diff --git a/VQI_PathwayEditor.js b/VQI_PathwayEditor.js
index 9ba5bab..9b45ac9 100755
--- a/VQI_PathwayEditor.js
+++ b/VQI_PathwayEditor.js
@@ -366,6 +366,10 @@ var VQI_PathwayEditor = function (parent) {
}
}
}
+
+ function setElementsNoGUI(obj) {
+ preAddProcessing(obj);
+ }
function setElements(obj) {
if (loadCounts == 0) {
@@ -374,13 +378,12 @@ var VQI_PathwayEditor = function (parent) {
} else {
// Pre-Add process
-
var cy = $('#' + parent + '-cy').cytoscape('get');
for (var i = 0; i < obj.elements.nodes.length; i++) {
obj.elements.nodes[i].position.x = obj.elements.nodes[i].position.x + 1000 * loadCounts;
}
- preProcessingAdd(obj);
+ preAddProcessing(obj);
// Add nodes
cy.add(obj.elements);
@@ -400,8 +403,7 @@ var VQI_PathwayEditor = function (parent) {
pid: id
}, function (data) {
removeHeroUnit();
- fixed_data = data.replace("-.", "-0.");
- var obj = JSON.parse(fixed_data);
+ var obj = JSON.parse(data);
setElements(obj);
});
}
@@ -454,7 +456,6 @@ var VQI_PathwayEditor = function (parent) {
for (var line = 1; line < list.length; line++) {
lines[line] = list[line].split('\t');
}
-
sprayColor(lines);
}
@@ -468,30 +469,6 @@ var VQI_PathwayEditor = function (parent) {
target.data('rna', rna);
target.data('cnv', cnv);
target.data('mut', mut);
-
- if (rna > 0) {
- setNodeStyle(target, 'red_bg', '', '');
- } else if (rna < 0) {
- setNodeStyle(target, 'green_bg', '', '');
- } else {
- setNodeStyle(target, '', '', '');
- }
-
- if (cnv > 0) {
- setNodeStyle(target, '', 'red_border', '');
- } else if (cnv < 0) {
- setNodeStyle(target, '', 'purple_border', '');
- } else {
- setNodeStyle(target, '', '', '');
- }
-
- if (mut > 0) {
- setNodeStyle(target, '', '', 'red_shadow');
- } else if (mut <= 0) {
- setNodeStyle(target, '', '', 'no_shadow');
- } else {
- setNodeStyle(target, '', '', '');
- }
}
}
@@ -579,6 +556,7 @@ var VQI_PathwayEditor = function (parent) {
}
}
+ //re-write
function unbundleRecursive(node, parents, edges, nodes, rCounter) {
rCounter++;
if (rCounter == 1 && node.isParent()) {
@@ -724,6 +702,7 @@ var VQI_PathwayEditor = function (parent) {
}
}
+ //re-write
function unbundle(event) {
var cy = $('#' + parent + '-cy').cytoscape('get');
var parents = [];
@@ -745,7 +724,8 @@ var VQI_PathwayEditor = function (parent) {
postAddProcessing();
saveState();
}
-
+
+ //re-write
function recursiveBundle(node, edges, nodes) {
nodes.push({
group: "nodes",
@@ -792,6 +772,7 @@ var VQI_PathwayEditor = function (parent) {
}
}
+ //re-write
function bundle(event) {
var cy = $('#' + parent + '-cy').cytoscape('get');
var type = document.getElementById(parent + "-type-bundle").value;
@@ -1080,14 +1061,11 @@ var VQI_PathwayEditor = function (parent) {
}, function (yue_data) {
var selectedPaths = findPath(JSON.parse(states[states.length - 1]), sid, vid);
var nodePaths = convertEdgePathtoNodePath(selectedPaths);
- console.log(JSON.stringify(nodePaths));
$.post(services['pathwayWeightedScorer'], {
data_paths: JSON.stringify(nodePaths)
}, function (tham_data) {
- console.log(tham_data)
var scoreJSON = JSON.parse(yue_data);
var fdrJSON = JSON.parse(tham_data);
- console.log(fdrJSON);
var table = document.getElementById(parent + "-inner-table");
var length = document.getElementById(parent + "-inner-table").rows.length;
@@ -1186,37 +1164,6 @@ var VQI_PathwayEditor = function (parent) {
return copy;
}
- function setNodeStyle(target, background, border, shadow) {
- if (background != '') {
- target.removeClass('green_bg');
- target.removeClass('red_bg');
- target.removeClass('white_bg');
- target.addClass(background);
- }
- if (border != '') {
- target.removeClass('purple_border');
- target.removeClass('red_border');
- target.removeClass('black_border');
- target.addClass(border);
- }
- if (shadow != '') {
- target.removeClass('red_shadow');
- target.removeClass('no_shadow');
- target.addClass(shadow);
- }
-
- if (background == '' && border == '' && shadow == '') {
- target.removeClass('green_bg');
- target.removeClass('red_bg');
- target.removeClass('white_bg');
- target.removeClass('purple_border');
- target.removeClass('red_border');
- target.removeClass('black_border');
- target.removeClass('red_shadow');
- target.removeClass('no_shadow');
- }
- }
-
function editEdge() {
var cy = $('#' + parent + '-cy').cytoscape('get');
var direction = document.getElementById(parent + "-direction").value;
@@ -1718,8 +1665,8 @@ var VQI_PathwayEditor = function (parent) {
'border-width': 1
})
- // collapse
- .selector('.collapsed').css({
+ // collapse
+ .selector('.collapsed').css({
'opacity': 0.01
}),
layout: {
@@ -2077,7 +2024,7 @@ var VQI_PathwayEditor = function (parent) {
document.getElementById(parent + '-undo').addEventListener('click', undo);
document.getElementById(parent + '-redo').addEventListener('click', redo);
- //external functions
+ //external GUI functions
self.loadPathwayExternal = function (id) {
loadPathway(id);
@@ -2087,11 +2034,34 @@ var VQI_PathwayEditor = function (parent) {
sprayColor(list);
}
- self.testExternal = function () {
- console.log(print);
- }
self.setDataToSpray = function (data) {
this.sprayData = data;
};
+
+ //external No GUI functions
+
+ self.loadPathwayExternalNoGUI = function (id) {
+ $.post(services['pathwayFinder'], {
+ pid: id
+ }, function (data) {
+ self.json = JSON.parse(data);
+ setElementsNoGUI(this.json);
+ });
+ }
+
+ self.findPathAndScoreExternalYueNoGUI = function (sid, did) {
+ var paths = findPath(this.json, sid, did);
+ $.post(services['pathwayScorer'], {
+ data_json: JSON.stringify(this.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], "score": score});
+ }
+ return result;
+ });
+ }
});
};
diff --git a/index.php b/index.php
index 6476c77..c5f5f55 100644
--- a/index.php
+++ b/index.php
@@ -15,7 +15,6 @@
-
-
+