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pathway/code.js
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// Globals | |
var selectedForQueryNodes = []; | |
var selectedForEditNodes = []; | |
var bundleCounter = 0; | |
var edgeCounter = 0; | |
var nodeCounter = 0; | |
var loadCounts = 0; | |
var target = 0; | |
var header =""; | |
var counts = {}; | |
var str_info; | |
$(function () { // on dom ready | |
function onChange(event) { | |
var reader = new FileReader(); | |
reader.onload = onReaderLoad; | |
reader.readAsText(event.target.files[0]); | |
} | |
function onReaderLoad(event) { | |
var obj = JSON.parse(event.target.result); | |
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) { | |
selectedForEditNodes.remove(); | |
} | |
function addNode(event) { | |
var name = "n"+nodeCounter; | |
var node = []; | |
node.push({ group: "nodes", | |
data: { | |
GraphId: name, | |
LabelSize: 10, | |
SUID: name, | |
Type: "Protein", | |
Valign: "Middle", | |
Width: 80.75, | |
Height: 100, | |
id: name, | |
name: name, | |
selected: false, | |
shared_name: name | |
}, | |
position: { | |
x: 500, | |
y: 500 | |
}, | |
css: { | |
'border-color': 'black', | |
'color': 'black' | |
} | |
}) | |
nodeCounter++; | |
window.cy.add(node); | |
} | |
function addEdge(event){ | |
var sourceE = prompt("Enter source."); | |
var targetE = prompt("Enter target."); | |
var typeE = prompt("Enter type."); | |
var edge = []; | |
edge.push({ | |
group: "edges", | |
data : { | |
id : "e"+edgeCounter, | |
SUID : "e"+edgeCounter, | |
LineThickness:1.0, | |
EndArrow:typeE, | |
Coords:[{"x":0,"y":0},{"x":0,"y":0}], | |
GraphId:"e"+edgeCounter, | |
ZOrder:"12288", | |
source:sourceE, | |
target:targetE, | |
StartArrow : typeE, | |
selected : false | |
}, | |
selected : false | |
}) | |
edgeCounter++; | |
window.cy.add(edge); | |
} | |
function bundle(event){ | |
var nodes = []; | |
var edges =[]; | |
// Create new parent | |
nodes.push({ group: "nodes", | |
data: { | |
GraphId: "n"+bundleCounter, | |
LabelSize: 10, | |
SUID: "b6fd7", | |
Type: "Protein", | |
Valign: "Middle", | |
Width: 80.75, | |
Height: 100, | |
id: "n"+bundleCounter, | |
name: "n"+bundleCounter, | |
selected: false, | |
shared_name: "n"+bundleCounter | |
}, | |
position: { | |
x: 500, | |
y: 500 | |
}, | |
css: { | |
"border-color": "red" | |
} | |
}) | |
// Create copies of old nodes | |
for (var i=0; i < selectedForEditNodes.size(); i++) { | |
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", | |
data : { | |
id : selectedForEditNodes[i].connectedEdges()[j].data('id'), | |
SUID : selectedForEditNodes[i].connectedEdges()[j].data('SUID'), | |
LineThickness: selectedForEditNodes[i].connectedEdges()[j].data('LineThickness'), | |
EndArrow: selectedForEditNodes[i].connectedEdges()[j].data('EndArrow'), | |
Coords: selectedForEditNodes[i].connectedEdges()[j].data('Coords'), | |
GraphId: selectedForEditNodes[i].connectedEdges()[j].data('GraphId'), | |
ZOrder: selectedForEditNodes[i].connectedEdges()[j].data('ZOrder'), | |
source: selectedForEditNodes[i].connectedEdges()[j].data('source'), | |
target: selectedForEditNodes[i].connectedEdges()[j].data('target'), | |
StartArrow : selectedForEditNodes[i].connectedEdges()[j].data('StartArrow'), | |
selected : selectedForEditNodes[i].connectedEdges()[j].data('selected') | |
}, | |
selected : selectedForEditNodes[i].connectedEdges()[j].selected | |
}) | |
} | |
} | |
// Remove old nodes | |
selectedForEditNodes.remove(); | |
// Add new nodes | |
window.cy.add(nodes.concat(edges)); | |
bundleCounter++; | |
} | |
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) { | |
$('#cy').cytoscape({ | |
style: cytoscape.stylesheet() | |
// node elements default css (unselected state) | |
.selector('node').css({ | |
'content': 'data(name)', | |
'text-valign': 'center', | |
'color': 'black', | |
'padding-left': 2, | |
'padding-right': 2, | |
'font-family': 'data(LabelSize)', | |
'background-color': 'white' | |
}) | |
.selector('node[Type="GeneProduct"]').css({ | |
'shape': 'rectangle', | |
'width': 'data(Width)', | |
'height': 'data(Height)', | |
'text-valign': 'middle', | |
'background-color': 'white', | |
'border-color': 'black', | |
'border-width': 1 | |
}) | |
.selector('node[Type="Protein"]').css({ | |
'shape': 'rectangle', | |
'width': 'data(Width)', | |
'height': 'data(Height)', | |
'background-color': 'white', | |
'color': '#ff3333', | |
'border-color': '#ff3333', | |
'border-style': 'solid', | |
'border-width': 1 | |
}) | |
.selector('node[Shape="Brace"]').css({ | |
'shape': 'rectangle', | |
'width': '1', | |
'height': 'data(Width)', | |
'background-color': 'black', | |
'color': 'black', | |
'border-color': 'black', | |
'border-style': 'solid', | |
'border-width': 1 | |
}) | |
.selector('node[FillColor="ffffff"]').css({ | |
'background-color': 'white', | |
'color': 'blue', | |
'text-halign': 'center', | |
'text-valign': 'top' | |
}) | |
// edge elements default css (unselected) | |
.selector('edge').css({ | |
'line-color': 'black', | |
'line-style': 'solid', | |
'width': 1 | |
}) | |
.selector('edge[LineStyle="Dashed"]').css({ | |
'line-style': 'dashed', | |
'line-color': 'black', | |
'background-color': 'black', | |
'color': 'black' | |
}) | |
.selector('edge[EndArrow="Arrow"]').css({ | |
'target-arrow-shape': 'triangle', | |
'target-arrow-color': 'black', | |
'target-arrow-fill': 'filled' | |
}) | |
.selector('edge[EndArrow="TBar"]').css({ | |
'target-arrow-shape': 'tee', | |
'target-arrow-color': 'black', | |
'target-arrow-fill': 'filled' | |
}) | |
.selector('edge[ConnectorType="Elbow"]').css({ | |
'line-color': 'yellow', | |
'line-style': 'solid' | |
}) | |
// node & edge elements (selected state) | |
.selector('edge:selected').css({ | |
'background-color': 'black', | |
'line-color': 'black', | |
'target-arrow-color': 'black', | |
'source-arrow-color': 'black' | |
}) | |
.selector('node:selected').css({ | |
'background-color': 'yellow' | |
}) | |
// misc | |
.selector('.faded').css({ | |
'opacity': 1, | |
'text-opacity': 0 | |
}) | |
// query purpose | |
.selector('.green_bg').css({ | |
'background-color': 'LightGreen', | |
'color': 'black' | |
}) | |
.selector('.red_bg').css({ | |
'background-color': 'LightSalmon', | |
'color': 'black' | |
}) | |
.selector('.purple_border').css({ | |
'border-color': 'MediumPurple', | |
'border-width': 3 | |
}) | |
.selector('.red_border').css({ | |
'border-color': 'red', | |
'border-width': 3 | |
}) | |
.selector('.red_shadow').css({ | |
'shadow-opacity': 1, | |
'shadow-color': 'red', | |
'border-width': 1 | |
}) | |
.selector('.red_circle').css({ | |
'background-color': 'red', | |
'shape': 'ellipse', | |
'background-opacity': 0.5 | |
}) | |
.selector('.green_circle').css({ | |
'background-color': 'green', | |
'shape': 'ellipse', | |
'background-opacity': 0.5 | |
}) | |
.selector('.reset_all').css({ | |
'background-color': 'white', | |
'border-color': 'black', | |
'border-width': 1 | |
}), | |
elements: obj.elements, | |
layout: { | |
name: 'preset', | |
padding: 10 | |
}, | |
ready: function () { | |
window.cy = this; | |
var selectedNodes = []; | |
// custom event handlers | |
cy.off('click', 'node').on('click', 'node', function (e) { | |
e.preventDefault(); | |
var node = this; | |
var node_name = node.data("shared_name"); | |
selectedForQueryNodes.push(node_name); | |
var node_id = node.data("id"); | |
var count = selectedForQueryNodes.filter(function (value) { | |
return value === node_name; | |
}).length; | |
// RNA | |
if (count == 1) { | |
node.addClass('green_bg'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 2) { | |
node.removeClass('green_bg'); | |
node.addClass('red_bg'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
// CNV Added | |
if (count == 3) { | |
node.addClass('purple_border'); | |
node.addClass('green_bg'); | |
node.removeClass('red_bg'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 4) { | |
node.addClass('purple_border'); | |
node.addClass('red_bg'); | |
node.removeClass('green_bg'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 5) { | |
node.addClass('red_border'); | |
node.addClass('green_bg'); | |
node.removeClass('red_bg'); | |
node.removeClass('purple_border'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 6) { | |
node.addClass('red_border'); | |
node.addClass('red_bg'); | |
node.removeClass('green_bg'); | |
node.removeClass('purple_border'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 7) { | |
node.addClass('red_shadow'); | |
node.addClass('red_bg'); | |
node.addClass('purple_border'); | |
node.removeClass('green_bg'); | |
node.removeClass('red_border'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 8) { | |
node.addClass('red_shadow'); | |
node.addClass('red_bg'); | |
node.addClass('red_border'); | |
node.removeClass('green_bg'); | |
node.removeClass('purple_border'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 9) { | |
node.addClass('red_shadow'); | |
node.addClass('green_bg'); | |
node.addClass('red_border'); | |
node.removeClass('red_bg'); | |
node.removeClass('purple_border'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
if (count == 10) { | |
node.addClass('red_shadow'); | |
node.addClass('green_bg'); | |
node.addClass('purple_border'); | |
node.removeClass('red_bg'); | |
node.removeClass('red_border'); | |
$('#variable').val($('#variable').val() + node_name + " "); | |
} | |
}); | |
cy.on('cxttapstart ', 'node', function(event){ | |
target = event.cyTarget; | |
dialogNode.dialog("open"); | |
}); | |
cy.on('select', 'node', function(event){ | |
selectedForEditNodes = cy.$('node:selected'); | |
}); | |
}, | |
// initial viewport state: | |
zoom: 1, | |
pan: { x: 0, y: 0 }, | |
// interaction options: | |
minZoom: 1e-50, | |
maxZoom: 1e50, | |
zoomingEnabled: true, | |
userZoomingEnabled: true, | |
panningEnabled: true, | |
userPanningEnabled: true, | |
boxSelectionEnabled: true, | |
selectionType: 'single', | |
touchTapThreshold: 8, | |
desktopTapThreshold: 4, | |
autolock: false, | |
autoungrabify: false, | |
autounselectify: false, | |
// rendering options: | |
headless: false, | |
styleEnabled: true, | |
hideEdgesOnViewport: false, | |
hideLabelsOnViewport: false, | |
textureOnViewport: false, | |
motionBlur: false, | |
motionBlurOpacity: 0.2, | |
wheelSensitivity: 1, | |
pixelRatio: 1, | |
initrender: function(evt){ /* ... */ }, | |
renderer: { /* ... */ } | |
}); | |
} | |
document.getElementById('file').addEventListener('change', onChange); | |
document.getElementById('delete').addEventListener('click', remove); | |
document.getElementById('addNode').addEventListener('click', addNode); | |
document.getElementById('addEdge').addEventListener('click', addEdge); | |
document.getElementById('bundle').addEventListener('click',bundle); | |
document.getElementById('produceJSON').addEventListener('click',produceJSON); | |
}); // on dom ready |