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sending call back function to score finder
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Pujan Joshi committed Dec 16, 2015
1 parent 9ca16c5 commit 96efb5e
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Showing 2 changed files with 123 additions and 116 deletions.
152 changes: 77 additions & 75 deletions VQI_PathwayEditor.js
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Original file line number Diff line number Diff line change
Expand Up @@ -366,8 +366,8 @@ var VQI_PathwayEditor = function (parent) {
}
}
}
function setElementsNoGUI(obj) {

function setElementsNoGUI(obj) {
preAddProcessing(obj);
}

Expand Down Expand Up @@ -458,18 +458,18 @@ var VQI_PathwayEditor = function (parent) {
}
sprayColor(lines);
}
function sprayColorNoGUI(lines,obj) {
var lookup = {};
for (var i = 0, len = obj.elements.nodes.length; i < len; i++) {
lookup[obj.elements.nodes[i].data.name] = obj.elements.nodes[i].data;
}

function sprayColorNoGUI(lines, obj) {
var lookup = {};
for (var i = 0, len = obj.elements.nodes.length; i < len; i++) {
lookup[obj.elements.nodes[i].data.name] = obj.elements.nodes[i].data;
}

for (var line = 1; line < lines.length; line++) {
var target = lines[line][0];
lookup[target].mut = lines[line][1];
lookup[target].cnv = lines[line][1];
lookup[target].rna = lines[line][1];
lookup[target].mut = lines[line][1];
lookup[target].cnv = lines[line][2];
lookup[target].rna = lines[line][3];
}
}

Expand Down Expand Up @@ -570,7 +570,7 @@ var VQI_PathwayEditor = function (parent) {
}
}

//re-write
//re-write
function unbundleRecursive(node, parents, edges, nodes, rCounter) {
rCounter++;
if (rCounter == 1 && node.isParent()) {
Expand Down Expand Up @@ -716,7 +716,7 @@ var VQI_PathwayEditor = function (parent) {
}
}

//re-write
//re-write
function unbundle(event) {
var cy = $('#' + parent + '-cy').cytoscape('get');
var parents = [];
Expand All @@ -738,8 +738,8 @@ var VQI_PathwayEditor = function (parent) {
postAddProcessing();
saveState();
}
//re-write

//re-write
function recursiveBundle(node, edges, nodes) {
nodes.push({
group: "nodes",
Expand Down Expand Up @@ -786,7 +786,7 @@ var VQI_PathwayEditor = function (parent) {
}
}

//re-write
//re-write
function bundle(event) {
var cy = $('#' + parent + '-cy').cytoscape('get');
var type = document.getElementById(parent + "-type-bundle").value;
Expand Down Expand Up @@ -989,27 +989,27 @@ var VQI_PathwayEditor = function (parent) {
}
return parseFloat((sum / max).toFixed(5));
}
function convertEdgePathtoNodePathNoGUI(selectedPaths,obj) {
var nodePath = [];
var lookupNodes = {};
var lookupEdges = {};
for (var i = 0, len = obj.elements.nodes.length; i < len; i++) {
lookupNodes[obj.elements.nodes[i].data.id] = obj.elements.nodes[i].data;
}
for (var i = 0, len = obj.elements.edges.length; i < len; i++) {
lookupEdges[obj.elements.edges[i].data.id] = obj.elements.edges[i].data;
}
for (var i = 0, len = obj.elements.edges.length; i < len; i++) {
if(obj.elements.nodes[i].data.parent != ""){
if(typeof(lookupNodes[obj.elements.nodes[i].data.parent].children) != "undefined")
lookupNodes[obj.elements.nodes[i].data.parent].children.push(obj.elements.nodes[i].data);
else
lookupNodes[obj.elements.nodes[i].data.parent].children = [obj.elements.nodes[i].data];
}
}
for (var n = 0; n < selectedPaths.length; n++) {

function convertEdgePathtoNodePathNoGUI(selectedPaths, obj) {
var nodePath = [];
var lookupNodes = {};
var lookupEdges = {};

for (var i = 0, len = obj.elements.nodes.length; i < len; i++) {
lookupNodes[obj.elements.nodes[i].data.id] = obj.elements.nodes[i].data;
}
for (var i = 0, len = obj.elements.edges.length; i < len; i++) {
lookupEdges[obj.elements.edges[i].data.id] = obj.elements.edges[i].data;
}
for (var i = 0, len = obj.elements.edges.length; i < len; i++) {
if (obj.elements.nodes[i].data.parent != "") {
if (typeof (lookupNodes[obj.elements.nodes[i].data.parent].children) != "undefined")
lookupNodes[obj.elements.nodes[i].data.parent].children.push(obj.elements.nodes[i].data);
else
lookupNodes[obj.elements.nodes[i].data.parent].children = [obj.elements.nodes[i].data];
}
}
for (var n = 0; n < selectedPaths.length; n++) {
nodePath.push([])
for (var j = 0; j < selectedPaths[n].length; j++) {
if (j < selectedPaths[n].length - 1) {
Expand Down Expand Up @@ -1071,7 +1071,7 @@ var VQI_PathwayEditor = function (parent) {
}
}
}
return nodePath;
return nodePath;
}

function convertEdgePathtoNodePath(selectedPaths) {
Expand Down Expand Up @@ -1756,8 +1756,8 @@ var VQI_PathwayEditor = function (parent) {
'border-width': 1
})

// collapse
.selector('.collapsed').css({
// collapse
.selector('.collapsed').css({
'opacity': 0.01
}),
layout: {
Expand Down Expand Up @@ -1816,8 +1816,8 @@ var VQI_PathwayEditor = function (parent) {
else
orderedSelectedNodes.shift();
orderedSelectedNodes.push(event.cyTarget);
console.log(event.cyTarget._private.data.id)
console.log(event.cyTarget._private.data.name)
console.log(event.cyTarget._private.data.id)
console.log(event.cyTarget._private.data.name)
});

cy.on('doubleTap', 'node', function (event) {
Expand Down Expand Up @@ -2130,55 +2130,57 @@ var VQI_PathwayEditor = function (parent) {
self.setDataToSpray = function (data) {
this.sprayData = data;
};
//external No GUI functions
self.printGraph = function(){
console.log(self.json);
}
self.sprayColorExternalNoGUI = function(list){
sprayColorNoGUI(list,self.json);
}
self.loadPathwayExternalNoGUI = function (id) {

//external No GUI functions

self.printGraph = function () {
console.log(self.json);
}

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);
setElementsNoGUI(self.json);
});
}
self.findPathAndScoreExternalYueNoGUI = function (sid, did) {

self.findPathAndScoreExternalYueNoGUI = function (sid, did, f) {
var paths = findPath(self.json, sid, did);
$.post(services['pathwayScorer'], {
$.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 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], "score": score});
result.push({"path": n, "edges": paths[n], "score": score});
}
return result;
});
// return result;
f(result);
});
}
self.findPathAndScoreExternalThamNoGUI = function (sid, did) {

self.findPathAndScoreExternalThamNoGUI = function (sid, did, f) {
var paths = findPath(self.json, sid, did);
var nodes = convertEdgePathtoNodePathNoGUI(paths,self.json);
$.post(services['pathwayScorer'], {
var nodes = convertEdgePathtoNodePathNoGUI(paths, self.json);
$.post(services['pathwayWeightedScorer'], {
data_json: JSON.stringify(nodes)
}, function (tham_data) {
var result = []
var scoreJSON = JSON.parse(tham_data);
for (var n = 0; n < paths.length; n++) {
var result = []
var scoreJSON = JSON.parse(tham_data);
for (var n = 0; n < paths.length; n++) {
var score = getPathScore(paths[n], scoreJSON).toString();
result.push({"path": n, "nodes": nodes[n], "score": score});
result.push({"path": n, "nodes": nodes[n], "score": score});
}
return result;
});
// return result;
f(result);
});
}
});
};
87 changes: 46 additions & 41 deletions index.php
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Original file line number Diff line number Diff line change
@@ -1,44 +1,49 @@
<html>
<head>
<meta charset=utf-8/>
<link rel="stylesheet" href="style.css"/>
<link rel="stylesheet" href="dependencies/jquery-ui-1.11.4/jquery-ui.css"/>
<link rel="stylesheet" href="dependencies/bootstrap-3.3.5-dist/css/bootstrap.min.css">
<script src="dependencies/download.js"></script>
<script src="dependencies/jquery-1.11.3.min.js"></script>
<script src="dependencies/jquery-ui-1.11.4/jquery-ui.js"></script>
<script src="dependencies/d3/d3.min.js"></script>
<script src="dependencies/bootstrap-3.3.5-dist/js/bootstrap.min.js"></script>
<script src="dependencies/cytoscape.js-2.4.9/dist/cytoscape.js"></script>
</head>
<body>
<input type=button onclick="load()" value="load">
<input type=button onclick="findYue()" value="find Yue">
<input type=button onclick="findTham()" value="find Tham">
<input type=button onclick="spray()" value="spray">
<input type=button onclick="print()" value="print">
<div id="parent"></div>
<script src="VQI_Observable.js"></script>
<script src="VQI_PathwayEditor.js"></script>
<script>
var objVQI_PathwayEditor = new VQI_PathwayEditor("parent");
function load(){
objVQI_PathwayEditor.loadPathwayExternalNoGUI(302);
}
function findYue(){
objVQI_PathwayEditor.findPathAndScoreExternalYueNoGUI("n0","n22");
}
function findTham(){
objVQI_PathwayEditor.findPathAndScoreExternalThamNoGUI("n0","n22");
}
function spray(){
var data = [["AKT1", 1,2,3],["AKT1", 1,2,3]];
objVQI_PathwayEditor.sprayColorExternalNoGUI(data);
}
function print(){
objVQI_PathwayEditor.printGraph();
}
<head>
<meta charset=utf-8/>
<link rel="stylesheet" href="style.css"/>
<link rel="stylesheet" href="dependencies/jquery-ui-1.11.4/jquery-ui.css"/>
<link rel="stylesheet" href="dependencies/bootstrap-3.3.5-dist/css/bootstrap.min.css">
<script src="dependencies/download.js"></script>
<script src="dependencies/jquery-1.11.3.min.js"></script>
<script src="dependencies/jquery-ui-1.11.4/jquery-ui.js"></script>
<script src="dependencies/d3/d3.min.js"></script>
<script src="dependencies/bootstrap-3.3.5-dist/js/bootstrap.min.js"></script>
<script src="dependencies/cytoscape.js-2.4.9/dist/cytoscape.js"></script>
</head>
<body>
<input type=button onclick="load()" value="load">
<input type=button onclick="spray()" value="spray">
<input type=button onclick="findYue()" value="find Yue">
<input type=button onclick="findTham()" value="find Tham">
<input type=button onclick="print()" value="print">
<div id="parent"></div>
<script src="VQI_Observable.js"></script>
<script src="VQI_PathwayEditor.js"></script>
<script>
var objVQI_PathwayEditor = new VQI_PathwayEditor("parent");
function load() {
objVQI_PathwayEditor.loadPathwayExternalNoGUI(302);
}
function findYue() {
objVQI_PathwayEditor.findPathAndScoreExternalYueNoGUI("n0", "n22", function (result) {
console.log(result)
});
}
function findTham() {
objVQI_PathwayEditor.findPathAndScoreExternalThamNoGUI("n0", "n22", function (result) {
console.log(result)
});
}
function spray() {
var data = [["AKT1", 1, 2, 3], ["AKT1", 1, 2, 3]];
objVQI_PathwayEditor.sprayColorExternalNoGUI(data);
}
function print() {
objVQI_PathwayEditor.printGraph();
}
</script>
</body>
</body>
</html>

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