diff --git a/code.js b/code.js
index 6b36a2b..5c61540 100644
--- a/code.js
+++ b/code.js
@@ -4,10 +4,11 @@ var selectedForQueryNodes = [];
var selectedForEditNodes = [];
var bundleCounter = 0;
var edgeCounter = 0;
+var loadCounts = 0;
+var header ="";
var counts = {};
var str_info;
-
$(function () { // on dom ready
function onChange(event) {
@@ -17,9 +18,17 @@ $(function () { // on dom ready
}
function onReaderLoad(event) {
- console.log(event.target.result);
var obj = JSON.parse(event.target.result);
- visual_pathway(obj);
+ if(loadCounts==0){
+ header = obj.data;
+ visual_pathway(obj);
+ } else {
+ for(var i=0; i < obj.elements.nodes.length; i++){
+ obj.elements.nodes[i].position.x = obj.elements.nodes[i].position.x+1000*loadCounts;
+ }
+ window.cy.add(obj.elements)
+ }
+ loadCounts++;
}
function remove(event) {
@@ -135,30 +144,57 @@ $(function () { // on dom ready
// Create copies of old nodes
for (var i=0; i < selectedForEditNodes.size(); i++) {
- nodes.push({
- group: "nodes",
- data: {
- GraphId: selectedForEditNodes[i].data('GraphId'),
- LabelSize: selectedForEditNodes[i].data('LabelSize'),
- SUID: selectedForEditNodes[i].data('SUID'),
- 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'),
- shared_name: selectedForEditNodes[i].data('shared_name'),
- parent: "n"+bundleCounter
- },
- position: {
- x: selectedForEditNodes[i].position('x'),
- y: selectedForEditNodes[i].position('y')
- },
- css: {
- 'border-color': 'red'
- }
- });
+ if(typeof selectedForEditNodes[i].data('parent') == 'undefined'){
+ nodes.push({
+ group: "nodes",
+ data: {
+ GraphId: selectedForEditNodes[i].data('GraphId'),
+ LabelSize: selectedForEditNodes[i].data('LabelSize'),
+ SUID: selectedForEditNodes[i].data('SUID'),
+ 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'),
+ shared_name: selectedForEditNodes[i].data('shared_name'),
+ parent: "n"+bundleCounter
+ },
+ position: {
+ x: selectedForEditNodes[i].position('x'),
+ y: selectedForEditNodes[i].position('y')
+ },
+ css: {
+ 'border-color': 'red'
+ }
+ });
+ } else {
+ nodes.push({
+ group: "nodes",
+ data: {
+ GraphId: selectedForEditNodes[i].data('GraphId'),
+ LabelSize: selectedForEditNodes[i].data('LabelSize'),
+ SUID: selectedForEditNodes[i].data('SUID'),
+ 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'),
+ shared_name: selectedForEditNodes[i].data('shared_name'),
+ parent: selectedForEditNodes[i].data('parent')
+ },
+ position: {
+ x: selectedForEditNodes[i].position('x'),
+ y: selectedForEditNodes[i].position('y')
+ },
+ css: {
+ 'border-color': 'red'
+ }
+ });
+ }
for (var j=0; j < selectedForEditNodes[i].connectedEdges().size(); j++) {
edges.push({
group: "edges",
@@ -175,7 +211,7 @@ $(function () { // on dom ready
StartArrow : selectedForEditNodes[i].connectedEdges()[j].data('StartArrow'),
selected : selectedForEditNodes[i].connectedEdges()[j].data('selected')
},
- selected : selectedForEditNodes[i].connectedEdges()[j].selected,
+ selected : selectedForEditNodes[i].connectedEdges()[j].selected
})
}
}
@@ -189,9 +225,21 @@ $(function () { // on dom ready
bundleCounter++;
}
- function produceJSON(event){
- var j = cy.elements().jsons();
- console.log(j);
+ function produceJSON(event){
+ var nodes = cy.$('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()) +
+ '}}';
+ console.log(data);
+// console.log(JSON.stringify(header));
+// console.log(JSON.stringify(nodes.jsons()));
+// console.log(JSON.stringify(edges.jsons()));
+// console.log(JSON.stringify(cy.elements().jsons()));
}
function visual_pathway(obj) {
@@ -332,6 +380,14 @@ $(function () { // on dom ready
});
+ cy.on('cxttapstart ', 'node', function(event){
+ var name = prompt("Enter new name.", event.cyTarget.data('name'));
+ if (name != null) {
+ event.cyTarget.data('name', name)
+ }
+ });
+
+
cy.on('select', 'node', function(event){
selectedForEditNodes = cy.$('node:selected');
});
diff --git a/index.php b/index.php
index cc25e37..8a39782 100644
--- a/index.php
+++ b/index.php
@@ -4,6 +4,8 @@
Json pathway file reader
+
+
diff --git a/workfile.cyjs b/workfile.cyjs
new file mode 100644
index 0000000..5ec30ad
--- /dev/null
+++ b/workfile.cyjs
@@ -0,0 +1 @@
+{"format_version" : "1.0","generated_by" : "cytoscape-3.2.1","target_cytoscapejs_version" : "~2.1","data" :{"shared_name":"Pathway","ID":"104","BOARDWIDTH":"1131","BOARDHEIGHT":"858","LICENSE":"CC BY 2.0","ORGANISM":"Homo sapiens","NAME":"TP53 Network","INSTRUCTION":"P53 is not a lonely genome guardian, it operates with the assistance of p73 and p63 within a complex network including distinct but complementary pathways. This protein family presents a high level of sequence homology in its DNA binding domain. The complexity of the family has been enriched by the alternatively spliced forms of the genes. At present pathway, the alternatively spliced forms of p63 and p73 and how they interact with p53 are shown . However, little is known about the transcriptional regulation of p53 family members. Further studies will tell us whether the three genes of the family also share others regulatory activities.","AUTHOR":"","VERSION":"","SUID":104,"__Annotations":[],"selected":true},"elements" : {"nodes" :[{"data":{"id":"b6fd7","SUID":"b6fd7","dbId":"13032","shared_name":"TP73alpha","name":"TP73alpha","Type":"Protein","XrefId":"O15350","Height":27,"Width":80.75,"LabelSize":10,"GraphId":"b6fd7","Valign":"Middle","NODE_TYPE":"DATANODE","Color":"ff0033","XrefDatasource":"Uniprot-TrEMBL","GroupRef":"c95d9","selected":false},"position":{"x":941.125,"y":125.5},"group":"nodes","removed":false,"selected":false,"selectable":true,"locked":false,"grabbed":false,"grabbable":true,"classes":""},{"data":{"id":"e2998","SUID":"e2998","dbId":"13033","shared_name":"ATM","name":"ATM","Type":"GeneProduct","XrefId":"ENSG00000149311","Height":21.5,"Width":77.5,"LabelSize":10,"GraphId":"e2998","Valign":"Middle","NODE_TYPE":"DATANODE","XrefDatasource":"Ensembl","selected":false},"position":{"x":513.75,"y":205.25},"group":"nodes","removed":false,"selected":false,"selectable":true,"locked":false,"grabbed":false,"grabbable":true,"classes":""},{"data":{"id":"b1117","SUID":"b1117","dbId":"13034","shared_name":"ABL1","name":"ABL1","Type":"GeneProduct","XrefId":"25","Height":20.5,"Width":78.5,"LabelSize":10,"GraphId":"b1117","Valign":"Middle","NODE_TYPE":"DATANODE","XrefDatasource":"Entrez Gene","selected":false},"position":{"x":632.25,"y":205.25},"group":"nodes","removed":false,"selected":false,"selectable":true,"locked":false,"grabbed":false,"grabbable":true,"classes":""},{"data":{"id":"acbaf","SUID":"acbaf","dbId":"13035","shared_name":"TP73zeta","name":"TP73zeta","Type":"Protein","XrefId":"O15350","Height":29,"Width":83,"LabelSize":10,"GraphId":"acbaf","Valign":"Middle","NODE_TYPE":"DATANODE","Color":"ff3333","XrefDatasource":"Uniprot-TrEMBL","GroupRef":"c95d9","selected":false},"position":{"x":941.5,"y":226.5},"group":"nodes","removed":false,"selected":false,"selectable":true,"locked":false,"grabbed":false,"grabbable":true,"classes":""},{"data":{"id":"baf57","SUID":"baf57","dbId":"13036","shared_name":"BAX","name":"BAX","Type":"GeneProduct","XrefId":"581","Height":22,"Width":64,"LabelSize":10,"GraphId":"baf57","Valign":"Middle","NODE_TYPE":"DATANODE","XrefDatasource":"Entrez 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