border-color': 'black',
                     'border-style': 'solid',
                     'border-width': 1
-                }).selector('node[Type="bundleTwo"]').css({
+                }).selector('node[Type="bundletwo"]').css({
                     'shape': 'roundrectangle',
                     'background-color': 'gray',
                     'color': 'black',
@@ -1616,7 +1620,7 @@ var VQI_PathwayEditorGUI = function (parent) {
                     'border-color': 'black',
                     'border-style': 'solid',
                     'border-width': 1
-                }).selector('node[Type="geneProduct"]').css({
+                }).selector('node[Type="geneproduct"]').css({
                     'shape': 'circle',
                     'radius': 5,
                     'color': 'black',
@@ -1644,7 +1648,7 @@ var VQI_PathwayEditorGUI = function (parent) {
                     'border-color': 'black',
                     'border-style': 'dotted',
                     'border-width': 1
-                }).selector('node[Type="microRNA"]').css({
+                }).selector('node[Type="microrna"]').css({
                     'shape': 'circle',
                     'radius': 5,
                     'color': 'black',
@@ -1683,7 +1687,7 @@ var VQI_PathwayEditorGUI = function (parent) {
                     'border-color': 'black',
                     'border-style': 'double',
                     'border-width': 1
-                }).selector('node[Type="biologicalProcess"]').css({
+                }).selector('node[Type="biologicalprocess"]').css({
                     'shape': 'roundrectangle',
                     'width': 'data(Width)',
                     'height': 'data(Height)',
@@ -1939,8 +1943,8 @@ var VQI_PathwayEditorGUI = function (parent) {
                     'height': .01
                 }).selector('.collapsed_informative').css({
                     'shape': 'circle',
-                    'width': 7,
-                    'height': 7,
+                    'width': 6,
+                    'height': 6,
                     'color': 'black',
                     'text-valign': 'center',
                     'border-color': 'black',
diff --git a/index.php b/index.php
index 1d2e194..199586a 100644
--- a/index.php
+++ b/index.php
@@ -13,12 +13,13 @@
         <script src="dependencies/cytoscape.js-2.5.4/cytoscape.js"></script>
     </head>
     <body>
-        <input type=button onclick="load()" value="load">
+<!--    <input type=button onclick="load()" value="load">
         <input type=button onclick="spray()" value="spray">
 		<input type=button onclick="setPersonId()" value="set Person id">
         <input type=button onclick="print()" value="print">
 		<input type=button onclick="save()" value="save">
 		<input id="file" type=file value="spray from file">
+-->
         <div id="parent"></div>
         <script src="VQI_Observable.js"></script>
         <script src="VQI_PathwayEditorGUI.js"></script>
@@ -62,7 +63,7 @@ function save() {
                 objVQI_PathwayEditorNoGUI.produceJSONExternalNoGUI();
             }
 			
-			document.getElementById("file").addEventListener("change", sprayFromFile); 
+//			document.getElementById("file").addEventListener("change", sprayFromFile); 
         </script>
     </body>
 </html>