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NoGUI API
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@ivp08001
ivp08001 committed Dec 16, 2015
1 parent e0d4477 commit 9ca16c5
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Showing 3 changed files with 153 additions and 14 deletions.
139 changes: 128 additions & 11 deletions VQI_PathwayEditor.js
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Original file line number Diff line number Diff line change
Expand Up @@ -458,6 +458,20 @@ 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;
}

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];
}
}

function sprayColor(lines) {
var cy = $('#' + parent + '-cy').cytoscape('get');
Expand Down Expand Up @@ -903,9 +917,8 @@ var VQI_PathwayEditor = function (parent) {
if (item['data']['NODE_TYPE'] !== 'GROUP') {
return true;
}

});
//console.log(nodes);

var edges = Json['elements']['edges'];
var result = [];
//array of arrays containing the graphids for edges in the path
Expand All @@ -923,7 +936,6 @@ var VQI_PathwayEditor = function (parent) {

if (x > x0 - w / 2 - deta & x < x0 + w / 2 + deta & y > y0 - h / 2 - deta & y < y0 + h / 2 + deta) {
return nodes[j]['data']['SUID'];

}
}
}
Expand All @@ -939,21 +951,18 @@ var VQI_PathwayEditor = function (parent) {
var s = (!('source' in edges[i]['data']) ? mapLocation(edges[i]['data']['Coords'][0]['x'], edges[i]['data']['Coords'][0]['y']) : edges[i]['data']['source']);

if (s == gid) {

var cl = edges[i]['data']['Coords'].length;
var t = (!('target' in edges[i]['data']) ? mapLocation(edges[i]['data']['Coords'][cl - 1]['x'], edges[i]['data']['Coords'][cl - 1]['y']) : edges[i]['data']['target']);

if (t == vid) {
var p = path.slice();
p.push(eid);
result.push(p);

continue;

} else if (nodeTrack.indexOf(eid) == -1 & t !== undefined & t !== '0') {
path.push(eid);
nodeTrack.push(eid);

findEdgeBySource(t);
} else {
continue;
Expand All @@ -963,11 +972,9 @@ var VQI_PathwayEditor = function (parent) {
if (end == true) {
path.pop();
nodeTrack.pop();

}
return true;
}

findEdgeBySource(sid);
return result;

Expand All @@ -982,6 +989,90 @@ 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++) {
nodePath.push([])
for (var j = 0; j < selectedPaths[n].length; j++) {
if (j < selectedPaths[n].length - 1) {
var sourceNodeId = lookupEdges[selectedPaths[n][j]].source;
var sourceNodeName = lookupNodes[sourceNodeId].name;
var sourceNodeCnv = lookupNodes[sourceNodeId].cnv;
var sourceNodeRna = lookupNodes[sourceNodeId].rna;
var sourceNodeMut = lookupNodes[sourceNodeId].mut;
if (lookupNodes[sourceNodeId].parent != "") {
nodePath[n].push([]);
for (var k = 0; k < lookupNodes[lookupNodes[sourceNodeId].parent].children.length; k++) {
var sourceNodeName = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].name
var sourceNodeCnv = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].cnv
var sourceNodeRna = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].rna
var sourceNodeMut = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].mut
nodePath[n][j].push({"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut});
}
} else {
nodePath[n].push([{"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut}]);
}
} else {
var sourceNodeId = lookupEdges[selectedPaths[n][j]].source;
var targetNodeId = lookupEdges[selectedPaths[n][j]].target;

var sourceNodeName = lookupNodes[sourceNodeId].name;
var sourceNodeCnv = lookupNodes[sourceNodeId].cnv;
var sourceNodeRna = lookupNodes[sourceNodeId].rna;
var sourceNodeMut = lookupNodes[sourceNodeId].mut;

var targetNodeName = lookupNodes[targetNodeId].name;
var targetNodeCnv = lookupNodes[targetNodeId].cnv;
var targetNodeRna = lookupNodes[targetNodeId].rna;
var targetNodeMut = lookupNodes[targetNodeId].mut;

if (lookupNodes[sourceNodeId].parent != "") {
nodePath[n].push([]);
for (var k = 0; k < lookupNodes[lookupNodes[sourceNodeId].parent].children.length; k++) {
var sourceNodeName = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].name
var sourceNodeCnv = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].cnv
var sourceNodeRna = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].rna
var sourceNodeMut = lookupNodes[lookupNodes[sourceNodeId].parent].children[k].mut
nodePath[n][j].push({"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut});
}
} else {
nodePath[n].push([{"name": sourceNodeName, "cnv": sourceNodeCnv, "rna": sourceNodeRna, "mut": sourceNodeMut}]);
}
if (lookupNodes[targetNodeId].parent != "") {
nodePath[n].push([]);
for (var k = 0; k < lookupNodes[lookupNodes[targetNodeId].parent].children.length; k++) {
var sourceNodeName = lookupNodes[lookupNodes[targetNodeId].parent].children[k].name
var sourceNodeCnv = lookupNodes[lookupNodes[targetNodeId].parent].children[k].cnv
var sourceNodeRna = lookupNodes[lookupNodes[targetNodeId].parent].children[k].rna
var sourceNodeMut = lookupNodes[lookupNodes[targetNodeId].parent].children[k].mut
nodePath[n][j].push({"name": targetNodeName, "cnv": targetNodeCnv, "rna": targetNodeRna, "mut": targetNodeMut});
}
} else {
nodePath[n].push([{"name": targetNodeName, "cnv": targetNodeCnv, "rna": targetNodeRna, "mut": targetNodeMut}]);
}
}
}
}
return nodePath;
}

function convertEdgePathtoNodePath(selectedPaths) {
var cy = $('#' + parent + '-cy').cytoscape('get');
Expand Down Expand Up @@ -1725,6 +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)
});

cy.on('doubleTap', 'node', function (event) {
Expand Down Expand Up @@ -2040,19 +2133,27 @@ var VQI_PathwayEditor = function (parent) {

//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(this.json);
setElementsNoGUI(self.json);
});
}

self.findPathAndScoreExternalYueNoGUI = function (sid, did) {
var paths = findPath(this.json, sid, did);
var paths = findPath(self.json, sid, did);
$.post(services['pathwayScorer'], {
data_json: JSON.stringify(this.json)
data_json: JSON.stringify(self.json)
}, function (yue_data) {
var result = []
var scoreJSON = JSON.parse(yue_data);
Expand All @@ -2062,6 +2163,22 @@ var VQI_PathwayEditor = function (parent) {
}
return result;
});
}

self.findPathAndScoreExternalThamNoGUI = function (sid, did) {
var paths = findPath(self.json, sid, did);
var nodes = convertEdgePathtoNodePathNoGUI(paths,self.json);
$.post(services['pathwayScorer'], {
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 score = getPathScore(paths[n], scoreJSON).toString();
result.push({"path": n, "nodes": nodes[n], "score": score});
}
return result;
});
}
});
};
26 changes: 25 additions & 1 deletion index.php
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,33 @@
<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 src="main.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();
}
</script>
</body>
</html>
2 changes: 0 additions & 2 deletions main.js
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