GUIDE
- Left-click and drag the background to move the graph
- Left-click and drag the nodes to reorganize
- Left-click a node to view first level connections
- Double left-click a node to navigate to its page
- Double left-click the background to zoom in
- Right-click the background to zoom out
sigma.utils.pkg('sigma.canvas.nodes');
sigma.canvas.nodes.image = (function() {
var _cache = {},
_loading = {},
_callbacks = {};
// Return the renderer itself:
var renderer = function(node, context, settings) {
var args = arguments,
prefix = settings('prefix') || '',
size = node[prefix + 'size'],
color = node.color || settings('defaultNodeColor'),
url = node.url;
if (_cache[url]) {
context.save();
// Draw the clipping disc:
context.beginPath();
context.arc(
node[prefix + 'x'],
node[prefix + 'y'],
node[prefix + 'size'],
0,
Math.PI * 2,
true
);
context.closePath();
context.clip();
// Draw the image
context.drawImage(
_cache[url],
node[prefix + 'x'] - size,
node[prefix + 'y'] - size,
2 * size,
2 * size
);
// Quit the "clipping mode":
context.restore();
// Draw the border:
context.beginPath();
context.arc(
node[prefix + 'x'],
node[prefix + 'y'],
node[prefix + 'size'],
0,
Math.PI * 2,
true
);
context.lineWidth = 1;
context.strokeStyle = node.color || settings('defaultNodeColor');
context.stroke();
} else {
sigma.canvas.nodes.image.cache(url);
sigma.canvas.nodes.def.apply(
sigma.canvas.nodes,
args
);
}
};
// Let's add a public method to cache images, to make it possible to
// preload images before the initial rendering:
renderer.cache = function(url, callback) {
if (callback)
_callbacks[url] = callback;
if (_loading[url])
return;
var img = new Image();
img.onload = function() {
_loading[url] = false;
_cache[url] = img;
if (_callbacks[url]) {
_callbacks[url].call(this, img);
delete _callbacks[url];
}
};
_loading[url] = true;
img.src = url;
};
return renderer;
})();
var i,
s,
o,
offset_left = 0.5,
N = 1,
E = 40,
C = 5,
d = 0.5,
cs = [],
g = {
nodes: [],
edges: []
};
if (!sigma.classes.graph.hasMethod('neighbors')){
sigma.classes.graph.addMethod('neighbors', function(nodeId) {
var k,
neighbors = {},
index = this.allNeighborsIndex[nodeId] || {};
for (k in index)
neighbors[k] = this.nodesIndex[k];
return neighbors;
});
}
//adding the central node
g.nodes.push({
id: 4297,
label: 'Olivera Francetic',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/09/research.pasteur.fr_o-francetic-150x150.jpg',
x: 0,
y: 0,
size: 30,
color: '#DDDDDD'
});
var biggest_node_size = 0;
N=11
// adding node
var x_node = Math.cos(2 * 0 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 0 * Math.PI / N) * 10;
g.nodes.push({
id: 200275,
label: 'PROJECT: Electrogenetic control of bacterial metabolism, communication, and biofilm formation',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/project/electrogenetic-control-of-bacterial-metabolism-communication-and-biofilm-formation/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4297200275,
size: 0.5,
source: 4297,
target: 200275,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 2002754297,
size: 0.5,
source: 200275,
target: 4297 });
// adding node
var x_node = Math.cos(2 * 1 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 1 * Math.PI / N) * 10;
g.nodes.push({
id: 200248,
label: 'PROJECT: Bacterial nanowires',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/project/bacterial-nanowires/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4297200248,
size: 0.5,
source: 4297,
target: 200248,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 2002484297,
size: 0.5,
source: 200248,
target: 4297 });
// adding node
var x_node = Math.cos(2 * 2 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 2 * Math.PI / N) * 10;
g.nodes.push({
id: 195937,
label: 'NEWS: Bacterial pathogenicity: improving understanding of an essential process – molecule secretion',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/news/bacterial-pathogenicity-improving-understanding-of-an-essential-process-molecule-secretion/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4297195937,
size: 0.5,
source: 4297,
target: 195937,
});
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4148,
label: 'Nadia Izadi-Pruneyre',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/08/research.pasteur.fr_photo_site-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/nadia-izadi-pruneyre/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1959374148,
size: 0.5,
source: 195937,
target: 4148 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4611,
label: 'Benjamin Bardiaux',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/07/research.pasteur.fr_bardiaux-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/benjamin-bardiaux/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1959374611,
size: 0.5,
source: 195937,
target: 4611 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1959374297,
size: 0.5,
source: 195937,
target: 4297 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4623,
label: 'Michael Nilges',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2017/02/research.pasteur.fr_dsc3513-copy-1-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/michael-nilges/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1959374623,
size: 0.5,
source: 195937,
target: 4623 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 796,
label: 'Ahmed Haouz',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/04/ahmed-haouz-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/ahmed-haouz/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 195937796,
size: 0.5,
source: 195937,
target: 796 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4147,
label: 'Florence Cordier',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/08/research_pasteur-photo_flo_2019.06.25a_crop-2-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/florence-cordier/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1959374147,
size: 0.5,
source: 195937,
target: 4147 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 98461,
label: 'Ariel Mechaly',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2018/03/research_pasteur-njg1njqx-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/fr-ariel-mechaly/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 19593798461,
size: 0.5,
source: 195937,
target: 98461 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4046,
label: 'Sébastien Brier',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/11/research_pasteur-dsc_1803_hd.jpg-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/sebastien-brier/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1959374046,
size: 0.5,
source: 195937,
target: 4046 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 117593,
label: 'Yuanyuan Li',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2019/07/research_pasteur-2-1-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/fr-yuanyuan-li/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 195937117593,
size: 0.5,
source: 195937,
target: 117593 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 140402,
label: 'Régine Dazzoni',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2020/03/research_pasteur-enregine-dazzonifrregine-dazzoni-fotbb28-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/regine-dazzoni-2/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 195937140402,
size: 0.5,
source: 195937,
target: 140402 });
// adding node
var x_node = Math.cos(2 * 3 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 3 * Math.PI / N) * 10;
g.nodes.push({
id: 96944,
label: 'PROJECT: Biogenesis of extracytoplasmic proteins in Gram-negative bacteria',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/project/biogenesis-of-extracytoplasmic-proteins-in-gram-negative-bacteria/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 429796944,
size: 0.5,
source: 4297,
target: 96944,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 969444297,
size: 0.5,
source: 96944,
target: 4297 });
// adding node
var x_node = Math.cos(2 * 4 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 4 * Math.PI / N) * 10;
g.nodes.push({
id: 130091,
label: 'PROJECT: Synergy_T2SS',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/project/synergy_t2ss/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4297130091,
size: 0.5,
source: 4297,
target: 130091,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 117593) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 130091117593,
size: 0.5,
source: 130091,
target: 117593 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 4301,
label: 'Ingrid Guilvout',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/09/research.pasteur.fr_ingrid-guilvout-new-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/ingrid-guilvout/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 1300914301,
size: 0.5,
source: 130091,
target: 4301 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4611) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1300914611,
size: 0.5,
source: 130091,
target: 4611 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1300914297,
size: 0.5,
source: 130091,
target: 4297 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4148) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1300914148,
size: 0.5,
source: 130091,
target: 4148 });
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4623) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1300914623,
size: 0.5,
source: 130091,
target: 4623 });
// adding node
var x_node = Math.cos(2 * 5 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 5 * Math.PI / N) * 10;
g.nodes.push({
id: 109268,
label: 'EVENT: Enterobacterial type IV pili: structure, assembly and molecular function',
x: x_node,
y: y_node,
type: 'image',
url: '',
page_url: 'https://research.pasteur.fr/en/event/enterobacterial-type-iv-pili-structure-assembly-and-molecular-function/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 4297109268,
size: 0.5,
source: 4297,
target: 109268,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 1092684297,
size: 0.5,
source: 109268,
target: 4297 });
// adding node
var x_node = Math.cos(2 * 6 * Math.PI / N) * 10;
var y_node = Math.sin(2 * 6 * Math.PI / N) * 10;
g.nodes.push({
id: 62445,
label: 'NEWS: The pullulanase secretion signal',
x: x_node,
y: y_node,
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2016/01/research.pasteur.fr_cover.tif-1-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/news/the-pullulanase-secretion-signal/',
size: 35,
color: '#DDDDDD'
});
//link content to central post
g.edges.push({
id: 429762445,
size: 0.5,
source: 4297,
target: 62445,
});
//check if content already exist
// update node size depending on the amount of edges
g.nodes.forEach(function(n) {
if (n.id == 4297) {
n.size = n.size + 8;
}
});
//link to content
g.edges.push({
id: 624454297,
size: 0.5,
source: 62445,
target: 4297 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 2487,
label: 'Pedro Alzari',
type: 'image',
url: 'https://research.pasteur.fr/wp-content/uploads/2015/03/palzari-150x150.jpg',
page_url: 'https://research.pasteur.fr/en/member/pedro-alzari/',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 624452487,
size: 0.5,
source: 62445,
target: 2487 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 47478,
label: '',
type: 'image',
url: '',
page_url: '',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6244547478,
size: 0.5,
source: 62445,
target: 47478 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 53112,
label: '',
type: 'image',
url: '',
page_url: '',
x: x_site,
y: y_site,
size: 10,
color: '#dddddd'
});
//link to content
g.edges.push({
id: 6244553112,
size: 0.5,
source: 62445,
target: 53112 });
//check if content already exist
if (x_node<0){
x_site = x_node + ((Math.random() * 2)-1) - offset_left;
}else{
x_site = x_node + ((Math.random() * 2)-1) + offset_left;
}
if (y_node<0){
y_site = y_node + ((Math.random() * 2)-1) - offset_left;
}else{
y_site = y_node + ((Math.random() * 2)-1) + offset_left;
}
// adding site
g.nodes.push({
id: 7802,
label: '',
type: 'image',
url: '',
page_url: '',
x: x_site,
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graph: g,
renderer: {
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container: document.getElementById('graph-main'),
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font: 'Montserrat',
labelThreshold:25,
borderSize:1,
defaultNodeBorderColor: '#999',
sideMargin:25,
}
});
// We first need to save the original colors of our
// nodes and edges, like this:
s.graph.nodes().forEach(function(n) {
n.originalColor = n.color;
});
s.graph.edges().forEach(function(e) {
e.originalColor = e.color;
});
// When a node is clicked, we check for each node
// if it is a neighbor of the clicked one. If not,
// we set its color as grey, and else, it takes its
// original color.
// We do the same for the edges, and we only keep
// edges that have both extremities colored.
s.bind('clickNode', function(e) {
var nodeId = e.data.node.id,
toKeep = s.graph.neighbors(nodeId);
toKeep[nodeId] = e.data.node;
s.graph.nodes().forEach(function(n) {
if (toKeep[n.id])
n.color = '#35a9f5';
else
n.color = '#dddddd';
});
s.graph.edges().forEach(function(e) {
if (toKeep[e.source] && toKeep[e.target])
e.color = '#35a9f5';
else
e.color = '#dddddd';
});
// Since the data has been modified, we need to
// call the refresh method to make the colors
// update effective.
s.refresh();
});
// When the stage is clicked, we just color each
// node and edge with its original color.
s.bind('clickStage', function(e) {
s.graph.nodes().forEach(function(n) {
n.color = n.originalColor;
});
s.graph.edges().forEach(function(e) {
e.color = e.originalColor;
});
// Same as in the previous event:
s.refresh();
});
s.bind("doubleClickNode", function (e) {
$("#canvas-wrap, .sigma-scene, .sigma-mouse").val();
ajax_load_page( e.data.node.page_url );
});
var c = s.camera;
s.bind("rightClickStage", function (e) {
sigma.misc.animation.camera(c, {
ratio: c.ratio * c.settings('zoomingRatio')
}, {
duration: 200
});
});
// Configure the noverlap layout:
var noverlapListener = s.configNoverlap({
nodeMargin: 10,
scaleNodes: 0.3,
gridSize: 1,
easing: 'quadraticInOut', // animation transition function
duration: 4000 // animation duration. Long here for the purposes of this example only
});
// Bind the events:
noverlapListener.bind('start stop interpolate', function(e) {
//console.log(e.type);
if(e.type === 'start') {
//console.time('noverlap');
}
if(e.type === 'interpolate') {
//console.timeEnd('noverlap');
}
});
// Start the layout:
s.startNoverlap();
//s.refresh();
// Initialize the dragNodes plugin:
var dragListener = sigma.plugins.dragNodes(s, s.renderers[0]);
dragListener.bind('startdrag', function(event) {
});
dragListener.bind('drag', function(event) {
});
dragListener.bind('drop', function(event) {
});
dragListener.bind('dragend', function(event) {
});