Reworked all code to commonjs modules. Replaced the build script with Gulp

Jakefile.js

@@ -1,208 +0,0 @@
-/**
- * Jake build script
- */
-var jake = require('jake'),
-    browserify = require('browserify'),
-    wrench = require('wrench'),
-    CleanCSS = require('clean-css'),
-    fs = require('fs');
-
-require('jake-utils');
-
-// constants
-var DIST = './dist';
-var VIS = DIST + '/vis.js';
-var VIS_CSS = DIST + '/vis.css';
-var VIS_TMP = DIST + '/vis.js.tmp';
-var VIS_MIN = DIST + '/vis.min.js';
-var VIS_MIN_CSS = DIST + '/vis.min.css';
-
-/**
- * default task
- */
-desc('Default task: build all libraries');
-task('default', ['build', 'minify'], function () {
-  console.log('done');
-});
-
-/**
- * build the visualization library vis.js
- */
-desc('Build the visualization library vis.js');
-task('build', {async: true}, function () {
-  jake.mkdirP(DIST);
-  jake.mkdirP(DIST + '/img');
-
-  // concatenate and stringify the css files
-  concat({
-    src: [
-      './lib/timeline/component/css/timeline.css',
-      './lib/timeline/component/css/panel.css',
-      './lib/timeline/component/css/labelset.css',
-      './lib/timeline/component/css/itemset.css',
-      './lib/timeline/component/css/item.css',
-      './lib/timeline/component/css/timeaxis.css',
-      './lib/timeline/component/css/currenttime.css',
-      './lib/timeline/component/css/customtime.css',
-      './lib/timeline/component/css/animation.css',
-
-      './lib/timeline/component/css/dataaxis.css',
-      './lib/timeline/component/css/pathStyles.css',
-
-      './lib/network/css/network-manipulation.css',
-      './lib/network/css/network-navigation.css'
-    ],
-    dest: VIS_CSS,
-    separator: '\n'
-  });
-  console.log('created ' + VIS_CSS);
-
-  // concatenate the script files
-  concat({
-    dest: VIS_TMP,
-    src: [
-      './lib/module/imports.js',
-
-      './lib/shim.js',
-      './lib/util.js',
-      './lib/DOMutil.js',
-      './lib/DataSet.js',
-      './lib/DataView.js',
-
-      './lib/timeline/component/GraphGroup.js',
-      './lib/timeline/component/Legend.js',
-      './lib/timeline/component/DataAxis.js',
-      './lib/timeline/component/LineGraph.js',
-      './lib/timeline/DataStep.js',
-
-      './lib/timeline/Stack.js',
-      './lib/timeline/TimeStep.js',
-      './lib/timeline/Range.js',
-      './lib/timeline/component/Component.js',
-      './lib/timeline/component/TimeAxis.js',
-      './lib/timeline/component/CurrentTime.js',
-      './lib/timeline/component/CustomTime.js',
-      './lib/timeline/component/ItemSet.js',
-      './lib/timeline/component/item/*.js',
-      './lib/timeline/component/Group.js',
-      './lib/timeline/Timeline.js',
-      './lib/timeline/Graph2d.js',
-
-      './lib/network/dotparser.js',
-      './lib/network/shapes.js',
-      './lib/network/Node.js',
-      './lib/network/Edge.js',
-      './lib/network/Popup.js',
-      './lib/network/Groups.js',
-      './lib/network/Images.js',
-      './lib/network/networkMixins/physics/PhysicsMixin.js',
-      './lib/network/networkMixins/physics/HierarchialRepulsion.js',
-      './lib/network/networkMixins/physics/BarnesHut.js',
-      './lib/network/networkMixins/physics/Repulsion.js',
-      './lib/network/networkMixins/HierarchicalLayoutMixin.js',
-      './lib/network/networkMixins/ManipulationMixin.js',
-      './lib/network/networkMixins/SectorsMixin.js',
-      './lib/network/networkMixins/ClusterMixin.js',
-      './lib/network/networkMixins/SelectionMixin.js',
-      './lib/network/networkMixins/NavigationMixin.js',
-      './lib/network/networkMixins/MixinLoader.js',
-      './lib/network/Network.js',
-
-      './lib/graph3d/Graph3d.js',
-
-      './lib/module/exports.js'
-    ],
-
-    separator: '\n'
-  });
-
-  // copy images
-  wrench.copyDirSyncRecursive('./lib/network/img', DIST + '/img/network', {
-    forceDelete: true
-  });
-  wrench.copyDirSyncRecursive('./lib/timeline/img', DIST + '/img/timeline', {
-    forceDelete: true
-  });
-
-  var timeStart = Date.now();
-  // bundle the concatenated script and dependencies into one file
-  var b = browserify();
-  b.add(VIS_TMP);
-  b.bundle({
-    standalone: 'vis'
-  }, function (err, code) {
-    if(err) {
-      throw err;
-    }
-    console.log("browserify",Date.now() - timeStart); timeStart = Date.now();
-    // add header and footer
-    var lib = read('./lib/module/header.js') + code;
-
-    // write bundled file
-    write(VIS, lib);
-    console.log('created js' + VIS);
-
-    // remove temporary file
-    fs.unlinkSync(VIS_TMP);
-
-    // update version number and stuff in the javascript files
-    replacePlaceholders(VIS);
-
-    complete();
-  });
-});
-
-/**
- * minify the visualization library vis.js
- */
-desc('Minify the visualization library vis.js');
-task('minify', {async: true}, function () {
-  // minify javascript
-  minify({
-    src: VIS,
-    dest: VIS_MIN,
-    header: read('./lib/module/header.js')
-  });
-
-  // update version number and stuff in the javascript files
-  replacePlaceholders(VIS_MIN);
-
-  console.log('created minified ' + VIS_MIN);
-
-  var minified = new CleanCSS().minify(read(VIS_CSS));
-  write(VIS_MIN_CSS, minified);
-  console.log('created minified ' + VIS_MIN_CSS);
-});
-
-/**
- * test task
- */
-desc('Test the library');
-task('test', function () {
-  // TODO: use a testing suite for testing: nodeunit, mocha, tap, ...
-  var filelist = new jake.FileList();
-  filelist.include([
-    './test/**/*.js'
-  ]);
-
-  var files = filelist.toArray();
-  files.forEach(function (file) {
-    require('./' + file);
-  });
-
-  console.log('Executed ' + files.length + ' test files successfully');
-});
-
-/**
- * replace version, date, and name placeholders in the provided file
- * @param {String} filename
- */
-var replacePlaceholders = function (filename) {
-  replace({
-    replacements: [
-      {pattern: '@@date',    replacement: today()},
-      {pattern: '@@version', replacement: version()}
-    ],
-    src: filename
-  });
-};

README.md

@@ -124,15 +124,9 @@ To build the library from source, clone the project from github
 
     git clone git://github.com/almende/vis.git
 
-The project uses [jake](https://github.com/mde/jake) as build tool.
-The build script uses [Browserify](http://browserify.org/) to
-bundle the source code into a library,
-and uses [UglifyJS](http://lisperator.net/uglifyjs/) to minify the code.
 The source code uses the module style of node (require and module.exports) to
-organize dependencies.
-
-To install all dependencies and build the library, run `npm install` in the
-root of the project.
+organize dependencies. To install all dependencies and build the library, 
+run `npm install` in the root of the project.
 
     cd vis
     npm install

dist/vis.css

@@ -703,4 +703,4 @@ div.network-navigation.zoomExtends {
     background-image: url("img/network/zoomExtends.png");
     bottom:50px;
     right:15px;
-}
+}

examples/network/07_selections.html

@@ -56,7 +56,7 @@
   });
 
   // set initial selection (id's of some nodes)
-  network.setSelection([3, 4, 5]);
+  network.selectNodes([3, 4, 5]);
 </script>
 
 </body>

gulpfile.js

@@ -0,0 +1,138 @@
+var fs = require('fs');
+var gulp = require('gulp');
+var gutil = require('gulp-util');
+var concat = require('gulp-concat');
+var minifyCSS = require('gulp-minify-css');
+var rename = require("gulp-rename");
+var webpack = require('webpack');
+var uglify = require('uglify-js');
+var rimraf = require('rimraf');
+var merge = require('merge-stream');
+
+var ENTRY             = './index.js';
+var HEADER            = './lib/header.js';
+var DIST              = './dist';
+var VIS_JS            = 'vis.js';
+var VIS_MAP           = 'vis.map';
+var VIS_CSS           = 'vis.css';
+var VIS_MIN_CSS       = 'vis.min.css';
+var DIST_VIS_MIN_JS   = DIST + '/vis.min.js';
+var DIST_VIS_MAP      = DIST + '/' + VIS_MAP;
+
+// generate banner with today's date and correct version
+function createBanner() {
+  var today = gutil.date(new Date(), 'yyyy-mm-dd'); // today, formatted as yyyy-mm-dd
+  var version = require('./package.json').version;
+
+  return String(fs.readFileSync(HEADER))
+      .replace('@@date', today)
+      .replace('@@version', version);
+}
+
+var bannerPlugin = new webpack.BannerPlugin(createBanner(), {
+  entryOnly: true,
+  raw: true
+});
+
+var webpackConfig = {
+  entry: ENTRY,
+  output: {
+    library: 'vis',
+    libraryTarget: 'umd',
+    path: DIST,
+    filename: VIS_JS,
+    sourcePrefix: '  '
+  },
+  plugins: [ bannerPlugin ],
+  cache: true
+};
+
+var uglifyConfig = {
+  outSourceMap: VIS_MAP,
+  output: {
+    comments: /@license/
+  }
+};
+
+// create a single instance of the compiler to allow caching
+var compiler = webpack(webpackConfig);
+
+// clean the dist directory
+gulp.task('clean', function (cb) {
+  rimraf(DIST, cb);
+});
+
+gulp.task('bundle-js', ['clean'], function (cb) {
+  // update the banner contents (has a date in it which should stay up to date)
+  bannerPlugin.banner = createBanner();
+
+  compiler.run(function (err, stats) {
+    if (err) gutil.log(err);
+    cb();
+  });
+});
+
+// bundle and minify css
+gulp.task('bundle-css', ['clean'], function () {
+  var files = [
+    './lib/timeline/component/css/timeline.css',
+    './lib/timeline/component/css/panel.css',
+    './lib/timeline/component/css/labelset.css',
+    './lib/timeline/component/css/itemset.css',
+    './lib/timeline/component/css/item.css',
+    './lib/timeline/component/css/timeaxis.css',
+    './lib/timeline/component/css/currenttime.css',
+    './lib/timeline/component/css/customtime.css',
+    './lib/timeline/component/css/animation.css',
+
+    './lib/timeline/component/css/dataaxis.css',
+    './lib/timeline/component/css/pathStyles.css',
+
+    './lib/network/css/network-manipulation.css',
+    './lib/network/css/network-navigation.css'
+  ];
+
+  return gulp.src(files)
+      .pipe(concat(VIS_CSS))
+      .pipe(gulp.dest(DIST))
+
+    // TODO: nicer to put minifying css in a separate task?
+      .pipe(minifyCSS())
+      .pipe(rename(VIS_MIN_CSS))
+      .pipe(gulp.dest(DIST));
+});
+
+gulp.task('copy-img', ['clean'], function () {
+  var network = gulp.src('./lib/network/img/**/*')
+      .pipe(gulp.dest(DIST + '/img/network'));
+
+  var timeline = gulp.src('./lib/timeline/img/**/*')
+      .pipe(gulp.dest(DIST + '/img/timeline'));
+
+  return merge(network, timeline);
+});
+
+gulp.task('minify', ['bundle-js'], function (cb) {
+  var result = uglify.minify([DIST + '/' + VIS_JS], uglifyConfig);
+
+  fs.writeFileSync(DIST_VIS_MIN_JS, result.code);
+  fs.writeFileSync(DIST_VIS_MAP, result.map);
+
+  cb();
+});
+
+gulp.task('bundle', ['bundle-js', 'bundle-css', 'copy-img']);
+
+// The watch task (to automatically rebuild when the source code changes)
+gulp.task('watch', ['bundle', 'minify'], function () {
+  gulp.watch(['index.js', 'lib/**/*.js'], ['bundle', 'minify']);
+});
+
+// The watch task (to automatically rebuild when the source code changes)
+// this watch only rebuilds vis.js, not vis.min.js
+gulp.task('watch-dev', ['bundle'], function () {
+  gulp.watch(['index.js', 'lib/**/*.js'], ['bundle']);
+});
+
+// The default task (called when you run `gulp`)
+gulp.task('default', ['clean', 'bundle', 'minify']);

index.js

@@ -0,0 +1,56 @@
+// utils
+exports.util = require('./lib/util');
+exports.DOMutil = require('./lib/DOMutil');
+
+// data
+exports.DataSet = require('./lib/DataSet');
+exports.DataView = require('./lib/DataView');
+
+// Graph3d
+exports.Graph3d = require('./lib/graph3d/Graph3d');
+
+// Timeline
+exports.Timeline = require('./lib/timeline/Timeline');
+exports.Graph2d = require('./lib/timeline/Graph2d');
+exports.timeline= {
+  DataStep: require('./lib/timeline/DataStep'),
+  Range: require('./lib/timeline/Range'),
+  stack: require('./lib/timeline/Stack'),
+  TimeStep: require('./lib/timeline/TimeStep'),
+
+  components: {
+    items: {
+      Item: require('./lib/timeline/component/item/Item'),
+      ItemBox: require('./lib/timeline/component/item/ItemBox'),
+      ItemPoint: require('./lib/timeline/component/item/ItemPoint'),
+      ItemRange: require('./lib/timeline/component/item/ItemRange')
+    },
+
+    Component: require('./lib/timeline/component/Component'),
+    CurrentTime: require('./lib/timeline/component/CurrentTime'),
+    CustomTime: require('./lib/timeline/component/CustomTime'),
+    DataAxis: require('./lib/timeline/component/DataAxis'),
+    GraphGroup: require('./lib/timeline/component/GraphGroup'),
+    Group: require('./lib/timeline/component/Group'),
+    ItemSet: require('./lib/timeline/component/ItemSet'),
+    Legend: require('./lib/timeline/component/Legend'),
+    LineGraph: require('./lib/timeline/component/LineGraph'),
+    TimeAxis: require('./lib/timeline/component/TimeAxis')
+  }
+};
+
+// Network
+exports.Network = require('./lib/network/Network');
+exports.network = {
+  Edge: require('./lib/network/Edge'),
+  Groups: require('./lib/network/Groups'),
+  Images: require('./lib/network/Images'),
+  Node: require('./lib/network/Node'),
+  Popup: require('./lib/network/Popup'),
+  dotparser: require('./lib/network/dotparser')
+};
+
+// Deprecated since v3.0.0
+exports.Graph = function () {
+  throw new Error('Graph is renamed to Network. Please create a graph as new vis.Network(...)');
+};

lib/DOMutil.js

@@ -1,15 +1,11 @@
-/**
- * Created by Alex on 6/20/14.
- */
-
-var DOMutil = {};
+// DOM utility methods
 
 /**
  * this prepares the JSON container for allocating SVG elements
  * @param JSONcontainer
  * @private
  */
-DOMutil.prepareElements = function(JSONcontainer) {
+exports.prepareElements = function(JSONcontainer) {
   // cleanup the redundant svgElements;
   for (var elementType in JSONcontainer) {
     if (JSONcontainer.hasOwnProperty(elementType)) {
@@ -26,7 +22,7 @@ DOMutil.prepareElements = function(JSONcontainer) {
  * @param JSONcontainer
  * @private
  */
-DOMutil.cleanupElements = function(JSONcontainer) {
+exports.cleanupElements = function(JSONcontainer) {
   // cleanup the redundant svgElements;
   for (var elementType in JSONcontainer) {
     if (JSONcontainer.hasOwnProperty(elementType)) {
@@ -50,7 +46,7 @@ DOMutil.cleanupElements = function(JSONcontainer) {
  * @returns {*}
  * @private
  */
-DOMutil.getSVGElement = function (elementType, JSONcontainer, svgContainer) {
+exports.getSVGElement = function (elementType, JSONcontainer, svgContainer) {
   var element;
   // allocate SVG element, if it doesnt yet exist, create one.
   if (JSONcontainer.hasOwnProperty(elementType)) { // this element has been created before
@@ -86,7 +82,7 @@ DOMutil.getSVGElement = function (elementType, JSONcontainer, svgContainer) {
  * @returns {*}
  * @private
  */
-DOMutil.getDOMElement = function (elementType, JSONcontainer, DOMContainer) {
+exports.getDOMElement = function (elementType, JSONcontainer, DOMContainer) {
   var element;
   // allocate SVG element, if it doesnt yet exist, create one.
   if (JSONcontainer.hasOwnProperty(elementType)) { // this element has been created before
@@ -126,17 +122,17 @@ DOMutil.getDOMElement = function (elementType, JSONcontainer, DOMContainer) {
  * @param svgContainer
  * @returns {*}
  */
-DOMutil.drawPoint = function(x, y, group, JSONcontainer, svgContainer) {
+exports.drawPoint = function(x, y, group, JSONcontainer, svgContainer) {
   var point;
   if (group.options.drawPoints.style == 'circle') {
-    point = DOMutil.getSVGElement('circle',JSONcontainer,svgContainer);
+    point = exports.getSVGElement('circle',JSONcontainer,svgContainer);
     point.setAttributeNS(null, "cx", x);
     point.setAttributeNS(null, "cy", y);
     point.setAttributeNS(null, "r", 0.5 * group.options.drawPoints.size);
     point.setAttributeNS(null, "class", group.className + " point");
   }
   else {
-    point = DOMutil.getSVGElement('rect',JSONcontainer,svgContainer);
+    point = exports.getSVGElement('rect',JSONcontainer,svgContainer);
     point.setAttributeNS(null, "x", x - 0.5*group.options.drawPoints.size);
     point.setAttributeNS(null, "y", y - 0.5*group.options.drawPoints.size);
     point.setAttributeNS(null, "width", group.options.drawPoints.size);
@@ -153,8 +149,8 @@ DOMutil.drawPoint = function(x, y, group, JSONcontainer, svgContainer) {
  * @param y
  * @param className
  */
-DOMutil.drawBar = function (x, y, width, height, className, JSONcontainer, svgContainer) {
-  var rect = DOMutil.getSVGElement('rect',JSONcontainer, svgContainer);
+exports.drawBar = function (x, y, width, height, className, JSONcontainer, svgContainer) {
+  var rect = exports.getSVGElement('rect',JSONcontainer, svgContainer);
   rect.setAttributeNS(null, "x", x - 0.5 * width);
   rect.setAttributeNS(null, "y", y);
   rect.setAttributeNS(null, "width", width);

lib/DataSet.js

@@ -1,3 +1,5 @@
+var util = require('./util');
+
 /**
  * DataSet
  *
@@ -932,3 +934,5 @@ DataSet.prototype._appendRow = function (dataTable, columns, item) {
     dataTable.setValue(row, col, item[field]);
   }
 };
+
+module.exports = DataSet;

lib/DataView.js

@@ -1,3 +1,6 @@
+var util = require('./util');
+var DataSet = require('./DataSet');
+
 /**
  * DataView
  *
@@ -294,3 +297,5 @@ DataView.prototype._trigger = DataSet.prototype._trigger;
 // TODO: make these functions deprecated (replaced with `on` and `off` since version 0.5)
 DataView.prototype.subscribe = DataView.prototype.on;
 DataView.prototype.unsubscribe = DataView.prototype.off;
+
+module.exports = DataView;

lib/graph3d/Filter.js

@@ -0,0 +1,218 @@
+var DataView = require('../DataView');
+
+/**
+ * @class Filter
+ *
+ * @param {DataSet} data The google data table
+ * @param {Number}  column             The index of the column to be filtered
+ * @param {Graph} graph           The graph
+ */
+function Filter (data, column, graph) {
+  this.data = data;
+  this.column = column;
+  this.graph = graph; // the parent graph
+
+  this.index = undefined;
+  this.value = undefined;
+
+  // read all distinct values and select the first one
+  this.values = graph.getDistinctValues(data.get(), this.column);
+
+  // sort both numeric and string values correctly
+  this.values.sort(function (a, b) {
+    return a > b ? 1 : a < b ? -1 : 0;
+  });
+
+  if (this.values.length > 0) {
+    this.selectValue(0);
+  }
+
+  // create an array with the filtered datapoints. this will be loaded afterwards
+  this.dataPoints = [];
+
+  this.loaded = false;
+  this.onLoadCallback = undefined;
+
+  if (graph.animationPreload) {
+    this.loaded = false;
+    this.loadInBackground();
+  }
+  else {
+    this.loaded = true;
+  }
+};
+
+
+/**
+ * Return the label
+ * @return {string} label
+ */
+Filter.prototype.isLoaded = function() {
+  return this.loaded;
+};
+
+
+/**
+ * Return the loaded progress
+ * @return {Number} percentage between 0 and 100
+ */
+Filter.prototype.getLoadedProgress = function() {
+  var len = this.values.length;
+
+  var i = 0;
+  while (this.dataPoints[i]) {
+    i++;
+  }
+
+  return Math.round(i / len * 100);
+};
+
+
+/**
+ * Return the label
+ * @return {string} label
+ */
+Filter.prototype.getLabel = function() {
+  return this.graph.filterLabel;
+};
+
+
+/**
+ * Return the columnIndex of the filter
+ * @return {Number} columnIndex
+ */
+Filter.prototype.getColumn = function() {
+  return this.column;
+};
+
+/**
+ * Return the currently selected value. Returns undefined if there is no selection
+ * @return {*} value
+ */
+Filter.prototype.getSelectedValue = function() {
+  if (this.index === undefined)
+    return undefined;
+
+  return this.values[this.index];
+};
+
+/**
+ * Retrieve all values of the filter
+ * @return {Array} values
+ */
+Filter.prototype.getValues = function() {
+  return this.values;
+};
+
+/**
+ * Retrieve one value of the filter
+ * @param {Number}  index
+ * @return {*} value
+ */
+Filter.prototype.getValue = function(index) {
+  if (index >= this.values.length)
+    throw 'Error: index out of range';
+
+  return this.values[index];
+};
+
+
+/**
+ * Retrieve the (filtered) dataPoints for the currently selected filter index
+ * @param {Number} [index] (optional)
+ * @return {Array} dataPoints
+ */
+Filter.prototype._getDataPoints = function(index) {
+  if (index === undefined)
+    index = this.index;
+
+  if (index === undefined)
+    return [];
+
+  var dataPoints;
+  if (this.dataPoints[index]) {
+    dataPoints = this.dataPoints[index];
+  }
+  else {
+    var f = {};
+    f.column = this.column;
+    f.value = this.values[index];
+
+    var dataView = new DataView(this.data,{filter: function (item) {return (item[f.column] == f.value);}}).get();
+    dataPoints = this.graph._getDataPoints(dataView);
+
+    this.dataPoints[index] = dataPoints;
+  }
+
+  return dataPoints;
+};
+
+
+
+/**
+ * Set a callback function when the filter is fully loaded.
+ */
+Filter.prototype.setOnLoadCallback = function(callback) {
+  this.onLoadCallback = callback;
+};
+
+
+/**
+ * Add a value to the list with available values for this filter
+ * No double entries will be created.
+ * @param {Number} index
+ */
+Filter.prototype.selectValue = function(index) {
+  if (index >= this.values.length)
+    throw 'Error: index out of range';
+
+  this.index = index;
+  this.value = this.values[index];
+};
+
+/**
+ * Load all filtered rows in the background one by one
+ * Start this method without providing an index!
+ */
+Filter.prototype.loadInBackground = function(index) {
+  if (index === undefined)
+    index = 0;
+
+  var frame = this.graph.frame;
+
+  if (index < this.values.length) {
+    var dataPointsTemp = this._getDataPoints(index);
+    //this.graph.redrawInfo(); // TODO: not neat
+
+    // create a progress box
+    if (frame.progress === undefined) {
+      frame.progress = document.createElement('DIV');
+      frame.progress.style.position = 'absolute';
+      frame.progress.style.color = 'gray';
+      frame.appendChild(frame.progress);
+    }
+    var progress = this.getLoadedProgress();
+    frame.progress.innerHTML = 'Loading animation... ' + progress + '%';
+    // TODO: this is no nice solution...
+    frame.progress.style.bottom = 60 + 'px'; // TODO: use height of slider
+    frame.progress.style.left = 10 + 'px';
+
+    var me = this;
+    setTimeout(function() {me.loadInBackground(index+1);}, 10);
+    this.loaded = false;
+  }
+  else {
+    this.loaded = true;
+
+    // remove the progress box
+    if (frame.progress !== undefined) {
+      frame.removeChild(frame.progress);
+      frame.progress = undefined;
+    }
+
+    if (this.onLoadCallback)
+      this.onLoadCallback();
+  }
+};
+
+module.exports = Filter;

lib/graph3d/Graph3d.js

@@ -1,3 +1,11 @@
+var Emitter = require('emitter-component');
+var DataSet = require('../DataSet');
+var DataView = require('../DataView');
+var Point3d = require('./Point3d');
+var Point2d = require('./Point2d');
+var Filter = require('./Filter');
+var StepNumber = require('./StepNumber');
+
 /**
  * @constructor Graph3d
  * Graph3d displays data in 3d.
@@ -715,19 +723,6 @@ Graph3d.prototype._getDataPoints = function (data) {
   return dataPoints;
 };
 
-
-
-
-/**
- * Append suffix 'px' to provided value x
- * @param {int}   x  An integer value
- * @return {string} the string value of x, followed by the suffix 'px'
- */
-Graph3d.px = function(x) {
-  return x + 'px';
-};
-
-
 /**
  * Create the main frame for the Graph3d.
  * This function is executed once when a Graph3d object is created. The frame
@@ -2455,458 +2450,6 @@ G3DpreventDefault = function (event) {
   }
 };
 
-
-
-/**
- * @prototype Point3d
- * @param {Number} x
- * @param {Number} y
- * @param {Number} z
- */
-function Point3d(x, y, z) {
-  this.x = x !== undefined ? x : 0;
-  this.y = y !== undefined ? y : 0;
-  this.z = z !== undefined ? z : 0;
-};
-
-/**
- * Subtract the two provided points, returns a-b
- * @param {Point3d} a
- * @param {Point3d} b
- * @return {Point3d} a-b
- */
-Point3d.subtract = function(a, b) {
-  var sub = new Point3d();
-  sub.x = a.x - b.x;
-  sub.y = a.y - b.y;
-  sub.z = a.z - b.z;
-  return sub;
-};
-
-/**
- * Add the two provided points, returns a+b
- * @param {Point3d} a
- * @param {Point3d} b
- * @return {Point3d} a+b
- */
-Point3d.add = function(a, b) {
-  var sum = new Point3d();
-  sum.x = a.x + b.x;
-  sum.y = a.y + b.y;
-  sum.z = a.z + b.z;
-  return sum;
-};
-
-/**
- * Calculate the average of two 3d points
- * @param {Point3d} a
- * @param {Point3d} b
- * @return {Point3d} The average, (a+b)/2
- */
-Point3d.avg = function(a, b) {
-  return new Point3d(
-      (a.x + b.x) / 2,
-      (a.y + b.y) / 2,
-      (a.z + b.z) / 2
-  );
-};
-
-/**
- * Calculate the cross product of the two provided points, returns axb
- * Documentation: http://en.wikipedia.org/wiki/Cross_product
- * @param {Point3d} a
- * @param {Point3d} b
- * @return {Point3d} cross product axb
- */
-Point3d.crossProduct = function(a, b) {
-  var crossproduct = new Point3d();
-
-  crossproduct.x = a.y * b.z - a.z * b.y;
-  crossproduct.y = a.z * b.x - a.x * b.z;
-  crossproduct.z = a.x * b.y - a.y * b.x;
-
-  return crossproduct;
-};
-
-
-/**
- * Rtrieve the length of the vector (or the distance from this point to the origin
- * @return {Number}  length
- */
-Point3d.prototype.length = function() {
-  return Math.sqrt(
-      this.x * this.x +
-      this.y * this.y +
-      this.z * this.z
-  );
-};
-
-/**
- * @prototype Point2d
- */
-Point2d = function (x, y) {
-  this.x = x !== undefined ? x : 0;
-  this.y = y !== undefined ? y : 0;
-};
-
-
-/**
- * @class Filter
- *
- * @param {DataSet} data The google data table
- * @param {Number}  column             The index of the column to be filtered
- * @param {Graph} graph           The graph
- */
-function Filter (data, column, graph) {
-  this.data = data;
-  this.column = column;
-  this.graph = graph; // the parent graph
-
-  this.index = undefined;
-  this.value = undefined;
-
-  // read all distinct values and select the first one
-  this.values = graph.getDistinctValues(data.get(), this.column);
-
-  // sort both numeric and string values correctly
-  this.values.sort(function (a, b) {
-    return a > b ? 1 : a < b ? -1 : 0;
-  });
-
-  if (this.values.length > 0) {
-    this.selectValue(0);
-  }
-
-  // create an array with the filtered datapoints. this will be loaded afterwards
-  this.dataPoints = [];
-
-  this.loaded = false;
-  this.onLoadCallback = undefined;
-
-  if (graph.animationPreload) {
-    this.loaded = false;
-    this.loadInBackground();
-  }
-  else {
-    this.loaded = true;
-  }
-};
-
-
-/**
- * Return the label
- * @return {string} label
- */
-Filter.prototype.isLoaded = function() {
-  return this.loaded;
-};
-
-
-/**
- * Return the loaded progress
- * @return {Number} percentage between 0 and 100
- */
-Filter.prototype.getLoadedProgress = function() {
-  var len = this.values.length;
-
-  var i = 0;
-  while (this.dataPoints[i]) {
-    i++;
-  }
-
-  return Math.round(i / len * 100);
-};
-
-
-/**
- * Return the label
- * @return {string} label
- */
-Filter.prototype.getLabel = function() {
-  return this.graph.filterLabel;
-};
-
-
-/**
- * Return the columnIndex of the filter
- * @return {Number} columnIndex
- */
-Filter.prototype.getColumn = function() {
-  return this.column;
-};
-
-/**
- * Return the currently selected value. Returns undefined if there is no selection
- * @return {*} value
- */
-Filter.prototype.getSelectedValue = function() {
-  if (this.index === undefined)
-    return undefined;
-
-  return this.values[this.index];
-};
-
-/**
- * Retrieve all values of the filter
- * @return {Array} values
- */
-Filter.prototype.getValues = function() {
-  return this.values;
-};
-
-/**
- * Retrieve one value of the filter
- * @param {Number}  index
- * @return {*} value
- */
-Filter.prototype.getValue = function(index) {
-  if (index >= this.values.length)
-    throw 'Error: index out of range';
-
-  return this.values[index];
-};
-
-
-/**
- * Retrieve the (filtered) dataPoints for the currently selected filter index
- * @param {Number} [index] (optional)
- * @return {Array} dataPoints
- */
-Filter.prototype._getDataPoints = function(index) {
-  if (index === undefined)
-    index = this.index;
-
-  if (index === undefined)
-    return [];
-
-  var dataPoints;
-  if (this.dataPoints[index]) {
-    dataPoints = this.dataPoints[index];
-  }
-  else {
-    var f = {};
-    f.column = this.column;
-    f.value = this.values[index];
-
-    var dataView = new DataView(this.data,{filter: function (item) {return (item[f.column] == f.value);}}).get();
-    dataPoints = this.graph._getDataPoints(dataView);
-
-    this.dataPoints[index] = dataPoints;
-  }
-
-  return dataPoints;
-};
-
-
-
-/**
- * Set a callback function when the filter is fully loaded.
- */
-Filter.prototype.setOnLoadCallback = function(callback) {
-  this.onLoadCallback = callback;
-};
-
-
-/**
- * Add a value to the list with available values for this filter
- * No double entries will be created.
- * @param {Number} index
- */
-Filter.prototype.selectValue = function(index) {
-  if (index >= this.values.length)
-    throw 'Error: index out of range';
-
-  this.index = index;
-  this.value = this.values[index];
-};
-
-/**
- * Load all filtered rows in the background one by one
- * Start this method without providing an index!
- */
-Filter.prototype.loadInBackground = function(index) {
-  if (index === undefined)
-    index = 0;
-
-  var frame = this.graph.frame;
-
-  if (index < this.values.length) {
-    var dataPointsTemp = this._getDataPoints(index);
-    //this.graph.redrawInfo(); // TODO: not neat
-
-    // create a progress box
-    if (frame.progress === undefined) {
-      frame.progress = document.createElement('DIV');
-      frame.progress.style.position = 'absolute';
-      frame.progress.style.color = 'gray';
-      frame.appendChild(frame.progress);
-    }
-    var progress = this.getLoadedProgress();
-    frame.progress.innerHTML = 'Loading animation... ' + progress + '%';
-    // TODO: this is no nice solution...
-    frame.progress.style.bottom = Graph3d.px(60); // TODO: use height of slider
-    frame.progress.style.left = Graph3d.px(10);
-
-    var me = this;
-    setTimeout(function() {me.loadInBackground(index+1);}, 10);
-    this.loaded = false;
-  }
-  else {
-    this.loaded = true;
-
-    // remove the progress box
-    if (frame.progress !== undefined) {
-      frame.removeChild(frame.progress);
-      frame.progress = undefined;
-    }
-
-    if (this.onLoadCallback)
-      this.onLoadCallback();
-  }
-};
-
-
-
-/**
- * @prototype StepNumber
- * The class StepNumber is an iterator for Numbers. You provide a start and end
- * value, and a best step size. StepNumber itself rounds to fixed values and
- * a finds the step that best fits the provided step.
- *
- * If prettyStep is true, the step size is chosen as close as possible to the
- * provided step, but being a round value like 1, 2, 5, 10, 20, 50, ....
- *
- * Example usage:
- *   var step = new StepNumber(0, 10, 2.5, true);
- *   step.start();
- *   while (!step.end()) {
- *   alert(step.getCurrent());
- *   step.next();
- *   }
- *
- * Version: 1.0
- *
- * @param {Number} start     The start value
- * @param {Number} end     The end value
- * @param {Number} step    Optional. Step size. Must be a positive value.
- * @param {boolean} prettyStep Optional. If true, the step size is rounded
- *               To a pretty step size (like 1, 2, 5, 10, 20, 50, ...)
- */
-StepNumber = function (start, end, step, prettyStep) {
-  // set default values
-  this._start = 0;
-  this._end = 0;
-  this._step = 1;
-  this.prettyStep = true;
-  this.precision = 5;
-
-  this._current = 0;
-  this.setRange(start, end, step, prettyStep);
-};
-
-/**
- * Set a new range: start, end and step.
- *
- * @param {Number} start     The start value
- * @param {Number} end     The end value
- * @param {Number} step    Optional. Step size. Must be a positive value.
- * @param {boolean} prettyStep Optional. If true, the step size is rounded
- *               To a pretty step size (like 1, 2, 5, 10, 20, 50, ...)
- */
-StepNumber.prototype.setRange = function(start, end, step, prettyStep) {
-  this._start = start ? start : 0;
-  this._end = end ? end : 0;
-
-  this.setStep(step, prettyStep);
-};
-
-/**
- * Set a new step size
- * @param {Number} step    New step size. Must be a positive value
- * @param {boolean} prettyStep Optional. If true, the provided step is rounded
- *               to a pretty step size (like 1, 2, 5, 10, 20, 50, ...)
- */
-StepNumber.prototype.setStep = function(step, prettyStep) {
-  if (step === undefined || step <= 0)
-    return;
-
-  if (prettyStep !== undefined)
-    this.prettyStep = prettyStep;
-
-  if (this.prettyStep === true)
-    this._step = StepNumber.calculatePrettyStep(step);
-  else
-    this._step = step;
-};
-
-/**
- * Calculate a nice step size, closest to the desired step size.
- * Returns a value in one of the ranges 1*10^n, 2*10^n, or 5*10^n, where n is an
- * integer Number. For example 1, 2, 5, 10, 20, 50, etc...
- * @param {Number}  step  Desired step size
- * @return {Number}     Nice step size
- */
-StepNumber.calculatePrettyStep = function (step) {
-  var log10 = function (x) {return Math.log(x) / Math.LN10;};
-
-  // try three steps (multiple of 1, 2, or 5
-  var step1 = Math.pow(10, Math.round(log10(step))),
-    step2 = 2 * Math.pow(10, Math.round(log10(step / 2))),
-    step5 = 5 * Math.pow(10, Math.round(log10(step / 5)));
-
-  // choose the best step (closest to minimum step)
-  var prettyStep = step1;
-  if (Math.abs(step2 - step) <= Math.abs(prettyStep - step)) prettyStep = step2;
-  if (Math.abs(step5 - step) <= Math.abs(prettyStep - step)) prettyStep = step5;
-
-  // for safety
-  if (prettyStep <= 0) {
-    prettyStep = 1;
-  }
-
-  return prettyStep;
-};
-
-/**
- * returns the current value of the step
- * @return {Number} current value
- */
-StepNumber.prototype.getCurrent = function () {
-  return parseFloat(this._current.toPrecision(this.precision));
-};
-
-/**
- * returns the current step size
- * @return {Number} current step size
- */
-StepNumber.prototype.getStep = function () {
-  return this._step;
-};
-
-/**
- * Set the current value to the largest value smaller than start, which
- * is a multiple of the step size
- */
-StepNumber.prototype.start = function() {
-  this._current = this._start - this._start % this._step;
-};
-
-/**
- * Do a step, add the step size to the current value
- */
-StepNumber.prototype.next = function () {
-  this._current += this._step;
-};
-
-/**
- * Returns true whether the end is reached
- * @return {boolean}  True if the current value has passed the end value.
- */
-StepNumber.prototype.end = function () {
-  return (this._current > this._end);
-};
-
-
 /**
  * @constructor Slider
  *
@@ -2981,7 +2524,7 @@ function Slider(container, options) {
   this.playTimeout = undefined;
   this.playInterval = 1000; // milliseconds
   this.playLoop = true;
-};
+}
 
 /**
  * Select the previous index
@@ -3308,3 +2851,4 @@ getMouseY = function(event) {
   return event.targetTouches[0] && event.targetTouches[0].clientY || 0;
 };
 
+module.exports = Graph3d;

lib/graph3d/Point2d.js

@@ -0,0 +1,11 @@
+/**
+ * @prototype Point2d
+ * @param {Number} [x]
+ * @param {Number} [y]
+ */
+Point2d = function (x, y) {
+  this.x = x !== undefined ? x : 0;
+  this.y = y !== undefined ? y : 0;
+};
+
+module.exports = Point2d;

lib/graph3d/Point3d.js

@@ -0,0 +1,85 @@
+/**
+ * @prototype Point3d
+ * @param {Number} [x]
+ * @param {Number} [y]
+ * @param {Number} [z]
+ */
+function Point3d(x, y, z) {
+  this.x = x !== undefined ? x : 0;
+  this.y = y !== undefined ? y : 0;
+  this.z = z !== undefined ? z : 0;
+};
+
+/**
+ * Subtract the two provided points, returns a-b
+ * @param {Point3d} a
+ * @param {Point3d} b
+ * @return {Point3d} a-b
+ */
+Point3d.subtract = function(a, b) {
+  var sub = new Point3d();
+  sub.x = a.x - b.x;
+  sub.y = a.y - b.y;
+  sub.z = a.z - b.z;
+  return sub;
+};
+
+/**
+ * Add the two provided points, returns a+b
+ * @param {Point3d} a
+ * @param {Point3d} b
+ * @return {Point3d} a+b
+ */
+Point3d.add = function(a, b) {
+  var sum = new Point3d();
+  sum.x = a.x + b.x;
+  sum.y = a.y + b.y;
+  sum.z = a.z + b.z;
+  return sum;
+};
+
+/**
+ * Calculate the average of two 3d points
+ * @param {Point3d} a
+ * @param {Point3d} b
+ * @return {Point3d} The average, (a+b)/2
+ */
+Point3d.avg = function(a, b) {
+  return new Point3d(
+          (a.x + b.x) / 2,
+          (a.y + b.y) / 2,
+          (a.z + b.z) / 2
+  );
+};
+
+/**
+ * Calculate the cross product of the two provided points, returns axb
+ * Documentation: http://en.wikipedia.org/wiki/Cross_product
+ * @param {Point3d} a
+ * @param {Point3d} b
+ * @return {Point3d} cross product axb
+ */
+Point3d.crossProduct = function(a, b) {
+  var crossproduct = new Point3d();
+
+  crossproduct.x = a.y * b.z - a.z * b.y;
+  crossproduct.y = a.z * b.x - a.x * b.z;
+  crossproduct.z = a.x * b.y - a.y * b.x;
+
+  return crossproduct;
+};
+
+
+/**
+ * Rtrieve the length of the vector (or the distance from this point to the origin
+ * @return {Number}  length
+ */
+Point3d.prototype.length = function() {
+  return Math.sqrt(
+          this.x * this.x +
+          this.y * this.y +
+          this.z * this.z
+  );
+};
+
+module.exports = Point3d;

lib/graph3d/StepNumber.js

@@ -0,0 +1,140 @@
+/**
+ * @prototype StepNumber
+ * The class StepNumber is an iterator for Numbers. You provide a start and end
+ * value, and a best step size. StepNumber itself rounds to fixed values and
+ * a finds the step that best fits the provided step.
+ *
+ * If prettyStep is true, the step size is chosen as close as possible to the
+ * provided step, but being a round value like 1, 2, 5, 10, 20, 50, ....
+ *
+ * Example usage:
+ *   var step = new StepNumber(0, 10, 2.5, true);
+ *   step.start();
+ *   while (!step.end()) {
+ *   alert(step.getCurrent());
+ *   step.next();
+ *   }
+ *
+ * Version: 1.0
+ *
+ * @param {Number} start     The start value
+ * @param {Number} end     The end value
+ * @param {Number} step    Optional. Step size. Must be a positive value.
+ * @param {boolean} prettyStep Optional. If true, the step size is rounded
+ *               To a pretty step size (like 1, 2, 5, 10, 20, 50, ...)
+ */
+function StepNumber(start, end, step, prettyStep) {
+  // set default values
+  this._start = 0;
+  this._end = 0;
+  this._step = 1;
+  this.prettyStep = true;
+  this.precision = 5;
+
+  this._current = 0;
+  this.setRange(start, end, step, prettyStep);
+};
+
+/**
+ * Set a new range: start, end and step.
+ *
+ * @param {Number} start     The start value
+ * @param {Number} end     The end value
+ * @param {Number} step    Optional. Step size. Must be a positive value.
+ * @param {boolean} prettyStep Optional. If true, the step size is rounded
+ *               To a pretty step size (like 1, 2, 5, 10, 20, 50, ...)
+ */
+StepNumber.prototype.setRange = function(start, end, step, prettyStep) {
+  this._start = start ? start : 0;
+  this._end = end ? end : 0;
+
+  this.setStep(step, prettyStep);
+};
+
+/**
+ * Set a new step size
+ * @param {Number} step    New step size. Must be a positive value
+ * @param {boolean} prettyStep Optional. If true, the provided step is rounded
+ *               to a pretty step size (like 1, 2, 5, 10, 20, 50, ...)
+ */
+StepNumber.prototype.setStep = function(step, prettyStep) {
+  if (step === undefined || step <= 0)
+    return;
+
+  if (prettyStep !== undefined)
+    this.prettyStep = prettyStep;
+
+  if (this.prettyStep === true)
+    this._step = StepNumber.calculatePrettyStep(step);
+  else
+    this._step = step;
+};
+
+/**
+ * Calculate a nice step size, closest to the desired step size.
+ * Returns a value in one of the ranges 1*10^n, 2*10^n, or 5*10^n, where n is an
+ * integer Number. For example 1, 2, 5, 10, 20, 50, etc...
+ * @param {Number}  step  Desired step size
+ * @return {Number}     Nice step size
+ */
+StepNumber.calculatePrettyStep = function (step) {
+  var log10 = function (x) {return Math.log(x) / Math.LN10;};
+
+  // try three steps (multiple of 1, 2, or 5
+  var step1 = Math.pow(10, Math.round(log10(step))),
+      step2 = 2 * Math.pow(10, Math.round(log10(step / 2))),
+      step5 = 5 * Math.pow(10, Math.round(log10(step / 5)));
+
+  // choose the best step (closest to minimum step)
+  var prettyStep = step1;
+  if (Math.abs(step2 - step) <= Math.abs(prettyStep - step)) prettyStep = step2;
+  if (Math.abs(step5 - step) <= Math.abs(prettyStep - step)) prettyStep = step5;
+
+  // for safety
+  if (prettyStep <= 0) {
+    prettyStep = 1;
+  }
+
+  return prettyStep;
+};
+
+/**
+ * returns the current value of the step
+ * @return {Number} current value
+ */
+StepNumber.prototype.getCurrent = function () {
+  return parseFloat(this._current.toPrecision(this.precision));
+};
+
+/**
+ * returns the current step size
+ * @return {Number} current step size
+ */
+StepNumber.prototype.getStep = function () {
+  return this._step;
+};
+
+/**
+ * Set the current value to the largest value smaller than start, which
+ * is a multiple of the step size
+ */
+StepNumber.prototype.start = function() {
+  this._current = this._start - this._start % this._step;
+};
+
+/**
+ * Do a step, add the step size to the current value
+ */
+StepNumber.prototype.next = function () {
+  this._current += this._step;
+};
+
+/**
+ * Returns true whether the end is reached
+ * @return {boolean}  True if the current value has passed the end value.
+ */
+StepNumber.prototype.end = function () {
+  return (this._current > this._end);
+};
+
+module.exports = StepNumber;

lib/module/exports.js

@@ -1,84 +0,0 @@
-/**
- * vis.js module exports
- */
-var vis = {
-  moment: moment,
-
-  util: util,
-  DOMutil: DOMutil,
-
-  DataSet: DataSet,
-  DataView: DataView,
-
-  Timeline: Timeline,
-  Graph2d: Graph2d,
-  timeline: {
-    DataStep: DataStep,
-    Range: Range,
-    stack: stack,
-    TimeStep: TimeStep,
-
-    components: {
-      items: {
-        Item: Item,
-        ItemBox: ItemBox,
-        ItemPoint: ItemPoint,
-        ItemRange: ItemRange
-      },
-
-      Component: Component,
-      CurrentTime: CurrentTime,
-      CustomTime: CustomTime,
-      DataAxis: DataAxis,
-      GraphGroup: GraphGroup,
-      Group: Group,
-      ItemSet: ItemSet,
-      Legend: Legend,
-      LineGraph: LineGraph,
-      TimeAxis: TimeAxis
-    }
-  },
-
-  Network: Network,
-  network: {
-    Edge: Edge,
-    Groups: Groups,
-    Images: Images,
-    Node: Node,
-    Popup: Popup
-  },
-
-  // Deprecated since v3.0.0
-  Graph: function () {
-    throw new Error('Graph is renamed to Network. Please create a graph as new vis.Network(...)');
-  },
-
-  Graph3d: Graph3d
-};
-
-/**
- * CommonJS module exports
- */
-if (typeof exports !== 'undefined') {
-  exports = vis;
-}
-if (typeof module !== 'undefined' && typeof module.exports !== 'undefined') {
-  module.exports = vis;
-}
-
-/**
- * AMD module exports
- */
-if (typeof(define) === 'function') {
-  define(function () {
-    return vis;
-  });
-}
-
-/**
- * Window exports
- */
-if (typeof window !== 'undefined') {
-  // attach the module to the window, load as a regular javascript file
-  window['vis'] = vis;
-}

lib/module/hammer.js

@@ -0,0 +1,10 @@
+// Only load hammer.js when in a browser environment
+// (loading hammer.js in a node.js environment gives errors)
+if (typeof window !== 'undefined') {
+  module.exports = require('hammerjs');
+}
+else {
+  module.exports = function () {
+    throw Error('hammer.js is only available in a browser, not in node.js.');
+  }
+}

lib/module/imports.js

@@ -1,31 +0,0 @@
-/**
- * vis.js module imports
- */
-
-// Try to load dependencies from the global window object.
-// If not available there, load via require.
-
-var moment = (typeof window !== 'undefined') && window['moment'] || require('moment');
-var Emitter = require('emitter-component');
-
-var Hammer;
-if (typeof window !== 'undefined') {
-  // load hammer.js only when running in a browser (where window is available)
-  Hammer = window['Hammer'] || require('hammerjs');
-}
-else {
-  Hammer = function () {
-    throw Error('hammer.js is only available in a browser, not in node.js.');
-  }
-}
-
-var mousetrap;
-if (typeof window !== 'undefined') {
-  // load mousetrap.js only when running in a browser (where window is available)
-  mousetrap = window['mousetrap'] || require('mousetrap');
-}
-else {
-  mousetrap = function () {
-    throw Error('mouseTrap is only available in a browser, not in node.js.');
-  }
-}

lib/module/moment.js

@@ -0,0 +1,3 @@
+// first check if moment.js is already loaded in the browser window, if so,
+// use this instance. Else, load via commonjs.
+module.exports = (typeof window !== 'undefined') && window['moment'] || require('moment');

lib/network/Edge.js

@@ -1,3 +1,5 @@
+var util = require('../util');
+
 /**
  * @class Edge
  *
@@ -861,7 +863,7 @@ Edge.prototype._drawControlNodes = function(ctx) {
   else {
     this.controlNodes = {from:null, to:null, positions:{}};
   }
-}
+};
 
 /**
  * Enable control nodes.
@@ -869,7 +871,7 @@ Edge.prototype._drawControlNodes = function(ctx) {
  */
 Edge.prototype._enableControlNodes = function() {
   this.controlNodesEnabled = true;
-}
+};
 
 /**
  * disable control nodes
@@ -877,7 +879,7 @@ Edge.prototype._enableControlNodes = function() {
  */
 Edge.prototype._disableControlNodes = function() {
   this.controlNodesEnabled = false;
-}
+};
 
 /**
  * This checks if one of the control nodes is selected and if so, returns the control node object. Else it returns null.
@@ -904,7 +906,7 @@ Edge.prototype._getSelectedControlNode = function(x,y) {
   else {
     return null;
   }
-}
+};
 
 
 /**
@@ -922,7 +924,7 @@ Edge.prototype._restoreControlNodes = function() {
     this.connectedNode = null;
     this.controlNodes.to.unselect();
   }
-}
+};
 
 /**
  * this calculates the position of the control nodes on the edges of the parent nodes.
@@ -961,4 +963,6 @@ Edge.prototype.getControlNodePositions = function(ctx) {
   }
 
   return {from:{x:xFrom,y:yFrom},to:{x:xTo,y:yTo}};
-}
+};
+
+module.exports = Edge;

lib/network/Groups.js

@@ -1,3 +1,5 @@
+var util = require('../util');
+
 /**
  * @class Groups
  * This class can store groups and properties specific for groups.
@@ -78,3 +80,5 @@ Groups.prototype.add = function (groupname, style) {
   }
   return style;
 };
+
+module.exports = Groups;

lib/network/Images.js

@@ -39,3 +39,5 @@ Images.prototype.load = function(url) {
 
   return img;
 };
+
+module.exports = Images;

lib/network/Network.js

@@ -1,3 +1,20 @@
+var Emitter = require('emitter-component');
+var Hammer = require('hammerjs');
+var mousetrap = require('mousetrap');
+var util = require('../util');
+var DataSet = require('../DataSet');
+var DataView = require('../DataView');
+var dotparser = require('./dotparser');
+var Groups = require('./Groups');
+var Images = require('./Images');
+var Node = require('./Node');
+var Edge = require('./Edge');
+var Popup = require('./Popup');
+var MixinLoader = require('./mixins/MixinLoader');
+
+// Load custom shapes into CanvasRenderingContext2D
+require('./shapes');
+
 /**
  * @constructor Network
  * Create a network visualization, displaying nodes and edges.
@@ -495,7 +512,7 @@ Network.prototype.setData = function(data, disableStart) {
   if (data && data.dot) {
     // parse DOT file
     if(data && data.dot) {
-      var dotData = vis.util.DOTToGraph(data.dot);
+      var dotData = dotparser.DOTToGraph(data.dot);
       this.setData(dotData);
       return;
     }
@@ -874,8 +891,8 @@ Network.prototype._createKeyBinds = function() {
  */
 Network.prototype._getPointer = function (touch) {
   return {
-    x: touch.pageX - vis.util.getAbsoluteLeft(this.frame.canvas),
-    y: touch.pageY - vis.util.getAbsoluteTop(this.frame.canvas)
+    x: touch.pageX - util.getAbsoluteLeft(this.frame.canvas),
+    y: touch.pageY - util.getAbsoluteTop(this.frame.canvas)
   };
 };
 
@@ -2232,9 +2249,9 @@ Network.prototype._createBezierNodes = function() {
  * @private
  */
 Network.prototype._initializeMixinLoaders = function () {
-  for (var mixinFunction in networkMixinLoaders) {
-    if (networkMixinLoaders.hasOwnProperty(mixinFunction)) {
-      Network.prototype[mixinFunction] = networkMixinLoaders[mixinFunction];
+  for (var mixin in MixinLoader) {
+    if (MixinLoader.hasOwnProperty(mixin)) {
+      Network.prototype[mixin] = MixinLoader[mixin];
     }
   }
 };
@@ -2289,11 +2306,4 @@ Network.prototype.focusOnNode = function (nodeId, zoomLevel) {
   }
 };
 
-
-
-
-
-
-
-
-
+module.exports = Network;

lib/network/Node.js

@@ -1,3 +1,5 @@
+var util = require('../util');
+
 /**
  * @class Node
  * A node. A node can be connected to other nodes via one or multiple edges.
@@ -967,3 +969,4 @@ Node.prototype.updateVelocity = function(massBeforeClustering) {
   this.vy = Math.sqrt(energyBefore/this.mass);
 };
 
+module.exports = Node;

lib/network/Popup.js

@@ -130,3 +130,5 @@ Popup.prototype.show = function (show) {
 Popup.prototype.hide = function () {
   this.frame.style.visibility = "hidden";
 };
+
+module.exports = Popup;

lib/network/mixins/HierarchicalLayoutMixin.js

@@ -0,0 +1,304 @@
+exports._resetLevels = function() {
+  for (var nodeId in this.nodes) {
+    if (this.nodes.hasOwnProperty(nodeId)) {
+      var node = this.nodes[nodeId];
+      if (node.preassignedLevel == false) {
+        node.level = -1;
+      }
+    }
+  }
+};
+
+/**
+ * This is the main function to layout the nodes in a hierarchical way.
+ * It checks if the node details are supplied correctly
+ *
+ * @private
+ */
+exports._setupHierarchicalLayout = function() {
+  if (this.constants.hierarchicalLayout.enabled == true && this.nodeIndices.length > 0) {
+    if (this.constants.hierarchicalLayout.direction == "RL" || this.constants.hierarchicalLayout.direction == "DU") {
+      this.constants.hierarchicalLayout.levelSeparation *= -1;
+    }
+    else {
+      this.constants.hierarchicalLayout.levelSeparation = Math.abs(this.constants.hierarchicalLayout.levelSeparation);
+    }
+    // get the size of the largest hubs and check if the user has defined a level for a node.
+    var hubsize = 0;
+    var node, nodeId;
+    var definedLevel = false;
+    var undefinedLevel = false;
+
+    for (nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        node = this.nodes[nodeId];
+        if (node.level != -1) {
+          definedLevel = true;
+        }
+        else {
+          undefinedLevel = true;
+        }
+        if (hubsize < node.edges.length) {
+          hubsize = node.edges.length;
+        }
+      }
+    }
+
+    // if the user defined some levels but not all, alert and run without hierarchical layout
+    if (undefinedLevel == true && definedLevel == true) {
+      alert("To use the hierarchical layout, nodes require either no predefined levels or levels have to be defined for all nodes.");
+      this.zoomExtent(true,this.constants.clustering.enabled);
+      if (!this.constants.clustering.enabled) {
+        this.start();
+      }
+    }
+    else {
+      // setup the system to use hierarchical method.
+      this._changeConstants();
+
+      // define levels if undefined by the users. Based on hubsize
+      if (undefinedLevel == true) {
+        this._determineLevels(hubsize);
+      }
+      // check the distribution of the nodes per level.
+      var distribution = this._getDistribution();
+
+      // place the nodes on the canvas. This also stablilizes the system.
+      this._placeNodesByHierarchy(distribution);
+
+      // start the simulation.
+      this.start();
+    }
+  }
+};
+
+
+/**
+ * This function places the nodes on the canvas based on the hierarchial distribution.
+ *
+ * @param {Object} distribution | obtained by the function this._getDistribution()
+ * @private
+ */
+exports._placeNodesByHierarchy = function(distribution) {
+  var nodeId, node;
+
+  // start placing all the level 0 nodes first. Then recursively position their branches.
+  for (nodeId in distribution[0].nodes) {
+    if (distribution[0].nodes.hasOwnProperty(nodeId)) {
+      node = distribution[0].nodes[nodeId];
+      if (this.constants.hierarchicalLayout.direction == "UD" || this.constants.hierarchicalLayout.direction == "DU") {
+        if (node.xFixed) {
+          node.x = distribution[0].minPos;
+          node.xFixed = false;
+
+          distribution[0].minPos += distribution[0].nodeSpacing;
+        }
+      }
+      else {
+        if (node.yFixed) {
+          node.y = distribution[0].minPos;
+          node.yFixed = false;
+
+          distribution[0].minPos += distribution[0].nodeSpacing;
+        }
+      }
+      this._placeBranchNodes(node.edges,node.id,distribution,node.level);
+    }
+  }
+
+  // stabilize the system after positioning. This function calls zoomExtent.
+  this._stabilize();
+};
+
+
+/**
+ * This function get the distribution of levels based on hubsize
+ *
+ * @returns {Object}
+ * @private
+ */
+exports._getDistribution = function() {
+  var distribution = {};
+  var nodeId, node, level;
+
+  // we fix Y because the hierarchy is vertical, we fix X so we do not give a node an x position for a second time.
+  // the fix of X is removed after the x value has been set.
+  for (nodeId in this.nodes) {
+    if (this.nodes.hasOwnProperty(nodeId)) {
+      node = this.nodes[nodeId];
+      node.xFixed = true;
+      node.yFixed = true;
+      if (this.constants.hierarchicalLayout.direction == "UD" || this.constants.hierarchicalLayout.direction == "DU") {
+        node.y = this.constants.hierarchicalLayout.levelSeparation*node.level;
+      }
+      else {
+        node.x = this.constants.hierarchicalLayout.levelSeparation*node.level;
+      }
+      if (!distribution.hasOwnProperty(node.level)) {
+        distribution[node.level] = {amount: 0, nodes: {}, minPos:0, nodeSpacing:0};
+      }
+      distribution[node.level].amount += 1;
+      distribution[node.level].nodes[node.id] = node;
+    }
+  }
+
+  // determine the largest amount of nodes of all levels
+  var maxCount = 0;
+  for (level in distribution) {
+    if (distribution.hasOwnProperty(level)) {
+      if (maxCount < distribution[level].amount) {
+        maxCount = distribution[level].amount;
+      }
+    }
+  }
+
+  // set the initial position and spacing of each nodes accordingly
+  for (level in distribution) {
+    if (distribution.hasOwnProperty(level)) {
+      distribution[level].nodeSpacing = (maxCount + 1) * this.constants.hierarchicalLayout.nodeSpacing;
+      distribution[level].nodeSpacing /= (distribution[level].amount + 1);
+      distribution[level].minPos = distribution[level].nodeSpacing - (0.5 * (distribution[level].amount + 1) * distribution[level].nodeSpacing);
+    }
+  }
+
+  return distribution;
+};
+
+
+/**
+ * this function allocates nodes in levels based on the recursive branching from the largest hubs.
+ *
+ * @param hubsize
+ * @private
+ */
+exports._determineLevels = function(hubsize) {
+  var nodeId, node;
+
+  // determine hubs
+  for (nodeId in this.nodes) {
+    if (this.nodes.hasOwnProperty(nodeId)) {
+      node = this.nodes[nodeId];
+      if (node.edges.length == hubsize) {
+        node.level = 0;
+      }
+    }
+  }
+
+  // branch from hubs
+  for (nodeId in this.nodes) {
+    if (this.nodes.hasOwnProperty(nodeId)) {
+      node = this.nodes[nodeId];
+      if (node.level == 0) {
+        this._setLevel(1,node.edges,node.id);
+      }
+    }
+  }
+};
+
+
+/**
+ * Since hierarchical layout does not support:
+ *    - smooth curves (based on the physics),
+ *    - clustering (based on dynamic node counts)
+ *
+ * We disable both features so there will be no problems.
+ *
+ * @private
+ */
+exports._changeConstants = function() {
+  this.constants.clustering.enabled = false;
+  this.constants.physics.barnesHut.enabled = false;
+  this.constants.physics.hierarchicalRepulsion.enabled = true;
+  this._loadSelectedForceSolver();
+  this.constants.smoothCurves = false;
+  this._configureSmoothCurves();
+};
+
+
+/**
+ * This is a recursively called function to enumerate the branches from the largest hubs and place the nodes
+ * on a X position that ensures there will be no overlap.
+ *
+ * @param edges
+ * @param parentId
+ * @param distribution
+ * @param parentLevel
+ * @private
+ */
+exports._placeBranchNodes = function(edges, parentId, distribution, parentLevel) {
+  for (var i = 0; i < edges.length; i++) {
+    var childNode = null;
+    if (edges[i].toId == parentId) {
+      childNode = edges[i].from;
+    }
+    else {
+      childNode = edges[i].to;
+    }
+
+    // if a node is conneceted to another node on the same level (or higher (means lower level))!, this is not handled here.
+    var nodeMoved = false;
+    if (this.constants.hierarchicalLayout.direction == "UD" || this.constants.hierarchicalLayout.direction == "DU") {
+      if (childNode.xFixed && childNode.level > parentLevel) {
+        childNode.xFixed = false;
+        childNode.x = distribution[childNode.level].minPos;
+        nodeMoved = true;
+      }
+    }
+    else {
+      if (childNode.yFixed && childNode.level > parentLevel) {
+        childNode.yFixed = false;
+        childNode.y = distribution[childNode.level].minPos;
+        nodeMoved = true;
+      }
+    }
+
+    if (nodeMoved == true) {
+      distribution[childNode.level].minPos += distribution[childNode.level].nodeSpacing;
+      if (childNode.edges.length > 1) {
+        this._placeBranchNodes(childNode.edges,childNode.id,distribution,childNode.level);
+      }
+    }
+  }
+};
+
+
+/**
+ * this function is called recursively to enumerate the barnches of the largest hubs and give each node a level.
+ *
+ * @param level
+ * @param edges
+ * @param parentId
+ * @private
+ */
+exports._setLevel = function(level, edges, parentId) {
+  for (var i = 0; i < edges.length; i++) {
+    var childNode = null;
+    if (edges[i].toId == parentId) {
+      childNode = edges[i].from;
+    }
+    else {
+      childNode = edges[i].to;
+    }
+    if (childNode.level == -1 || childNode.level > level) {
+      childNode.level = level;
+      if (edges.length > 1) {
+        this._setLevel(level+1, childNode.edges, childNode.id);
+      }
+    }
+  }
+};
+
+
+/**
+ * Unfix nodes
+ *
+ * @private
+ */
+exports._restoreNodes = function() {
+  for (var nodeId in this.nodes) {
+    if (this.nodes.hasOwnProperty(nodeId)) {
+      this.nodes[nodeId].xFixed = false;
+      this.nodes[nodeId].yFixed = false;
+    }
+  }
+};

lib/network/mixins/ManipulationMixin.js

@@ -0,0 +1,571 @@
+var util = require('../../util');
+
+/**
+ * clears the toolbar div element of children
+ *
+ * @private
+ */
+exports._clearManipulatorBar = function() {
+  while (this.manipulationDiv.hasChildNodes()) {
+    this.manipulationDiv.removeChild(this.manipulationDiv.firstChild);
+  }
+};
+
+/**
+ * Manipulation UI temporarily overloads certain functions to extend or replace them. To be able to restore
+ * these functions to their original functionality, we saved them in this.cachedFunctions.
+ * This function restores these functions to their original function.
+ *
+ * @private
+ */
+exports._restoreOverloadedFunctions = function() {
+  for (var functionName in this.cachedFunctions) {
+    if (this.cachedFunctions.hasOwnProperty(functionName)) {
+      this[functionName] = this.cachedFunctions[functionName];
+    }
+  }
+};
+
+/**
+ * Enable or disable edit-mode.
+ *
+ * @private
+ */
+exports._toggleEditMode = function() {
+  this.editMode = !this.editMode;
+  var toolbar = document.getElementById("network-manipulationDiv");
+  var closeDiv = document.getElementById("network-manipulation-closeDiv");
+  var editModeDiv = document.getElementById("network-manipulation-editMode");
+  if (this.editMode == true) {
+    toolbar.style.display="block";
+    closeDiv.style.display="block";
+    editModeDiv.style.display="none";
+    closeDiv.onclick = this._toggleEditMode.bind(this);
+  }
+  else {
+    toolbar.style.display="none";
+    closeDiv.style.display="none";
+    editModeDiv.style.display="block";
+    closeDiv.onclick = null;
+  }
+  this._createManipulatorBar()
+};
+
+/**
+ * main function, creates the main toolbar. Removes functions bound to the select event. Binds all the buttons of the toolbar.
+ *
+ * @private
+ */
+exports._createManipulatorBar = function() {
+  // remove bound functions
+  if (this.boundFunction) {
+    this.off('select', this.boundFunction);
+  }
+  if (this.edgeBeingEdited !== undefined) {
+    this.edgeBeingEdited._disableControlNodes();
+    this.edgeBeingEdited = undefined;
+    this.selectedControlNode = null;
+  }
+
+  // restore overloaded functions
+  this._restoreOverloadedFunctions();
+
+  // resume calculation
+  this.freezeSimulation = false;
+
+  // reset global variables
+  this.blockConnectingEdgeSelection = false;
+  this.forceAppendSelection = false;
+
+  if (this.editMode == true) {
+    while (this.manipulationDiv.hasChildNodes()) {
+      this.manipulationDiv.removeChild(this.manipulationDiv.firstChild);
+    }
+    // add the icons to the manipulator div
+    this.manipulationDiv.innerHTML = "" +
+      "<span class='network-manipulationUI add' id='network-manipulate-addNode'>" +
+        "<span class='network-manipulationLabel'>"+this.constants.labels['add'] +"</span></span>" +
+      "<div class='network-seperatorLine'></div>" +
+      "<span class='network-manipulationUI connect' id='network-manipulate-connectNode'>" +
+        "<span class='network-manipulationLabel'>"+this.constants.labels['link'] +"</span></span>";
+    if (this._getSelectedNodeCount() == 1 && this.triggerFunctions.edit) {
+      this.manipulationDiv.innerHTML += "" +
+        "<div class='network-seperatorLine'></div>" +
+        "<span class='network-manipulationUI edit' id='network-manipulate-editNode'>" +
+          "<span class='network-manipulationLabel'>"+this.constants.labels['editNode'] +"</span></span>";
+    }
+    else if (this._getSelectedEdgeCount() == 1 && this._getSelectedNodeCount() == 0) {
+      this.manipulationDiv.innerHTML += "" +
+        "<div class='network-seperatorLine'></div>" +
+        "<span class='network-manipulationUI edit' id='network-manipulate-editEdge'>" +
+        "<span class='network-manipulationLabel'>"+this.constants.labels['editEdge'] +"</span></span>";
+    }
+    if (this._selectionIsEmpty() == false) {
+      this.manipulationDiv.innerHTML += "" +
+        "<div class='network-seperatorLine'></div>" +
+        "<span class='network-manipulationUI delete' id='network-manipulate-delete'>" +
+          "<span class='network-manipulationLabel'>"+this.constants.labels['del'] +"</span></span>";
+    }
+
+
+    // bind the icons
+    var addNodeButton = document.getElementById("network-manipulate-addNode");
+    addNodeButton.onclick = this._createAddNodeToolbar.bind(this);
+    var addEdgeButton = document.getElementById("network-manipulate-connectNode");
+    addEdgeButton.onclick = this._createAddEdgeToolbar.bind(this);
+    if (this._getSelectedNodeCount() == 1 && this.triggerFunctions.edit) {
+      var editButton = document.getElementById("network-manipulate-editNode");
+      editButton.onclick = this._editNode.bind(this);
+    }
+    else if (this._getSelectedEdgeCount() == 1 && this._getSelectedNodeCount() == 0) {
+      var editButton = document.getElementById("network-manipulate-editEdge");
+      editButton.onclick = this._createEditEdgeToolbar.bind(this);
+    }
+    if (this._selectionIsEmpty() == false) {
+      var deleteButton = document.getElementById("network-manipulate-delete");
+      deleteButton.onclick = this._deleteSelected.bind(this);
+    }
+    var closeDiv = document.getElementById("network-manipulation-closeDiv");
+    closeDiv.onclick = this._toggleEditMode.bind(this);
+
+    this.boundFunction = this._createManipulatorBar.bind(this);
+    this.on('select', this.boundFunction);
+  }
+  else {
+    this.editModeDiv.innerHTML = "" +
+      "<span class='network-manipulationUI edit editmode' id='network-manipulate-editModeButton'>" +
+      "<span class='network-manipulationLabel'>" + this.constants.labels['edit'] + "</span></span>";
+    var editModeButton = document.getElementById("network-manipulate-editModeButton");
+    editModeButton.onclick = this._toggleEditMode.bind(this);
+  }
+};
+
+
+
+/**
+ * Create the toolbar for adding Nodes
+ *
+ * @private
+ */
+exports._createAddNodeToolbar = function() {
+  // clear the toolbar
+  this._clearManipulatorBar();
+  if (this.boundFunction) {
+    this.off('select', this.boundFunction);
+  }
+
+  // create the toolbar contents
+  this.manipulationDiv.innerHTML = "" +
+    "<span class='network-manipulationUI back' id='network-manipulate-back'>" +
+    "<span class='network-manipulationLabel'>" + this.constants.labels['back'] + " </span></span>" +
+    "<div class='network-seperatorLine'></div>" +
+    "<span class='network-manipulationUI none' id='network-manipulate-back'>" +
+    "<span id='network-manipulatorLabel' class='network-manipulationLabel'>" + this.constants.labels['addDescription'] + "</span></span>";
+
+  // bind the icon
+  var backButton = document.getElementById("network-manipulate-back");
+  backButton.onclick = this._createManipulatorBar.bind(this);
+
+  // we use the boundFunction so we can reference it when we unbind it from the "select" event.
+  this.boundFunction = this._addNode.bind(this);
+  this.on('select', this.boundFunction);
+};
+
+
+/**
+ * create the toolbar to connect nodes
+ *
+ * @private
+ */
+exports._createAddEdgeToolbar = function() {
+  // clear the toolbar
+  this._clearManipulatorBar();
+  this._unselectAll(true);
+  this.freezeSimulation = true;
+
+  if (this.boundFunction) {
+    this.off('select', this.boundFunction);
+  }
+
+  this._unselectAll();
+  this.forceAppendSelection = false;
+  this.blockConnectingEdgeSelection = true;
+
+  this.manipulationDiv.innerHTML = "" +
+    "<span class='network-manipulationUI back' id='network-manipulate-back'>" +
+      "<span class='network-manipulationLabel'>" + this.constants.labels['back'] + " </span></span>" +
+    "<div class='network-seperatorLine'></div>" +
+    "<span class='network-manipulationUI none' id='network-manipulate-back'>" +
+      "<span id='network-manipulatorLabel' class='network-manipulationLabel'>" + this.constants.labels['linkDescription'] + "</span></span>";
+
+  // bind the icon
+  var backButton = document.getElementById("network-manipulate-back");
+  backButton.onclick = this._createManipulatorBar.bind(this);
+
+  // we use the boundFunction so we can reference it when we unbind it from the "select" event.
+  this.boundFunction = this._handleConnect.bind(this);
+  this.on('select', this.boundFunction);
+
+  // temporarily overload functions
+  this.cachedFunctions["_handleTouch"] = this._handleTouch;
+  this.cachedFunctions["_handleOnRelease"] = this._handleOnRelease;
+  this._handleTouch = this._handleConnect;
+  this._handleOnRelease = this._finishConnect;
+
+  // redraw to show the unselect
+  this._redraw();
+};
+
+/**
+ * create the toolbar to edit edges
+ *
+ * @private
+ */
+exports._createEditEdgeToolbar = function() {
+  // clear the toolbar
+  this._clearManipulatorBar();
+
+  if (this.boundFunction) {
+    this.off('select', this.boundFunction);
+  }
+
+  this.edgeBeingEdited = this._getSelectedEdge();
+  this.edgeBeingEdited._enableControlNodes();
+
+  this.manipulationDiv.innerHTML = "" +
+    "<span class='network-manipulationUI back' id='network-manipulate-back'>" +
+    "<span class='network-manipulationLabel'>" + this.constants.labels['back'] + " </span></span>" +
+    "<div class='network-seperatorLine'></div>" +
+    "<span class='network-manipulationUI none' id='network-manipulate-back'>" +
+    "<span id='network-manipulatorLabel' class='network-manipulationLabel'>" + this.constants.labels['editEdgeDescription'] + "</span></span>";
+
+  // bind the icon
+  var backButton = document.getElementById("network-manipulate-back");
+  backButton.onclick = this._createManipulatorBar.bind(this);
+
+  // temporarily overload functions
+  this.cachedFunctions["_handleTouch"]      = this._handleTouch;
+  this.cachedFunctions["_handleOnRelease"]  = this._handleOnRelease;
+  this.cachedFunctions["_handleTap"]        = this._handleTap;
+  this.cachedFunctions["_handleDragStart"]  = this._handleDragStart;
+  this.cachedFunctions["_handleOnDrag"]     = this._handleOnDrag;
+  this._handleTouch     = this._selectControlNode;
+  this._handleTap       = function () {};
+  this._handleOnDrag    = this._controlNodeDrag;
+  this._handleDragStart = function () {}
+  this._handleOnRelease = this._releaseControlNode;
+
+  // redraw to show the unselect
+  this._redraw();
+};
+
+
+
+
+
+/**
+ * the function bound to the selection event. It checks if you want to connect a cluster and changes the description
+ * to walk the user through the process.
+ *
+ * @private
+ */
+exports._selectControlNode = function(pointer) {
+  this.edgeBeingEdited.controlNodes.from.unselect();
+  this.edgeBeingEdited.controlNodes.to.unselect();
+  this.selectedControlNode = this.edgeBeingEdited._getSelectedControlNode(this._XconvertDOMtoCanvas(pointer.x),this._YconvertDOMtoCanvas(pointer.y));
+  if (this.selectedControlNode !== null) {
+    this.selectedControlNode.select();
+    this.freezeSimulation = true;
+  }
+  this._redraw();
+};
+
+/**
+ * the function bound to the selection event. It checks if you want to connect a cluster and changes the description
+ * to walk the user through the process.
+ *
+ * @private
+ */
+exports._controlNodeDrag = function(event) {
+  var pointer = this._getPointer(event.gesture.center);
+  if (this.selectedControlNode !== null && this.selectedControlNode !== undefined) {
+    this.selectedControlNode.x = this._XconvertDOMtoCanvas(pointer.x);
+    this.selectedControlNode.y = this._YconvertDOMtoCanvas(pointer.y);
+  }
+  this._redraw();
+};
+
+exports._releaseControlNode = function(pointer) {
+  var newNode = this._getNodeAt(pointer);
+  if (newNode != null) {
+    if (this.edgeBeingEdited.controlNodes.from.selected == true) {
+      this._editEdge(newNode.id, this.edgeBeingEdited.to.id);
+      this.edgeBeingEdited.controlNodes.from.unselect();
+    }
+    if (this.edgeBeingEdited.controlNodes.to.selected == true) {
+      this._editEdge(this.edgeBeingEdited.from.id, newNode.id);
+      this.edgeBeingEdited.controlNodes.to.unselect();
+    }
+  }
+  else {
+    this.edgeBeingEdited._restoreControlNodes();
+  }
+  this.freezeSimulation = false;
+  this._redraw();
+};
+
+/**
+ * the function bound to the selection event. It checks if you want to connect a cluster and changes the description
+ * to walk the user through the process.
+ *
+ * @private
+ */
+exports._handleConnect = function(pointer) {
+  if (this._getSelectedNodeCount() == 0) {
+    var node = this._getNodeAt(pointer);
+    if (node != null) {
+      if (node.clusterSize > 1) {
+        alert("Cannot create edges to a cluster.")
+      }
+      else {
+        this._selectObject(node,false);
+        // create a node the temporary line can look at
+        this.sectors['support']['nodes']['targetNode'] = new Node({id:'targetNode'},{},{},this.constants);
+        this.sectors['support']['nodes']['targetNode'].x = node.x;
+        this.sectors['support']['nodes']['targetNode'].y = node.y;
+        this.sectors['support']['nodes']['targetViaNode'] = new Node({id:'targetViaNode'},{},{},this.constants);
+        this.sectors['support']['nodes']['targetViaNode'].x = node.x;
+        this.sectors['support']['nodes']['targetViaNode'].y = node.y;
+        this.sectors['support']['nodes']['targetViaNode'].parentEdgeId = "connectionEdge";
+
+        // create a temporary edge
+        this.edges['connectionEdge'] = new Edge({id:"connectionEdge",from:node.id,to:this.sectors['support']['nodes']['targetNode'].id}, this, this.constants);
+        this.edges['connectionEdge'].from = node;
+        this.edges['connectionEdge'].connected = true;
+        this.edges['connectionEdge'].smooth = true;
+        this.edges['connectionEdge'].selected = true;
+        this.edges['connectionEdge'].to = this.sectors['support']['nodes']['targetNode'];
+        this.edges['connectionEdge'].via = this.sectors['support']['nodes']['targetViaNode'];
+
+        this.cachedFunctions["_handleOnDrag"] = this._handleOnDrag;
+        this._handleOnDrag = function(event) {
+          var pointer = this._getPointer(event.gesture.center);
+          this.sectors['support']['nodes']['targetNode'].x = this._XconvertDOMtoCanvas(pointer.x);
+          this.sectors['support']['nodes']['targetNode'].y = this._YconvertDOMtoCanvas(pointer.y);
+          this.sectors['support']['nodes']['targetViaNode'].x = 0.5 * (this._XconvertDOMtoCanvas(pointer.x) + this.edges['connectionEdge'].from.x);
+          this.sectors['support']['nodes']['targetViaNode'].y = this._YconvertDOMtoCanvas(pointer.y);
+        };
+
+        this.moving = true;
+        this.start();
+      }
+    }
+  }
+};
+
+exports._finishConnect = function(pointer) {
+  if (this._getSelectedNodeCount() == 1) {
+
+    // restore the drag function
+    this._handleOnDrag = this.cachedFunctions["_handleOnDrag"];
+    delete this.cachedFunctions["_handleOnDrag"];
+
+    // remember the edge id
+    var connectFromId = this.edges['connectionEdge'].fromId;
+
+    // remove the temporary nodes and edge
+    delete this.edges['connectionEdge'];
+    delete this.sectors['support']['nodes']['targetNode'];
+    delete this.sectors['support']['nodes']['targetViaNode'];
+
+    var node = this._getNodeAt(pointer);
+    if (node != null) {
+      if (node.clusterSize > 1) {
+        alert("Cannot create edges to a cluster.")
+      }
+      else {
+        this._createEdge(connectFromId,node.id);
+        this._createManipulatorBar();
+      }
+    }
+    this._unselectAll();
+  }
+};
+
+
+/**
+ * Adds a node on the specified location
+ */
+exports._addNode = function() {
+  if (this._selectionIsEmpty() && this.editMode == true) {
+    var positionObject = this._pointerToPositionObject(this.pointerPosition);
+    var defaultData = {id:util.randomUUID(),x:positionObject.left,y:positionObject.top,label:"new",allowedToMoveX:true,allowedToMoveY:true};
+    if (this.triggerFunctions.add) {
+      if (this.triggerFunctions.add.length == 2) {
+        var me = this;
+        this.triggerFunctions.add(defaultData, function(finalizedData) {
+          me.nodesData.add(finalizedData);
+          me._createManipulatorBar();
+          me.moving = true;
+          me.start();
+        });
+      }
+      else {
+        alert(this.constants.labels['addError']);
+        this._createManipulatorBar();
+        this.moving = true;
+        this.start();
+      }
+    }
+    else {
+      this.nodesData.add(defaultData);
+      this._createManipulatorBar();
+      this.moving = true;
+      this.start();
+    }
+  }
+};
+
+
+/**
+ * connect two nodes with a new edge.
+ *
+ * @private
+ */
+exports._createEdge = function(sourceNodeId,targetNodeId) {
+  if (this.editMode == true) {
+    var defaultData = {from:sourceNodeId, to:targetNodeId};
+    if (this.triggerFunctions.connect) {
+      if (this.triggerFunctions.connect.length == 2) {
+        var me = this;
+        this.triggerFunctions.connect(defaultData, function(finalizedData) {
+          me.edgesData.add(finalizedData);
+          me.moving = true;
+          me.start();
+        });
+      }
+      else {
+        alert(this.constants.labels["linkError"]);
+        this.moving = true;
+        this.start();
+      }
+    }
+    else {
+      this.edgesData.add(defaultData);
+      this.moving = true;
+      this.start();
+    }
+  }
+};
+
+/**
+ * connect two nodes with a new edge.
+ *
+ * @private
+ */
+exports._editEdge = function(sourceNodeId,targetNodeId) {
+  if (this.editMode == true) {
+    var defaultData = {id: this.edgeBeingEdited.id, from:sourceNodeId, to:targetNodeId};
+    if (this.triggerFunctions.editEdge) {
+      if (this.triggerFunctions.editEdge.length == 2) {
+        var me = this;
+        this.triggerFunctions.editEdge(defaultData, function(finalizedData) {
+          me.edgesData.update(finalizedData);
+          me.moving = true;
+          me.start();
+        });
+      }
+      else {
+        alert(this.constants.labels["linkError"]);
+        this.moving = true;
+        this.start();
+      }
+    }
+    else {
+      this.edgesData.update(defaultData);
+      this.moving = true;
+      this.start();
+    }
+  }
+};
+
+/**
+ * Create the toolbar to edit the selected node. The label and the color can be changed. Other colors are derived from the chosen color.
+ *
+ * @private
+ */
+exports._editNode = function() {
+  if (this.triggerFunctions.edit && this.editMode == true) {
+    var node = this._getSelectedNode();
+    var data = {id:node.id,
+      label: node.label,
+      group: node.group,
+      shape: node.shape,
+      color: {
+        background:node.color.background,
+        border:node.color.border,
+        highlight: {
+          background:node.color.highlight.background,
+          border:node.color.highlight.border
+        }
+      }};
+    if (this.triggerFunctions.edit.length == 2) {
+      var me = this;
+      this.triggerFunctions.edit(data, function (finalizedData) {
+        me.nodesData.update(finalizedData);
+        me._createManipulatorBar();
+        me.moving = true;
+        me.start();
+      });
+    }
+    else {
+      alert(this.constants.labels["editError"]);
+    }
+  }
+  else {
+    alert(this.constants.labels["editBoundError"]);
+  }
+};
+
+
+
+
+/**
+ * delete everything in the selection
+ *
+ * @private
+ */
+exports._deleteSelected = function() {
+  if (!this._selectionIsEmpty() && this.editMode == true) {
+    if (!this._clusterInSelection()) {
+      var selectedNodes = this.getSelectedNodes();
+      var selectedEdges = this.getSelectedEdges();
+      if (this.triggerFunctions.del) {
+        var me = this;
+        var data = {nodes: selectedNodes, edges: selectedEdges};
+        if (this.triggerFunctions.del.length = 2) {
+          this.triggerFunctions.del(data, function (finalizedData) {
+            me.edgesData.remove(finalizedData.edges);
+            me.nodesData.remove(finalizedData.nodes);
+            me._unselectAll();
+            me.moving = true;
+            me.start();
+          });
+        }
+        else {
+          alert(this.constants.labels["deleteError"])
+        }
+      }
+      else {
+        this.edgesData.remove(selectedEdges);
+        this.nodesData.remove(selectedNodes);
+        this._unselectAll();
+        this.moving = true;
+        this.start();
+      }
+    }
+    else {
+      alert(this.constants.labels["deleteClusterError"]);
+    }
+  }
+};

lib/network/mixins/MixinLoader.js

@@ -0,0 +1,198 @@
+var PhysicsMixin = require('./physics/PhysicsMixin');
+var ClusterMixin = require('./ClusterMixin');
+var SectorsMixin = require('./SectorsMixin');
+var SelectionMixin = require('./SelectionMixin');
+var ManipulationMixin = require('./ManipulationMixin');
+var NavigationMixin = require('./NavigationMixin');
+var HierarchicalLayoutMixin = require('./HierarchicalLayoutMixin');
+
+/**
+ * Load a mixin into the network object
+ *
+ * @param {Object} sourceVariable | this object has to contain functions.
+ * @private
+ */
+exports._loadMixin = function (sourceVariable) {
+  for (var mixinFunction in sourceVariable) {
+    if (sourceVariable.hasOwnProperty(mixinFunction)) {
+      this[mixinFunction] = sourceVariable[mixinFunction];
+    }
+  }
+};
+
+
+/**
+ * removes a mixin from the network object.
+ *
+ * @param {Object} sourceVariable | this object has to contain functions.
+ * @private
+ */
+exports._clearMixin = function (sourceVariable) {
+  for (var mixinFunction in sourceVariable) {
+    if (sourceVariable.hasOwnProperty(mixinFunction)) {
+      this[mixinFunction] = undefined;
+    }
+  }
+};
+
+
+/**
+ * Mixin the physics system and initialize the parameters required.
+ *
+ * @private
+ */
+exports._loadPhysicsSystem = function () {
+  this._loadMixin(PhysicsMixin);
+  this._loadSelectedForceSolver();
+  if (this.constants.configurePhysics == true) {
+    this._loadPhysicsConfiguration();
+  }
+};
+
+
+/**
+ * Mixin the cluster system and initialize the parameters required.
+ *
+ * @private
+ */
+exports._loadClusterSystem = function () {
+  this.clusterSession = 0;
+  this.hubThreshold = 5;
+  this._loadMixin(ClusterMixin);
+};
+
+
+/**
+ * Mixin the sector system and initialize the parameters required
+ *
+ * @private
+ */
+exports._loadSectorSystem = function () {
+  this.sectors = {};
+  this.activeSector = ["default"];
+  this.sectors["active"] = {};
+  this.sectors["active"]["default"] = {"nodes": {},
+    "edges": {},
+    "nodeIndices": [],
+    "formationScale": 1.0,
+    "drawingNode": undefined };
+  this.sectors["frozen"] = {};
+  this.sectors["support"] = {"nodes": {},
+    "edges": {},
+    "nodeIndices": [],
+    "formationScale": 1.0,
+    "drawingNode": undefined };
+
+  this.nodeIndices = this.sectors["active"]["default"]["nodeIndices"];  // the node indices list is used to speed up the computation of the repulsion fields
+
+  this._loadMixin(SectorsMixin);
+};
+
+
+/**
+ * Mixin the selection system and initialize the parameters required
+ *
+ * @private
+ */
+exports._loadSelectionSystem = function () {
+  this.selectionObj = {nodes: {}, edges: {}};
+
+  this._loadMixin(SelectionMixin);
+};
+
+
+/**
+ * Mixin the navigationUI (User Interface) system and initialize the parameters required
+ *
+ * @private
+ */
+exports._loadManipulationSystem = function () {
+  // reset global variables -- these are used by the selection of nodes and edges.
+  this.blockConnectingEdgeSelection = false;
+  this.forceAppendSelection = false;
+
+  if (this.constants.dataManipulation.enabled == true) {
+    // load the manipulator HTML elements. All styling done in css.
+    if (this.manipulationDiv === undefined) {
+      this.manipulationDiv = document.createElement('div');
+      this.manipulationDiv.className = 'network-manipulationDiv';
+      this.manipulationDiv.id = 'network-manipulationDiv';
+      if (this.editMode == true) {
+        this.manipulationDiv.style.display = "block";
+      }
+      else {
+        this.manipulationDiv.style.display = "none";
+      }
+      this.containerElement.insertBefore(this.manipulationDiv, this.frame);
+    }
+
+    if (this.editModeDiv === undefined) {
+      this.editModeDiv = document.createElement('div');
+      this.editModeDiv.className = 'network-manipulation-editMode';
+      this.editModeDiv.id = 'network-manipulation-editMode';
+      if (this.editMode == true) {
+        this.editModeDiv.style.display = "none";
+      }
+      else {
+        this.editModeDiv.style.display = "block";
+      }
+      this.containerElement.insertBefore(this.editModeDiv, this.frame);
+    }
+
+    if (this.closeDiv === undefined) {
+      this.closeDiv = document.createElement('div');
+      this.closeDiv.className = 'network-manipulation-closeDiv';
+      this.closeDiv.id = 'network-manipulation-closeDiv';
+      this.closeDiv.style.display = this.manipulationDiv.style.display;
+      this.containerElement.insertBefore(this.closeDiv, this.frame);
+    }
+
+    // load the manipulation functions
+    this._loadMixin(ManipulationMixin);
+
+    // create the manipulator toolbar
+    this._createManipulatorBar();
+  }
+  else {
+    if (this.manipulationDiv !== undefined) {
+      // removes all the bindings and overloads
+      this._createManipulatorBar();
+      // remove the manipulation divs
+      this.containerElement.removeChild(this.manipulationDiv);
+      this.containerElement.removeChild(this.editModeDiv);
+      this.containerElement.removeChild(this.closeDiv);
+
+      this.manipulationDiv = undefined;
+      this.editModeDiv = undefined;
+      this.closeDiv = undefined;
+      // remove the mixin functions
+      this._clearMixin(ManipulationMixin);
+    }
+  }
+};
+
+
+/**
+ * Mixin the navigation (User Interface) system and initialize the parameters required
+ *
+ * @private
+ */
+exports._loadNavigationControls = function () {
+  this._loadMixin(NavigationMixin);
+
+  // the clean function removes the button divs, this is done to remove the bindings.
+  this._cleanNavigation();
+  if (this.constants.navigation.enabled == true) {
+    this._loadNavigationElements();
+  }
+};
+
+
+/**
+ * Mixin the hierarchical layout system.
+ *
+ * @private
+ */
+exports._loadHierarchySystem = function () {
+  this._loadMixin(HierarchicalLayoutMixin);
+};

lib/network/mixins/NavigationMixin.js

@@ -0,0 +1,196 @@
+exports._cleanNavigation = function() {
+  // clean up previous navigation items
+  var wrapper = document.getElementById('network-navigation_wrapper');
+  if (wrapper != null) {
+    this.containerElement.removeChild(wrapper);
+  }
+  document.onmouseup = null;
+};
+
+/**
+ * Creation of the navigation controls nodes. They are drawn over the rest of the nodes and are not affected by scale and translation
+ * they have a triggerFunction which is called on click. If the position of the navigation controls is dependent
+ * on this.frame.canvas.clientWidth or this.frame.canvas.clientHeight, we flag horizontalAlignLeft and verticalAlignTop false.
+ * This means that the location will be corrected by the _relocateNavigation function on a size change of the canvas.
+ *
+ * @private
+ */
+exports._loadNavigationElements = function() {
+  this._cleanNavigation();
+
+  this.navigationDivs = {};
+  var navigationDivs = ['up','down','left','right','zoomIn','zoomOut','zoomExtends'];
+  var navigationDivActions = ['_moveUp','_moveDown','_moveLeft','_moveRight','_zoomIn','_zoomOut','zoomExtent'];
+
+  this.navigationDivs['wrapper'] = document.createElement('div');
+  this.navigationDivs['wrapper'].id = "network-navigation_wrapper";
+  this.navigationDivs['wrapper'].style.position = "absolute";
+  this.navigationDivs['wrapper'].style.width = this.frame.canvas.clientWidth + "px";
+  this.navigationDivs['wrapper'].style.height = this.frame.canvas.clientHeight + "px";
+  this.containerElement.insertBefore(this.navigationDivs['wrapper'],this.frame);
+
+  for (var i = 0; i < navigationDivs.length; i++) {
+    this.navigationDivs[navigationDivs[i]] = document.createElement('div');
+    this.navigationDivs[navigationDivs[i]].id = "network-navigation_" + navigationDivs[i];
+    this.navigationDivs[navigationDivs[i]].className = "network-navigation " + navigationDivs[i];
+    this.navigationDivs['wrapper'].appendChild(this.navigationDivs[navigationDivs[i]]);
+    this.navigationDivs[navigationDivs[i]].onmousedown = this[navigationDivActions[i]].bind(this);
+  }
+
+  document.onmouseup = this._stopMovement.bind(this);
+};
+
+/**
+ * this stops all movement induced by the navigation buttons
+ *
+ * @private
+ */
+exports._stopMovement = function() {
+  this._xStopMoving();
+  this._yStopMoving();
+  this._stopZoom();
+};
+
+
+/**
+ * stops the actions performed by page up and down etc.
+ *
+ * @param event
+ * @private
+ */
+exports._preventDefault = function(event) {
+  if (event !== undefined) {
+    if (event.preventDefault) {
+      event.preventDefault();
+    } else {
+      event.returnValue = false;
+    }
+  }
+};
+
+
+/**
+ * move the screen up
+ * By using the increments, instead of adding a fixed number to the translation, we keep fluent and
+ * instant movement. The onKeypress event triggers immediately, then pauses, then triggers frequently
+ * To avoid this behaviour, we do the translation in the start loop.
+ *
+ * @private
+ */
+exports._moveUp = function(event) {
+  this.yIncrement = this.constants.keyboard.speed.y;
+  this.start(); // if there is no node movement, the calculation wont be done
+  this._preventDefault(event);
+  if (this.navigationDivs) {
+    this.navigationDivs['up'].className += " active";
+  }
+};
+
+
+/**
+ * move the screen down
+ * @private
+ */
+exports._moveDown = function(event) {
+  this.yIncrement = -this.constants.keyboard.speed.y;
+  this.start(); // if there is no node movement, the calculation wont be done
+  this._preventDefault(event);
+  if (this.navigationDivs) {
+    this.navigationDivs['down'].className += " active";
+  }
+};
+
+
+/**
+ * move the screen left
+ * @private
+ */
+exports._moveLeft = function(event) {
+  this.xIncrement = this.constants.keyboard.speed.x;
+  this.start(); // if there is no node movement, the calculation wont be done
+  this._preventDefault(event);
+  if (this.navigationDivs) {
+    this.navigationDivs['left'].className += " active";
+  }
+};
+
+
+/**
+ * move the screen right
+ * @private
+ */
+exports._moveRight = function(event) {
+  this.xIncrement = -this.constants.keyboard.speed.y;
+  this.start(); // if there is no node movement, the calculation wont be done
+  this._preventDefault(event);
+  if (this.navigationDivs) {
+    this.navigationDivs['right'].className += " active";
+  }
+};
+
+
+/**
+ * Zoom in, using the same method as the movement.
+ * @private
+ */
+exports._zoomIn = function(event) {
+  this.zoomIncrement = this.constants.keyboard.speed.zoom;
+  this.start(); // if there is no node movement, the calculation wont be done
+  this._preventDefault(event);
+  if (this.navigationDivs) {
+    this.navigationDivs['zoomIn'].className += " active";
+  }
+};
+
+
+/**
+ * Zoom out
+ * @private
+ */
+exports._zoomOut = function() {
+  this.zoomIncrement = -this.constants.keyboard.speed.zoom;
+  this.start(); // if there is no node movement, the calculation wont be done
+  this._preventDefault(event);
+  if (this.navigationDivs) {
+    this.navigationDivs['zoomOut'].className += " active";
+  }
+};
+
+
+/**
+ * Stop zooming and unhighlight the zoom controls
+ * @private
+ */
+exports._stopZoom = function() {
+  this.zoomIncrement = 0;
+  if (this.navigationDivs) {
+    this.navigationDivs['zoomIn'].className = this.navigationDivs['zoomIn'].className.replace(" active","");
+    this.navigationDivs['zoomOut'].className = this.navigationDivs['zoomOut'].className.replace(" active","");
+  }
+};
+
+
+/**
+ * Stop moving in the Y direction and unHighlight the up and down
+ * @private
+ */
+exports._yStopMoving = function() {
+  this.yIncrement = 0;
+  if (this.navigationDivs) {
+    this.navigationDivs['up'].className = this.navigationDivs['up'].className.replace(" active","");
+    this.navigationDivs['down'].className = this.navigationDivs['down'].className.replace(" active","");
+  }
+};
+
+
+/**
+ * Stop moving in the X direction and unHighlight left and right.
+ * @private
+ */
+exports._xStopMoving = function() {
+  this.xIncrement = 0;
+  if (this.navigationDivs) {
+    this.navigationDivs['left'].className = this.navigationDivs['left'].className.replace(" active","");
+    this.navigationDivs['right'].className = this.navigationDivs['right'].className.replace(" active","");
+  }
+};

lib/network/mixins/SectorsMixin.js

@@ -0,0 +1,548 @@
+var util = require('../../util');
+
+/**
+ * Creation of the SectorMixin var.
+ *
+ * This contains all the functions the Network object can use to employ the sector system.
+ * The sector system is always used by Network, though the benefits only apply to the use of clustering.
+ * If clustering is not used, there is no overhead except for a duplicate object with references to nodes and edges.
+ */
+
+/**
+ * This function is only called by the setData function of the Network object.
+ * This loads the global references into the active sector. This initializes the sector.
+ *
+ * @private
+ */
+exports._putDataInSector = function() {
+  this.sectors["active"][this._sector()].nodes = this.nodes;
+  this.sectors["active"][this._sector()].edges = this.edges;
+  this.sectors["active"][this._sector()].nodeIndices = this.nodeIndices;
+};
+
+
+/**
+ *  /**
+ * This function sets the global references to nodes, edges and nodeIndices back to
+ * those of the supplied (active) sector. If a type is defined, do the specific type
+ *
+ * @param {String} sectorId
+ * @param {String} [sectorType] | "active" or "frozen"
+ * @private
+ */
+exports._switchToSector = function(sectorId, sectorType) {
+  if (sectorType === undefined || sectorType == "active") {
+    this._switchToActiveSector(sectorId);
+  }
+  else {
+    this._switchToFrozenSector(sectorId);
+  }
+};
+
+
+/**
+ * This function sets the global references to nodes, edges and nodeIndices back to
+ * those of the supplied active sector.
+ *
+ * @param sectorId
+ * @private
+ */
+exports._switchToActiveSector = function(sectorId) {
+  this.nodeIndices = this.sectors["active"][sectorId]["nodeIndices"];
+  this.nodes       = this.sectors["active"][sectorId]["nodes"];
+  this.edges       = this.sectors["active"][sectorId]["edges"];
+};
+
+
+/**
+ * This function sets the global references to nodes, edges and nodeIndices back to
+ * those of the supplied active sector.
+ *
+ * @private
+ */
+exports._switchToSupportSector = function() {
+  this.nodeIndices = this.sectors["support"]["nodeIndices"];
+  this.nodes       = this.sectors["support"]["nodes"];
+  this.edges       = this.sectors["support"]["edges"];
+};
+
+
+/**
+ * This function sets the global references to nodes, edges and nodeIndices back to
+ * those of the supplied frozen sector.
+ *
+ * @param sectorId
+ * @private
+ */
+exports._switchToFrozenSector = function(sectorId) {
+  this.nodeIndices = this.sectors["frozen"][sectorId]["nodeIndices"];
+  this.nodes       = this.sectors["frozen"][sectorId]["nodes"];
+  this.edges       = this.sectors["frozen"][sectorId]["edges"];
+};
+
+
+/**
+ * This function sets the global references to nodes, edges and nodeIndices back to
+ * those of the currently active sector.
+ *
+ * @private
+ */
+exports._loadLatestSector = function() {
+  this._switchToSector(this._sector());
+};
+
+
+/**
+ * This function returns the currently active sector Id
+ *
+ * @returns {String}
+ * @private
+ */
+exports._sector = function() {
+  return this.activeSector[this.activeSector.length-1];
+};
+
+
+/**
+ * This function returns the previously active sector Id
+ *
+ * @returns {String}
+ * @private
+ */
+exports._previousSector = function() {
+  if (this.activeSector.length > 1) {
+    return this.activeSector[this.activeSector.length-2];
+  }
+  else {
+    throw new TypeError('there are not enough sectors in the this.activeSector array.');
+  }
+};
+
+
+/**
+ * We add the active sector at the end of the this.activeSector array
+ * This ensures it is the currently active sector returned by _sector() and it reaches the top
+ * of the activeSector stack. When we reverse our steps we move from the end to the beginning of this stack.
+ *
+ * @param newId
+ * @private
+ */
+exports._setActiveSector = function(newId) {
+  this.activeSector.push(newId);
+};
+
+
+/**
+ * We remove the currently active sector id from the active sector stack. This happens when
+ * we reactivate the previously active sector
+ *
+ * @private
+ */
+exports._forgetLastSector = function() {
+  this.activeSector.pop();
+};
+
+
+/**
+ * This function creates a new active sector with the supplied newId. This newId
+ * is the expanding node id.
+ *
+ * @param {String} newId   | Id of the new active sector
+ * @private
+ */
+exports._createNewSector = function(newId) {
+  // create the new sector
+  this.sectors["active"][newId] = {"nodes":{},
+                                   "edges":{},
+                                   "nodeIndices":[],
+                                   "formationScale": this.scale,
+                                   "drawingNode": undefined};
+
+  // create the new sector render node. This gives visual feedback that you are in a new sector.
+  this.sectors["active"][newId]['drawingNode'] = new Node(
+      {id:newId,
+        color: {
+          background: "#eaefef",
+          border: "495c5e"
+        }
+      },{},{},this.constants);
+  this.sectors["active"][newId]['drawingNode'].clusterSize = 2;
+};
+
+
+/**
+ * This function removes the currently active sector. This is called when we create a new
+ * active sector.
+ *
+ * @param {String} sectorId   | Id of the active sector that will be removed
+ * @private
+ */
+exports._deleteActiveSector = function(sectorId) {
+  delete this.sectors["active"][sectorId];
+};
+
+
+/**
+ * This function removes the currently active sector. This is called when we reactivate
+ * the previously active sector.
+ *
+ * @param {String} sectorId   | Id of the active sector that will be removed
+ * @private
+ */
+exports._deleteFrozenSector = function(sectorId) {
+  delete this.sectors["frozen"][sectorId];
+};
+
+
+/**
+ * Freezing an active sector means moving it from the "active" object to the "frozen" object.
+ * We copy the references, then delete the active entree.
+ *
+ * @param sectorId
+ * @private
+ */
+exports._freezeSector = function(sectorId) {
+  // we move the set references from the active to the frozen stack.
+  this.sectors["frozen"][sectorId] = this.sectors["active"][sectorId];
+
+  // we have moved the sector data into the frozen set, we now remove it from the active set
+  this._deleteActiveSector(sectorId);
+};
+
+
+/**
+ * This is the reverse operation of _freezeSector. Activating means moving the sector from the "frozen"
+ * object to the "active" object.
+ *
+ * @param sectorId
+ * @private
+ */
+exports._activateSector = function(sectorId) {
+  // we move the set references from the frozen to the active stack.
+  this.sectors["active"][sectorId] = this.sectors["frozen"][sectorId];
+
+  // we have moved the sector data into the active set, we now remove it from the frozen stack
+  this._deleteFrozenSector(sectorId);
+};
+
+
+/**
+ * This function merges the data from the currently active sector with a frozen sector. This is used
+ * in the process of reverting back to the previously active sector.
+ * The data that is placed in the frozen (the previously active) sector is the node that has been removed from it
+ * upon the creation of a new active sector.
+ *
+ * @param sectorId
+ * @private
+ */
+exports._mergeThisWithFrozen = function(sectorId) {
+  // copy all nodes
+  for (var nodeId in this.nodes) {
+    if (this.nodes.hasOwnProperty(nodeId)) {
+      this.sectors["frozen"][sectorId]["nodes"][nodeId] = this.nodes[nodeId];
+    }
+  }
+
+  // copy all edges (if not fully clustered, else there are no edges)
+  for (var edgeId in this.edges) {
+    if (this.edges.hasOwnProperty(edgeId)) {
+      this.sectors["frozen"][sectorId]["edges"][edgeId] = this.edges[edgeId];
+    }
+  }
+
+  // merge the nodeIndices
+  for (var i = 0; i < this.nodeIndices.length; i++) {
+    this.sectors["frozen"][sectorId]["nodeIndices"].push(this.nodeIndices[i]);
+  }
+};
+
+
+/**
+ * This clusters the sector to one cluster. It was a single cluster before this process started so
+ * we revert to that state. The clusterToFit function with a maximum size of 1 node does this.
+ *
+ * @private
+ */
+exports._collapseThisToSingleCluster = function() {
+  this.clusterToFit(1,false);
+};
+
+
+/**
+ * We create a new active sector from the node that we want to open.
+ *
+ * @param node
+ * @private
+ */
+exports._addSector = function(node) {
+  // this is the currently active sector
+  var sector = this._sector();
+
+//    // this should allow me to select nodes from a frozen set.
+//    if (this.sectors['active'][sector]["nodes"].hasOwnProperty(node.id)) {
+//      console.log("the node is part of the active sector");
+//    }
+//    else {
+//      console.log("I dont know what the fuck happened!!");
+//    }
+
+  // when we switch to a new sector, we remove the node that will be expanded from the current nodes list.
+  delete this.nodes[node.id];
+
+  var unqiueIdentifier = util.randomUUID();
+
+  // we fully freeze the currently active sector
+  this._freezeSector(sector);
+
+  // we create a new active sector. This sector has the Id of the node to ensure uniqueness
+  this._createNewSector(unqiueIdentifier);
+
+  // we add the active sector to the sectors array to be able to revert these steps later on
+  this._setActiveSector(unqiueIdentifier);
+
+  // we redirect the global references to the new sector's references. this._sector() now returns unqiueIdentifier
+  this._switchToSector(this._sector());
+
+  // finally we add the node we removed from our previous active sector to the new active sector
+  this.nodes[node.id] = node;
+};
+
+
+/**
+ * We close the sector that is currently open and revert back to the one before.
+ * If the active sector is the "default" sector, nothing happens.
+ *
+ * @private
+ */
+exports._collapseSector = function() {
+  // the currently active sector
+  var sector = this._sector();
+
+  // we cannot collapse the default sector
+  if (sector != "default") {
+    if ((this.nodeIndices.length == 1) ||
+     (this.sectors["active"][sector]["drawingNode"].width*this.scale < this.constants.clustering.screenSizeThreshold * this.frame.canvas.clientWidth) ||
+     (this.sectors["active"][sector]["drawingNode"].height*this.scale < this.constants.clustering.screenSizeThreshold * this.frame.canvas.clientHeight)) {
+      var previousSector = this._previousSector();
+
+      // we collapse the sector back to a single cluster
+      this._collapseThisToSingleCluster();
+
+      // we move the remaining nodes, edges and nodeIndices to the previous sector.
+      // This previous sector is the one we will reactivate
+      this._mergeThisWithFrozen(previousSector);
+
+      // the previously active (frozen) sector now has all the data from the currently active sector.
+      // we can now delete the active sector.
+      this._deleteActiveSector(sector);
+
+      // we activate the previously active (and currently frozen) sector.
+      this._activateSector(previousSector);
+
+      // we load the references from the newly active sector into the global references
+      this._switchToSector(previousSector);
+
+      // we forget the previously active sector because we reverted to the one before
+      this._forgetLastSector();
+
+      // finally, we update the node index list.
+      this._updateNodeIndexList();
+
+      // we refresh the list with calulation nodes and calculation node indices.
+      this._updateCalculationNodes();
+    }
+  }
+};
+
+
+/**
+ * This runs a function in all active sectors. This is used in _redraw() and the _initializeForceCalculation().
+ *
+ * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
+ *                              |   we dont pass the function itself because then the "this" is the window object
+ *                              |   instead of the Network object
+ * @param {*} [argument]            |   Optional: arguments to pass to the runFunction
+ * @private
+ */
+exports._doInAllActiveSectors = function(runFunction,argument) {
+  if (argument === undefined) {
+    for (var sector in this.sectors["active"]) {
+      if (this.sectors["active"].hasOwnProperty(sector)) {
+        // switch the global references to those of this sector
+        this._switchToActiveSector(sector);
+        this[runFunction]();
+      }
+    }
+  }
+  else {
+    for (var sector in this.sectors["active"]) {
+      if (this.sectors["active"].hasOwnProperty(sector)) {
+        // switch the global references to those of this sector
+        this._switchToActiveSector(sector);
+        var args = Array.prototype.splice.call(arguments, 1);
+        if (args.length > 1) {
+          this[runFunction](args[0],args[1]);
+        }
+        else {
+          this[runFunction](argument);
+        }
+      }
+    }
+  }
+  // we revert the global references back to our active sector
+  this._loadLatestSector();
+};
+
+
+/**
+ * This runs a function in all active sectors. This is used in _redraw() and the _initializeForceCalculation().
+ *
+ * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
+ *                              |   we dont pass the function itself because then the "this" is the window object
+ *                              |   instead of the Network object
+ * @param {*} [argument]        |   Optional: arguments to pass to the runFunction
+ * @private
+ */
+exports._doInSupportSector = function(runFunction,argument) {
+  if (argument === undefined) {
+    this._switchToSupportSector();
+    this[runFunction]();
+  }
+  else {
+    this._switchToSupportSector();
+    var args = Array.prototype.splice.call(arguments, 1);
+    if (args.length > 1) {
+      this[runFunction](args[0],args[1]);
+    }
+    else {
+      this[runFunction](argument);
+    }
+  }
+  // we revert the global references back to our active sector
+  this._loadLatestSector();
+};
+
+
+/**
+ * This runs a function in all frozen sectors. This is used in the _redraw().
+ *
+ * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
+ *                              |   we don't pass the function itself because then the "this" is the window object
+ *                              |   instead of the Network object
+ * @param {*} [argument]            |   Optional: arguments to pass to the runFunction
+ * @private
+ */
+exports._doInAllFrozenSectors = function(runFunction,argument) {
+  if (argument === undefined) {
+    for (var sector in this.sectors["frozen"]) {
+      if (this.sectors["frozen"].hasOwnProperty(sector)) {
+        // switch the global references to those of this sector
+        this._switchToFrozenSector(sector);
+        this[runFunction]();
+      }
+    }
+  }
+  else {
+    for (var sector in this.sectors["frozen"]) {
+      if (this.sectors["frozen"].hasOwnProperty(sector)) {
+        // switch the global references to those of this sector
+        this._switchToFrozenSector(sector);
+        var args = Array.prototype.splice.call(arguments, 1);
+        if (args.length > 1) {
+          this[runFunction](args[0],args[1]);
+        }
+        else {
+          this[runFunction](argument);
+        }
+      }
+    }
+  }
+  this._loadLatestSector();
+};
+
+
+/**
+ * This runs a function in all sectors. This is used in the _redraw().
+ *
+ * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
+ *                              |   we don't pass the function itself because then the "this" is the window object
+ *                              |   instead of the Network object
+ * @param {*} [argument]        |   Optional: arguments to pass to the runFunction
+ * @private
+ */
+exports._doInAllSectors = function(runFunction,argument) {
+  var args = Array.prototype.splice.call(arguments, 1);
+  if (argument === undefined) {
+    this._doInAllActiveSectors(runFunction);
+    this._doInAllFrozenSectors(runFunction);
+  }
+  else {
+    if (args.length > 1) {
+      this._doInAllActiveSectors(runFunction,args[0],args[1]);
+      this._doInAllFrozenSectors(runFunction,args[0],args[1]);
+    }
+    else {
+      this._doInAllActiveSectors(runFunction,argument);
+      this._doInAllFrozenSectors(runFunction,argument);
+    }
+  }
+};
+
+
+/**
+ * This clears the nodeIndices list. We cannot use this.nodeIndices = [] because we would break the link with the
+ * active sector. Thus we clear the nodeIndices in the active sector, then reconnect the this.nodeIndices to it.
+ *
+ * @private
+ */
+exports._clearNodeIndexList = function() {
+  var sector = this._sector();
+  this.sectors["active"][sector]["nodeIndices"] = [];
+  this.nodeIndices = this.sectors["active"][sector]["nodeIndices"];
+};
+
+
+/**
+ * Draw the encompassing sector node
+ *
+ * @param ctx
+ * @param sectorType
+ * @private
+ */
+exports._drawSectorNodes = function(ctx,sectorType) {
+  var minY = 1e9, maxY = -1e9, minX = 1e9, maxX = -1e9, node;
+  for (var sector in this.sectors[sectorType]) {
+    if (this.sectors[sectorType].hasOwnProperty(sector)) {
+      if (this.sectors[sectorType][sector]["drawingNode"] !== undefined) {
+
+        this._switchToSector(sector,sectorType);
+
+        minY = 1e9; maxY = -1e9; minX = 1e9; maxX = -1e9;
+        for (var nodeId in this.nodes) {
+          if (this.nodes.hasOwnProperty(nodeId)) {
+            node = this.nodes[nodeId];
+            node.resize(ctx);
+            if (minX > node.x - 0.5 * node.width) {minX = node.x - 0.5 * node.width;}
+            if (maxX < node.x + 0.5 * node.width) {maxX = node.x + 0.5 * node.width;}
+            if (minY > node.y - 0.5 * node.height) {minY = node.y - 0.5 * node.height;}
+            if (maxY < node.y + 0.5 * node.height) {maxY = node.y + 0.5 * node.height;}
+          }
+        }
+        node = this.sectors[sectorType][sector]["drawingNode"];
+        node.x = 0.5 * (maxX + minX);
+        node.y = 0.5 * (maxY + minY);
+        node.width = 2 * (node.x - minX);
+        node.height = 2 * (node.y - minY);
+        node.radius = Math.sqrt(Math.pow(0.5*node.width,2) + Math.pow(0.5*node.height,2));
+        node.setScale(this.scale);
+        node._drawCircle(ctx);
+      }
+    }
+  }
+};
+
+exports._drawAllSectorNodes = function(ctx) {
+  this._drawSectorNodes(ctx,"frozen");
+  this._drawSectorNodes(ctx,"active");
+  this._loadLatestSector();
+};

lib/network/mixins/SelectionMixin.js

@@ -0,0 +1,705 @@
+var Node = require('../Node');
+
+/**
+ * This function can be called from the _doInAllSectors function
+ *
+ * @param object
+ * @param overlappingNodes
+ * @private
+ */
+exports._getNodesOverlappingWith = function(object, overlappingNodes) {
+  var nodes = this.nodes;
+  for (var nodeId in nodes) {
+    if (nodes.hasOwnProperty(nodeId)) {
+      if (nodes[nodeId].isOverlappingWith(object)) {
+        overlappingNodes.push(nodeId);
+      }
+    }
+  }
+};
+
+/**
+ * retrieve all nodes overlapping with given object
+ * @param {Object} object  An object with parameters left, top, right, bottom
+ * @return {Number[]}   An array with id's of the overlapping nodes
+ * @private
+ */
+exports._getAllNodesOverlappingWith = function (object) {
+  var overlappingNodes = [];
+  this._doInAllActiveSectors("_getNodesOverlappingWith",object,overlappingNodes);
+  return overlappingNodes;
+};
+
+
+/**
+ * Return a position object in canvasspace from a single point in screenspace
+ *
+ * @param pointer
+ * @returns {{left: number, top: number, right: number, bottom: number}}
+ * @private
+ */
+exports._pointerToPositionObject = function(pointer) {
+  var x = this._XconvertDOMtoCanvas(pointer.x);
+  var y = this._YconvertDOMtoCanvas(pointer.y);
+
+  return {
+    left:   x,
+    top:    y,
+    right:  x,
+    bottom: y
+  };
+};
+
+
+/**
+ * Get the top node at the a specific point (like a click)
+ *
+ * @param {{x: Number, y: Number}} pointer
+ * @return {Node | null} node
+ * @private
+ */
+exports._getNodeAt = function (pointer) {
+  // we first check if this is an navigation controls element
+  var positionObject = this._pointerToPositionObject(pointer);
+  var overlappingNodes = this._getAllNodesOverlappingWith(positionObject);
+
+  // if there are overlapping nodes, select the last one, this is the
+  // one which is drawn on top of the others
+  if (overlappingNodes.length > 0) {
+     return this.nodes[overlappingNodes[overlappingNodes.length - 1]];
+  }
+  else {
+    return null;
+  }
+};
+
+
+/**
+ * retrieve all edges overlapping with given object, selector is around center
+ * @param {Object} object  An object with parameters left, top, right, bottom
+ * @return {Number[]}   An array with id's of the overlapping nodes
+ * @private
+ */
+exports._getEdgesOverlappingWith = function (object, overlappingEdges) {
+  var edges = this.edges;
+  for (var edgeId in edges) {
+    if (edges.hasOwnProperty(edgeId)) {
+      if (edges[edgeId].isOverlappingWith(object)) {
+        overlappingEdges.push(edgeId);
+      }
+    }
+  }
+};
+
+
+/**
+ * retrieve all nodes overlapping with given object
+ * @param {Object} object  An object with parameters left, top, right, bottom
+ * @return {Number[]}   An array with id's of the overlapping nodes
+ * @private
+ */
+exports._getAllEdgesOverlappingWith = function (object) {
+  var overlappingEdges = [];
+  this._doInAllActiveSectors("_getEdgesOverlappingWith",object,overlappingEdges);
+  return overlappingEdges;
+};
+
+/**
+ * Place holder. To implement change the _getNodeAt to a _getObjectAt. Have the _getObjectAt call
+ * _getNodeAt and _getEdgesAt, then priortize the selection to user preferences.
+ *
+ * @param pointer
+ * @returns {null}
+ * @private
+ */
+exports._getEdgeAt = function(pointer) {
+  var positionObject = this._pointerToPositionObject(pointer);
+  var overlappingEdges = this._getAllEdgesOverlappingWith(positionObject);
+
+  if (overlappingEdges.length > 0) {
+    return this.edges[overlappingEdges[overlappingEdges.length - 1]];
+  }
+  else {
+    return null;
+  }
+};
+
+
+/**
+ * Add object to the selection array.
+ *
+ * @param obj
+ * @private
+ */
+exports._addToSelection = function(obj) {
+  if (obj instanceof Node) {
+    this.selectionObj.nodes[obj.id] = obj;
+  }
+  else {
+    this.selectionObj.edges[obj.id] = obj;
+  }
+};
+
+/**
+ * Add object to the selection array.
+ *
+ * @param obj
+ * @private
+ */
+exports._addToHover = function(obj) {
+  if (obj instanceof Node) {
+    this.hoverObj.nodes[obj.id] = obj;
+  }
+  else {
+    this.hoverObj.edges[obj.id] = obj;
+  }
+};
+
+
+/**
+ * Remove a single option from selection.
+ *
+ * @param {Object} obj
+ * @private
+ */
+exports._removeFromSelection = function(obj) {
+  if (obj instanceof Node) {
+    delete this.selectionObj.nodes[obj.id];
+  }
+  else {
+    delete this.selectionObj.edges[obj.id];
+  }
+};
+
+/**
+ * Unselect all. The selectionObj is useful for this.
+ *
+ * @param {Boolean} [doNotTrigger] | ignore trigger
+ * @private
+ */
+exports._unselectAll = function(doNotTrigger) {
+  if (doNotTrigger === undefined) {
+    doNotTrigger = false;
+  }
+  for(var nodeId in this.selectionObj.nodes) {
+    if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      this.selectionObj.nodes[nodeId].unselect();
+    }
+  }
+  for(var edgeId in this.selectionObj.edges) {
+    if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      this.selectionObj.edges[edgeId].unselect();
+    }
+  }
+
+  this.selectionObj = {nodes:{},edges:{}};
+
+  if (doNotTrigger == false) {
+    this.emit('select', this.getSelection());
+  }
+};
+
+/**
+ * Unselect all clusters. The selectionObj is useful for this.
+ *
+ * @param {Boolean} [doNotTrigger] | ignore trigger
+ * @private
+ */
+exports._unselectClusters = function(doNotTrigger) {
+  if (doNotTrigger === undefined) {
+    doNotTrigger = false;
+  }
+
+  for (var nodeId in this.selectionObj.nodes) {
+    if (this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      if (this.selectionObj.nodes[nodeId].clusterSize > 1) {
+        this.selectionObj.nodes[nodeId].unselect();
+        this._removeFromSelection(this.selectionObj.nodes[nodeId]);
+      }
+    }
+  }
+
+  if (doNotTrigger == false) {
+    this.emit('select', this.getSelection());
+  }
+};
+
+
+/**
+ * return the number of selected nodes
+ *
+ * @returns {number}
+ * @private
+ */
+exports._getSelectedNodeCount = function() {
+  var count = 0;
+  for (var nodeId in this.selectionObj.nodes) {
+    if (this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      count += 1;
+    }
+  }
+  return count;
+};
+
+/**
+ * return the selected node
+ *
+ * @returns {number}
+ * @private
+ */
+exports._getSelectedNode = function() {
+  for (var nodeId in this.selectionObj.nodes) {
+    if (this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      return this.selectionObj.nodes[nodeId];
+    }
+  }
+  return null;
+};
+
+/**
+ * return the selected edge
+ *
+ * @returns {number}
+ * @private
+ */
+exports._getSelectedEdge = function() {
+  for (var edgeId in this.selectionObj.edges) {
+    if (this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      return this.selectionObj.edges[edgeId];
+    }
+  }
+  return null;
+};
+
+
+/**
+ * return the number of selected edges
+ *
+ * @returns {number}
+ * @private
+ */
+exports._getSelectedEdgeCount = function() {
+  var count = 0;
+  for (var edgeId in this.selectionObj.edges) {
+    if (this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      count += 1;
+    }
+  }
+  return count;
+};
+
+
+/**
+ * return the number of selected objects.
+ *
+ * @returns {number}
+ * @private
+ */
+exports._getSelectedObjectCount = function() {
+  var count = 0;
+  for(var nodeId in this.selectionObj.nodes) {
+    if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      count += 1;
+    }
+  }
+  for(var edgeId in this.selectionObj.edges) {
+    if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      count += 1;
+    }
+  }
+  return count;
+};
+
+/**
+ * Check if anything is selected
+ *
+ * @returns {boolean}
+ * @private
+ */
+exports._selectionIsEmpty = function() {
+  for(var nodeId in this.selectionObj.nodes) {
+    if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      return false;
+    }
+  }
+  for(var edgeId in this.selectionObj.edges) {
+    if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      return false;
+    }
+  }
+  return true;
+};
+
+
+/**
+ * check if one of the selected nodes is a cluster.
+ *
+ * @returns {boolean}
+ * @private
+ */
+exports._clusterInSelection = function() {
+  for(var nodeId in this.selectionObj.nodes) {
+    if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      if (this.selectionObj.nodes[nodeId].clusterSize > 1) {
+        return true;
+      }
+    }
+  }
+  return false;
+};
+
+/**
+ * select the edges connected to the node that is being selected
+ *
+ * @param {Node} node
+ * @private
+ */
+exports._selectConnectedEdges = function(node) {
+  for (var i = 0; i < node.dynamicEdges.length; i++) {
+    var edge = node.dynamicEdges[i];
+    edge.select();
+    this._addToSelection(edge);
+  }
+};
+
+/**
+ * select the edges connected to the node that is being selected
+ *
+ * @param {Node} node
+ * @private
+ */
+exports._hoverConnectedEdges = function(node) {
+  for (var i = 0; i < node.dynamicEdges.length; i++) {
+    var edge = node.dynamicEdges[i];
+    edge.hover = true;
+    this._addToHover(edge);
+  }
+};
+
+
+/**
+ * unselect the edges connected to the node that is being selected
+ *
+ * @param {Node} node
+ * @private
+ */
+exports._unselectConnectedEdges = function(node) {
+  for (var i = 0; i < node.dynamicEdges.length; i++) {
+    var edge = node.dynamicEdges[i];
+    edge.unselect();
+    this._removeFromSelection(edge);
+  }
+};
+
+
+
+
+/**
+ * This is called when someone clicks on a node. either select or deselect it.
+ * If there is an existing selection and we don't want to append to it, clear the existing selection
+ *
+ * @param {Node || Edge} object
+ * @param {Boolean} append
+ * @param {Boolean} [doNotTrigger] | ignore trigger
+ * @private
+ */
+exports._selectObject = function(object, append, doNotTrigger, highlightEdges) {
+  if (doNotTrigger === undefined) {
+    doNotTrigger = false;
+  }
+  if (highlightEdges === undefined) {
+    highlightEdges = true;
+  }
+
+  if (this._selectionIsEmpty() == false && append == false && this.forceAppendSelection == false) {
+    this._unselectAll(true);
+  }
+
+  if (object.selected == false) {
+    object.select();
+    this._addToSelection(object);
+    if (object instanceof Node && this.blockConnectingEdgeSelection == false && highlightEdges == true) {
+      this._selectConnectedEdges(object);
+    }
+  }
+  else {
+    object.unselect();
+    this._removeFromSelection(object);
+  }
+
+  if (doNotTrigger == false) {
+    this.emit('select', this.getSelection());
+  }
+};
+
+
+/**
+ * This is called when someone clicks on a node. either select or deselect it.
+ * If there is an existing selection and we don't want to append to it, clear the existing selection
+ *
+ * @param {Node || Edge} object
+ * @private
+ */
+exports._blurObject = function(object) {
+  if (object.hover == true) {
+    object.hover = false;
+    this.emit("blurNode",{node:object.id});
+  }
+};
+
+/**
+ * This is called when someone clicks on a node. either select or deselect it.
+ * If there is an existing selection and we don't want to append to it, clear the existing selection
+ *
+ * @param {Node || Edge} object
+ * @private
+ */
+exports._hoverObject = function(object) {
+  if (object.hover == false) {
+    object.hover = true;
+    this._addToHover(object);
+    if (object instanceof Node) {
+      this.emit("hoverNode",{node:object.id});
+    }
+  }
+  if (object instanceof Node) {
+    this._hoverConnectedEdges(object);
+  }
+};
+
+
+/**
+ * handles the selection part of the touch, only for navigation controls elements;
+ * Touch is triggered before tap, also before hold. Hold triggers after a while.
+ * This is the most responsive solution
+ *
+ * @param {Object} pointer
+ * @private
+ */
+exports._handleTouch = function(pointer) {
+};
+
+
+/**
+ * handles the selection part of the tap;
+ *
+ * @param {Object} pointer
+ * @private
+ */
+exports._handleTap = function(pointer) {
+  var node = this._getNodeAt(pointer);
+  if (node != null) {
+    this._selectObject(node,false);
+  }
+  else {
+    var edge = this._getEdgeAt(pointer);
+    if (edge != null) {
+      this._selectObject(edge,false);
+    }
+    else {
+      this._unselectAll();
+    }
+  }
+  this.emit("click", this.getSelection());
+  this._redraw();
+};
+
+
+/**
+ * handles the selection part of the double tap and opens a cluster if needed
+ *
+ * @param {Object} pointer
+ * @private
+ */
+exports._handleDoubleTap = function(pointer) {
+  var node = this._getNodeAt(pointer);
+  if (node != null && node !== undefined) {
+    // we reset the areaCenter here so the opening of the node will occur
+    this.areaCenter =  {"x" : this._XconvertDOMtoCanvas(pointer.x),
+                        "y" : this._YconvertDOMtoCanvas(pointer.y)};
+    this.openCluster(node);
+  }
+  this.emit("doubleClick", this.getSelection());
+};
+
+
+/**
+ * Handle the onHold selection part
+ *
+ * @param pointer
+ * @private
+ */
+exports._handleOnHold = function(pointer) {
+  var node = this._getNodeAt(pointer);
+  if (node != null) {
+    this._selectObject(node,true);
+  }
+  else {
+    var edge = this._getEdgeAt(pointer);
+    if (edge != null) {
+      this._selectObject(edge,true);
+    }
+  }
+  this._redraw();
+};
+
+
+/**
+ * handle the onRelease event. These functions are here for the navigation controls module.
+ *
+  * @private
+ */
+exports._handleOnRelease = function(pointer) {
+
+};
+
+
+
+/**
+ *
+ * retrieve the currently selected objects
+ * @return {{nodes: Array.<String>, edges: Array.<String>}} selection
+ */
+exports.getSelection = function() {
+  var nodeIds = this.getSelectedNodes();
+  var edgeIds = this.getSelectedEdges();
+  return {nodes:nodeIds, edges:edgeIds};
+};
+
+/**
+ *
+ * retrieve the currently selected nodes
+ * @return {String[]} selection    An array with the ids of the
+ *                                            selected nodes.
+ */
+exports.getSelectedNodes = function() {
+  var idArray = [];
+  for(var nodeId in this.selectionObj.nodes) {
+    if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      idArray.push(nodeId);
+    }
+  }
+  return idArray
+};
+
+/**
+ *
+ * retrieve the currently selected edges
+ * @return {Array} selection    An array with the ids of the
+ *                                            selected nodes.
+ */
+exports.getSelectedEdges = function() {
+  var idArray = [];
+  for(var edgeId in this.selectionObj.edges) {
+    if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      idArray.push(edgeId);
+    }
+  }
+  return idArray;
+};
+
+
+/**
+ * select zero or more nodes
+ * @param {Number[] | String[]} selection     An array with the ids of the
+ *                                            selected nodes.
+ */
+exports.setSelection = function(selection) {
+  var i, iMax, id;
+
+  if (!selection || (selection.length == undefined))
+    throw 'Selection must be an array with ids';
+
+  // first unselect any selected node
+  this._unselectAll(true);
+
+  for (i = 0, iMax = selection.length; i < iMax; i++) {
+    id = selection[i];
+
+    var node = this.nodes[id];
+    if (!node) {
+      throw new RangeError('Node with id "' + id + '" not found');
+    }
+    this._selectObject(node,true,true);
+  }
+
+  console.log("setSelection is deprecated. Please use selectNodes instead.")
+
+  this.redraw();
+};
+
+
+/**
+ * select zero or more nodes with the option to highlight edges
+ * @param {Number[] | String[]} selection     An array with the ids of the
+ *                                            selected nodes.
+ * @param {boolean} [highlightEdges]
+ */
+exports.selectNodes = function(selection, highlightEdges) {
+  var i, iMax, id;
+
+  if (!selection || (selection.length == undefined))
+    throw 'Selection must be an array with ids';
+
+  // first unselect any selected node
+  this._unselectAll(true);
+
+  for (i = 0, iMax = selection.length; i < iMax; i++) {
+    id = selection[i];
+
+    var node = this.nodes[id];
+    if (!node) {
+      throw new RangeError('Node with id "' + id + '" not found');
+    }
+    this._selectObject(node,true,true,highlightEdges);
+  }
+  this.redraw();
+};
+
+
+/**
+ * select zero or more edges
+ * @param {Number[] | String[]} selection     An array with the ids of the
+ *                                            selected nodes.
+ */
+exports.selectEdges = function(selection) {
+  var i, iMax, id;
+
+  if (!selection || (selection.length == undefined))
+    throw 'Selection must be an array with ids';
+
+  // first unselect any selected node
+  this._unselectAll(true);
+
+  for (i = 0, iMax = selection.length; i < iMax; i++) {
+    id = selection[i];
+
+    var edge = this.edges[id];
+    if (!edge) {
+      throw new RangeError('Edge with id "' + id + '" not found');
+    }
+    this._selectObject(edge,true,true,highlightEdges);
+  }
+  this.redraw();
+};
+
+/**
+ * Validate the selection: remove ids of nodes which no longer exist
+ * @private
+ */
+exports._updateSelection = function () {
+  for(var nodeId in this.selectionObj.nodes) {
+    if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
+      if (!this.nodes.hasOwnProperty(nodeId)) {
+        delete this.selectionObj.nodes[nodeId];
+      }
+    }
+  }
+  for(var edgeId in this.selectionObj.edges) {
+    if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
+      if (!this.edges.hasOwnProperty(edgeId)) {
+        delete this.selectionObj.edges[edgeId];
+      }
+    }
+  }
+};

lib/network/mixins/physics/BarnesHutMixin.js

@@ -0,0 +1,393 @@
+/**
+ * This function calculates the forces the nodes apply on eachother based on a gravitational model.
+ * The Barnes Hut method is used to speed up this N-body simulation.
+ *
+ * @private
+ */
+exports._calculateNodeForces = function() {
+  if (this.constants.physics.barnesHut.gravitationalConstant != 0) {
+    var node;
+    var nodes = this.calculationNodes;
+    var nodeIndices = this.calculationNodeIndices;
+    var nodeCount = nodeIndices.length;
+
+    this._formBarnesHutTree(nodes,nodeIndices);
+
+    var barnesHutTree = this.barnesHutTree;
+
+    // place the nodes one by one recursively
+    for (var i = 0; i < nodeCount; i++) {
+      node = nodes[nodeIndices[i]];
+      // starting with root is irrelevant, it never passes the BarnesHut condition
+      this._getForceContribution(barnesHutTree.root.children.NW,node);
+      this._getForceContribution(barnesHutTree.root.children.NE,node);
+      this._getForceContribution(barnesHutTree.root.children.SW,node);
+      this._getForceContribution(barnesHutTree.root.children.SE,node);
+    }
+  }
+};
+
+
+/**
+ * This function traverses the barnesHutTree. It checks when it can approximate distant nodes with their center of mass.
+ * If a region contains a single node, we check if it is not itself, then we apply the force.
+ *
+ * @param parentBranch
+ * @param node
+ * @private
+ */
+exports._getForceContribution = function(parentBranch,node) {
+  // we get no force contribution from an empty region
+  if (parentBranch.childrenCount > 0) {
+    var dx,dy,distance;
+
+    // get the distance from the center of mass to the node.
+    dx = parentBranch.centerOfMass.x - node.x;
+    dy = parentBranch.centerOfMass.y - node.y;
+    distance = Math.sqrt(dx * dx + dy * dy);
+
+    // BarnesHut condition
+    // original condition : s/d < theta = passed  ===  d/s > 1/theta = passed
+    // calcSize = 1/s --> d * 1/s > 1/theta = passed
+    if (distance * parentBranch.calcSize > this.constants.physics.barnesHut.theta) {
+      // duplicate code to reduce function calls to speed up program
+      if (distance == 0) {
+        distance = 0.1*Math.random();
+        dx = distance;
+      }
+      var gravityForce = this.constants.physics.barnesHut.gravitationalConstant * parentBranch.mass * node.mass / (distance * distance * distance);
+      var fx = dx * gravityForce;
+      var fy = dy * gravityForce;
+      node.fx += fx;
+      node.fy += fy;
+    }
+    else {
+      // Did not pass the condition, go into children if available
+      if (parentBranch.childrenCount == 4) {
+        this._getForceContribution(parentBranch.children.NW,node);
+        this._getForceContribution(parentBranch.children.NE,node);
+        this._getForceContribution(parentBranch.children.SW,node);
+        this._getForceContribution(parentBranch.children.SE,node);
+      }
+      else { // parentBranch must have only one node, if it was empty we wouldnt be here
+        if (parentBranch.children.data.id != node.id) { // if it is not self
+          // duplicate code to reduce function calls to speed up program
+          if (distance == 0) {
+            distance = 0.5*Math.random();
+            dx = distance;
+          }
+          var gravityForce = this.constants.physics.barnesHut.gravitationalConstant * parentBranch.mass * node.mass / (distance * distance * distance);
+          var fx = dx * gravityForce;
+          var fy = dy * gravityForce;
+          node.fx += fx;
+          node.fy += fy;
+        }
+      }
+    }
+  }
+};
+
+/**
+ * This function constructs the barnesHut tree recursively. It creates the root, splits it and starts placing the nodes.
+ *
+ * @param nodes
+ * @param nodeIndices
+ * @private
+ */
+exports._formBarnesHutTree = function(nodes,nodeIndices) {
+  var node;
+  var nodeCount = nodeIndices.length;
+
+  var minX = Number.MAX_VALUE,
+    minY = Number.MAX_VALUE,
+    maxX =-Number.MAX_VALUE,
+    maxY =-Number.MAX_VALUE;
+
+  // get the range of the nodes
+  for (var i = 0; i < nodeCount; i++) {
+    var x = nodes[nodeIndices[i]].x;
+    var y = nodes[nodeIndices[i]].y;
+    if (x < minX) { minX = x; }
+    if (x > maxX) { maxX = x; }
+    if (y < minY) { minY = y; }
+    if (y > maxY) { maxY = y; }
+  }
+  // make the range a square
+  var sizeDiff = Math.abs(maxX - minX) - Math.abs(maxY - minY); // difference between X and Y
+  if (sizeDiff > 0) {minY -= 0.5 * sizeDiff; maxY += 0.5 * sizeDiff;} // xSize > ySize
+  else              {minX += 0.5 * sizeDiff; maxX -= 0.5 * sizeDiff;} // xSize < ySize
+
+
+  var minimumTreeSize = 1e-5;
+  var rootSize = Math.max(minimumTreeSize,Math.abs(maxX - minX));
+  var halfRootSize = 0.5 * rootSize;
+  var centerX = 0.5 * (minX + maxX), centerY = 0.5 * (minY + maxY);
+
+  // construct the barnesHutTree
+  var barnesHutTree = {
+    root:{
+      centerOfMass: {x:0, y:0},
+      mass:0,
+      range: {
+        minX: centerX-halfRootSize,maxX:centerX+halfRootSize,
+        minY: centerY-halfRootSize,maxY:centerY+halfRootSize
+      },
+      size: rootSize,
+      calcSize: 1 / rootSize,
+      children: { data:null},
+      maxWidth: 0,
+      level: 0,
+      childrenCount: 4
+    }
+  };
+  this._splitBranch(barnesHutTree.root);
+
+  // place the nodes one by one recursively
+  for (i = 0; i < nodeCount; i++) {
+    node = nodes[nodeIndices[i]];
+    this._placeInTree(barnesHutTree.root,node);
+  }
+
+  // make global
+  this.barnesHutTree = barnesHutTree
+};
+
+
+/**
+ * this updates the mass of a branch. this is increased by adding a node.
+ *
+ * @param parentBranch
+ * @param node
+ * @private
+ */
+exports._updateBranchMass = function(parentBranch, node) {
+  var totalMass = parentBranch.mass + node.mass;
+  var totalMassInv = 1/totalMass;
+
+  parentBranch.centerOfMass.x = parentBranch.centerOfMass.x * parentBranch.mass + node.x * node.mass;
+  parentBranch.centerOfMass.x *= totalMassInv;
+
+  parentBranch.centerOfMass.y = parentBranch.centerOfMass.y * parentBranch.mass + node.y * node.mass;
+  parentBranch.centerOfMass.y *= totalMassInv;
+
+  parentBranch.mass = totalMass;
+  var biggestSize = Math.max(Math.max(node.height,node.radius),node.width);
+  parentBranch.maxWidth = (parentBranch.maxWidth < biggestSize) ? biggestSize : parentBranch.maxWidth;
+
+};
+
+
+/**
+ * determine in which branch the node will be placed.
+ *
+ * @param parentBranch
+ * @param node
+ * @param skipMassUpdate
+ * @private
+ */
+exports._placeInTree = function(parentBranch,node,skipMassUpdate) {
+  if (skipMassUpdate != true || skipMassUpdate === undefined) {
+    // update the mass of the branch.
+    this._updateBranchMass(parentBranch,node);
+  }
+
+  if (parentBranch.children.NW.range.maxX > node.x) { // in NW or SW
+    if (parentBranch.children.NW.range.maxY > node.y) { // in NW
+      this._placeInRegion(parentBranch,node,"NW");
+    }
+    else { // in SW
+      this._placeInRegion(parentBranch,node,"SW");
+    }
+  }
+  else { // in NE or SE
+    if (parentBranch.children.NW.range.maxY > node.y) { // in NE
+      this._placeInRegion(parentBranch,node,"NE");
+    }
+    else { // in SE
+      this._placeInRegion(parentBranch,node,"SE");
+    }
+  }
+};
+
+
+/**
+ * actually place the node in a region (or branch)
+ *
+ * @param parentBranch
+ * @param node
+ * @param region
+ * @private
+ */
+exports._placeInRegion = function(parentBranch,node,region) {
+  switch (parentBranch.children[region].childrenCount) {
+    case 0: // place node here
+      parentBranch.children[region].children.data = node;
+      parentBranch.children[region].childrenCount = 1;
+      this._updateBranchMass(parentBranch.children[region],node);
+      break;
+    case 1: // convert into children
+      // if there are two nodes exactly overlapping (on init, on opening of cluster etc.)
+      // we move one node a pixel and we do not put it in the tree.
+      if (parentBranch.children[region].children.data.x == node.x &&
+          parentBranch.children[region].children.data.y == node.y) {
+        node.x += Math.random();
+        node.y += Math.random();
+      }
+      else {
+        this._splitBranch(parentBranch.children[region]);
+        this._placeInTree(parentBranch.children[region],node);
+      }
+      break;
+    case 4: // place in branch
+      this._placeInTree(parentBranch.children[region],node);
+      break;
+  }
+};
+
+
+/**
+ * this function splits a branch into 4 sub branches. If the branch contained a node, we place it in the subbranch
+ * after the split is complete.
+ *
+ * @param parentBranch
+ * @private
+ */
+exports._splitBranch = function(parentBranch) {
+  // if the branch is shaded with a node, replace the node in the new subset.
+  var containedNode = null;
+  if (parentBranch.childrenCount == 1) {
+    containedNode = parentBranch.children.data;
+    parentBranch.mass = 0; parentBranch.centerOfMass.x = 0; parentBranch.centerOfMass.y = 0;
+  }
+  parentBranch.childrenCount = 4;
+  parentBranch.children.data = null;
+  this._insertRegion(parentBranch,"NW");
+  this._insertRegion(parentBranch,"NE");
+  this._insertRegion(parentBranch,"SW");
+  this._insertRegion(parentBranch,"SE");
+
+  if (containedNode != null) {
+    this._placeInTree(parentBranch,containedNode);
+  }
+};
+
+
+/**
+ * This function subdivides the region into four new segments.
+ * Specifically, this inserts a single new segment.
+ * It fills the children section of the parentBranch
+ *
+ * @param parentBranch
+ * @param region
+ * @param parentRange
+ * @private
+ */
+exports._insertRegion = function(parentBranch, region) {
+  var minX,maxX,minY,maxY;
+  var childSize = 0.5 * parentBranch.size;
+  switch (region) {
+    case "NW":
+      minX = parentBranch.range.minX;
+      maxX = parentBranch.range.minX + childSize;
+      minY = parentBranch.range.minY;
+      maxY = parentBranch.range.minY + childSize;
+      break;
+    case "NE":
+      minX = parentBranch.range.minX + childSize;
+      maxX = parentBranch.range.maxX;
+      minY = parentBranch.range.minY;
+      maxY = parentBranch.range.minY + childSize;
+      break;
+    case "SW":
+      minX = parentBranch.range.minX;
+      maxX = parentBranch.range.minX + childSize;
+      minY = parentBranch.range.minY + childSize;
+      maxY = parentBranch.range.maxY;
+      break;
+    case "SE":
+      minX = parentBranch.range.minX + childSize;
+      maxX = parentBranch.range.maxX;
+      minY = parentBranch.range.minY + childSize;
+      maxY = parentBranch.range.maxY;
+      break;
+  }
+
+
+  parentBranch.children[region] = {
+    centerOfMass:{x:0,y:0},
+    mass:0,
+    range:{minX:minX,maxX:maxX,minY:minY,maxY:maxY},
+    size: 0.5 * parentBranch.size,
+    calcSize: 2 * parentBranch.calcSize,
+    children: {data:null},
+    maxWidth: 0,
+    level: parentBranch.level+1,
+    childrenCount: 0
+  };
+};
+
+
+/**
+ * This function is for debugging purposed, it draws the tree.
+ *
+ * @param ctx
+ * @param color
+ * @private
+ */
+exports._drawTree = function(ctx,color) {
+  if (this.barnesHutTree !== undefined) {
+
+    ctx.lineWidth = 1;
+
+    this._drawBranch(this.barnesHutTree.root,ctx,color);
+  }
+};
+
+
+/**
+ * This function is for debugging purposes. It draws the branches recursively.
+ *
+ * @param branch
+ * @param ctx
+ * @param color
+ * @private
+ */
+exports._drawBranch = function(branch,ctx,color) {
+  if (color === undefined) {
+    color = "#FF0000";
+  }
+
+  if (branch.childrenCount == 4) {
+    this._drawBranch(branch.children.NW,ctx);
+    this._drawBranch(branch.children.NE,ctx);
+    this._drawBranch(branch.children.SE,ctx);
+    this._drawBranch(branch.children.SW,ctx);
+  }
+  ctx.strokeStyle = color;
+  ctx.beginPath();
+  ctx.moveTo(branch.range.minX,branch.range.minY);
+  ctx.lineTo(branch.range.maxX,branch.range.minY);
+  ctx.stroke();
+
+  ctx.beginPath();
+  ctx.moveTo(branch.range.maxX,branch.range.minY);
+  ctx.lineTo(branch.range.maxX,branch.range.maxY);
+  ctx.stroke();
+
+  ctx.beginPath();
+  ctx.moveTo(branch.range.maxX,branch.range.maxY);
+  ctx.lineTo(branch.range.minX,branch.range.maxY);
+  ctx.stroke();
+
+  ctx.beginPath();
+  ctx.moveTo(branch.range.minX,branch.range.maxY);
+  ctx.lineTo(branch.range.minX,branch.range.minY);
+  ctx.stroke();
+
+  /*
+   if (branch.mass > 0) {
+   ctx.circle(branch.centerOfMass.x, branch.centerOfMass.y, 3*branch.mass);
+   ctx.stroke();
+   }
+   */
+};

lib/network/mixins/physics/HierarchialRepulsionMixin.js

@@ -0,0 +1,125 @@
+/**
+ * Calculate the forces the nodes apply on eachother based on a repulsion field.
+ * This field is linearly approximated.
+ *
+ * @private
+ */
+exports._calculateNodeForces = function () {
+  var dx, dy, distance, fx, fy, combinedClusterSize,
+    repulsingForce, node1, node2, i, j;
+
+  var nodes = this.calculationNodes;
+  var nodeIndices = this.calculationNodeIndices;
+
+  // approximation constants
+  var b = 5;
+  var a_base = 0.5 * -b;
+
+
+  // repulsing forces between nodes
+  var nodeDistance = this.constants.physics.hierarchicalRepulsion.nodeDistance;
+  var minimumDistance = nodeDistance;
+  var a = a_base / minimumDistance;
+
+  // we loop from i over all but the last entree in the array
+  // j loops from i+1 to the last. This way we do not double count any of the indices, nor i == j
+  for (i = 0; i < nodeIndices.length - 1; i++) {
+
+    node1 = nodes[nodeIndices[i]];
+    for (j = i + 1; j < nodeIndices.length; j++) {
+      node2 = nodes[nodeIndices[j]];
+      if (node1.level == node2.level) {
+
+        dx = node2.x - node1.x;
+        dy = node2.y - node1.y;
+        distance = Math.sqrt(dx * dx + dy * dy);
+
+
+        if (distance < 2 * minimumDistance) {
+          repulsingForce = a * distance + b;
+          var c = 0.05;
+          var d = 2 * minimumDistance * 2 * c;
+          repulsingForce = c * Math.pow(distance,2) - d * distance + d*d/(4*c);
+
+          // normalize force with
+          if (distance == 0) {
+            distance = 0.01;
+          }
+          else {
+            repulsingForce = repulsingForce / distance;
+          }
+          fx = dx * repulsingForce;
+          fy = dy * repulsingForce;
+
+          node1.fx -= fx;
+          node1.fy -= fy;
+          node2.fx += fx;
+          node2.fy += fy;
+        }
+      }
+    }
+  }
+};
+
+
+/**
+ * this function calculates the effects of the springs in the case of unsmooth curves.
+ *
+ * @private
+ */
+exports._calculateHierarchicalSpringForces = function () {
+  var edgeLength, edge, edgeId;
+  var dx, dy, fx, fy, springForce, distance;
+  var edges = this.edges;
+
+  // forces caused by the edges, modelled as springs
+  for (edgeId in edges) {
+    if (edges.hasOwnProperty(edgeId)) {
+      edge = edges[edgeId];
+      if (edge.connected) {
+        // only calculate forces if nodes are in the same sector
+        if (this.nodes.hasOwnProperty(edge.toId) && this.nodes.hasOwnProperty(edge.fromId)) {
+          edgeLength = edge.customLength ? edge.length : this.constants.physics.springLength;
+          // this implies that the edges between big clusters are longer
+          edgeLength += (edge.to.clusterSize + edge.from.clusterSize - 2) * this.constants.clustering.edgeGrowth;
+
+          dx = (edge.from.x - edge.to.x);
+          dy = (edge.from.y - edge.to.y);
+          distance = Math.sqrt(dx * dx + dy * dy);
+
+          if (distance == 0) {
+            distance = 0.01;
+          }
+
+          distance = Math.max(0.8*edgeLength,Math.min(5*edgeLength, distance));
+
+          // the 1/distance is so the fx and fy can be calculated without sine or cosine.
+          springForce = this.constants.physics.springConstant * (edgeLength - distance) / distance;
+
+          fx = dx * springForce;
+          fy = dy * springForce;
+
+          edge.to.fx -= fx;
+          edge.to.fy -= fy;
+          edge.from.fx += fx;
+          edge.from.fy += fy;
+
+
+          var factor = 5;
+          if (distance > edgeLength) {
+            factor = 25;
+          }
+
+          if (edge.from.level > edge.to.level) {
+            edge.to.fx -= factor*fx;
+            edge.to.fy -= factor*fy;
+          }
+          else if (edge.from.level < edge.to.level) {
+            edge.from.fx += factor*fx;
+            edge.from.fy += factor*fy;
+          }
+        }
+      }
+    }
+  }
+};

lib/network/mixins/physics/PhysicsMixin.js

@@ -0,0 +1,700 @@
+var util = require('../../../util');
+var RepulsionMixin = require('./RepulsionMixin');
+var HierarchialRepulsionMixin = require('./HierarchialRepulsionMixin');
+var BarnesHutMixin = require('./BarnesHutMixin');
+
+/**
+ * Toggling barnes Hut calculation on and off.
+ *
+ * @private
+ */
+exports._toggleBarnesHut = function () {
+  this.constants.physics.barnesHut.enabled = !this.constants.physics.barnesHut.enabled;
+  this._loadSelectedForceSolver();
+  this.moving = true;
+  this.start();
+};
+
+
+/**
+ * This loads the node force solver based on the barnes hut or repulsion algorithm
+ *
+ * @private
+ */
+exports._loadSelectedForceSolver = function () {
+  // this overloads the this._calculateNodeForces
+  if (this.constants.physics.barnesHut.enabled == true) {
+    this._clearMixin(RepulsionMixin);
+    this._clearMixin(HierarchialRepulsionMixin);
+
+    this.constants.physics.centralGravity = this.constants.physics.barnesHut.centralGravity;
+    this.constants.physics.springLength = this.constants.physics.barnesHut.springLength;
+    this.constants.physics.springConstant = this.constants.physics.barnesHut.springConstant;
+    this.constants.physics.damping = this.constants.physics.barnesHut.damping;
+
+    this._loadMixin(BarnesHutMixin);
+  }
+  else if (this.constants.physics.hierarchicalRepulsion.enabled == true) {
+    this._clearMixin(BarnesHutMixin);
+    this._clearMixin(RepulsionMixin);
+
+    this.constants.physics.centralGravity = this.constants.physics.hierarchicalRepulsion.centralGravity;
+    this.constants.physics.springLength = this.constants.physics.hierarchicalRepulsion.springLength;
+    this.constants.physics.springConstant = this.constants.physics.hierarchicalRepulsion.springConstant;
+    this.constants.physics.damping = this.constants.physics.hierarchicalRepulsion.damping;
+
+    this._loadMixin(HierarchialRepulsionMixin);
+  }
+  else {
+    this._clearMixin(BarnesHutMixin);
+    this._clearMixin(HierarchialRepulsionMixin);
+    this.barnesHutTree = undefined;
+
+    this.constants.physics.centralGravity = this.constants.physics.repulsion.centralGravity;
+    this.constants.physics.springLength = this.constants.physics.repulsion.springLength;
+    this.constants.physics.springConstant = this.constants.physics.repulsion.springConstant;
+    this.constants.physics.damping = this.constants.physics.repulsion.damping;
+
+    this._loadMixin(RepulsionMixin);
+  }
+};
+
+/**
+ * Before calculating the forces, we check if we need to cluster to keep up performance and we check
+ * if there is more than one node. If it is just one node, we dont calculate anything.
+ *
+ * @private
+ */
+exports._initializeForceCalculation = function () {
+  // stop calculation if there is only one node
+  if (this.nodeIndices.length == 1) {
+    this.nodes[this.nodeIndices[0]]._setForce(0, 0);
+  }
+  else {
+    // if there are too many nodes on screen, we cluster without repositioning
+    if (this.nodeIndices.length > this.constants.clustering.clusterThreshold && this.constants.clustering.enabled == true) {
+      this.clusterToFit(this.constants.clustering.reduceToNodes, false);
+    }
+
+    // we now start the force calculation
+    this._calculateForces();
+  }
+};
+
+
+/**
+ * Calculate the external forces acting on the nodes
+ * Forces are caused by: edges, repulsing forces between nodes, gravity
+ * @private
+ */
+exports._calculateForces = function () {
+  // Gravity is required to keep separated groups from floating off
+  // the forces are reset to zero in this loop by using _setForce instead
+  // of _addForce
+
+  this._calculateGravitationalForces();
+  this._calculateNodeForces();
+
+  if (this.constants.smoothCurves == true) {
+    this._calculateSpringForcesWithSupport();
+  }
+  else {
+    if (this.constants.physics.hierarchicalRepulsion.enabled == true) {
+      this._calculateHierarchicalSpringForces();
+    }
+    else {
+      this._calculateSpringForces();
+    }
+  }
+};
+
+
+/**
+ * Smooth curves are created by adding invisible nodes in the center of the edges. These nodes are also
+ * handled in the calculateForces function. We then use a quadratic curve with the center node as control.
+ * This function joins the datanodes and invisible (called support) nodes into one object.
+ * We do this so we do not contaminate this.nodes with the support nodes.
+ *
+ * @private
+ */
+exports._updateCalculationNodes = function () {
+  if (this.constants.smoothCurves == true) {
+    this.calculationNodes = {};
+    this.calculationNodeIndices = [];
+
+    for (var nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        this.calculationNodes[nodeId] = this.nodes[nodeId];
+      }
+    }
+    var supportNodes = this.sectors['support']['nodes'];
+    for (var supportNodeId in supportNodes) {
+      if (supportNodes.hasOwnProperty(supportNodeId)) {
+        if (this.edges.hasOwnProperty(supportNodes[supportNodeId].parentEdgeId)) {
+          this.calculationNodes[supportNodeId] = supportNodes[supportNodeId];
+        }
+        else {
+          supportNodes[supportNodeId]._setForce(0, 0);
+        }
+      }
+    }
+
+    for (var idx in this.calculationNodes) {
+      if (this.calculationNodes.hasOwnProperty(idx)) {
+        this.calculationNodeIndices.push(idx);
+      }
+    }
+  }
+  else {
+    this.calculationNodes = this.nodes;
+    this.calculationNodeIndices = this.nodeIndices;
+  }
+};
+
+
+/**
+ * this function applies the central gravity effect to keep groups from floating off
+ *
+ * @private
+ */
+exports._calculateGravitationalForces = function () {
+  var dx, dy, distance, node, i;
+  var nodes = this.calculationNodes;
+  var gravity = this.constants.physics.centralGravity;
+  var gravityForce = 0;
+
+  for (i = 0; i < this.calculationNodeIndices.length; i++) {
+    node = nodes[this.calculationNodeIndices[i]];
+    node.damping = this.constants.physics.damping; // possibly add function to alter damping properties of clusters.
+    // gravity does not apply when we are in a pocket sector
+    if (this._sector() == "default" && gravity != 0) {
+      dx = -node.x;
+      dy = -node.y;
+      distance = Math.sqrt(dx * dx + dy * dy);
+
+      gravityForce = (distance == 0) ? 0 : (gravity / distance);
+      node.fx = dx * gravityForce;
+      node.fy = dy * gravityForce;
+    }
+    else {
+      node.fx = 0;
+      node.fy = 0;
+    }
+  }
+};
+
+
+
+
+/**
+ * this function calculates the effects of the springs in the case of unsmooth curves.
+ *
+ * @private
+ */
+exports._calculateSpringForces = function () {
+  var edgeLength, edge, edgeId;
+  var dx, dy, fx, fy, springForce, distance;
+  var edges = this.edges;
+
+  // forces caused by the edges, modelled as springs
+  for (edgeId in edges) {
+    if (edges.hasOwnProperty(edgeId)) {
+      edge = edges[edgeId];
+      if (edge.connected) {
+        // only calculate forces if nodes are in the same sector
+        if (this.nodes.hasOwnProperty(edge.toId) && this.nodes.hasOwnProperty(edge.fromId)) {
+          edgeLength = edge.customLength ? edge.length : this.constants.physics.springLength;
+          // this implies that the edges between big clusters are longer
+          edgeLength += (edge.to.clusterSize + edge.from.clusterSize - 2) * this.constants.clustering.edgeGrowth;
+
+          dx = (edge.from.x - edge.to.x);
+          dy = (edge.from.y - edge.to.y);
+          distance = Math.sqrt(dx * dx + dy * dy);
+
+          if (distance == 0) {
+            distance = 0.01;
+          }
+
+          // the 1/distance is so the fx and fy can be calculated without sine or cosine.
+          springForce = this.constants.physics.springConstant * (edgeLength - distance) / distance;
+
+          fx = dx * springForce;
+          fy = dy * springForce;
+
+          edge.from.fx += fx;
+          edge.from.fy += fy;
+          edge.to.fx -= fx;
+          edge.to.fy -= fy;
+        }
+      }
+    }
+  }
+};
+
+
+
+
+/**
+ * This function calculates the springforces on the nodes, accounting for the support nodes.
+ *
+ * @private
+ */
+exports._calculateSpringForcesWithSupport = function () {
+  var edgeLength, edge, edgeId, combinedClusterSize;
+  var edges = this.edges;
+
+  // forces caused by the edges, modelled as springs
+  for (edgeId in edges) {
+    if (edges.hasOwnProperty(edgeId)) {
+      edge = edges[edgeId];
+      if (edge.connected) {
+        // only calculate forces if nodes are in the same sector
+        if (this.nodes.hasOwnProperty(edge.toId) && this.nodes.hasOwnProperty(edge.fromId)) {
+          if (edge.via != null) {
+            var node1 = edge.to;
+            var node2 = edge.via;
+            var node3 = edge.from;
+
+            edgeLength = edge.customLength ? edge.length : this.constants.physics.springLength;
+
+            combinedClusterSize = node1.clusterSize + node3.clusterSize - 2;
+
+            // this implies that the edges between big clusters are longer
+            edgeLength += combinedClusterSize * this.constants.clustering.edgeGrowth;
+            this._calculateSpringForce(node1, node2, 0.5 * edgeLength);
+            this._calculateSpringForce(node2, node3, 0.5 * edgeLength);
+          }
+        }
+      }
+    }
+  }
+};
+
+
+/**
+ * This is the code actually performing the calculation for the function above. It is split out to avoid repetition.
+ *
+ * @param node1
+ * @param node2
+ * @param edgeLength
+ * @private
+ */
+exports._calculateSpringForce = function (node1, node2, edgeLength) {
+  var dx, dy, fx, fy, springForce, distance;
+
+  dx = (node1.x - node2.x);
+  dy = (node1.y - node2.y);
+  distance = Math.sqrt(dx * dx + dy * dy);
+
+  if (distance == 0) {
+    distance = 0.01;
+  }
+
+  // the 1/distance is so the fx and fy can be calculated without sine or cosine.
+  springForce = this.constants.physics.springConstant * (edgeLength - distance) / distance;
+
+  fx = dx * springForce;
+  fy = dy * springForce;
+
+  node1.fx += fx;
+  node1.fy += fy;
+  node2.fx -= fx;
+  node2.fy -= fy;
+};
+
+
+/**
+ * Load the HTML for the physics config and bind it
+ * @private
+ */
+exports._loadPhysicsConfiguration = function () {
+  if (this.physicsConfiguration === undefined) {
+    this.backupConstants = {};
+    util.deepExtend(this.backupConstants,this.constants);
+
+    var hierarchicalLayoutDirections = ["LR", "RL", "UD", "DU"];
+    this.physicsConfiguration = document.createElement('div');
+    this.physicsConfiguration.className = "PhysicsConfiguration";
+    this.physicsConfiguration.innerHTML = '' +
+      '<table><tr><td><b>Simulation Mode:</b></td></tr>' +
+      '<tr>' +
+      '<td width="120px"><input type="radio" name="graph_physicsMethod" id="graph_physicsMethod1" value="BH" checked="checked">Barnes Hut</td>' +
+      '<td width="120px"><input type="radio" name="graph_physicsMethod" id="graph_physicsMethod2" value="R">Repulsion</td>' +
+      '<td width="120px"><input type="radio" name="graph_physicsMethod" id="graph_physicsMethod3" value="H">Hierarchical</td>' +
+      '</tr>' +
+      '</table>' +
+      '<table id="graph_BH_table" style="display:none">' +
+      '<tr><td><b>Barnes Hut</b></td></tr>' +
+      '<tr>' +
+      '<td width="150px">gravitationalConstant</td><td>0</td><td><input type="range" min="0" max="20000" value="' + (-1 * this.constants.physics.barnesHut.gravitationalConstant) + '" step="25" style="width:300px" id="graph_BH_gc"></td><td  width="50px">-20000</td><td><input value="' + (-1 * this.constants.physics.barnesHut.gravitationalConstant) + '" id="graph_BH_gc_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">centralGravity</td><td>0</td><td><input type="range" min="0" max="3"  value="' + this.constants.physics.barnesHut.centralGravity + '" step="0.05"  style="width:300px" id="graph_BH_cg"></td><td>3</td><td><input value="' + this.constants.physics.barnesHut.centralGravity + '" id="graph_BH_cg_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">springLength</td><td>0</td><td><input type="range" min="0" max="500" value="' + this.constants.physics.barnesHut.springLength + '" step="1" style="width:300px" id="graph_BH_sl"></td><td>500</td><td><input value="' + this.constants.physics.barnesHut.springLength + '" id="graph_BH_sl_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">springConstant</td><td>0</td><td><input type="range" min="0" max="0.5" value="' + this.constants.physics.barnesHut.springConstant + '" step="0.001" style="width:300px" id="graph_BH_sc"></td><td>0.5</td><td><input value="' + this.constants.physics.barnesHut.springConstant + '" id="graph_BH_sc_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">damping</td><td>0</td><td><input type="range" min="0" max="0.3" value="' + this.constants.physics.barnesHut.damping + '" step="0.005" style="width:300px" id="graph_BH_damp"></td><td>0.3</td><td><input value="' + this.constants.physics.barnesHut.damping + '" id="graph_BH_damp_value" style="width:60px"></td>' +
+      '</tr>' +
+      '</table>' +
+      '<table id="graph_R_table" style="display:none">' +
+      '<tr><td><b>Repulsion</b></td></tr>' +
+      '<tr>' +
+      '<td width="150px">nodeDistance</td><td>0</td><td><input type="range" min="0" max="300" value="' + this.constants.physics.repulsion.nodeDistance + '" step="1" style="width:300px" id="graph_R_nd"></td><td width="50px">300</td><td><input value="' + this.constants.physics.repulsion.nodeDistance + '" id="graph_R_nd_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">centralGravity</td><td>0</td><td><input type="range" min="0" max="3"  value="' + this.constants.physics.repulsion.centralGravity + '" step="0.05"  style="width:300px" id="graph_R_cg"></td><td>3</td><td><input value="' + this.constants.physics.repulsion.centralGravity + '" id="graph_R_cg_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">springLength</td><td>0</td><td><input type="range" min="0" max="500" value="' + this.constants.physics.repulsion.springLength + '" step="1" style="width:300px" id="graph_R_sl"></td><td>500</td><td><input value="' + this.constants.physics.repulsion.springLength + '" id="graph_R_sl_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">springConstant</td><td>0</td><td><input type="range" min="0" max="0.5" value="' + this.constants.physics.repulsion.springConstant + '" step="0.001" style="width:300px" id="graph_R_sc"></td><td>0.5</td><td><input value="' + this.constants.physics.repulsion.springConstant + '" id="graph_R_sc_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">damping</td><td>0</td><td><input type="range" min="0" max="0.3" value="' + this.constants.physics.repulsion.damping + '" step="0.005" style="width:300px" id="graph_R_damp"></td><td>0.3</td><td><input value="' + this.constants.physics.repulsion.damping + '" id="graph_R_damp_value" style="width:60px"></td>' +
+      '</tr>' +
+      '</table>' +
+      '<table id="graph_H_table" style="display:none">' +
+      '<tr><td width="150"><b>Hierarchical</b></td></tr>' +
+      '<tr>' +
+      '<td width="150px">nodeDistance</td><td>0</td><td><input type="range" min="0" max="300" value="' + this.constants.physics.hierarchicalRepulsion.nodeDistance + '" step="1" style="width:300px" id="graph_H_nd"></td><td width="50px">300</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.nodeDistance + '" id="graph_H_nd_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">centralGravity</td><td>0</td><td><input type="range" min="0" max="3"  value="' + this.constants.physics.hierarchicalRepulsion.centralGravity + '" step="0.05"  style="width:300px" id="graph_H_cg"></td><td>3</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.centralGravity + '" id="graph_H_cg_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">springLength</td><td>0</td><td><input type="range" min="0" max="500" value="' + this.constants.physics.hierarchicalRepulsion.springLength + '" step="1" style="width:300px" id="graph_H_sl"></td><td>500</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.springLength + '" id="graph_H_sl_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">springConstant</td><td>0</td><td><input type="range" min="0" max="0.5" value="' + this.constants.physics.hierarchicalRepulsion.springConstant + '" step="0.001" style="width:300px" id="graph_H_sc"></td><td>0.5</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.springConstant + '" id="graph_H_sc_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">damping</td><td>0</td><td><input type="range" min="0" max="0.3" value="' + this.constants.physics.hierarchicalRepulsion.damping + '" step="0.005" style="width:300px" id="graph_H_damp"></td><td>0.3</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.damping + '" id="graph_H_damp_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">direction</td><td>1</td><td><input type="range" min="0" max="3" value="' + hierarchicalLayoutDirections.indexOf(this.constants.hierarchicalLayout.direction) + '" step="1" style="width:300px" id="graph_H_direction"></td><td>4</td><td><input value="' + this.constants.hierarchicalLayout.direction + '" id="graph_H_direction_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">levelSeparation</td><td>1</td><td><input type="range" min="0" max="500" value="' + this.constants.hierarchicalLayout.levelSeparation + '" step="1" style="width:300px" id="graph_H_levsep"></td><td>500</td><td><input value="' + this.constants.hierarchicalLayout.levelSeparation + '" id="graph_H_levsep_value" style="width:60px"></td>' +
+      '</tr>' +
+      '<tr>' +
+      '<td width="150px">nodeSpacing</td><td>1</td><td><input type="range" min="0" max="500" value="' + this.constants.hierarchicalLayout.nodeSpacing + '" step="1" style="width:300px" id="graph_H_nspac"></td><td>500</td><td><input value="' + this.constants.hierarchicalLayout.nodeSpacing + '" id="graph_H_nspac_value" style="width:60px"></td>' +
+      '</tr>' +
+      '</table>' +
+      '<table><tr><td><b>Options:</b></td></tr>' +
+      '<tr>' +
+      '<td width="180px"><input type="button" id="graph_toggleSmooth" value="Toggle smoothCurves" style="width:150px"></td>' +
+      '<td width="180px"><input type="button" id="graph_repositionNodes" value="Reinitialize" style="width:150px"></td>' +
+      '<td width="180px"><input type="button" id="graph_generateOptions" value="Generate Options" style="width:150px"></td>' +
+      '</tr>' +
+      '</table>'
+    this.containerElement.parentElement.insertBefore(this.physicsConfiguration, this.containerElement);
+    this.optionsDiv = document.createElement("div");
+    this.optionsDiv.style.fontSize = "14px";
+    this.optionsDiv.style.fontFamily = "verdana";
+    this.containerElement.parentElement.insertBefore(this.optionsDiv, this.containerElement);
+
+    var rangeElement;
+    rangeElement = document.getElementById('graph_BH_gc');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_gc', -1, "physics_barnesHut_gravitationalConstant");
+    rangeElement = document.getElementById('graph_BH_cg');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_cg', 1, "physics_centralGravity");
+    rangeElement = document.getElementById('graph_BH_sc');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_sc', 1, "physics_springConstant");
+    rangeElement = document.getElementById('graph_BH_sl');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_sl', 1, "physics_springLength");
+    rangeElement = document.getElementById('graph_BH_damp');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_damp', 1, "physics_damping");
+
+    rangeElement = document.getElementById('graph_R_nd');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_nd', 1, "physics_repulsion_nodeDistance");
+    rangeElement = document.getElementById('graph_R_cg');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_cg', 1, "physics_centralGravity");
+    rangeElement = document.getElementById('graph_R_sc');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_sc', 1, "physics_springConstant");
+    rangeElement = document.getElementById('graph_R_sl');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_sl', 1, "physics_springLength");
+    rangeElement = document.getElementById('graph_R_damp');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_damp', 1, "physics_damping");
+
+    rangeElement = document.getElementById('graph_H_nd');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_nd', 1, "physics_hierarchicalRepulsion_nodeDistance");
+    rangeElement = document.getElementById('graph_H_cg');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_cg', 1, "physics_centralGravity");
+    rangeElement = document.getElementById('graph_H_sc');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_sc', 1, "physics_springConstant");
+    rangeElement = document.getElementById('graph_H_sl');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_sl', 1, "physics_springLength");
+    rangeElement = document.getElementById('graph_H_damp');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_damp', 1, "physics_damping");
+    rangeElement = document.getElementById('graph_H_direction');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_direction', hierarchicalLayoutDirections, "hierarchicalLayout_direction");
+    rangeElement = document.getElementById('graph_H_levsep');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_levsep', 1, "hierarchicalLayout_levelSeparation");
+    rangeElement = document.getElementById('graph_H_nspac');
+    rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_nspac', 1, "hierarchicalLayout_nodeSpacing");
+
+    var radioButton1 = document.getElementById("graph_physicsMethod1");
+    var radioButton2 = document.getElementById("graph_physicsMethod2");
+    var radioButton3 = document.getElementById("graph_physicsMethod3");
+    radioButton2.checked = true;
+    if (this.constants.physics.barnesHut.enabled) {
+      radioButton1.checked = true;
+    }
+    if (this.constants.hierarchicalLayout.enabled) {
+      radioButton3.checked = true;
+    }
+
+    var graph_toggleSmooth = document.getElementById("graph_toggleSmooth");
+    var graph_repositionNodes = document.getElementById("graph_repositionNodes");
+    var graph_generateOptions = document.getElementById("graph_generateOptions");
+
+    graph_toggleSmooth.onclick = graphToggleSmoothCurves.bind(this);
+    graph_repositionNodes.onclick = graphRepositionNodes.bind(this);
+    graph_generateOptions.onclick = graphGenerateOptions.bind(this);
+    if (this.constants.smoothCurves == true) {
+      graph_toggleSmooth.style.background = "#A4FF56";
+    }
+    else {
+      graph_toggleSmooth.style.background = "#FF8532";
+    }
+
+
+    switchConfigurations.apply(this);
+
+    radioButton1.onchange = switchConfigurations.bind(this);
+    radioButton2.onchange = switchConfigurations.bind(this);
+    radioButton3.onchange = switchConfigurations.bind(this);
+  }
+};
+
+/**
+ * This overwrites the this.constants.
+ *
+ * @param constantsVariableName
+ * @param value
+ * @private
+ */
+exports._overWriteGraphConstants = function (constantsVariableName, value) {
+  var nameArray = constantsVariableName.split("_");
+  if (nameArray.length == 1) {
+    this.constants[nameArray[0]] = value;
+  }
+  else if (nameArray.length == 2) {
+    this.constants[nameArray[0]][nameArray[1]] = value;
+  }
+  else if (nameArray.length == 3) {
+    this.constants[nameArray[0]][nameArray[1]][nameArray[2]] = value;
+  }
+};
+
+
+/**
+ * this function is bound to the toggle smooth curves button. That is also why it is not in the prototype.
+ */
+function graphToggleSmoothCurves () {
+  this.constants.smoothCurves = !this.constants.smoothCurves;
+  var graph_toggleSmooth = document.getElementById("graph_toggleSmooth");
+  if (this.constants.smoothCurves == true) {graph_toggleSmooth.style.background = "#A4FF56";}
+  else                                     {graph_toggleSmooth.style.background = "#FF8532";}
+
+  this._configureSmoothCurves(false);
+}
+
+/**
+ * this function is used to scramble the nodes
+ *
+ */
+function graphRepositionNodes () {
+  for (var nodeId in this.calculationNodes) {
+    if (this.calculationNodes.hasOwnProperty(nodeId)) {
+      this.calculationNodes[nodeId].vx = 0;  this.calculationNodes[nodeId].vy = 0;
+      this.calculationNodes[nodeId].fx = 0;  this.calculationNodes[nodeId].fy = 0;
+    }
+  }
+  if (this.constants.hierarchicalLayout.enabled == true) {
+    this._setupHierarchicalLayout();
+  }
+  else {
+    this.repositionNodes();
+  }
+  this.moving = true;
+  this.start();
+}
+
+/**
+ *  this is used to generate an options file from the playing with physics system.
+ */
+function graphGenerateOptions () {
+  var options = "No options are required, default values used.";
+  var optionsSpecific = [];
+  var radioButton1 = document.getElementById("graph_physicsMethod1");
+  var radioButton2 = document.getElementById("graph_physicsMethod2");
+  if (radioButton1.checked == true) {
+    if (this.constants.physics.barnesHut.gravitationalConstant != this.backupConstants.physics.barnesHut.gravitationalConstant) {optionsSpecific.push("gravitationalConstant: " + this.constants.physics.barnesHut.gravitationalConstant);}
+    if (this.constants.physics.centralGravity != this.backupConstants.physics.barnesHut.centralGravity)                         {optionsSpecific.push("centralGravity: " + this.constants.physics.centralGravity);}
+    if (this.constants.physics.springLength != this.backupConstants.physics.barnesHut.springLength)                             {optionsSpecific.push("springLength: " + this.constants.physics.springLength);}
+    if (this.constants.physics.springConstant != this.backupConstants.physics.barnesHut.springConstant)                         {optionsSpecific.push("springConstant: " + this.constants.physics.springConstant);}
+    if (this.constants.physics.damping != this.backupConstants.physics.barnesHut.damping)                                       {optionsSpecific.push("damping: " + this.constants.physics.damping);}
+    if (optionsSpecific.length != 0) {
+      options = "var options = {";
+      options += "physics: {barnesHut: {";
+      for (var i = 0; i < optionsSpecific.length; i++) {
+        options += optionsSpecific[i];
+        if (i < optionsSpecific.length - 1) {
+          options += ", "
+        }
+      }
+      options += '}}'
+    }
+    if (this.constants.smoothCurves != this.backupConstants.smoothCurves) {
+      if (optionsSpecific.length == 0) {options = "var options = {";}
+      else {options += ", "}
+      options += "smoothCurves: " + this.constants.smoothCurves;
+    }
+    if (options != "No options are required, default values used.") {
+      options += '};'
+    }
+  }
+  else if (radioButton2.checked == true) {
+    options = "var options = {";
+    options += "physics: {barnesHut: {enabled: false}";
+    if (this.constants.physics.repulsion.nodeDistance != this.backupConstants.physics.repulsion.nodeDistance)  {optionsSpecific.push("nodeDistance: " + this.constants.physics.repulsion.nodeDistance);}
+    if (this.constants.physics.centralGravity != this.backupConstants.physics.repulsion.centralGravity)        {optionsSpecific.push("centralGravity: " + this.constants.physics.centralGravity);}
+    if (this.constants.physics.springLength != this.backupConstants.physics.repulsion.springLength)            {optionsSpecific.push("springLength: " + this.constants.physics.springLength);}
+    if (this.constants.physics.springConstant != this.backupConstants.physics.repulsion.springConstant)        {optionsSpecific.push("springConstant: " + this.constants.physics.springConstant);}
+    if (this.constants.physics.damping != this.backupConstants.physics.repulsion.damping)                      {optionsSpecific.push("damping: " + this.constants.physics.damping);}
+    if (optionsSpecific.length != 0) {
+      options += ", repulsion: {";
+      for (var i = 0; i < optionsSpecific.length; i++) {
+        options += optionsSpecific[i];
+        if (i < optionsSpecific.length - 1) {
+          options += ", "
+        }
+      }
+      options += '}}'
+    }
+    if (optionsSpecific.length == 0) {options += "}"}
+    if (this.constants.smoothCurves != this.backupConstants.smoothCurves) {
+      options += ", smoothCurves: " + this.constants.smoothCurves;
+    }
+    options += '};'
+  }
+  else {
+    options = "var options = {";
+    if (this.constants.physics.hierarchicalRepulsion.nodeDistance != this.backupConstants.physics.hierarchicalRepulsion.nodeDistance)  {optionsSpecific.push("nodeDistance: " + this.constants.physics.hierarchicalRepulsion.nodeDistance);}
+    if (this.constants.physics.centralGravity != this.backupConstants.physics.hierarchicalRepulsion.centralGravity)        {optionsSpecific.push("centralGravity: " + this.constants.physics.centralGravity);}
+    if (this.constants.physics.springLength != this.backupConstants.physics.hierarchicalRepulsion.springLength)            {optionsSpecific.push("springLength: " + this.constants.physics.springLength);}
+    if (this.constants.physics.springConstant != this.backupConstants.physics.hierarchicalRepulsion.springConstant)        {optionsSpecific.push("springConstant: " + this.constants.physics.springConstant);}
+    if (this.constants.physics.damping != this.backupConstants.physics.hierarchicalRepulsion.damping)                      {optionsSpecific.push("damping: " + this.constants.physics.damping);}
+    if (optionsSpecific.length != 0) {
+      options += "physics: {hierarchicalRepulsion: {";
+      for (var i = 0; i < optionsSpecific.length; i++) {
+        options += optionsSpecific[i];
+        if (i < optionsSpecific.length - 1) {
+          options += ", ";
+        }
+      }
+      options += '}},';
+    }
+    options += 'hierarchicalLayout: {';
+    optionsSpecific = [];
+    if (this.constants.hierarchicalLayout.direction != this.backupConstants.hierarchicalLayout.direction)                       {optionsSpecific.push("direction: " + this.constants.hierarchicalLayout.direction);}
+    if (Math.abs(this.constants.hierarchicalLayout.levelSeparation) != this.backupConstants.hierarchicalLayout.levelSeparation) {optionsSpecific.push("levelSeparation: " + this.constants.hierarchicalLayout.levelSeparation);}
+    if (this.constants.hierarchicalLayout.nodeSpacing != this.backupConstants.hierarchicalLayout.nodeSpacing)                   {optionsSpecific.push("nodeSpacing: " + this.constants.hierarchicalLayout.nodeSpacing);}
+    if (optionsSpecific.length != 0) {
+      for (var i = 0; i < optionsSpecific.length; i++) {
+        options += optionsSpecific[i];
+        if (i < optionsSpecific.length - 1) {
+          options += ", "
+        }
+      }
+      options += '}'
+    }
+    else {
+      options += "enabled:true}";
+    }
+    options += '};'
+  }
+
+
+  this.optionsDiv.innerHTML = options;
+}
+
+/**
+ * this is used to switch between barnesHut, repulsion and hierarchical.
+ *
+ */
+function switchConfigurations () {
+  var ids = ["graph_BH_table", "graph_R_table", "graph_H_table"];
+  var radioButton = document.querySelector('input[name="graph_physicsMethod"]:checked').value;
+  var tableId = "graph_" + radioButton + "_table";
+  var table = document.getElementById(tableId);
+  table.style.display = "block";
+  for (var i = 0; i < ids.length; i++) {
+    if (ids[i] != tableId) {
+      table = document.getElementById(ids[i]);
+      table.style.display = "none";
+    }
+  }
+  this._restoreNodes();
+  if (radioButton == "R") {
+    this.constants.hierarchicalLayout.enabled = false;
+    this.constants.physics.hierarchicalRepulsion.enabled = false;
+    this.constants.physics.barnesHut.enabled = false;
+  }
+  else if (radioButton == "H") {
+    if (this.constants.hierarchicalLayout.enabled == false) {
+      this.constants.hierarchicalLayout.enabled = true;
+      this.constants.physics.hierarchicalRepulsion.enabled = true;
+      this.constants.physics.barnesHut.enabled = false;
+      this._setupHierarchicalLayout();
+    }
+  }
+  else {
+    this.constants.hierarchicalLayout.enabled = false;
+    this.constants.physics.hierarchicalRepulsion.enabled = false;
+    this.constants.physics.barnesHut.enabled = true;
+  }
+  this._loadSelectedForceSolver();
+  var graph_toggleSmooth = document.getElementById("graph_toggleSmooth");
+  if (this.constants.smoothCurves == true) {graph_toggleSmooth.style.background = "#A4FF56";}
+  else                                     {graph_toggleSmooth.style.background = "#FF8532";}
+  this.moving = true;
+  this.start();
+}
+
+
+/**
+ * this generates the ranges depending on the iniital values.
+ *
+ * @param id
+ * @param map
+ * @param constantsVariableName
+ */
+function showValueOfRange (id,map,constantsVariableName) {
+  var valueId = id + "_value";
+  var rangeValue = document.getElementById(id).value;
+
+  if (map instanceof Array) {
+    document.getElementById(valueId).value = map[parseInt(rangeValue)];
+    this._overWriteGraphConstants(constantsVariableName,map[parseInt(rangeValue)]);
+  }
+  else {
+    document.getElementById(valueId).value = parseInt(map) * parseFloat(rangeValue);
+    this._overWriteGraphConstants(constantsVariableName, parseInt(map) * parseFloat(rangeValue));
+  }
+
+  if (constantsVariableName == "hierarchicalLayout_direction" ||
+    constantsVariableName == "hierarchicalLayout_levelSeparation" ||
+    constantsVariableName == "hierarchicalLayout_nodeSpacing") {
+    this._setupHierarchicalLayout();
+  }
+  this.moving = true;
+  this.start();
+}

lib/network/mixins/physics/RepulsionMixin.js

@@ -0,0 +1,58 @@
+/**
+ * Calculate the forces the nodes apply on each other based on a repulsion field.
+ * This field is linearly approximated.
+ *
+ * @private
+ */
+exports._calculateNodeForces = function () {
+  var dx, dy, angle, distance, fx, fy, combinedClusterSize,
+    repulsingForce, node1, node2, i, j;
+
+  var nodes = this.calculationNodes;
+  var nodeIndices = this.calculationNodeIndices;
+
+  // approximation constants
+  var a_base = -2 / 3;
+  var b = 4 / 3;
+
+  // repulsing forces between nodes
+  var nodeDistance = this.constants.physics.repulsion.nodeDistance;
+  var minimumDistance = nodeDistance;
+
+  // we loop from i over all but the last entree in the array
+  // j loops from i+1 to the last. This way we do not double count any of the indices, nor i == j
+  for (i = 0; i < nodeIndices.length - 1; i++) {
+    node1 = nodes[nodeIndices[i]];
+    for (j = i + 1; j < nodeIndices.length; j++) {
+      node2 = nodes[nodeIndices[j]];
+      combinedClusterSize = node1.clusterSize + node2.clusterSize - 2;
+
+      dx = node2.x - node1.x;
+      dy = node2.y - node1.y;
+      distance = Math.sqrt(dx * dx + dy * dy);
+
+      minimumDistance = (combinedClusterSize == 0) ? nodeDistance : (nodeDistance * (1 + combinedClusterSize * this.constants.clustering.distanceAmplification));
+      var a = a_base / minimumDistance;
+      if (distance < 2 * minimumDistance) {
+        if (distance < 0.5 * minimumDistance) {
+          repulsingForce = 1.0;
+        }
+        else {
+          repulsingForce = a * distance + b; // linear approx of  1 / (1 + Math.exp((distance / minimumDistance - 1) * steepness))
+        }
+
+        // amplify the repulsion for clusters.
+        repulsingForce *= (combinedClusterSize == 0) ? 1 : 1 + combinedClusterSize * this.constants.clustering.forceAmplification;
+        repulsingForce = repulsingForce / distance;
+
+        fx = dx * repulsingForce;
+        fy = dy * repulsingForce;
+
+        node1.fx -= fx;
+        node1.fy -= fy;
+        node2.fx += fx;
+        node2.fy += fy;
+      }
+    }
+  }
+};

lib/network/networkMixins/HierarchicalLayoutMixin.js

@@ -1,311 +0,0 @@
-var HierarchicalLayoutMixin = {
-
-
-
-  _resetLevels : function() {
-    for (var nodeId in this.nodes) {
-      if (this.nodes.hasOwnProperty(nodeId)) {
-        var node = this.nodes[nodeId];
-        if (node.preassignedLevel == false) {
-          node.level = -1;
-        }
-      }
-    }
-  },
-
-  /**
-   * This is the main function to layout the nodes in a hierarchical way.
-   * It checks if the node details are supplied correctly
-   *
-   * @private
-   */
-  _setupHierarchicalLayout : function() {
-    if (this.constants.hierarchicalLayout.enabled == true && this.nodeIndices.length > 0) {
-      if (this.constants.hierarchicalLayout.direction == "RL" || this.constants.hierarchicalLayout.direction == "DU") {
-        this.constants.hierarchicalLayout.levelSeparation *= -1;
-      }
-      else {
-        this.constants.hierarchicalLayout.levelSeparation = Math.abs(this.constants.hierarchicalLayout.levelSeparation);
-      }
-      // get the size of the largest hubs and check if the user has defined a level for a node.
-      var hubsize = 0;
-      var node, nodeId;
-      var definedLevel = false;
-      var undefinedLevel = false;
-
-      for (nodeId in this.nodes) {
-        if (this.nodes.hasOwnProperty(nodeId)) {
-          node = this.nodes[nodeId];
-          if (node.level != -1) {
-            definedLevel = true;
-          }
-          else {
-            undefinedLevel = true;
-          }
-          if (hubsize < node.edges.length) {
-            hubsize = node.edges.length;
-          }
-        }
-      }
-
-      // if the user defined some levels but not all, alert and run without hierarchical layout
-      if (undefinedLevel == true && definedLevel == true) {
-        alert("To use the hierarchical layout, nodes require either no predefined levels or levels have to be defined for all nodes.");
-        this.zoomExtent(true,this.constants.clustering.enabled);
-        if (!this.constants.clustering.enabled) {
-          this.start();
-        }
-      }
-      else {
-        // setup the system to use hierarchical method.
-        this._changeConstants();
-
-        // define levels if undefined by the users. Based on hubsize
-        if (undefinedLevel == true) {
-          this._determineLevels(hubsize);
-        }
-        // check the distribution of the nodes per level.
-        var distribution = this._getDistribution();
-
-        // place the nodes on the canvas. This also stablilizes the system.
-        this._placeNodesByHierarchy(distribution);
-
-        // start the simulation.
-        this.start();
-      }
-    }
-  },
-
-
-  /**
-   * This function places the nodes on the canvas based on the hierarchial distribution.
-   *
-   * @param {Object} distribution | obtained by the function this._getDistribution()
-   * @private
-   */
-  _placeNodesByHierarchy : function(distribution) {
-    var nodeId, node;
-
-    // start placing all the level 0 nodes first. Then recursively position their branches.
-    for (nodeId in distribution[0].nodes) {
-      if (distribution[0].nodes.hasOwnProperty(nodeId)) {
-        node = distribution[0].nodes[nodeId];
-        if (this.constants.hierarchicalLayout.direction == "UD" || this.constants.hierarchicalLayout.direction == "DU") {
-          if (node.xFixed) {
-            node.x = distribution[0].minPos;
-            node.xFixed = false;
-
-            distribution[0].minPos += distribution[0].nodeSpacing;
-          }
-        }
-        else {
-          if (node.yFixed) {
-            node.y = distribution[0].minPos;
-            node.yFixed = false;
-
-            distribution[0].minPos += distribution[0].nodeSpacing;
-          }
-        }
-        this._placeBranchNodes(node.edges,node.id,distribution,node.level);
-      }
-    }
-
-    // stabilize the system after positioning. This function calls zoomExtent.
-    this._stabilize();
-  },
-
-
-  /**
-   * This function get the distribution of levels based on hubsize
-   *
-   * @returns {Object}
-   * @private
-   */
-  _getDistribution : function() {
-    var distribution = {};
-    var nodeId, node, level;
-
-    // we fix Y because the hierarchy is vertical, we fix X so we do not give a node an x position for a second time.
-    // the fix of X is removed after the x value has been set.
-    for (nodeId in this.nodes) {
-      if (this.nodes.hasOwnProperty(nodeId)) {
-        node = this.nodes[nodeId];
-        node.xFixed = true;
-        node.yFixed = true;
-        if (this.constants.hierarchicalLayout.direction == "UD" || this.constants.hierarchicalLayout.direction == "DU") {
-          node.y = this.constants.hierarchicalLayout.levelSeparation*node.level;
-        }
-        else {
-          node.x = this.constants.hierarchicalLayout.levelSeparation*node.level;
-        }
-        if (!distribution.hasOwnProperty(node.level)) {
-          distribution[node.level] = {amount: 0, nodes: {}, minPos:0, nodeSpacing:0};
-        }
-        distribution[node.level].amount += 1;
-        distribution[node.level].nodes[node.id] = node;
-      }
-    }
-
-    // determine the largest amount of nodes of all levels
-    var maxCount = 0;
-    for (level in distribution) {
-      if (distribution.hasOwnProperty(level)) {
-        if (maxCount < distribution[level].amount) {
-          maxCount = distribution[level].amount;
-        }
-      }
-    }
-
-    // set the initial position and spacing of each nodes accordingly
-    for (level in distribution) {
-      if (distribution.hasOwnProperty(level)) {
-        distribution[level].nodeSpacing = (maxCount + 1) * this.constants.hierarchicalLayout.nodeSpacing;
-        distribution[level].nodeSpacing /= (distribution[level].amount + 1);
-        distribution[level].minPos = distribution[level].nodeSpacing - (0.5 * (distribution[level].amount + 1) * distribution[level].nodeSpacing);
-      }
-    }
-
-    return distribution;
-  },
-
-
-  /**
-   * this function allocates nodes in levels based on the recursive branching from the largest hubs.
-   *
-   * @param hubsize
-   * @private
-   */
-  _determineLevels : function(hubsize) {
-    var nodeId, node;
-
-    // determine hubs
-    for (nodeId in this.nodes) {
-      if (this.nodes.hasOwnProperty(nodeId)) {
-        node = this.nodes[nodeId];
-        if (node.edges.length == hubsize) {
-          node.level = 0;
-        }
-      }
-    }
-
-    // branch from hubs
-    for (nodeId in this.nodes) {
-      if (this.nodes.hasOwnProperty(nodeId)) {
-        node = this.nodes[nodeId];
-        if (node.level == 0) {
-          this._setLevel(1,node.edges,node.id);
-        }
-      }
-    }
-  },
-
-
-  /**
-   * Since hierarchical layout does not support:
-   *    - smooth curves (based on the physics),
-   *    - clustering (based on dynamic node counts)
-   *
-   * We disable both features so there will be no problems.
-   *
-   * @private
-   */
-  _changeConstants : function() {
-    this.constants.clustering.enabled = false;
-    this.constants.physics.barnesHut.enabled = false;
-    this.constants.physics.hierarchicalRepulsion.enabled = true;
-    this._loadSelectedForceSolver();
-    this.constants.smoothCurves = false;
-    this._configureSmoothCurves();
-  },
-
-
-  /**
-   * This is a recursively called function to enumerate the branches from the largest hubs and place the nodes
-   * on a X position that ensures there will be no overlap.
-   *
-   * @param edges
-   * @param parentId
-   * @param distribution
-   * @param parentLevel
-   * @private
-   */
-  _placeBranchNodes : function(edges, parentId, distribution, parentLevel) {
-    for (var i = 0; i < edges.length; i++) {
-      var childNode = null;
-      if (edges[i].toId == parentId) {
-        childNode = edges[i].from;
-      }
-      else {
-        childNode = edges[i].to;
-      }
-
-      // if a node is conneceted to another node on the same level (or higher (means lower level))!, this is not handled here.
-      var nodeMoved = false;
-      if (this.constants.hierarchicalLayout.direction == "UD" || this.constants.hierarchicalLayout.direction == "DU") {
-        if (childNode.xFixed && childNode.level > parentLevel) {
-          childNode.xFixed = false;
-          childNode.x = distribution[childNode.level].minPos;
-          nodeMoved = true;
-        }
-      }
-      else {
-        if (childNode.yFixed && childNode.level > parentLevel) {
-          childNode.yFixed = false;
-          childNode.y = distribution[childNode.level].minPos;
-          nodeMoved = true;
-        }
-      }
-
-      if (nodeMoved == true) {
-        distribution[childNode.level].minPos += distribution[childNode.level].nodeSpacing;
-        if (childNode.edges.length > 1) {
-          this._placeBranchNodes(childNode.edges,childNode.id,distribution,childNode.level);
-        }
-      }
-    }
-  },
-
-
-  /**
-   * this function is called recursively to enumerate the barnches of the largest hubs and give each node a level.
-   *
-   * @param level
-   * @param edges
-   * @param parentId
-   * @private
-   */
-  _setLevel : function(level, edges, parentId) {
-    for (var i = 0; i < edges.length; i++) {
-      var childNode = null;
-      if (edges[i].toId == parentId) {
-        childNode = edges[i].from;
-      }
-      else {
-        childNode = edges[i].to;
-      }
-      if (childNode.level == -1 || childNode.level > level) {
-        childNode.level = level;
-        if (edges.length > 1) {
-          this._setLevel(level+1, childNode.edges, childNode.id);
-        }
-      }
-    }
-  },
-
-
-  /**
-   * Unfix nodes
-   *
-   * @private
-   */
-  _restoreNodes : function() {
-    for (nodeId in this.nodes) {
-      if (this.nodes.hasOwnProperty(nodeId)) {
-        this.nodes[nodeId].xFixed = false;
-        this.nodes[nodeId].yFixed = false;
-      }
-    }
-  }
-
-
-};

lib/network/networkMixins/ManipulationMixin.js

@@ -1,576 +0,0 @@
-/**
- * Created by Alex on 2/4/14.
- */
-
-var manipulationMixin = {
-
-  /**
-   * clears the toolbar div element of children
-   *
-   * @private
-   */
-  _clearManipulatorBar : function() {
-    while (this.manipulationDiv.hasChildNodes()) {
-      this.manipulationDiv.removeChild(this.manipulationDiv.firstChild);
-    }
-  },
-
-  /**
-   * Manipulation UI temporarily overloads certain functions to extend or replace them. To be able to restore
-   * these functions to their original functionality, we saved them in this.cachedFunctions.
-   * This function restores these functions to their original function.
-   *
-   * @private
-   */
-  _restoreOverloadedFunctions : function() {
-    for (var functionName in this.cachedFunctions) {
-      if (this.cachedFunctions.hasOwnProperty(functionName)) {
-        this[functionName] = this.cachedFunctions[functionName];
-      }
-    }
-  },
-
-  /**
-   * Enable or disable edit-mode.
-   *
-   * @private
-   */
-  _toggleEditMode : function() {
-    this.editMode = !this.editMode;
-    var toolbar = document.getElementById("network-manipulationDiv");
-    var closeDiv = document.getElementById("network-manipulation-closeDiv");
-    var editModeDiv = document.getElementById("network-manipulation-editMode");
-    if (this.editMode == true) {
-      toolbar.style.display="block";
-      closeDiv.style.display="block";
-      editModeDiv.style.display="none";
-      closeDiv.onclick = this._toggleEditMode.bind(this);
-    }
-    else {
-      toolbar.style.display="none";
-      closeDiv.style.display="none";
-      editModeDiv.style.display="block";
-      closeDiv.onclick = null;
-    }
-    this._createManipulatorBar()
-  },
-
-  /**
-   * main function, creates the main toolbar. Removes functions bound to the select event. Binds all the buttons of the toolbar.
-   *
-   * @private
-   */
-  _createManipulatorBar : function() {
-    // remove bound functions
-    if (this.boundFunction) {
-      this.off('select', this.boundFunction);
-    }
-    if (this.edgeBeingEdited !== undefined) {
-      this.edgeBeingEdited._disableControlNodes();
-      this.edgeBeingEdited = undefined;
-      this.selectedControlNode = null;
-    }
-
-    // restore overloaded functions
-    this._restoreOverloadedFunctions();
-
-    // resume calculation
-    this.freezeSimulation = false;
-
-    // reset global variables
-    this.blockConnectingEdgeSelection = false;
-    this.forceAppendSelection = false;
-
-    if (this.editMode == true) {
-      while (this.manipulationDiv.hasChildNodes()) {
-        this.manipulationDiv.removeChild(this.manipulationDiv.firstChild);
-      }
-      // add the icons to the manipulator div
-      this.manipulationDiv.innerHTML = "" +
-        "<span class='network-manipulationUI add' id='network-manipulate-addNode'>" +
-          "<span class='network-manipulationLabel'>"+this.constants.labels['add'] +"</span></span>" +
-        "<div class='network-seperatorLine'></div>" +
-        "<span class='network-manipulationUI connect' id='network-manipulate-connectNode'>" +
-          "<span class='network-manipulationLabel'>"+this.constants.labels['link'] +"</span></span>";
-      if (this._getSelectedNodeCount() == 1 && this.triggerFunctions.edit) {
-        this.manipulationDiv.innerHTML += "" +
-          "<div class='network-seperatorLine'></div>" +
-          "<span class='network-manipulationUI edit' id='network-manipulate-editNode'>" +
-            "<span class='network-manipulationLabel'>"+this.constants.labels['editNode'] +"</span></span>";
-      }
-      else if (this._getSelectedEdgeCount() == 1 && this._getSelectedNodeCount() == 0) {
-        this.manipulationDiv.innerHTML += "" +
-          "<div class='network-seperatorLine'></div>" +
-          "<span class='network-manipulationUI edit' id='network-manipulate-editEdge'>" +
-          "<span class='network-manipulationLabel'>"+this.constants.labels['editEdge'] +"</span></span>";
-      }
-      if (this._selectionIsEmpty() == false) {
-        this.manipulationDiv.innerHTML += "" +
-          "<div class='network-seperatorLine'></div>" +
-          "<span class='network-manipulationUI delete' id='network-manipulate-delete'>" +
-            "<span class='network-manipulationLabel'>"+this.constants.labels['del'] +"</span></span>";
-      }
-
-
-      // bind the icons
-      var addNodeButton = document.getElementById("network-manipulate-addNode");
-      addNodeButton.onclick = this._createAddNodeToolbar.bind(this);
-      var addEdgeButton = document.getElementById("network-manipulate-connectNode");
-      addEdgeButton.onclick = this._createAddEdgeToolbar.bind(this);
-      if (this._getSelectedNodeCount() == 1 && this.triggerFunctions.edit) {
-        var editButton = document.getElementById("network-manipulate-editNode");
-        editButton.onclick = this._editNode.bind(this);
-      }
-      else if (this._getSelectedEdgeCount() == 1 && this._getSelectedNodeCount() == 0) {
-        var editButton = document.getElementById("network-manipulate-editEdge");
-        editButton.onclick = this._createEditEdgeToolbar.bind(this);
-      }
-      if (this._selectionIsEmpty() == false) {
-        var deleteButton = document.getElementById("network-manipulate-delete");
-        deleteButton.onclick = this._deleteSelected.bind(this);
-      }
-      var closeDiv = document.getElementById("network-manipulation-closeDiv");
-      closeDiv.onclick = this._toggleEditMode.bind(this);
-
-      this.boundFunction = this._createManipulatorBar.bind(this);
-      this.on('select', this.boundFunction);
-    }
-    else {
-      this.editModeDiv.innerHTML = "" +
-        "<span class='network-manipulationUI edit editmode' id='network-manipulate-editModeButton'>" +
-        "<span class='network-manipulationLabel'>" + this.constants.labels['edit'] + "</span></span>";
-      var editModeButton = document.getElementById("network-manipulate-editModeButton");
-      editModeButton.onclick = this._toggleEditMode.bind(this);
-    }
-  },
-
-
-
-  /**
-   * Create the toolbar for adding Nodes
-   *
-   * @private
-   */
-  _createAddNodeToolbar : function() {
-    // clear the toolbar
-    this._clearManipulatorBar();
-    if (this.boundFunction) {
-      this.off('select', this.boundFunction);
-    }
-
-    // create the toolbar contents
-    this.manipulationDiv.innerHTML = "" +
-      "<span class='network-manipulationUI back' id='network-manipulate-back'>" +
-      "<span class='network-manipulationLabel'>" + this.constants.labels['back'] + " </span></span>" +
-      "<div class='network-seperatorLine'></div>" +
-      "<span class='network-manipulationUI none' id='network-manipulate-back'>" +
-      "<span id='network-manipulatorLabel' class='network-manipulationLabel'>" + this.constants.labels['addDescription'] + "</span></span>";
-
-    // bind the icon
-    var backButton = document.getElementById("network-manipulate-back");
-    backButton.onclick = this._createManipulatorBar.bind(this);
-
-    // we use the boundFunction so we can reference it when we unbind it from the "select" event.
-    this.boundFunction = this._addNode.bind(this);
-    this.on('select', this.boundFunction);
-  },
-
-
-  /**
-   * create the toolbar to connect nodes
-   *
-   * @private
-   */
-  _createAddEdgeToolbar : function() {
-    // clear the toolbar
-    this._clearManipulatorBar();
-    this._unselectAll(true);
-    this.freezeSimulation = true;
-
-    if (this.boundFunction) {
-      this.off('select', this.boundFunction);
-    }
-
-    this._unselectAll();
-    this.forceAppendSelection = false;
-    this.blockConnectingEdgeSelection = true;
-
-    this.manipulationDiv.innerHTML = "" +
-      "<span class='network-manipulationUI back' id='network-manipulate-back'>" +
-        "<span class='network-manipulationLabel'>" + this.constants.labels['back'] + " </span></span>" +
-      "<div class='network-seperatorLine'></div>" +
-      "<span class='network-manipulationUI none' id='network-manipulate-back'>" +
-        "<span id='network-manipulatorLabel' class='network-manipulationLabel'>" + this.constants.labels['linkDescription'] + "</span></span>";
-
-    // bind the icon
-    var backButton = document.getElementById("network-manipulate-back");
-    backButton.onclick = this._createManipulatorBar.bind(this);
-
-    // we use the boundFunction so we can reference it when we unbind it from the "select" event.
-    this.boundFunction = this._handleConnect.bind(this);
-    this.on('select', this.boundFunction);
-
-    // temporarily overload functions
-    this.cachedFunctions["_handleTouch"] = this._handleTouch;
-    this.cachedFunctions["_handleOnRelease"] = this._handleOnRelease;
-    this._handleTouch = this._handleConnect;
-    this._handleOnRelease = this._finishConnect;
-
-    // redraw to show the unselect
-    this._redraw();
-  },
-
-  /**
-   * create the toolbar to edit edges
-   *
-   * @private
-   */
-  _createEditEdgeToolbar : function() {
-    // clear the toolbar
-    this._clearManipulatorBar();
-
-    if (this.boundFunction) {
-      this.off('select', this.boundFunction);
-    }
-
-    this.edgeBeingEdited = this._getSelectedEdge();
-    this.edgeBeingEdited._enableControlNodes();
-
-    this.manipulationDiv.innerHTML = "" +
-      "<span class='network-manipulationUI back' id='network-manipulate-back'>" +
-      "<span class='network-manipulationLabel'>" + this.constants.labels['back'] + " </span></span>" +
-      "<div class='network-seperatorLine'></div>" +
-      "<span class='network-manipulationUI none' id='network-manipulate-back'>" +
-      "<span id='network-manipulatorLabel' class='network-manipulationLabel'>" + this.constants.labels['editEdgeDescription'] + "</span></span>";
-
-    // bind the icon
-    var backButton = document.getElementById("network-manipulate-back");
-    backButton.onclick = this._createManipulatorBar.bind(this);
-
-    // temporarily overload functions
-    this.cachedFunctions["_handleTouch"]      = this._handleTouch;
-    this.cachedFunctions["_handleOnRelease"]  = this._handleOnRelease;
-    this.cachedFunctions["_handleTap"]        = this._handleTap;
-    this.cachedFunctions["_handleDragStart"]  = this._handleDragStart;
-    this.cachedFunctions["_handleOnDrag"]     = this._handleOnDrag;
-    this._handleTouch     = this._selectControlNode;
-    this._handleTap       = function () {};
-    this._handleOnDrag    = this._controlNodeDrag;
-    this._handleDragStart = function () {}
-    this._handleOnRelease = this._releaseControlNode;
-
-    // redraw to show the unselect
-    this._redraw();
-  },
-
-
-
-
-
-  /**
-   * the function bound to the selection event. It checks if you want to connect a cluster and changes the description
-   * to walk the user through the process.
-   *
-   * @private
-   */
-  _selectControlNode : function(pointer) {
-    this.edgeBeingEdited.controlNodes.from.unselect();
-    this.edgeBeingEdited.controlNodes.to.unselect();
-    this.selectedControlNode = this.edgeBeingEdited._getSelectedControlNode(this._XconvertDOMtoCanvas(pointer.x),this._YconvertDOMtoCanvas(pointer.y));
-    if (this.selectedControlNode !== null) {
-      this.selectedControlNode.select();
-      this.freezeSimulation = true;
-    }
-    this._redraw();
-  },
-
-  /**
-   * the function bound to the selection event. It checks if you want to connect a cluster and changes the description
-   * to walk the user through the process.
-   *
-   * @private
-   */
-  _controlNodeDrag : function(event) {
-    var pointer = this._getPointer(event.gesture.center);
-    if (this.selectedControlNode !== null && this.selectedControlNode !== undefined) {
-      this.selectedControlNode.x = this._XconvertDOMtoCanvas(pointer.x);
-      this.selectedControlNode.y = this._YconvertDOMtoCanvas(pointer.y);
-    }
-    this._redraw();
-  },
-
-  _releaseControlNode : function(pointer) {
-    var newNode = this._getNodeAt(pointer);
-    if (newNode != null) {
-      if (this.edgeBeingEdited.controlNodes.from.selected == true) {
-        this._editEdge(newNode.id, this.edgeBeingEdited.to.id);
-        this.edgeBeingEdited.controlNodes.from.unselect();
-      }
-      if (this.edgeBeingEdited.controlNodes.to.selected == true) {
-        this._editEdge(this.edgeBeingEdited.from.id, newNode.id);
-        this.edgeBeingEdited.controlNodes.to.unselect();
-      }
-    }
-    else {
-      this.edgeBeingEdited._restoreControlNodes();
-    }
-    this.freezeSimulation = false;
-    this._redraw();
-  },
-
-  /**
-   * the function bound to the selection event. It checks if you want to connect a cluster and changes the description
-   * to walk the user through the process.
-   *
-   * @private
-   */
-  _handleConnect : function(pointer) {
-    if (this._getSelectedNodeCount() == 0) {
-      var node = this._getNodeAt(pointer);
-      if (node != null) {
-        if (node.clusterSize > 1) {
-          alert("Cannot create edges to a cluster.")
-        }
-        else {
-          this._selectObject(node,false);
-          // create a node the temporary line can look at
-          this.sectors['support']['nodes']['targetNode'] = new Node({id:'targetNode'},{},{},this.constants);
-          this.sectors['support']['nodes']['targetNode'].x = node.x;
-          this.sectors['support']['nodes']['targetNode'].y = node.y;
-          this.sectors['support']['nodes']['targetViaNode'] = new Node({id:'targetViaNode'},{},{},this.constants);
-          this.sectors['support']['nodes']['targetViaNode'].x = node.x;
-          this.sectors['support']['nodes']['targetViaNode'].y = node.y;
-          this.sectors['support']['nodes']['targetViaNode'].parentEdgeId = "connectionEdge";
-
-          // create a temporary edge
-          this.edges['connectionEdge'] = new Edge({id:"connectionEdge",from:node.id,to:this.sectors['support']['nodes']['targetNode'].id}, this, this.constants);
-          this.edges['connectionEdge'].from = node;
-          this.edges['connectionEdge'].connected = true;
-          this.edges['connectionEdge'].smooth = true;
-          this.edges['connectionEdge'].selected = true;
-          this.edges['connectionEdge'].to = this.sectors['support']['nodes']['targetNode'];
-          this.edges['connectionEdge'].via = this.sectors['support']['nodes']['targetViaNode'];
-
-          this.cachedFunctions["_handleOnDrag"] = this._handleOnDrag;
-          this._handleOnDrag = function(event) {
-            var pointer = this._getPointer(event.gesture.center);
-            this.sectors['support']['nodes']['targetNode'].x = this._XconvertDOMtoCanvas(pointer.x);
-            this.sectors['support']['nodes']['targetNode'].y = this._YconvertDOMtoCanvas(pointer.y);
-            this.sectors['support']['nodes']['targetViaNode'].x = 0.5 * (this._XconvertDOMtoCanvas(pointer.x) + this.edges['connectionEdge'].from.x);
-            this.sectors['support']['nodes']['targetViaNode'].y = this._YconvertDOMtoCanvas(pointer.y);
-          };
-
-          this.moving = true;
-          this.start();
-        }
-      }
-    }
-  },
-
-  _finishConnect : function(pointer) {
-    if (this._getSelectedNodeCount() == 1) {
-
-      // restore the drag function
-      this._handleOnDrag = this.cachedFunctions["_handleOnDrag"];
-      delete this.cachedFunctions["_handleOnDrag"];
-
-      // remember the edge id
-      var connectFromId = this.edges['connectionEdge'].fromId;
-
-      // remove the temporary nodes and edge
-      delete this.edges['connectionEdge'];
-      delete this.sectors['support']['nodes']['targetNode'];
-      delete this.sectors['support']['nodes']['targetViaNode'];
-
-      var node = this._getNodeAt(pointer);
-      if (node != null) {
-        if (node.clusterSize > 1) {
-          alert("Cannot create edges to a cluster.")
-        }
-        else {
-          this._createEdge(connectFromId,node.id);
-          this._createManipulatorBar();
-        }
-      }
-      this._unselectAll();
-    }
-  },
-
-
-  /**
-   * Adds a node on the specified location
-   */
-  _addNode : function() {
-    if (this._selectionIsEmpty() && this.editMode == true) {
-      var positionObject = this._pointerToPositionObject(this.pointerPosition);
-      var defaultData = {id:util.randomUUID(),x:positionObject.left,y:positionObject.top,label:"new",allowedToMoveX:true,allowedToMoveY:true};
-      if (this.triggerFunctions.add) {
-        if (this.triggerFunctions.add.length == 2) {
-          var me = this;
-          this.triggerFunctions.add(defaultData, function(finalizedData) {
-            me.nodesData.add(finalizedData);
-            me._createManipulatorBar();
-            me.moving = true;
-            me.start();
-          });
-        }
-        else {
-          alert(this.constants.labels['addError']);
-          this._createManipulatorBar();
-          this.moving = true;
-          this.start();
-        }
-      }
-      else {
-        this.nodesData.add(defaultData);
-        this._createManipulatorBar();
-        this.moving = true;
-        this.start();
-      }
-    }
-  },
-
-
-  /**
-   * connect two nodes with a new edge.
-   *
-   * @private
-   */
-  _createEdge : function(sourceNodeId,targetNodeId) {
-    if (this.editMode == true) {
-      var defaultData = {from:sourceNodeId, to:targetNodeId};
-      if (this.triggerFunctions.connect) {
-        if (this.triggerFunctions.connect.length == 2) {
-          var me = this;
-          this.triggerFunctions.connect(defaultData, function(finalizedData) {
-            me.edgesData.add(finalizedData);
-            me.moving = true;
-            me.start();
-          });
-        }
-        else {
-          alert(this.constants.labels["linkError"]);
-          this.moving = true;
-          this.start();
-        }
-      }
-      else {
-        this.edgesData.add(defaultData);
-        this.moving = true;
-        this.start();
-      }
-    }
-  },
-
-  /**
-   * connect two nodes with a new edge.
-   *
-   * @private
-   */
-  _editEdge : function(sourceNodeId,targetNodeId) {
-    if (this.editMode == true) {
-      var defaultData = {id: this.edgeBeingEdited.id, from:sourceNodeId, to:targetNodeId};
-      if (this.triggerFunctions.editEdge) {
-        if (this.triggerFunctions.editEdge.length == 2) {
-          var me = this;
-          this.triggerFunctions.editEdge(defaultData, function(finalizedData) {
-            me.edgesData.update(finalizedData);
-            me.moving = true;
-            me.start();
-          });
-        }
-        else {
-          alert(this.constants.labels["linkError"]);
-          this.moving = true;
-          this.start();
-        }
-      }
-      else {
-        this.edgesData.update(defaultData);
-        this.moving = true;
-        this.start();
-      }
-    }
-  },
-
-  /**
-   * Create the toolbar to edit the selected node. The label and the color can be changed. Other colors are derived from the chosen color.
-   *
-   * @private
-   */
-  _editNode : function() {
-    if (this.triggerFunctions.edit && this.editMode == true) {
-      var node = this._getSelectedNode();
-      var data = {id:node.id,
-        label: node.label,
-        group: node.group,
-        shape: node.shape,
-        color: {
-          background:node.color.background,
-          border:node.color.border,
-          highlight: {
-            background:node.color.highlight.background,
-            border:node.color.highlight.border
-          }
-        }};
-      if (this.triggerFunctions.edit.length == 2) {
-        var me = this;
-        this.triggerFunctions.edit(data, function (finalizedData) {
-          me.nodesData.update(finalizedData);
-          me._createManipulatorBar();
-          me.moving = true;
-          me.start();
-        });
-      }
-      else {
-        alert(this.constants.labels["editError"]);
-      }
-    }
-    else {
-      alert(this.constants.labels["editBoundError"]);
-    }
-  },
-
-
-
-
-  /**
-   * delete everything in the selection
-   *
-   * @private
-   */
-  _deleteSelected : function() {
-    if (!this._selectionIsEmpty() && this.editMode == true) {
-      if (!this._clusterInSelection()) {
-        var selectedNodes = this.getSelectedNodes();
-        var selectedEdges = this.getSelectedEdges();
-        if (this.triggerFunctions.del) {
-          var me = this;
-          var data = {nodes: selectedNodes, edges: selectedEdges};
-          if (this.triggerFunctions.del.length = 2) {
-            this.triggerFunctions.del(data, function (finalizedData) {
-              me.edgesData.remove(finalizedData.edges);
-              me.nodesData.remove(finalizedData.nodes);
-              me._unselectAll();
-              me.moving = true;
-              me.start();
-            });
-          }
-          else {
-            alert(this.constants.labels["deleteError"])
-          }
-        }
-        else {
-          this.edgesData.remove(selectedEdges);
-          this.nodesData.remove(selectedNodes);
-          this._unselectAll();
-          this.moving = true;
-          this.start();
-        }
-      }
-      else {
-        alert(this.constants.labels["deleteClusterError"]);
-      }
-    }
-  }
-};

lib/network/networkMixins/MixinLoader.js

@@ -1,199 +0,0 @@
-/**
- * Created by Alex on 2/10/14.
- */
-
-
-var networkMixinLoaders = {
-
-  /**
-   * Load a mixin into the network object
-   *
-   * @param {Object} sourceVariable | this object has to contain functions.
-   * @private
-   */
-  _loadMixin: function (sourceVariable) {
-    for (var mixinFunction in sourceVariable) {
-      if (sourceVariable.hasOwnProperty(mixinFunction)) {
-        Network.prototype[mixinFunction] = sourceVariable[mixinFunction];
-      }
-    }
-  },
-
-
-  /**
-   * removes a mixin from the network object.
-   *
-   * @param {Object} sourceVariable | this object has to contain functions.
-   * @private
-   */
-  _clearMixin: function (sourceVariable) {
-    for (var mixinFunction in sourceVariable) {
-      if (sourceVariable.hasOwnProperty(mixinFunction)) {
-        Network.prototype[mixinFunction] = undefined;
-      }
-    }
-  },
-
-
-  /**
-   * Mixin the physics system and initialize the parameters required.
-   *
-   * @private
-   */
-  _loadPhysicsSystem: function () {
-    this._loadMixin(physicsMixin);
-    this._loadSelectedForceSolver();
-    if (this.constants.configurePhysics == true) {
-      this._loadPhysicsConfiguration();
-    }
-  },
-
-
-  /**
-   * Mixin the cluster system and initialize the parameters required.
-   *
-   * @private
-   */
-  _loadClusterSystem: function () {
-    this.clusterSession = 0;
-    this.hubThreshold = 5;
-    this._loadMixin(ClusterMixin);
-  },
-
-
-  /**
-   * Mixin the sector system and initialize the parameters required
-   *
-   * @private
-   */
-  _loadSectorSystem: function () {
-    this.sectors = {};
-    this.activeSector = ["default"];
-    this.sectors["active"] = {};
-    this.sectors["active"]["default"] = {"nodes": {},
-        "edges": {},
-        "nodeIndices": [],
-        "formationScale": 1.0,
-        "drawingNode": undefined };
-    this.sectors["frozen"] = {};
-      this.sectors["support"] = {"nodes": {},
-        "edges": {},
-        "nodeIndices": [],
-        "formationScale": 1.0,
-        "drawingNode": undefined };
-
-    this.nodeIndices = this.sectors["active"]["default"]["nodeIndices"];  // the node indices list is used to speed up the computation of the repulsion fields
-
-    this._loadMixin(SectorMixin);
-  },
-
-
-  /**
-   * Mixin the selection system and initialize the parameters required
-   *
-   * @private
-   */
-  _loadSelectionSystem: function () {
-    this.selectionObj = {nodes: {}, edges: {}};
-
-    this._loadMixin(SelectionMixin);
-  },
-
-
-  /**
-   * Mixin the navigationUI (User Interface) system and initialize the parameters required
-   *
-   * @private
-   */
-  _loadManipulationSystem: function () {
-    // reset global variables -- these are used by the selection of nodes and edges.
-    this.blockConnectingEdgeSelection = false;
-    this.forceAppendSelection = false;
-
-    if (this.constants.dataManipulation.enabled == true) {
-      // load the manipulator HTML elements. All styling done in css.
-      if (this.manipulationDiv === undefined) {
-        this.manipulationDiv = document.createElement('div');
-        this.manipulationDiv.className = 'network-manipulationDiv';
-        this.manipulationDiv.id = 'network-manipulationDiv';
-        if (this.editMode == true) {
-          this.manipulationDiv.style.display = "block";
-        }
-        else {
-          this.manipulationDiv.style.display = "none";
-        }
-        this.containerElement.insertBefore(this.manipulationDiv, this.frame);
-      }
-
-      if (this.editModeDiv === undefined) {
-        this.editModeDiv = document.createElement('div');
-        this.editModeDiv.className = 'network-manipulation-editMode';
-        this.editModeDiv.id = 'network-manipulation-editMode';
-        if (this.editMode == true) {
-          this.editModeDiv.style.display = "none";
-        }
-        else {
-          this.editModeDiv.style.display = "block";
-        }
-        this.containerElement.insertBefore(this.editModeDiv, this.frame);
-      }
-
-      if (this.closeDiv === undefined) {
-        this.closeDiv = document.createElement('div');
-        this.closeDiv.className = 'network-manipulation-closeDiv';
-        this.closeDiv.id = 'network-manipulation-closeDiv';
-        this.closeDiv.style.display = this.manipulationDiv.style.display;
-        this.containerElement.insertBefore(this.closeDiv, this.frame);
-      }
-
-      // load the manipulation functions
-      this._loadMixin(manipulationMixin);
-
-      // create the manipulator toolbar
-      this._createManipulatorBar();
-    }
-    else {
-      if (this.manipulationDiv !== undefined) {
-        // removes all the bindings and overloads
-        this._createManipulatorBar();
-        // remove the manipulation divs
-        this.containerElement.removeChild(this.manipulationDiv);
-        this.containerElement.removeChild(this.editModeDiv);
-        this.containerElement.removeChild(this.closeDiv);
-
-        this.manipulationDiv = undefined;
-        this.editModeDiv = undefined;
-        this.closeDiv = undefined;
-        // remove the mixin functions
-        this._clearMixin(manipulationMixin);
-      }
-    }
-  },
-
-
-  /**
-   * Mixin the navigation (User Interface) system and initialize the parameters required
-   *
-   * @private
-   */
-  _loadNavigationControls: function () {
-    this._loadMixin(NavigationMixin);
-
-    // the clean function removes the button divs, this is done to remove the bindings.
-    this._cleanNavigation();
-    if (this.constants.navigation.enabled == true) {
-      this._loadNavigationElements();
-    }
-  },
-
-
-  /**
-   * Mixin the hierarchical layout system.
-   *
-   * @private
-   */
-  _loadHierarchySystem: function () {
-    this._loadMixin(HierarchicalLayoutMixin);
-  }
-
-};

lib/network/networkMixins/NavigationMixin.js

@@ -1,205 +0,0 @@
-/**
- * Created by Alex on 1/22/14.
- */
-
-var NavigationMixin = {
-
-  _cleanNavigation : function() {
-    // clean up previosu navigation items
-    var wrapper = document.getElementById('network-navigation_wrapper');
-    if (wrapper != null) {
-      this.containerElement.removeChild(wrapper);
-    }
-    document.onmouseup = null;
-  },
-
-  /**
-   * Creation of the navigation controls nodes. They are drawn over the rest of the nodes and are not affected by scale and translation
-   * they have a triggerFunction which is called on click. If the position of the navigation controls is dependent
-   * on this.frame.canvas.clientWidth or this.frame.canvas.clientHeight, we flag horizontalAlignLeft and verticalAlignTop false.
-   * This means that the location will be corrected by the _relocateNavigation function on a size change of the canvas.
-   *
-   * @private
-   */
-  _loadNavigationElements : function() {
-    this._cleanNavigation();
-
-    this.navigationDivs = {};
-    var navigationDivs = ['up','down','left','right','zoomIn','zoomOut','zoomExtends'];
-    var navigationDivActions = ['_moveUp','_moveDown','_moveLeft','_moveRight','_zoomIn','_zoomOut','zoomExtent'];
-
-    this.navigationDivs['wrapper'] = document.createElement('div');
-    this.navigationDivs['wrapper'].id = "network-navigation_wrapper";
-    this.navigationDivs['wrapper'].style.position = "absolute";
-    this.navigationDivs['wrapper'].style.width = this.frame.canvas.clientWidth + "px";
-    this.navigationDivs['wrapper'].style.height = this.frame.canvas.clientHeight + "px";
-    this.containerElement.insertBefore(this.navigationDivs['wrapper'],this.frame);
-
-    for (var i = 0; i < navigationDivs.length; i++) {
-      this.navigationDivs[navigationDivs[i]] = document.createElement('div');
-      this.navigationDivs[navigationDivs[i]].id = "network-navigation_" + navigationDivs[i];
-      this.navigationDivs[navigationDivs[i]].className = "network-navigation " + navigationDivs[i];
-      this.navigationDivs['wrapper'].appendChild(this.navigationDivs[navigationDivs[i]]);
-      this.navigationDivs[navigationDivs[i]].onmousedown = this[navigationDivActions[i]].bind(this);
-    }
-
-    document.onmouseup = this._stopMovement.bind(this);
-  },
-
-  /**
-   * this stops all movement induced by the navigation buttons
-   *
-   * @private
-   */
-  _stopMovement : function() {
-    this._xStopMoving();
-    this._yStopMoving();
-    this._stopZoom();
-  },
-
-
-  /**
-   * stops the actions performed by page up and down etc.
-   *
-   * @param event
-   * @private
-   */
-  _preventDefault : function(event) {
-    if (event !== undefined) {
-      if (event.preventDefault) {
-        event.preventDefault();
-      } else {
-        event.returnValue = false;
-      }
-    }
-  },
-
-
-  /**
-   * move the screen up
-   * By using the increments, instead of adding a fixed number to the translation, we keep fluent and
-   * instant movement. The onKeypress event triggers immediately, then pauses, then triggers frequently
-   * To avoid this behaviour, we do the translation in the start loop.
-   *
-   * @private
-   */
-  _moveUp : function(event) {
-    this.yIncrement = this.constants.keyboard.speed.y;
-    this.start(); // if there is no node movement, the calculation wont be done
-    this._preventDefault(event);
-    if (this.navigationDivs) {
-      this.navigationDivs['up'].className += " active";
-    }
-  },
-
-
-  /**
-   * move the screen down
-   * @private
-   */
-  _moveDown : function(event) {
-    this.yIncrement = -this.constants.keyboard.speed.y;
-    this.start(); // if there is no node movement, the calculation wont be done
-    this._preventDefault(event);
-    if (this.navigationDivs) {
-      this.navigationDivs['down'].className += " active";
-    }
-  },
-
-
-  /**
-   * move the screen left
-   * @private
-   */
-  _moveLeft : function(event) {
-    this.xIncrement = this.constants.keyboard.speed.x;
-    this.start(); // if there is no node movement, the calculation wont be done
-    this._preventDefault(event);
-    if (this.navigationDivs) {
-      this.navigationDivs['left'].className += " active";
-    }
-  },
-
-
-  /**
-   * move the screen right
-   * @private
-   */
-  _moveRight : function(event) {
-    this.xIncrement = -this.constants.keyboard.speed.y;
-    this.start(); // if there is no node movement, the calculation wont be done
-    this._preventDefault(event);
-    if (this.navigationDivs) {
-      this.navigationDivs['right'].className += " active";
-    }
-  },
-
-
-  /**
-   * Zoom in, using the same method as the movement.
-   * @private
-   */
-  _zoomIn : function(event) {
-    this.zoomIncrement = this.constants.keyboard.speed.zoom;
-    this.start(); // if there is no node movement, the calculation wont be done
-    this._preventDefault(event);
-    if (this.navigationDivs) {
-      this.navigationDivs['zoomIn'].className += " active";
-    }
-  },
-
-
-  /**
-   * Zoom out
-   * @private
-   */
-  _zoomOut : function() {
-    this.zoomIncrement = -this.constants.keyboard.speed.zoom;
-    this.start(); // if there is no node movement, the calculation wont be done
-    this._preventDefault(event);
-    if (this.navigationDivs) {
-      this.navigationDivs['zoomOut'].className += " active";
-    }
-  },
-
-
-  /**
-   * Stop zooming and unhighlight the zoom controls
-   * @private
-   */
-  _stopZoom : function() {
-    this.zoomIncrement = 0;
-    if (this.navigationDivs) {
-      this.navigationDivs['zoomIn'].className = this.navigationDivs['zoomIn'].className.replace(" active","");
-      this.navigationDivs['zoomOut'].className = this.navigationDivs['zoomOut'].className.replace(" active","");
-    }
-  },
-
-
-  /**
-   * Stop moving in the Y direction and unHighlight the up and down
-   * @private
-   */
-  _yStopMoving : function() {
-    this.yIncrement = 0;
-    if (this.navigationDivs) {
-      this.navigationDivs['up'].className = this.navigationDivs['up'].className.replace(" active","");
-      this.navigationDivs['down'].className = this.navigationDivs['down'].className.replace(" active","");
-    }
-  },
-
-
-  /**
-   * Stop moving in the X direction and unHighlight left and right.
-   * @private
-   */
-  _xStopMoving : function() {
-    this.xIncrement = 0;
-    if (this.navigationDivs) {
-      this.navigationDivs['left'].className = this.navigationDivs['left'].className.replace(" active","");
-      this.navigationDivs['right'].className = this.navigationDivs['right'].className.replace(" active","");
-    }
-  }
-
-
-};

lib/network/networkMixins/SectorsMixin.js

@@ -1,552 +0,0 @@
-/**
- * Creation of the SectorMixin var.
- *
- * This contains all the functions the Network object can use to employ the sector system.
- * The sector system is always used by Network, though the benefits only apply to the use of clustering.
- * If clustering is not used, there is no overhead except for a duplicate object with references to nodes and edges.
- *
- * Alex de Mulder
- * 21-01-2013
- */
-var SectorMixin = {
-
-  /**
-   * This function is only called by the setData function of the Network object.
-   * This loads the global references into the active sector. This initializes the sector.
-   *
-   * @private
-   */
-  _putDataInSector : function() {
-    this.sectors["active"][this._sector()].nodes = this.nodes;
-    this.sectors["active"][this._sector()].edges = this.edges;
-    this.sectors["active"][this._sector()].nodeIndices = this.nodeIndices;
-  },
-
-
-  /**
-   *  /**
-   * This function sets the global references to nodes, edges and nodeIndices back to
-   * those of the supplied (active) sector. If a type is defined, do the specific type
-   *
-   * @param {String} sectorId
-   * @param {String} [sectorType] | "active" or "frozen"
-   * @private
-   */
-  _switchToSector : function(sectorId, sectorType) {
-    if (sectorType === undefined || sectorType == "active") {
-      this._switchToActiveSector(sectorId);
-    }
-    else {
-      this._switchToFrozenSector(sectorId);
-    }
-  },
-
-
-  /**
-   * This function sets the global references to nodes, edges and nodeIndices back to
-   * those of the supplied active sector.
-   *
-   * @param sectorId
-   * @private
-   */
-  _switchToActiveSector : function(sectorId) {
-    this.nodeIndices = this.sectors["active"][sectorId]["nodeIndices"];
-    this.nodes       = this.sectors["active"][sectorId]["nodes"];
-    this.edges       = this.sectors["active"][sectorId]["edges"];
-  },
-
-
-  /**
-   * This function sets the global references to nodes, edges and nodeIndices back to
-   * those of the supplied active sector.
-   *
-   * @param sectorId
-   * @private
-   */
-  _switchToSupportSector : function() {
-    this.nodeIndices = this.sectors["support"]["nodeIndices"];
-    this.nodes       = this.sectors["support"]["nodes"];
-    this.edges       = this.sectors["support"]["edges"];
-  },
-
-
-  /**
-   * This function sets the global references to nodes, edges and nodeIndices back to
-   * those of the supplied frozen sector.
-   *
-   * @param sectorId
-   * @private
-   */
-  _switchToFrozenSector : function(sectorId) {
-    this.nodeIndices = this.sectors["frozen"][sectorId]["nodeIndices"];
-    this.nodes       = this.sectors["frozen"][sectorId]["nodes"];
-    this.edges       = this.sectors["frozen"][sectorId]["edges"];
-  },
-
-
-  /**
-   * This function sets the global references to nodes, edges and nodeIndices back to
-   * those of the currently active sector.
-   *
-   * @private
-   */
-  _loadLatestSector : function() {
-    this._switchToSector(this._sector());
-  },
-
-
-  /**
-   * This function returns the currently active sector Id
-   *
-   * @returns {String}
-   * @private
-   */
-  _sector : function() {
-    return this.activeSector[this.activeSector.length-1];
-  },
-
-
-  /**
-   * This function returns the previously active sector Id
-   *
-   * @returns {String}
-   * @private
-   */
-  _previousSector : function() {
-    if (this.activeSector.length > 1) {
-      return this.activeSector[this.activeSector.length-2];
-    }
-    else {
-      throw new TypeError('there are not enough sectors in the this.activeSector array.');
-    }
-  },
-
-
-  /**
-   * We add the active sector at the end of the this.activeSector array
-   * This ensures it is the currently active sector returned by _sector() and it reaches the top
-   * of the activeSector stack. When we reverse our steps we move from the end to the beginning of this stack.
-   *
-   * @param newId
-   * @private
-   */
-  _setActiveSector : function(newId) {
-    this.activeSector.push(newId);
-  },
-
-
-  /**
-   * We remove the currently active sector id from the active sector stack. This happens when
-   * we reactivate the previously active sector
-   *
-   * @private
-   */
-  _forgetLastSector : function() {
-    this.activeSector.pop();
-  },
-
-
-  /**
-   * This function creates a new active sector with the supplied newId. This newId
-   * is the expanding node id.
-   *
-   * @param {String} newId   | Id of the new active sector
-   * @private
-   */
-  _createNewSector : function(newId) {
-    // create the new sector
-    this.sectors["active"][newId] = {"nodes":{},
-                                     "edges":{},
-                                     "nodeIndices":[],
-                                     "formationScale": this.scale,
-                                     "drawingNode": undefined};
-
-    // create the new sector render node. This gives visual feedback that you are in a new sector.
-    this.sectors["active"][newId]['drawingNode'] = new Node(
-        {id:newId,
-          color: {
-            background: "#eaefef",
-            border: "495c5e"
-          }
-        },{},{},this.constants);
-    this.sectors["active"][newId]['drawingNode'].clusterSize = 2;
-  },
-
-
-  /**
-   * This function removes the currently active sector. This is called when we create a new
-   * active sector.
-   *
-   * @param {String} sectorId   | Id of the active sector that will be removed
-   * @private
-   */
-  _deleteActiveSector : function(sectorId) {
-    delete this.sectors["active"][sectorId];
-  },
-
-
-  /**
-   * This function removes the currently active sector. This is called when we reactivate
-   * the previously active sector.
-   *
-   * @param {String} sectorId   | Id of the active sector that will be removed
-   * @private
-   */
-  _deleteFrozenSector : function(sectorId) {
-    delete this.sectors["frozen"][sectorId];
-  },
-
-
-  /**
-   * Freezing an active sector means moving it from the "active" object to the "frozen" object.
-   * We copy the references, then delete the active entree.
-   *
-   * @param sectorId
-   * @private
-   */
-  _freezeSector : function(sectorId) {
-    // we move the set references from the active to the frozen stack.
-    this.sectors["frozen"][sectorId] = this.sectors["active"][sectorId];
-
-    // we have moved the sector data into the frozen set, we now remove it from the active set
-    this._deleteActiveSector(sectorId);
-  },
-
-
-  /**
-   * This is the reverse operation of _freezeSector. Activating means moving the sector from the "frozen"
-   * object to the "active" object.
-   *
-   * @param sectorId
-   * @private
-   */
-  _activateSector : function(sectorId) {
-    // we move the set references from the frozen to the active stack.
-    this.sectors["active"][sectorId] = this.sectors["frozen"][sectorId];
-
-    // we have moved the sector data into the active set, we now remove it from the frozen stack
-    this._deleteFrozenSector(sectorId);
-  },
-
-
-  /**
-   * This function merges the data from the currently active sector with a frozen sector. This is used
-   * in the process of reverting back to the previously active sector.
-   * The data that is placed in the frozen (the previously active) sector is the node that has been removed from it
-   * upon the creation of a new active sector.
-   *
-   * @param sectorId
-   * @private
-   */
-  _mergeThisWithFrozen : function(sectorId) {
-    // copy all nodes
-    for (var nodeId in this.nodes) {
-      if (this.nodes.hasOwnProperty(nodeId)) {
-        this.sectors["frozen"][sectorId]["nodes"][nodeId] = this.nodes[nodeId];
-      }
-    }
-
-    // copy all edges (if not fully clustered, else there are no edges)
-    for (var edgeId in this.edges) {
-      if (this.edges.hasOwnProperty(edgeId)) {
-        this.sectors["frozen"][sectorId]["edges"][edgeId] = this.edges[edgeId];
-      }
-    }
-
-    // merge the nodeIndices
-    for (var i = 0; i < this.nodeIndices.length; i++) {
-      this.sectors["frozen"][sectorId]["nodeIndices"].push(this.nodeIndices[i]);
-    }
-  },
-
-
-  /**
-   * This clusters the sector to one cluster. It was a single cluster before this process started so
-   * we revert to that state. The clusterToFit function with a maximum size of 1 node does this.
-   *
-   * @private
-   */
-  _collapseThisToSingleCluster : function() {
-    this.clusterToFit(1,false);
-  },
-
-
-  /**
-   * We create a new active sector from the node that we want to open.
-   *
-   * @param node
-   * @private
-   */
-  _addSector : function(node) {
-    // this is the currently active sector
-    var sector = this._sector();
-
-//    // this should allow me to select nodes from a frozen set.
-//    if (this.sectors['active'][sector]["nodes"].hasOwnProperty(node.id)) {
-//      console.log("the node is part of the active sector");
-//    }
-//    else {
-//      console.log("I dont know what the fuck happened!!");
-//    }
-
-    // when we switch to a new sector, we remove the node that will be expanded from the current nodes list.
-    delete this.nodes[node.id];
-
-    var unqiueIdentifier = util.randomUUID();
-
-    // we fully freeze the currently active sector
-    this._freezeSector(sector);
-
-    // we create a new active sector. This sector has the Id of the node to ensure uniqueness
-    this._createNewSector(unqiueIdentifier);
-
-    // we add the active sector to the sectors array to be able to revert these steps later on
-    this._setActiveSector(unqiueIdentifier);
-
-    // we redirect the global references to the new sector's references. this._sector() now returns unqiueIdentifier
-    this._switchToSector(this._sector());
-
-    // finally we add the node we removed from our previous active sector to the new active sector
-    this.nodes[node.id] = node;
-  },
-
-
-  /**
-   * We close the sector that is currently open and revert back to the one before.
-   * If the active sector is the "default" sector, nothing happens.
-   *
-   * @private
-   */
-  _collapseSector : function() {
-    // the currently active sector
-    var sector = this._sector();
-
-    // we cannot collapse the default sector
-    if (sector != "default") {
-      if ((this.nodeIndices.length == 1) ||
-       (this.sectors["active"][sector]["drawingNode"].width*this.scale < this.constants.clustering.screenSizeThreshold * this.frame.canvas.clientWidth) ||
-       (this.sectors["active"][sector]["drawingNode"].height*this.scale < this.constants.clustering.screenSizeThreshold * this.frame.canvas.clientHeight)) {
-        var previousSector = this._previousSector();
-
-        // we collapse the sector back to a single cluster
-        this._collapseThisToSingleCluster();
-
-        // we move the remaining nodes, edges and nodeIndices to the previous sector.
-        // This previous sector is the one we will reactivate
-        this._mergeThisWithFrozen(previousSector);
-
-        // the previously active (frozen) sector now has all the data from the currently active sector.
-        // we can now delete the active sector.
-        this._deleteActiveSector(sector);
-
-        // we activate the previously active (and currently frozen) sector.
-        this._activateSector(previousSector);
-
-        // we load the references from the newly active sector into the global references
-        this._switchToSector(previousSector);
-
-        // we forget the previously active sector because we reverted to the one before
-        this._forgetLastSector();
-
-        // finally, we update the node index list.
-        this._updateNodeIndexList();
-
-        // we refresh the list with calulation nodes and calculation node indices.
-        this._updateCalculationNodes();
-      }
-    }
-  },
-
-
-  /**
-   * This runs a function in all active sectors. This is used in _redraw() and the _initializeForceCalculation().
-   *
-   * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
-   *                              |   we dont pass the function itself because then the "this" is the window object
-   *                              |   instead of the Network object
-   * @param {*} [argument]            |   Optional: arguments to pass to the runFunction
-   * @private
-   */
-  _doInAllActiveSectors : function(runFunction,argument) {
-    if (argument === undefined) {
-      for (var sector in this.sectors["active"]) {
-        if (this.sectors["active"].hasOwnProperty(sector)) {
-          // switch the global references to those of this sector
-          this._switchToActiveSector(sector);
-          this[runFunction]();
-        }
-      }
-    }
-    else {
-      for (var sector in this.sectors["active"]) {
-        if (this.sectors["active"].hasOwnProperty(sector)) {
-          // switch the global references to those of this sector
-          this._switchToActiveSector(sector);
-          var args = Array.prototype.splice.call(arguments, 1);
-          if (args.length > 1) {
-            this[runFunction](args[0],args[1]);
-          }
-          else {
-            this[runFunction](argument);
-          }
-        }
-      }
-    }
-    // we revert the global references back to our active sector
-    this._loadLatestSector();
-  },
-
-
-  /**
-   * This runs a function in all active sectors. This is used in _redraw() and the _initializeForceCalculation().
-   *
-   * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
-   *                              |   we dont pass the function itself because then the "this" is the window object
-   *                              |   instead of the Network object
-   * @param {*} [argument]        |   Optional: arguments to pass to the runFunction
-   * @private
-   */
-  _doInSupportSector : function(runFunction,argument) {
-    if (argument === undefined) {
-      this._switchToSupportSector();
-      this[runFunction]();
-    }
-    else {
-      this._switchToSupportSector();
-      var args = Array.prototype.splice.call(arguments, 1);
-      if (args.length > 1) {
-        this[runFunction](args[0],args[1]);
-      }
-      else {
-        this[runFunction](argument);
-      }
-    }
-    // we revert the global references back to our active sector
-    this._loadLatestSector();
-  },
-
-
-  /**
-   * This runs a function in all frozen sectors. This is used in the _redraw().
-   *
-   * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
-   *                              |   we don't pass the function itself because then the "this" is the window object
-   *                              |   instead of the Network object
-   * @param {*} [argument]            |   Optional: arguments to pass to the runFunction
-   * @private
-   */
-  _doInAllFrozenSectors : function(runFunction,argument) {
-    if (argument === undefined) {
-      for (var sector in this.sectors["frozen"]) {
-        if (this.sectors["frozen"].hasOwnProperty(sector)) {
-          // switch the global references to those of this sector
-          this._switchToFrozenSector(sector);
-          this[runFunction]();
-        }
-      }
-    }
-    else {
-      for (var sector in this.sectors["frozen"]) {
-        if (this.sectors["frozen"].hasOwnProperty(sector)) {
-          // switch the global references to those of this sector
-          this._switchToFrozenSector(sector);
-          var args = Array.prototype.splice.call(arguments, 1);
-          if (args.length > 1) {
-            this[runFunction](args[0],args[1]);
-          }
-          else {
-            this[runFunction](argument);
-          }
-        }
-      }
-    }
-    this._loadLatestSector();
-  },
-
-
-  /**
-   * This runs a function in all sectors. This is used in the _redraw().
-   *
-   * @param {String} runFunction  |   This is the NAME of a function we want to call in all active sectors
-   *                              |   we don't pass the function itself because then the "this" is the window object
-   *                              |   instead of the Network object
-   * @param {*} [argument]        |   Optional: arguments to pass to the runFunction
-   * @private
-   */
-  _doInAllSectors : function(runFunction,argument) {
-    var args = Array.prototype.splice.call(arguments, 1);
-    if (argument === undefined) {
-      this._doInAllActiveSectors(runFunction);
-      this._doInAllFrozenSectors(runFunction);
-    }
-    else {
-      if (args.length > 1) {
-        this._doInAllActiveSectors(runFunction,args[0],args[1]);
-        this._doInAllFrozenSectors(runFunction,args[0],args[1]);
-      }
-      else {
-        this._doInAllActiveSectors(runFunction,argument);
-        this._doInAllFrozenSectors(runFunction,argument);
-      }
-    }
-  },
-
-
-  /**
-   * This clears the nodeIndices list. We cannot use this.nodeIndices = [] because we would break the link with the
-   * active sector. Thus we clear the nodeIndices in the active sector, then reconnect the this.nodeIndices to it.
-   *
-   * @private
-   */
-  _clearNodeIndexList : function() {
-    var sector = this._sector();
-    this.sectors["active"][sector]["nodeIndices"] = [];
-    this.nodeIndices = this.sectors["active"][sector]["nodeIndices"];
-  },
-
-
-  /**
-   * Draw the encompassing sector node
-   *
-   * @param ctx
-   * @param sectorType
-   * @private
-   */
-  _drawSectorNodes : function(ctx,sectorType) {
-    var minY = 1e9, maxY = -1e9, minX = 1e9, maxX = -1e9, node;
-    for (var sector in this.sectors[sectorType]) {
-      if (this.sectors[sectorType].hasOwnProperty(sector)) {
-        if (this.sectors[sectorType][sector]["drawingNode"] !== undefined) {
-
-          this._switchToSector(sector,sectorType);
-
-          minY = 1e9; maxY = -1e9; minX = 1e9; maxX = -1e9;
-          for (var nodeId in this.nodes) {
-            if (this.nodes.hasOwnProperty(nodeId)) {
-              node = this.nodes[nodeId];
-              node.resize(ctx);
-              if (minX > node.x - 0.5 * node.width) {minX = node.x - 0.5 * node.width;}
-              if (maxX < node.x + 0.5 * node.width) {maxX = node.x + 0.5 * node.width;}
-              if (minY > node.y - 0.5 * node.height) {minY = node.y - 0.5 * node.height;}
-              if (maxY < node.y + 0.5 * node.height) {maxY = node.y + 0.5 * node.height;}
-            }
-          }
-          node = this.sectors[sectorType][sector]["drawingNode"];
-          node.x = 0.5 * (maxX + minX);
-          node.y = 0.5 * (maxY + minY);
-          node.width = 2 * (node.x - minX);
-          node.height = 2 * (node.y - minY);
-          node.radius = Math.sqrt(Math.pow(0.5*node.width,2) + Math.pow(0.5*node.height,2));
-          node.setScale(this.scale);
-          node._drawCircle(ctx);
-        }
-      }
-    }
-  },
-
-  _drawAllSectorNodes : function(ctx) {
-    this._drawSectorNodes(ctx,"frozen");
-    this._drawSectorNodes(ctx,"active");
-    this._loadLatestSector();
-  }
-};

lib/network/networkMixins/SelectionMixin.js

@@ -1,708 +0,0 @@
-
-var SelectionMixin = {
-
-  /**
-   * This function can be called from the _doInAllSectors function
-   *
-   * @param object
-   * @param overlappingNodes
-   * @private
-   */
-  _getNodesOverlappingWith : function(object, overlappingNodes) {
-    var nodes = this.nodes;
-    for (var nodeId in nodes) {
-      if (nodes.hasOwnProperty(nodeId)) {
-        if (nodes[nodeId].isOverlappingWith(object)) {
-          overlappingNodes.push(nodeId);
-        }
-      }
-    }
-  },
-
-  /**
-   * retrieve all nodes overlapping with given object
-   * @param {Object} object  An object with parameters left, top, right, bottom
-   * @return {Number[]}   An array with id's of the overlapping nodes
-   * @private
-   */
-  _getAllNodesOverlappingWith : function (object) {
-    var overlappingNodes = [];
-    this._doInAllActiveSectors("_getNodesOverlappingWith",object,overlappingNodes);
-    return overlappingNodes;
-  },
-
-
-  /**
-   * Return a position object in canvasspace from a single point in screenspace
-   *
-   * @param pointer
-   * @returns {{left: number, top: number, right: number, bottom: number}}
-   * @private
-   */
-  _pointerToPositionObject : function(pointer) {
-    var x = this._XconvertDOMtoCanvas(pointer.x);
-    var y = this._YconvertDOMtoCanvas(pointer.y);
-
-    return {left:   x,
-            top:    y,
-            right:  x,
-            bottom: y};
-  },
-
-
-  /**
-   * Get the top node at the a specific point (like a click)
-   *
-   * @param {{x: Number, y: Number}} pointer
-   * @return {Node | null} node
-   * @private
-   */
-  _getNodeAt : function (pointer) {
-    // we first check if this is an navigation controls element
-    var positionObject = this._pointerToPositionObject(pointer);
-    var overlappingNodes = this._getAllNodesOverlappingWith(positionObject);
-
-    // if there are overlapping nodes, select the last one, this is the
-    // one which is drawn on top of the others
-    if (overlappingNodes.length > 0) {
-       return this.nodes[overlappingNodes[overlappingNodes.length - 1]];
-    }
-    else {
-      return null;
-    }
-  },
-
-
-  /**
-   * retrieve all edges overlapping with given object, selector is around center
-   * @param {Object} object  An object with parameters left, top, right, bottom
-   * @return {Number[]}   An array with id's of the overlapping nodes
-   * @private
-   */
-  _getEdgesOverlappingWith : function (object, overlappingEdges) {
-    var edges = this.edges;
-    for (var edgeId in edges) {
-      if (edges.hasOwnProperty(edgeId)) {
-        if (edges[edgeId].isOverlappingWith(object)) {
-          overlappingEdges.push(edgeId);
-        }
-      }
-    }
-  },
-
-
-  /**
-   * retrieve all nodes overlapping with given object
-   * @param {Object} object  An object with parameters left, top, right, bottom
-   * @return {Number[]}   An array with id's of the overlapping nodes
-   * @private
-   */
-  _getAllEdgesOverlappingWith : function (object) {
-    var overlappingEdges = [];
-    this._doInAllActiveSectors("_getEdgesOverlappingWith",object,overlappingEdges);
-    return overlappingEdges;
-  },
-
-  /**
-   * Place holder. To implement change the _getNodeAt to a _getObjectAt. Have the _getObjectAt call
-   * _getNodeAt and _getEdgesAt, then priortize the selection to user preferences.
-   *
-   * @param pointer
-   * @returns {null}
-   * @private
-   */
-  _getEdgeAt : function(pointer) {
-    var positionObject = this._pointerToPositionObject(pointer);
-    var overlappingEdges = this._getAllEdgesOverlappingWith(positionObject);
-
-    if (overlappingEdges.length > 0) {
-      return this.edges[overlappingEdges[overlappingEdges.length - 1]];
-    }
-    else {
-      return null;
-    }
-  },
-
-
-  /**
-   * Add object to the selection array.
-   *
-   * @param obj
-   * @private
-   */
-  _addToSelection : function(obj) {
-    if (obj instanceof Node) {
-      this.selectionObj.nodes[obj.id] = obj;
-    }
-    else {
-      this.selectionObj.edges[obj.id] = obj;
-    }
-  },
-
-  /**
-   * Add object to the selection array.
-   *
-   * @param obj
-   * @private
-   */
-  _addToHover : function(obj) {
-    if (obj instanceof Node) {
-      this.hoverObj.nodes[obj.id] = obj;
-    }
-    else {
-      this.hoverObj.edges[obj.id] = obj;
-    }
-  },
-
-
-  /**
-   * Remove a single option from selection.
-   *
-   * @param {Object} obj
-   * @private
-   */
-  _removeFromSelection : function(obj) {
-    if (obj instanceof Node) {
-      delete this.selectionObj.nodes[obj.id];
-    }
-    else {
-      delete this.selectionObj.edges[obj.id];
-    }
-  },
-
-  /**
-   * Unselect all. The selectionObj is useful for this.
-   *
-   * @param {Boolean} [doNotTrigger] | ignore trigger
-   * @private
-   */
-  _unselectAll : function(doNotTrigger) {
-    if (doNotTrigger === undefined) {
-      doNotTrigger = false;
-    }
-    for(var nodeId in this.selectionObj.nodes) {
-      if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        this.selectionObj.nodes[nodeId].unselect();
-      }
-    }
-    for(var edgeId in this.selectionObj.edges) {
-      if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        this.selectionObj.edges[edgeId].unselect();
-      }
-    }
-
-    this.selectionObj = {nodes:{},edges:{}};
-
-    if (doNotTrigger == false) {
-      this.emit('select', this.getSelection());
-    }
-  },
-
-  /**
-   * Unselect all clusters. The selectionObj is useful for this.
-   *
-   * @param {Boolean} [doNotTrigger] | ignore trigger
-   * @private
-   */
-  _unselectClusters : function(doNotTrigger) {
-    if (doNotTrigger === undefined) {
-      doNotTrigger = false;
-    }
-
-    for (var nodeId in this.selectionObj.nodes) {
-      if (this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        if (this.selectionObj.nodes[nodeId].clusterSize > 1) {
-          this.selectionObj.nodes[nodeId].unselect();
-          this._removeFromSelection(this.selectionObj.nodes[nodeId]);
-        }
-      }
-    }
-
-    if (doNotTrigger == false) {
-      this.emit('select', this.getSelection());
-    }
-  },
-
-
-  /**
-   * return the number of selected nodes
-   *
-   * @returns {number}
-   * @private
-   */
-  _getSelectedNodeCount : function() {
-    var count = 0;
-    for (var nodeId in this.selectionObj.nodes) {
-      if (this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        count += 1;
-      }
-    }
-    return count;
-  },
-
-  /**
-   * return the selected node
-   *
-   * @returns {number}
-   * @private
-   */
-  _getSelectedNode : function() {
-    for (var nodeId in this.selectionObj.nodes) {
-      if (this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        return this.selectionObj.nodes[nodeId];
-      }
-    }
-    return null;
-  },
-
-  /**
-   * return the selected edge
-   *
-   * @returns {number}
-   * @private
-   */
-  _getSelectedEdge : function() {
-    for (var edgeId in this.selectionObj.edges) {
-      if (this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        return this.selectionObj.edges[edgeId];
-      }
-    }
-    return null;
-  },
-
-
-  /**
-   * return the number of selected edges
-   *
-   * @returns {number}
-   * @private
-   */
-  _getSelectedEdgeCount : function() {
-    var count = 0;
-    for (var edgeId in this.selectionObj.edges) {
-      if (this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        count += 1;
-      }
-    }
-    return count;
-  },
-
-
-  /**
-   * return the number of selected objects.
-   *
-   * @returns {number}
-   * @private
-   */
-  _getSelectedObjectCount : function() {
-    var count = 0;
-    for(var nodeId in this.selectionObj.nodes) {
-      if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        count += 1;
-      }
-    }
-    for(var edgeId in this.selectionObj.edges) {
-      if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        count += 1;
-      }
-    }
-    return count;
-  },
-
-  /**
-   * Check if anything is selected
-   *
-   * @returns {boolean}
-   * @private
-   */
-  _selectionIsEmpty : function() {
-    for(var nodeId in this.selectionObj.nodes) {
-      if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        return false;
-      }
-    }
-    for(var edgeId in this.selectionObj.edges) {
-      if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        return false;
-      }
-    }
-    return true;
-  },
-
-
-  /**
-   * check if one of the selected nodes is a cluster.
-   *
-   * @returns {boolean}
-   * @private
-   */
-  _clusterInSelection : function() {
-    for(var nodeId in this.selectionObj.nodes) {
-      if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        if (this.selectionObj.nodes[nodeId].clusterSize > 1) {
-          return true;
-        }
-      }
-    }
-    return false;
-  },
-
-  /**
-   * select the edges connected to the node that is being selected
-   *
-   * @param {Node} node
-   * @private
-   */
-  _selectConnectedEdges : function(node) {
-    for (var i = 0; i < node.dynamicEdges.length; i++) {
-      var edge = node.dynamicEdges[i];
-      edge.select();
-      this._addToSelection(edge);
-    }
-  },
-
-  /**
-   * select the edges connected to the node that is being selected
-   *
-   * @param {Node} node
-   * @private
-   */
-  _hoverConnectedEdges : function(node) {
-    for (var i = 0; i < node.dynamicEdges.length; i++) {
-      var edge = node.dynamicEdges[i];
-      edge.hover = true;
-      this._addToHover(edge);
-    }
-  },
-
-
-  /**
-   * unselect the edges connected to the node that is being selected
-   *
-   * @param {Node} node
-   * @private
-   */
-  _unselectConnectedEdges : function(node) {
-    for (var i = 0; i < node.dynamicEdges.length; i++) {
-      var edge = node.dynamicEdges[i];
-      edge.unselect();
-      this._removeFromSelection(edge);
-    }
-  },
-
-
-
-
-  /**
-   * This is called when someone clicks on a node. either select or deselect it.
-   * If there is an existing selection and we don't want to append to it, clear the existing selection
-   *
-   * @param {Node || Edge} object
-   * @param {Boolean} append
-   * @param {Boolean} [doNotTrigger] | ignore trigger
-   * @private
-   */
-  _selectObject : function(object, append, doNotTrigger, highlightEdges) {
-    if (doNotTrigger === undefined) {
-      doNotTrigger = false;
-    }
-    if (highlightEdges === undefined) {
-      highlightEdges = true;
-    }
-
-    if (this._selectionIsEmpty() == false && append == false && this.forceAppendSelection == false) {
-      this._unselectAll(true);
-    }
-
-    if (object.selected == false) {
-      object.select();
-      this._addToSelection(object);
-      if (object instanceof Node && this.blockConnectingEdgeSelection == false && highlightEdges == true) {
-        this._selectConnectedEdges(object);
-      }
-    }
-    else {
-      object.unselect();
-      this._removeFromSelection(object);
-    }
-
-    if (doNotTrigger == false) {
-      this.emit('select', this.getSelection());
-    }
-  },
-
-
-  /**
-   * This is called when someone clicks on a node. either select or deselect it.
-   * If there is an existing selection and we don't want to append to it, clear the existing selection
-   *
-   * @param {Node || Edge} object
-   * @private
-   */
-  _blurObject : function(object) {
-    if (object.hover == true) {
-      object.hover = false;
-      this.emit("blurNode",{node:object.id});
-    }
-  },
-
-  /**
-   * This is called when someone clicks on a node. either select or deselect it.
-   * If there is an existing selection and we don't want to append to it, clear the existing selection
-   *
-   * @param {Node || Edge} object
-   * @private
-   */
-  _hoverObject : function(object) {
-    if (object.hover == false) {
-      object.hover = true;
-      this._addToHover(object);
-      if (object instanceof Node) {
-        this.emit("hoverNode",{node:object.id});
-      }
-    }
-    if (object instanceof Node) {
-      this._hoverConnectedEdges(object);
-    }
-  },
-
-
-  /**
-   * handles the selection part of the touch, only for navigation controls elements;
-   * Touch is triggered before tap, also before hold. Hold triggers after a while.
-   * This is the most responsive solution
-   *
-   * @param {Object} pointer
-   * @private
-   */
-  _handleTouch : function(pointer) {
-  },
-
-
-  /**
-   * handles the selection part of the tap;
-   *
-   * @param {Object} pointer
-   * @private
-   */
-  _handleTap : function(pointer) {
-    var node = this._getNodeAt(pointer);
-    if (node != null) {
-      this._selectObject(node,false);
-    }
-    else {
-      var edge = this._getEdgeAt(pointer);
-      if (edge != null) {
-        this._selectObject(edge,false);
-      }
-      else {
-        this._unselectAll();
-      }
-    }
-    this.emit("click", this.getSelection());
-    this._redraw();
-  },
-
-
-  /**
-   * handles the selection part of the double tap and opens a cluster if needed
-   *
-   * @param {Object} pointer
-   * @private
-   */
-  _handleDoubleTap : function(pointer) {
-    var node = this._getNodeAt(pointer);
-    if (node != null && node !== undefined) {
-      // we reset the areaCenter here so the opening of the node will occur
-      this.areaCenter =  {"x" : this._XconvertDOMtoCanvas(pointer.x),
-                          "y" : this._YconvertDOMtoCanvas(pointer.y)};
-      this.openCluster(node);
-    }
-    this.emit("doubleClick", this.getSelection());
-  },
-
-
-  /**
-   * Handle the onHold selection part
-   *
-   * @param pointer
-   * @private
-   */
-  _handleOnHold : function(pointer) {
-    var node = this._getNodeAt(pointer);
-    if (node != null) {
-      this._selectObject(node,true);
-    }
-    else {
-      var edge = this._getEdgeAt(pointer);
-      if (edge != null) {
-        this._selectObject(edge,true);
-      }
-    }
-    this._redraw();
-  },
-
-
-  /**
-   * handle the onRelease event. These functions are here for the navigation controls module.
-   *
-    * @private
-   */
-  _handleOnRelease : function(pointer) {
-
-  },
-
-
-
-  /**
-   *
-   * retrieve the currently selected objects
-   * @return {Number[] | String[]} selection    An array with the ids of the
-   *                                            selected nodes.
-   */
-  getSelection : function() {
-    var nodeIds = this.getSelectedNodes();
-    var edgeIds = this.getSelectedEdges();
-    return {nodes:nodeIds, edges:edgeIds};
-  },
-
-  /**
-   *
-   * retrieve the currently selected nodes
-   * @return {String} selection    An array with the ids of the
-   *                                            selected nodes.
-   */
-  getSelectedNodes : function() {
-    var idArray = [];
-    for(var nodeId in this.selectionObj.nodes) {
-      if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        idArray.push(nodeId);
-      }
-    }
-    return idArray
-  },
-
-  /**
-   *
-   * retrieve the currently selected edges
-   * @return {Array} selection    An array with the ids of the
-   *                                            selected nodes.
-   */
-  getSelectedEdges : function() {
-    var idArray = [];
-    for(var edgeId in this.selectionObj.edges) {
-      if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        idArray.push(edgeId);
-      }
-    }
-    return idArray;
-  },
-
-
-  /**
-   * select zero or more nodes
-   * @param {Number[] | String[]} selection     An array with the ids of the
-   *                                            selected nodes.
-   */
-  setSelection : function(selection) {
-    var i, iMax, id;
-
-    if (!selection || (selection.length == undefined))
-      throw 'Selection must be an array with ids';
-
-    // first unselect any selected node
-    this._unselectAll(true);
-
-    for (i = 0, iMax = selection.length; i < iMax; i++) {
-      id = selection[i];
-
-      var node = this.nodes[id];
-      if (!node) {
-        throw new RangeError('Node with id "' + id + '" not found');
-      }
-      this._selectObject(node,true,true);
-    }
-
-    console.log("setSelection is deprecated. Please use selectNodes instead.")
-
-    this.redraw();
-  },
-
-
-  /**
-   * select zero or more nodes with the option to highlight edges
-   * @param {Number[] | String[]} selection     An array with the ids of the
-   *                                            selected nodes.
-   * @param {boolean} [highlightEdges]
-   */
-  selectNodes : function(selection, highlightEdges) {
-    var i, iMax, id;
-
-    if (!selection || (selection.length == undefined))
-      throw 'Selection must be an array with ids';
-
-    // first unselect any selected node
-    this._unselectAll(true);
-
-    for (i = 0, iMax = selection.length; i < iMax; i++) {
-      id = selection[i];
-
-      var node = this.nodes[id];
-      if (!node) {
-        throw new RangeError('Node with id "' + id + '" not found');
-      }
-      this._selectObject(node,true,true,highlightEdges);
-    }
-    this.redraw();
-  },
-
-
-  /**
-   * select zero or more edges
-   * @param {Number[] | String[]} selection     An array with the ids of the
-   *                                            selected nodes.
-   */
-  selectEdges : function(selection) {
-    var i, iMax, id;
-
-    if (!selection || (selection.length == undefined))
-      throw 'Selection must be an array with ids';
-
-    // first unselect any selected node
-    this._unselectAll(true);
-
-    for (i = 0, iMax = selection.length; i < iMax; i++) {
-      id = selection[i];
-
-      var edge = this.edges[id];
-      if (!edge) {
-        throw new RangeError('Edge with id "' + id + '" not found');
-      }
-      this._selectObject(edge,true,true,highlightEdges);
-    }
-    this.redraw();
-  },
-
-  /**
-   * Validate the selection: remove ids of nodes which no longer exist
-   * @private
-   */
-  _updateSelection : function () {
-    for(var nodeId in this.selectionObj.nodes) {
-      if(this.selectionObj.nodes.hasOwnProperty(nodeId)) {
-        if (!this.nodes.hasOwnProperty(nodeId)) {
-          delete this.selectionObj.nodes[nodeId];
-        }
-      }
-    }
-    for(var edgeId in this.selectionObj.edges) {
-      if(this.selectionObj.edges.hasOwnProperty(edgeId)) {
-        if (!this.edges.hasOwnProperty(edgeId)) {
-          delete this.selectionObj.edges[edgeId];
-        }
-      }
-    }
-  }
-};
-
-

lib/network/networkMixins/physics/BarnesHut.js

@@ -1,398 +0,0 @@
-/**
- * Created by Alex on 2/10/14.
- */
-
-var barnesHutMixin = {
-
-  /**
-   * This function calculates the forces the nodes apply on eachother based on a gravitational model.
-   * The Barnes Hut method is used to speed up this N-body simulation.
-   *
-   * @private
-   */
-  _calculateNodeForces : function() {
-    if (this.constants.physics.barnesHut.gravitationalConstant != 0) {
-      var node;
-      var nodes = this.calculationNodes;
-      var nodeIndices = this.calculationNodeIndices;
-      var nodeCount = nodeIndices.length;
-
-      this._formBarnesHutTree(nodes,nodeIndices);
-
-      var barnesHutTree = this.barnesHutTree;
-
-      // place the nodes one by one recursively
-      for (var i = 0; i < nodeCount; i++) {
-        node = nodes[nodeIndices[i]];
-        // starting with root is irrelevant, it never passes the BarnesHut condition
-        this._getForceContribution(barnesHutTree.root.children.NW,node);
-        this._getForceContribution(barnesHutTree.root.children.NE,node);
-        this._getForceContribution(barnesHutTree.root.children.SW,node);
-        this._getForceContribution(barnesHutTree.root.children.SE,node);
-      }
-    }
-  },
-
-
-  /**
-   * This function traverses the barnesHutTree. It checks when it can approximate distant nodes with their center of mass.
-   * If a region contains a single node, we check if it is not itself, then we apply the force.
-   *
-   * @param parentBranch
-   * @param node
-   * @private
-   */
-  _getForceContribution : function(parentBranch,node) {
-    // we get no force contribution from an empty region
-    if (parentBranch.childrenCount > 0) {
-      var dx,dy,distance;
-
-      // get the distance from the center of mass to the node.
-      dx = parentBranch.centerOfMass.x - node.x;
-      dy = parentBranch.centerOfMass.y - node.y;
-      distance = Math.sqrt(dx * dx + dy * dy);
-
-      // BarnesHut condition
-      // original condition : s/d < theta = passed  ===  d/s > 1/theta = passed
-      // calcSize = 1/s --> d * 1/s > 1/theta = passed
-      if (distance * parentBranch.calcSize > this.constants.physics.barnesHut.theta) {
-        // duplicate code to reduce function calls to speed up program
-        if (distance == 0) {
-          distance = 0.1*Math.random();
-          dx = distance;
-        }
-        var gravityForce = this.constants.physics.barnesHut.gravitationalConstant * parentBranch.mass * node.mass / (distance * distance * distance);
-        var fx = dx * gravityForce;
-        var fy = dy * gravityForce;
-        node.fx += fx;
-        node.fy += fy;
-      }
-      else {
-        // Did not pass the condition, go into children if available
-        if (parentBranch.childrenCount == 4) {
-          this._getForceContribution(parentBranch.children.NW,node);
-          this._getForceContribution(parentBranch.children.NE,node);
-          this._getForceContribution(parentBranch.children.SW,node);
-          this._getForceContribution(parentBranch.children.SE,node);
-        }
-        else { // parentBranch must have only one node, if it was empty we wouldnt be here
-          if (parentBranch.children.data.id != node.id) { // if it is not self
-            // duplicate code to reduce function calls to speed up program
-            if (distance == 0) {
-              distance = 0.5*Math.random();
-              dx = distance;
-            }
-            var gravityForce = this.constants.physics.barnesHut.gravitationalConstant * parentBranch.mass * node.mass / (distance * distance * distance);
-            var fx = dx * gravityForce;
-            var fy = dy * gravityForce;
-            node.fx += fx;
-            node.fy += fy;
-          }
-        }
-      }
-    }
-  },
-
-  /**
-   * This function constructs the barnesHut tree recursively. It creates the root, splits it and starts placing the nodes.
-   *
-   * @param nodes
-   * @param nodeIndices
-   * @private
-   */
-  _formBarnesHutTree : function(nodes,nodeIndices) {
-    var node;
-    var nodeCount = nodeIndices.length;
-
-    var minX = Number.MAX_VALUE,
-      minY = Number.MAX_VALUE,
-      maxX =-Number.MAX_VALUE,
-      maxY =-Number.MAX_VALUE;
-
-    // get the range of the nodes
-    for (var i = 0; i < nodeCount; i++) {
-      var x = nodes[nodeIndices[i]].x;
-      var y = nodes[nodeIndices[i]].y;
-      if (x < minX) { minX = x; }
-      if (x > maxX) { maxX = x; }
-      if (y < minY) { minY = y; }
-      if (y > maxY) { maxY = y; }
-    }
-    // make the range a square
-    var sizeDiff = Math.abs(maxX - minX) - Math.abs(maxY - minY); // difference between X and Y
-    if (sizeDiff > 0) {minY -= 0.5 * sizeDiff; maxY += 0.5 * sizeDiff;} // xSize > ySize
-    else              {minX += 0.5 * sizeDiff; maxX -= 0.5 * sizeDiff;} // xSize < ySize
-
-
-    var minimumTreeSize = 1e-5;
-    var rootSize = Math.max(minimumTreeSize,Math.abs(maxX - minX));
-    var halfRootSize = 0.5 * rootSize;
-    var centerX = 0.5 * (minX + maxX), centerY = 0.5 * (minY + maxY);
-
-    // construct the barnesHutTree
-    var barnesHutTree = {root:{
-      centerOfMass:{x:0,y:0}, // Center of Mass
-      mass:0,
-      range: {minX:centerX-halfRootSize,maxX:centerX+halfRootSize,
-              minY:centerY-halfRootSize,maxY:centerY+halfRootSize},
-
-      size: rootSize,
-      calcSize: 1 / rootSize,
-      children: {data:null},
-      maxWidth: 0,
-      level: 0,
-      childrenCount: 4
-    }};
-    this._splitBranch(barnesHutTree.root);
-
-    // place the nodes one by one recursively
-    for (i = 0; i < nodeCount; i++) {
-      node = nodes[nodeIndices[i]];
-      this._placeInTree(barnesHutTree.root,node);
-    }
-
-    // make global
-    this.barnesHutTree = barnesHutTree
-  },
-
-
-  /**
-   * this updates the mass of a branch. this is increased by adding a node.
-   *
-   * @param parentBranch
-   * @param node
-   * @private
-   */
-  _updateBranchMass : function(parentBranch, node) {
-    var totalMass = parentBranch.mass + node.mass;
-    var totalMassInv = 1/totalMass;
-
-    parentBranch.centerOfMass.x = parentBranch.centerOfMass.x * parentBranch.mass + node.x * node.mass;
-    parentBranch.centerOfMass.x *= totalMassInv;
-
-    parentBranch.centerOfMass.y = parentBranch.centerOfMass.y * parentBranch.mass + node.y * node.mass;
-    parentBranch.centerOfMass.y *= totalMassInv;
-
-    parentBranch.mass = totalMass;
-    var biggestSize = Math.max(Math.max(node.height,node.radius),node.width);
-    parentBranch.maxWidth = (parentBranch.maxWidth < biggestSize) ? biggestSize : parentBranch.maxWidth;
-
-  },
-
-
-  /**
-   * determine in which branch the node will be placed.
-   *
-   * @param parentBranch
-   * @param node
-   * @param skipMassUpdate
-   * @private
-   */
-  _placeInTree : function(parentBranch,node,skipMassUpdate) {
-    if (skipMassUpdate != true || skipMassUpdate === undefined) {
-      // update the mass of the branch.
-      this._updateBranchMass(parentBranch,node);
-    }
-
-    if (parentBranch.children.NW.range.maxX > node.x) { // in NW or SW
-      if (parentBranch.children.NW.range.maxY > node.y) { // in NW
-        this._placeInRegion(parentBranch,node,"NW");
-      }
-      else { // in SW
-        this._placeInRegion(parentBranch,node,"SW");
-      }
-    }
-    else { // in NE or SE
-      if (parentBranch.children.NW.range.maxY > node.y) { // in NE
-        this._placeInRegion(parentBranch,node,"NE");
-      }
-      else { // in SE
-        this._placeInRegion(parentBranch,node,"SE");
-      }
-    }
-  },
-
-
-  /**
-   * actually place the node in a region (or branch)
-   *
-   * @param parentBranch
-   * @param node
-   * @param region
-   * @private
-   */
-  _placeInRegion : function(parentBranch,node,region) {
-    switch (parentBranch.children[region].childrenCount) {
-      case 0: // place node here
-        parentBranch.children[region].children.data = node;
-        parentBranch.children[region].childrenCount = 1;
-        this._updateBranchMass(parentBranch.children[region],node);
-        break;
-      case 1: // convert into children
-        // if there are two nodes exactly overlapping (on init, on opening of cluster etc.)
-        // we move one node a pixel and we do not put it in the tree.
-        if (parentBranch.children[region].children.data.x == node.x &&
-            parentBranch.children[region].children.data.y == node.y) {
-          node.x += Math.random();
-          node.y += Math.random();
-        }
-        else {
-          this._splitBranch(parentBranch.children[region]);
-          this._placeInTree(parentBranch.children[region],node);
-        }
-        break;
-      case 4: // place in branch
-        this._placeInTree(parentBranch.children[region],node);
-        break;
-    }
-  },
-
-
-  /**
-   * this function splits a branch into 4 sub branches. If the branch contained a node, we place it in the subbranch
-   * after the split is complete.
-   *
-   * @param parentBranch
-   * @private
-   */
-  _splitBranch : function(parentBranch) {
-    // if the branch is shaded with a node, replace the node in the new subset.
-    var containedNode = null;
-    if (parentBranch.childrenCount == 1) {
-      containedNode = parentBranch.children.data;
-      parentBranch.mass = 0; parentBranch.centerOfMass.x = 0; parentBranch.centerOfMass.y = 0;
-    }
-    parentBranch.childrenCount = 4;
-    parentBranch.children.data = null;
-    this._insertRegion(parentBranch,"NW");
-    this._insertRegion(parentBranch,"NE");
-    this._insertRegion(parentBranch,"SW");
-    this._insertRegion(parentBranch,"SE");
-
-    if (containedNode != null) {
-      this._placeInTree(parentBranch,containedNode);
-    }
-  },
-
-
-  /**
-   * This function subdivides the region into four new segments.
-   * Specifically, this inserts a single new segment.
-   * It fills the children section of the parentBranch
-   *
-   * @param parentBranch
-   * @param region
-   * @param parentRange
-   * @private
-   */
-  _insertRegion : function(parentBranch, region) {
-    var minX,maxX,minY,maxY;
-    var childSize = 0.5 * parentBranch.size;
-    switch (region) {
-      case "NW":
-        minX = parentBranch.range.minX;
-        maxX = parentBranch.range.minX + childSize;
-        minY = parentBranch.range.minY;
-        maxY = parentBranch.range.minY + childSize;
-        break;
-      case "NE":
-        minX = parentBranch.range.minX + childSize;
-        maxX = parentBranch.range.maxX;
-        minY = parentBranch.range.minY;
-        maxY = parentBranch.range.minY + childSize;
-        break;
-      case "SW":
-        minX = parentBranch.range.minX;
-        maxX = parentBranch.range.minX + childSize;
-        minY = parentBranch.range.minY + childSize;
-        maxY = parentBranch.range.maxY;
-        break;
-      case "SE":
-        minX = parentBranch.range.minX + childSize;
-        maxX = parentBranch.range.maxX;
-        minY = parentBranch.range.minY + childSize;
-        maxY = parentBranch.range.maxY;
-        break;
-    }
-
-
-    parentBranch.children[region] = {
-      centerOfMass:{x:0,y:0},
-      mass:0,
-      range:{minX:minX,maxX:maxX,minY:minY,maxY:maxY},
-      size: 0.5 * parentBranch.size,
-      calcSize: 2 * parentBranch.calcSize,
-      children: {data:null},
-      maxWidth: 0,
-      level: parentBranch.level+1,
-      childrenCount: 0
-    };
-  },
-
-
-  /**
-   * This function is for debugging purposed, it draws the tree.
-   *
-   * @param ctx
-   * @param color
-   * @private
-   */
-  _drawTree : function(ctx,color) {
-    if (this.barnesHutTree !== undefined) {
-
-      ctx.lineWidth = 1;
-
-      this._drawBranch(this.barnesHutTree.root,ctx,color);
-    }
-  },
-
-
-  /**
-   * This function is for debugging purposes. It draws the branches recursively.
-   *
-   * @param branch
-   * @param ctx
-   * @param color
-   * @private
-   */
-  _drawBranch : function(branch,ctx,color) {
-    if (color === undefined) {
-      color = "#FF0000";
-    }
-
-    if (branch.childrenCount == 4) {
-      this._drawBranch(branch.children.NW,ctx);
-      this._drawBranch(branch.children.NE,ctx);
-      this._drawBranch(branch.children.SE,ctx);
-      this._drawBranch(branch.children.SW,ctx);
-    }
-    ctx.strokeStyle = color;
-    ctx.beginPath();
-    ctx.moveTo(branch.range.minX,branch.range.minY);
-    ctx.lineTo(branch.range.maxX,branch.range.minY);
-    ctx.stroke();
-
-    ctx.beginPath();
-    ctx.moveTo(branch.range.maxX,branch.range.minY);
-    ctx.lineTo(branch.range.maxX,branch.range.maxY);
-    ctx.stroke();
-
-    ctx.beginPath();
-    ctx.moveTo(branch.range.maxX,branch.range.maxY);
-    ctx.lineTo(branch.range.minX,branch.range.maxY);
-    ctx.stroke();
-
-    ctx.beginPath();
-    ctx.moveTo(branch.range.minX,branch.range.maxY);
-    ctx.lineTo(branch.range.minX,branch.range.minY);
-    ctx.stroke();
-
-    /*
-     if (branch.mass > 0) {
-     ctx.circle(branch.centerOfMass.x, branch.centerOfMass.y, 3*branch.mass);
-     ctx.stroke();
-     }
-     */
-  }
-
-};

lib/network/networkMixins/physics/HierarchialRepulsion.js

@@ -1,133 +0,0 @@
-/**
- * Created by Alex on 2/10/14.
- */
-
-var hierarchalRepulsionMixin = {
-
-
-  /**
-   * Calculate the forces the nodes apply on eachother based on a repulsion field.
-   * This field is linearly approximated.
-   *
-   * @private
-   */
-  _calculateNodeForces: function () {
-    var dx, dy, distance, fx, fy, combinedClusterSize,
-      repulsingForce, node1, node2, i, j;
-
-    var nodes = this.calculationNodes;
-    var nodeIndices = this.calculationNodeIndices;
-
-    // approximation constants
-    var b = 5;
-    var a_base = 0.5 * -b;
-
-
-    // repulsing forces between nodes
-    var nodeDistance = this.constants.physics.hierarchicalRepulsion.nodeDistance;
-    var minimumDistance = nodeDistance;
-    var a = a_base / minimumDistance;
-
-    // we loop from i over all but the last entree in the array
-    // j loops from i+1 to the last. This way we do not double count any of the indices, nor i == j
-    for (i = 0; i < nodeIndices.length - 1; i++) {
-
-      node1 = nodes[nodeIndices[i]];
-      for (j = i + 1; j < nodeIndices.length; j++) {
-        node2 = nodes[nodeIndices[j]];
-        if (node1.level == node2.level) {
-
-          dx = node2.x - node1.x;
-          dy = node2.y - node1.y;
-          distance = Math.sqrt(dx * dx + dy * dy);
-
-
-          if (distance < 2 * minimumDistance) {
-            repulsingForce = a * distance + b;
-            var c = 0.05;
-            var d = 2 * minimumDistance * 2 * c;
-            repulsingForce = c * Math.pow(distance,2) - d * distance + d*d/(4*c);
-
-            // normalize force with
-            if (distance == 0) {
-              distance = 0.01;
-            }
-            else {
-              repulsingForce = repulsingForce / distance;
-            }
-            fx = dx * repulsingForce;
-            fy = dy * repulsingForce;
-
-            node1.fx -= fx;
-            node1.fy -= fy;
-            node2.fx += fx;
-            node2.fy += fy;
-          }
-        }
-      }
-    }
-  },
-
-
-  /**
-   * this function calculates the effects of the springs in the case of unsmooth curves.
-   *
-   * @private
-   */
-  _calculateHierarchicalSpringForces: function () {
-    var edgeLength, edge, edgeId;
-    var dx, dy, fx, fy, springForce, distance;
-    var edges = this.edges;
-
-    // forces caused by the edges, modelled as springs
-    for (edgeId in edges) {
-      if (edges.hasOwnProperty(edgeId)) {
-        edge = edges[edgeId];
-        if (edge.connected) {
-          // only calculate forces if nodes are in the same sector
-          if (this.nodes.hasOwnProperty(edge.toId) && this.nodes.hasOwnProperty(edge.fromId)) {
-            edgeLength = edge.customLength ? edge.length : this.constants.physics.springLength;
-            // this implies that the edges between big clusters are longer
-            edgeLength += (edge.to.clusterSize + edge.from.clusterSize - 2) * this.constants.clustering.edgeGrowth;
-
-            dx = (edge.from.x - edge.to.x);
-            dy = (edge.from.y - edge.to.y);
-            distance = Math.sqrt(dx * dx + dy * dy);
-
-            if (distance == 0) {
-              distance = 0.01;
-            }
-
-            distance = Math.max(0.8*edgeLength,Math.min(5*edgeLength, distance));
-
-            // the 1/distance is so the fx and fy can be calculated without sine or cosine.
-            springForce = this.constants.physics.springConstant * (edgeLength - distance) / distance;
-
-            fx = dx * springForce;
-            fy = dy * springForce;
-
-            edge.to.fx -= fx;
-            edge.to.fy -= fy;
-            edge.from.fx += fx;
-            edge.from.fy += fy;
-
-
-            var factor = 5;
-            if (distance > edgeLength) {
-              factor = 25;
-            }
-
-            if (edge.from.level > edge.to.level) {
-              edge.to.fx -= factor*fx;
-              edge.to.fy -= factor*fy;
-            }
-            else if (edge.from.level < edge.to.level) {
-              edge.from.fx += factor*fx;
-              edge.from.fy += factor*fy;
-            }
-          }
-        }
-      }
-    }
-  }
-};

lib/network/networkMixins/physics/PhysicsMixin.js

@@ -1,706 +0,0 @@
-/**
- * Created by Alex on 2/6/14.
- */
-
-
-var physicsMixin = {
-
-  /**
-   * Toggling barnes Hut calculation on and off.
-   *
-   * @private
-   */
-  _toggleBarnesHut: function () {
-    this.constants.physics.barnesHut.enabled = !this.constants.physics.barnesHut.enabled;
-    this._loadSelectedForceSolver();
-    this.moving = true;
-    this.start();
-  },
-
-
-  /**
-   * This loads the node force solver based on the barnes hut or repulsion algorithm
-   *
-   * @private
-   */
-  _loadSelectedForceSolver: function () {
-    // this overloads the this._calculateNodeForces
-    if (this.constants.physics.barnesHut.enabled == true) {
-      this._clearMixin(repulsionMixin);
-      this._clearMixin(hierarchalRepulsionMixin);
-
-      this.constants.physics.centralGravity = this.constants.physics.barnesHut.centralGravity;
-      this.constants.physics.springLength = this.constants.physics.barnesHut.springLength;
-      this.constants.physics.springConstant = this.constants.physics.barnesHut.springConstant;
-      this.constants.physics.damping = this.constants.physics.barnesHut.damping;
-
-      this._loadMixin(barnesHutMixin);
-    }
-    else if (this.constants.physics.hierarchicalRepulsion.enabled == true) {
-      this._clearMixin(barnesHutMixin);
-      this._clearMixin(repulsionMixin);
-
-      this.constants.physics.centralGravity = this.constants.physics.hierarchicalRepulsion.centralGravity;
-      this.constants.physics.springLength = this.constants.physics.hierarchicalRepulsion.springLength;
-      this.constants.physics.springConstant = this.constants.physics.hierarchicalRepulsion.springConstant;
-      this.constants.physics.damping = this.constants.physics.hierarchicalRepulsion.damping;
-
-      this._loadMixin(hierarchalRepulsionMixin);
-    }
-    else {
-      this._clearMixin(barnesHutMixin);
-      this._clearMixin(hierarchalRepulsionMixin);
-      this.barnesHutTree = undefined;
-
-      this.constants.physics.centralGravity = this.constants.physics.repulsion.centralGravity;
-      this.constants.physics.springLength = this.constants.physics.repulsion.springLength;
-      this.constants.physics.springConstant = this.constants.physics.repulsion.springConstant;
-      this.constants.physics.damping = this.constants.physics.repulsion.damping;
-
-      this._loadMixin(repulsionMixin);
-    }
-  },
-
-  /**
-   * Before calculating the forces, we check if we need to cluster to keep up performance and we check
-   * if there is more than one node. If it is just one node, we dont calculate anything.
-   *
-   * @private
-   */
-  _initializeForceCalculation: function () {
-    // stop calculation if there is only one node
-    if (this.nodeIndices.length == 1) {
-      this.nodes[this.nodeIndices[0]]._setForce(0, 0);
-    }
-    else {
-      // if there are too many nodes on screen, we cluster without repositioning
-      if (this.nodeIndices.length > this.constants.clustering.clusterThreshold && this.constants.clustering.enabled == true) {
-        this.clusterToFit(this.constants.clustering.reduceToNodes, false);
-      }
-
-      // we now start the force calculation
-      this._calculateForces();
-    }
-  },
-
-
-  /**
-   * Calculate the external forces acting on the nodes
-   * Forces are caused by: edges, repulsing forces between nodes, gravity
-   * @private
-   */
-  _calculateForces: function () {
-    // Gravity is required to keep separated groups from floating off
-    // the forces are reset to zero in this loop by using _setForce instead
-    // of _addForce
-
-    this._calculateGravitationalForces();
-    this._calculateNodeForces();
-
-    if (this.constants.smoothCurves == true) {
-      this._calculateSpringForcesWithSupport();
-    }
-    else {
-      if (this.constants.physics.hierarchicalRepulsion.enabled == true) {
-        this._calculateHierarchicalSpringForces();
-      }
-      else {
-        this._calculateSpringForces();
-      }
-    }
-  },
-
-
-  /**
-   * Smooth curves are created by adding invisible nodes in the center of the edges. These nodes are also
-   * handled in the calculateForces function. We then use a quadratic curve with the center node as control.
-   * This function joins the datanodes and invisible (called support) nodes into one object.
-   * We do this so we do not contaminate this.nodes with the support nodes.
-   *
-   * @private
-   */
-  _updateCalculationNodes: function () {
-    if (this.constants.smoothCurves == true) {
-      this.calculationNodes = {};
-      this.calculationNodeIndices = [];
-
-      for (var nodeId in this.nodes) {
-        if (this.nodes.hasOwnProperty(nodeId)) {
-          this.calculationNodes[nodeId] = this.nodes[nodeId];
-        }
-      }
-      var supportNodes = this.sectors['support']['nodes'];
-      for (var supportNodeId in supportNodes) {
-        if (supportNodes.hasOwnProperty(supportNodeId)) {
-          if (this.edges.hasOwnProperty(supportNodes[supportNodeId].parentEdgeId)) {
-            this.calculationNodes[supportNodeId] = supportNodes[supportNodeId];
-          }
-          else {
-            supportNodes[supportNodeId]._setForce(0, 0);
-          }
-        }
-      }
-
-      for (var idx in this.calculationNodes) {
-        if (this.calculationNodes.hasOwnProperty(idx)) {
-          this.calculationNodeIndices.push(idx);
-        }
-      }
-    }
-    else {
-      this.calculationNodes = this.nodes;
-      this.calculationNodeIndices = this.nodeIndices;
-    }
-  },
-
-
-  /**
-   * this function applies the central gravity effect to keep groups from floating off
-   *
-   * @private
-   */
-  _calculateGravitationalForces: function () {
-    var dx, dy, distance, node, i;
-    var nodes = this.calculationNodes;
-    var gravity = this.constants.physics.centralGravity;
-    var gravityForce = 0;
-
-    for (i = 0; i < this.calculationNodeIndices.length; i++) {
-      node = nodes[this.calculationNodeIndices[i]];
-      node.damping = this.constants.physics.damping; // possibly add function to alter damping properties of clusters.
-      // gravity does not apply when we are in a pocket sector
-      if (this._sector() == "default" && gravity != 0) {
-        dx = -node.x;
-        dy = -node.y;
-        distance = Math.sqrt(dx * dx + dy * dy);
-
-        gravityForce = (distance == 0) ? 0 : (gravity / distance);
-        node.fx = dx * gravityForce;
-        node.fy = dy * gravityForce;
-      }
-      else {
-        node.fx = 0;
-        node.fy = 0;
-      }
-    }
-  },
-
-
-
-
-  /**
-   * this function calculates the effects of the springs in the case of unsmooth curves.
-   *
-   * @private
-   */
-  _calculateSpringForces: function () {
-    var edgeLength, edge, edgeId;
-    var dx, dy, fx, fy, springForce, distance;
-    var edges = this.edges;
-
-    // forces caused by the edges, modelled as springs
-    for (edgeId in edges) {
-      if (edges.hasOwnProperty(edgeId)) {
-        edge = edges[edgeId];
-        if (edge.connected) {
-          // only calculate forces if nodes are in the same sector
-          if (this.nodes.hasOwnProperty(edge.toId) && this.nodes.hasOwnProperty(edge.fromId)) {
-            edgeLength = edge.customLength ? edge.length : this.constants.physics.springLength;
-            // this implies that the edges between big clusters are longer
-            edgeLength += (edge.to.clusterSize + edge.from.clusterSize - 2) * this.constants.clustering.edgeGrowth;
-
-            dx = (edge.from.x - edge.to.x);
-            dy = (edge.from.y - edge.to.y);
-            distance = Math.sqrt(dx * dx + dy * dy);
-
-            if (distance == 0) {
-              distance = 0.01;
-            }
-
-            // the 1/distance is so the fx and fy can be calculated without sine or cosine.
-            springForce = this.constants.physics.springConstant * (edgeLength - distance) / distance;
-
-            fx = dx * springForce;
-            fy = dy * springForce;
-
-            edge.from.fx += fx;
-            edge.from.fy += fy;
-            edge.to.fx -= fx;
-            edge.to.fy -= fy;
-          }
-        }
-      }
-    }
-  },
-
-
-
-
-  /**
-   * This function calculates the springforces on the nodes, accounting for the support nodes.
-   *
-   * @private
-   */
-  _calculateSpringForcesWithSupport: function () {
-    var edgeLength, edge, edgeId, combinedClusterSize;
-    var edges = this.edges;
-
-    // forces caused by the edges, modelled as springs
-    for (edgeId in edges) {
-      if (edges.hasOwnProperty(edgeId)) {
-        edge = edges[edgeId];
-        if (edge.connected) {
-          // only calculate forces if nodes are in the same sector
-          if (this.nodes.hasOwnProperty(edge.toId) && this.nodes.hasOwnProperty(edge.fromId)) {
-            if (edge.via != null) {
-              var node1 = edge.to;
-              var node2 = edge.via;
-              var node3 = edge.from;
-
-              edgeLength = edge.customLength ? edge.length : this.constants.physics.springLength;
-
-              combinedClusterSize = node1.clusterSize + node3.clusterSize - 2;
-
-              // this implies that the edges between big clusters are longer
-              edgeLength += combinedClusterSize * this.constants.clustering.edgeGrowth;
-              this._calculateSpringForce(node1, node2, 0.5 * edgeLength);
-              this._calculateSpringForce(node2, node3, 0.5 * edgeLength);
-            }
-          }
-        }
-      }
-    }
-  },
-
-
-  /**
-   * This is the code actually performing the calculation for the function above. It is split out to avoid repetition.
-   *
-   * @param node1
-   * @param node2
-   * @param edgeLength
-   * @private
-   */
-  _calculateSpringForce: function (node1, node2, edgeLength) {
-    var dx, dy, fx, fy, springForce, distance;
-
-    dx = (node1.x - node2.x);
-    dy = (node1.y - node2.y);
-    distance = Math.sqrt(dx * dx + dy * dy);
-
-    if (distance == 0) {
-      distance = 0.01;
-    }
-
-    // the 1/distance is so the fx and fy can be calculated without sine or cosine.
-    springForce = this.constants.physics.springConstant * (edgeLength - distance) / distance;
-
-    fx = dx * springForce;
-    fy = dy * springForce;
-
-    node1.fx += fx;
-    node1.fy += fy;
-    node2.fx -= fx;
-    node2.fy -= fy;
-  },
-
-
-  /**
-   * Load the HTML for the physics config and bind it
-   * @private
-   */
-  _loadPhysicsConfiguration: function () {
-    if (this.physicsConfiguration === undefined) {
-      this.backupConstants = {};
-      util.deepExtend(this.backupConstants,this.constants);
-
-      var hierarchicalLayoutDirections = ["LR", "RL", "UD", "DU"];
-      this.physicsConfiguration = document.createElement('div');
-      this.physicsConfiguration.className = "PhysicsConfiguration";
-      this.physicsConfiguration.innerHTML = '' +
-        '<table><tr><td><b>Simulation Mode:</b></td></tr>' +
-        '<tr>' +
-        '<td width="120px"><input type="radio" name="graph_physicsMethod" id="graph_physicsMethod1" value="BH" checked="checked">Barnes Hut</td>' +
-        '<td width="120px"><input type="radio" name="graph_physicsMethod" id="graph_physicsMethod2" value="R">Repulsion</td>' +
-        '<td width="120px"><input type="radio" name="graph_physicsMethod" id="graph_physicsMethod3" value="H">Hierarchical</td>' +
-        '</tr>' +
-        '</table>' +
-        '<table id="graph_BH_table" style="display:none">' +
-        '<tr><td><b>Barnes Hut</b></td></tr>' +
-        '<tr>' +
-        '<td width="150px">gravitationalConstant</td><td>0</td><td><input type="range" min="0" max="20000" value="' + (-1 * this.constants.physics.barnesHut.gravitationalConstant) + '" step="25" style="width:300px" id="graph_BH_gc"></td><td  width="50px">-20000</td><td><input value="' + (-1 * this.constants.physics.barnesHut.gravitationalConstant) + '" id="graph_BH_gc_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">centralGravity</td><td>0</td><td><input type="range" min="0" max="3"  value="' + this.constants.physics.barnesHut.centralGravity + '" step="0.05"  style="width:300px" id="graph_BH_cg"></td><td>3</td><td><input value="' + this.constants.physics.barnesHut.centralGravity + '" id="graph_BH_cg_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">springLength</td><td>0</td><td><input type="range" min="0" max="500" value="' + this.constants.physics.barnesHut.springLength + '" step="1" style="width:300px" id="graph_BH_sl"></td><td>500</td><td><input value="' + this.constants.physics.barnesHut.springLength + '" id="graph_BH_sl_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">springConstant</td><td>0</td><td><input type="range" min="0" max="0.5" value="' + this.constants.physics.barnesHut.springConstant + '" step="0.001" style="width:300px" id="graph_BH_sc"></td><td>0.5</td><td><input value="' + this.constants.physics.barnesHut.springConstant + '" id="graph_BH_sc_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">damping</td><td>0</td><td><input type="range" min="0" max="0.3" value="' + this.constants.physics.barnesHut.damping + '" step="0.005" style="width:300px" id="graph_BH_damp"></td><td>0.3</td><td><input value="' + this.constants.physics.barnesHut.damping + '" id="graph_BH_damp_value" style="width:60px"></td>' +
-        '</tr>' +
-        '</table>' +
-        '<table id="graph_R_table" style="display:none">' +
-        '<tr><td><b>Repulsion</b></td></tr>' +
-        '<tr>' +
-        '<td width="150px">nodeDistance</td><td>0</td><td><input type="range" min="0" max="300" value="' + this.constants.physics.repulsion.nodeDistance + '" step="1" style="width:300px" id="graph_R_nd"></td><td width="50px">300</td><td><input value="' + this.constants.physics.repulsion.nodeDistance + '" id="graph_R_nd_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">centralGravity</td><td>0</td><td><input type="range" min="0" max="3"  value="' + this.constants.physics.repulsion.centralGravity + '" step="0.05"  style="width:300px" id="graph_R_cg"></td><td>3</td><td><input value="' + this.constants.physics.repulsion.centralGravity + '" id="graph_R_cg_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">springLength</td><td>0</td><td><input type="range" min="0" max="500" value="' + this.constants.physics.repulsion.springLength + '" step="1" style="width:300px" id="graph_R_sl"></td><td>500</td><td><input value="' + this.constants.physics.repulsion.springLength + '" id="graph_R_sl_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">springConstant</td><td>0</td><td><input type="range" min="0" max="0.5" value="' + this.constants.physics.repulsion.springConstant + '" step="0.001" style="width:300px" id="graph_R_sc"></td><td>0.5</td><td><input value="' + this.constants.physics.repulsion.springConstant + '" id="graph_R_sc_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">damping</td><td>0</td><td><input type="range" min="0" max="0.3" value="' + this.constants.physics.repulsion.damping + '" step="0.005" style="width:300px" id="graph_R_damp"></td><td>0.3</td><td><input value="' + this.constants.physics.repulsion.damping + '" id="graph_R_damp_value" style="width:60px"></td>' +
-        '</tr>' +
-        '</table>' +
-        '<table id="graph_H_table" style="display:none">' +
-        '<tr><td width="150"><b>Hierarchical</b></td></tr>' +
-        '<tr>' +
-        '<td width="150px">nodeDistance</td><td>0</td><td><input type="range" min="0" max="300" value="' + this.constants.physics.hierarchicalRepulsion.nodeDistance + '" step="1" style="width:300px" id="graph_H_nd"></td><td width="50px">300</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.nodeDistance + '" id="graph_H_nd_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">centralGravity</td><td>0</td><td><input type="range" min="0" max="3"  value="' + this.constants.physics.hierarchicalRepulsion.centralGravity + '" step="0.05"  style="width:300px" id="graph_H_cg"></td><td>3</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.centralGravity + '" id="graph_H_cg_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">springLength</td><td>0</td><td><input type="range" min="0" max="500" value="' + this.constants.physics.hierarchicalRepulsion.springLength + '" step="1" style="width:300px" id="graph_H_sl"></td><td>500</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.springLength + '" id="graph_H_sl_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">springConstant</td><td>0</td><td><input type="range" min="0" max="0.5" value="' + this.constants.physics.hierarchicalRepulsion.springConstant + '" step="0.001" style="width:300px" id="graph_H_sc"></td><td>0.5</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.springConstant + '" id="graph_H_sc_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">damping</td><td>0</td><td><input type="range" min="0" max="0.3" value="' + this.constants.physics.hierarchicalRepulsion.damping + '" step="0.005" style="width:300px" id="graph_H_damp"></td><td>0.3</td><td><input value="' + this.constants.physics.hierarchicalRepulsion.damping + '" id="graph_H_damp_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">direction</td><td>1</td><td><input type="range" min="0" max="3" value="' + hierarchicalLayoutDirections.indexOf(this.constants.hierarchicalLayout.direction) + '" step="1" style="width:300px" id="graph_H_direction"></td><td>4</td><td><input value="' + this.constants.hierarchicalLayout.direction + '" id="graph_H_direction_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">levelSeparation</td><td>1</td><td><input type="range" min="0" max="500" value="' + this.constants.hierarchicalLayout.levelSeparation + '" step="1" style="width:300px" id="graph_H_levsep"></td><td>500</td><td><input value="' + this.constants.hierarchicalLayout.levelSeparation + '" id="graph_H_levsep_value" style="width:60px"></td>' +
-        '</tr>' +
-        '<tr>' +
-        '<td width="150px">nodeSpacing</td><td>1</td><td><input type="range" min="0" max="500" value="' + this.constants.hierarchicalLayout.nodeSpacing + '" step="1" style="width:300px" id="graph_H_nspac"></td><td>500</td><td><input value="' + this.constants.hierarchicalLayout.nodeSpacing + '" id="graph_H_nspac_value" style="width:60px"></td>' +
-        '</tr>' +
-        '</table>' +
-        '<table><tr><td><b>Options:</b></td></tr>' +
-        '<tr>' +
-        '<td width="180px"><input type="button" id="graph_toggleSmooth" value="Toggle smoothCurves" style="width:150px"></td>' +
-        '<td width="180px"><input type="button" id="graph_repositionNodes" value="Reinitialize" style="width:150px"></td>' +
-        '<td width="180px"><input type="button" id="graph_generateOptions" value="Generate Options" style="width:150px"></td>' +
-        '</tr>' +
-        '</table>'
-      this.containerElement.parentElement.insertBefore(this.physicsConfiguration, this.containerElement);
-      this.optionsDiv = document.createElement("div");
-      this.optionsDiv.style.fontSize = "14px";
-      this.optionsDiv.style.fontFamily = "verdana";
-      this.containerElement.parentElement.insertBefore(this.optionsDiv, this.containerElement);
-
-      var rangeElement;
-      rangeElement = document.getElementById('graph_BH_gc');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_gc', -1, "physics_barnesHut_gravitationalConstant");
-      rangeElement = document.getElementById('graph_BH_cg');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_cg', 1, "physics_centralGravity");
-      rangeElement = document.getElementById('graph_BH_sc');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_sc', 1, "physics_springConstant");
-      rangeElement = document.getElementById('graph_BH_sl');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_sl', 1, "physics_springLength");
-      rangeElement = document.getElementById('graph_BH_damp');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_BH_damp', 1, "physics_damping");
-
-      rangeElement = document.getElementById('graph_R_nd');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_nd', 1, "physics_repulsion_nodeDistance");
-      rangeElement = document.getElementById('graph_R_cg');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_cg', 1, "physics_centralGravity");
-      rangeElement = document.getElementById('graph_R_sc');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_sc', 1, "physics_springConstant");
-      rangeElement = document.getElementById('graph_R_sl');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_sl', 1, "physics_springLength");
-      rangeElement = document.getElementById('graph_R_damp');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_R_damp', 1, "physics_damping");
-
-      rangeElement = document.getElementById('graph_H_nd');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_nd', 1, "physics_hierarchicalRepulsion_nodeDistance");
-      rangeElement = document.getElementById('graph_H_cg');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_cg', 1, "physics_centralGravity");
-      rangeElement = document.getElementById('graph_H_sc');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_sc', 1, "physics_springConstant");
-      rangeElement = document.getElementById('graph_H_sl');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_sl', 1, "physics_springLength");
-      rangeElement = document.getElementById('graph_H_damp');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_damp', 1, "physics_damping");
-      rangeElement = document.getElementById('graph_H_direction');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_direction', hierarchicalLayoutDirections, "hierarchicalLayout_direction");
-      rangeElement = document.getElementById('graph_H_levsep');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_levsep', 1, "hierarchicalLayout_levelSeparation");
-      rangeElement = document.getElementById('graph_H_nspac');
-      rangeElement.onchange = showValueOfRange.bind(this, 'graph_H_nspac', 1, "hierarchicalLayout_nodeSpacing");
-
-      var radioButton1 = document.getElementById("graph_physicsMethod1");
-      var radioButton2 = document.getElementById("graph_physicsMethod2");
-      var radioButton3 = document.getElementById("graph_physicsMethod3");
-      radioButton2.checked = true;
-      if (this.constants.physics.barnesHut.enabled) {
-        radioButton1.checked = true;
-      }
-      if (this.constants.hierarchicalLayout.enabled) {
-        radioButton3.checked = true;
-      }
-
-      var graph_toggleSmooth = document.getElementById("graph_toggleSmooth");
-      var graph_repositionNodes = document.getElementById("graph_repositionNodes");
-      var graph_generateOptions = document.getElementById("graph_generateOptions");
-
-      graph_toggleSmooth.onclick = graphToggleSmoothCurves.bind(this);
-      graph_repositionNodes.onclick = graphRepositionNodes.bind(this);
-      graph_generateOptions.onclick = graphGenerateOptions.bind(this);
-      if (this.constants.smoothCurves == true) {
-        graph_toggleSmooth.style.background = "#A4FF56";
-      }
-      else {
-        graph_toggleSmooth.style.background = "#FF8532";
-      }
-
-
-      switchConfigurations.apply(this);
-
-      radioButton1.onchange = switchConfigurations.bind(this);
-      radioButton2.onchange = switchConfigurations.bind(this);
-      radioButton3.onchange = switchConfigurations.bind(this);
-    }
-  },
-
-  /**
-   * This overwrites the this.constants.
-   *
-   * @param constantsVariableName
-   * @param value
-   * @private
-   */
-  _overWriteGraphConstants: function (constantsVariableName, value) {
-    var nameArray = constantsVariableName.split("_");
-    if (nameArray.length == 1) {
-      this.constants[nameArray[0]] = value;
-    }
-    else if (nameArray.length == 2) {
-      this.constants[nameArray[0]][nameArray[1]] = value;
-    }
-    else if (nameArray.length == 3) {
-      this.constants[nameArray[0]][nameArray[1]][nameArray[2]] = value;
-    }
-  }
-};
-
-/**
- * this function is bound to the toggle smooth curves button. That is also why it is not in the prototype.
- */
-function graphToggleSmoothCurves () {
-  this.constants.smoothCurves = !this.constants.smoothCurves;
-  var graph_toggleSmooth = document.getElementById("graph_toggleSmooth");
-  if (this.constants.smoothCurves == true) {graph_toggleSmooth.style.background = "#A4FF56";}
-  else                                     {graph_toggleSmooth.style.background = "#FF8532";}
-
-  this._configureSmoothCurves(false);
-};
-
-/**
- * this function is used to scramble the nodes
- *
- */
-function graphRepositionNodes () {
-  for (var nodeId in this.calculationNodes) {
-    if (this.calculationNodes.hasOwnProperty(nodeId)) {
-      this.calculationNodes[nodeId].vx = 0;  this.calculationNodes[nodeId].vy = 0;
-      this.calculationNodes[nodeId].fx = 0;  this.calculationNodes[nodeId].fy = 0;
-    }
-  }
-  if (this.constants.hierarchicalLayout.enabled == true) {
-    this._setupHierarchicalLayout();
-  }
-  else {
-    this.repositionNodes();
-  }
-  this.moving = true;
-  this.start();
-};
-
-/**
- *  this is used to generate an options file from the playing with physics system.
- */
-function graphGenerateOptions () {
-  var options = "No options are required, default values used.";
-  var optionsSpecific = [];
-  var radioButton1 = document.getElementById("graph_physicsMethod1");
-  var radioButton2 = document.getElementById("graph_physicsMethod2");
-  if (radioButton1.checked == true) {
-    if (this.constants.physics.barnesHut.gravitationalConstant != this.backupConstants.physics.barnesHut.gravitationalConstant) {optionsSpecific.push("gravitationalConstant: " + this.constants.physics.barnesHut.gravitationalConstant);}
-    if (this.constants.physics.centralGravity != this.backupConstants.physics.barnesHut.centralGravity)                         {optionsSpecific.push("centralGravity: " + this.constants.physics.centralGravity);}
-    if (this.constants.physics.springLength != this.backupConstants.physics.barnesHut.springLength)                             {optionsSpecific.push("springLength: " + this.constants.physics.springLength);}
-    if (this.constants.physics.springConstant != this.backupConstants.physics.barnesHut.springConstant)                         {optionsSpecific.push("springConstant: " + this.constants.physics.springConstant);}
-    if (this.constants.physics.damping != this.backupConstants.physics.barnesHut.damping)                                       {optionsSpecific.push("damping: " + this.constants.physics.damping);}
-    if (optionsSpecific.length != 0) {
-      options = "var options = {";
-      options += "physics: {barnesHut: {";
-      for (var i = 0; i < optionsSpecific.length; i++) {
-        options += optionsSpecific[i];
-        if (i < optionsSpecific.length - 1) {
-          options += ", "
-        }
-      }
-      options += '}}'
-    }
-    if (this.constants.smoothCurves != this.backupConstants.smoothCurves) {
-      if (optionsSpecific.length == 0) {options = "var options = {";}
-      else {options += ", "}
-      options += "smoothCurves: " + this.constants.smoothCurves;
-    }
-    if (options != "No options are required, default values used.") {
-      options += '};'
-    }
-  }
-  else if (radioButton2.checked == true) {
-    options = "var options = {";
-    options += "physics: {barnesHut: {enabled: false}";
-    if (this.constants.physics.repulsion.nodeDistance != this.backupConstants.physics.repulsion.nodeDistance)  {optionsSpecific.push("nodeDistance: " + this.constants.physics.repulsion.nodeDistance);}
-    if (this.constants.physics.centralGravity != this.backupConstants.physics.repulsion.centralGravity)        {optionsSpecific.push("centralGravity: " + this.constants.physics.centralGravity);}
-    if (this.constants.physics.springLength != this.backupConstants.physics.repulsion.springLength)            {optionsSpecific.push("springLength: " + this.constants.physics.springLength);}
-    if (this.constants.physics.springConstant != this.backupConstants.physics.repulsion.springConstant)        {optionsSpecific.push("springConstant: " + this.constants.physics.springConstant);}
-    if (this.constants.physics.damping != this.backupConstants.physics.repulsion.damping)                      {optionsSpecific.push("damping: " + this.constants.physics.damping);}
-    if (optionsSpecific.length != 0) {
-      options += ", repulsion: {";
-      for (var i = 0; i < optionsSpecific.length; i++) {
-        options += optionsSpecific[i];
-        if (i < optionsSpecific.length - 1) {
-          options += ", "
-        }
-      }
-      options += '}}'
-    }
-    if (optionsSpecific.length == 0) {options += "}"}
-    if (this.constants.smoothCurves != this.backupConstants.smoothCurves) {
-      options += ", smoothCurves: " + this.constants.smoothCurves;
-    }
-    options += '};'
-  }
-  else {
-    options = "var options = {";
-    if (this.constants.physics.hierarchicalRepulsion.nodeDistance != this.backupConstants.physics.hierarchicalRepulsion.nodeDistance)  {optionsSpecific.push("nodeDistance: " + this.constants.physics.hierarchicalRepulsion.nodeDistance);}
-    if (this.constants.physics.centralGravity != this.backupConstants.physics.hierarchicalRepulsion.centralGravity)        {optionsSpecific.push("centralGravity: " + this.constants.physics.centralGravity);}
-    if (this.constants.physics.springLength != this.backupConstants.physics.hierarchicalRepulsion.springLength)            {optionsSpecific.push("springLength: " + this.constants.physics.springLength);}
-    if (this.constants.physics.springConstant != this.backupConstants.physics.hierarchicalRepulsion.springConstant)        {optionsSpecific.push("springConstant: " + this.constants.physics.springConstant);}
-    if (this.constants.physics.damping != this.backupConstants.physics.hierarchicalRepulsion.damping)                      {optionsSpecific.push("damping: " + this.constants.physics.damping);}
-    if (optionsSpecific.length != 0) {
-      options += "physics: {hierarchicalRepulsion: {";
-      for (var i = 0; i < optionsSpecific.length; i++) {
-        options += optionsSpecific[i];
-        if (i < optionsSpecific.length - 1) {
-          options += ", ";
-        }
-      }
-      options += '}},';
-    }
-    options += 'hierarchicalLayout: {';
-    optionsSpecific = [];
-    if (this.constants.hierarchicalLayout.direction != this.backupConstants.hierarchicalLayout.direction)                       {optionsSpecific.push("direction: " + this.constants.hierarchicalLayout.direction);}
-    if (Math.abs(this.constants.hierarchicalLayout.levelSeparation) != this.backupConstants.hierarchicalLayout.levelSeparation) {optionsSpecific.push("levelSeparation: " + this.constants.hierarchicalLayout.levelSeparation);}
-    if (this.constants.hierarchicalLayout.nodeSpacing != this.backupConstants.hierarchicalLayout.nodeSpacing)                   {optionsSpecific.push("nodeSpacing: " + this.constants.hierarchicalLayout.nodeSpacing);}
-    if (optionsSpecific.length != 0) {
-      for (var i = 0; i < optionsSpecific.length; i++) {
-        options += optionsSpecific[i];
-        if (i < optionsSpecific.length - 1) {
-          options += ", "
-        }
-      }
-      options += '}'
-    }
-    else {
-      options += "enabled:true}";
-    }
-    options += '};'
-  }
-
-
-  this.optionsDiv.innerHTML = options;
-
-};
-
-/**
- * this is used to switch between barnesHut, repulsion and hierarchical.
- *
- */
-function switchConfigurations () {
-  var ids = ["graph_BH_table", "graph_R_table", "graph_H_table"];
-  var radioButton = document.querySelector('input[name="graph_physicsMethod"]:checked').value;
-  var tableId = "graph_" + radioButton + "_table";
-  var table = document.getElementById(tableId);
-  table.style.display = "block";
-  for (var i = 0; i < ids.length; i++) {
-    if (ids[i] != tableId) {
-      table = document.getElementById(ids[i]);
-      table.style.display = "none";
-    }
-  }
-  this._restoreNodes();
-  if (radioButton == "R") {
-    this.constants.hierarchicalLayout.enabled = false;
-    this.constants.physics.hierarchicalRepulsion.enabled = false;
-    this.constants.physics.barnesHut.enabled = false;
-  }
-  else if (radioButton == "H") {
-    if (this.constants.hierarchicalLayout.enabled == false) {
-      this.constants.hierarchicalLayout.enabled = true;
-      this.constants.physics.hierarchicalRepulsion.enabled = true;
-      this.constants.physics.barnesHut.enabled = false;
-      this._setupHierarchicalLayout();
-    }
-  }
-  else {
-    this.constants.hierarchicalLayout.enabled = false;
-    this.constants.physics.hierarchicalRepulsion.enabled = false;
-    this.constants.physics.barnesHut.enabled = true;
-  }
-  this._loadSelectedForceSolver();
-  var graph_toggleSmooth = document.getElementById("graph_toggleSmooth");
-  if (this.constants.smoothCurves == true) {graph_toggleSmooth.style.background = "#A4FF56";}
-  else                                     {graph_toggleSmooth.style.background = "#FF8532";}
-  this.moving = true;
-  this.start();
-
-}
-
-
-/**
- * this generates the ranges depending on the iniital values.
- *
- * @param id
- * @param map
- * @param constantsVariableName
- */
-function showValueOfRange (id,map,constantsVariableName) {
-  var valueId = id + "_value";
-  var rangeValue = document.getElementById(id).value;
-
-  if (map instanceof Array) {
-    document.getElementById(valueId).value = map[parseInt(rangeValue)];
-    this._overWriteGraphConstants(constantsVariableName,map[parseInt(rangeValue)]);
-  }
-  else {
-    document.getElementById(valueId).value = parseInt(map) * parseFloat(rangeValue);
-    this._overWriteGraphConstants(constantsVariableName, parseInt(map) * parseFloat(rangeValue));
-  }
-
-  if (constantsVariableName == "hierarchicalLayout_direction" ||
-    constantsVariableName == "hierarchicalLayout_levelSeparation" ||
-    constantsVariableName == "hierarchicalLayout_nodeSpacing") {
-    this._setupHierarchicalLayout();
-  }
-  this.moving = true;
-  this.start();
-};
-
-

lib/network/networkMixins/physics/Repulsion.js

@@ -1,66 +0,0 @@
-/**
- * Created by Alex on 2/10/14.
- */
-
-var repulsionMixin = {
-
-
-  /**
-   * Calculate the forces the nodes apply on eachother based on a repulsion field.
-   * This field is linearly approximated.
-   *
-   * @private
-   */
-  _calculateNodeForces: function () {
-    var dx, dy, angle, distance, fx, fy, combinedClusterSize,
-      repulsingForce, node1, node2, i, j;
-
-    var nodes = this.calculationNodes;
-    var nodeIndices = this.calculationNodeIndices;
-
-    // approximation constants
-    var a_base = -2 / 3;
-    var b = 4 / 3;
-
-    // repulsing forces between nodes
-    var nodeDistance = this.constants.physics.repulsion.nodeDistance;
-    var minimumDistance = nodeDistance;
-
-    // we loop from i over all but the last entree in the array
-    // j loops from i+1 to the last. This way we do not double count any of the indices, nor i == j
-    for (i = 0; i < nodeIndices.length - 1; i++) {
-      node1 = nodes[nodeIndices[i]];
-      for (j = i + 1; j < nodeIndices.length; j++) {
-        node2 = nodes[nodeIndices[j]];
-        combinedClusterSize = node1.clusterSize + node2.clusterSize - 2;
-
-        dx = node2.x - node1.x;
-        dy = node2.y - node1.y;
-        distance = Math.sqrt(dx * dx + dy * dy);
-
-        minimumDistance = (combinedClusterSize == 0) ? nodeDistance : (nodeDistance * (1 + combinedClusterSize * this.constants.clustering.distanceAmplification));
-        var a = a_base / minimumDistance;
-        if (distance < 2 * minimumDistance) {
-          if (distance < 0.5 * minimumDistance) {
-            repulsingForce = 1.0;
-          }
-          else {
-            repulsingForce = a * distance + b; // linear approx of  1 / (1 + Math.exp((distance / minimumDistance - 1) * steepness))
-          }
-
-          // amplify the repulsion for clusters.
-          repulsingForce *= (combinedClusterSize == 0) ? 1 : 1 + combinedClusterSize * this.constants.clustering.forceAmplification;
-          repulsingForce = repulsingForce / distance;
-
-          fx = dx * repulsingForce;
-          fy = dy * repulsingForce;
-
-          node1.fx -= fx;
-          node1.fy -= fy;
-          node2.fx += fx;
-          node2.fy += fy;
-        }
-      }
-    }
-  }
-};

lib/shim.js

@@ -1,252 +0,0 @@
-
-// Internet Explorer 8 and older does not support Array.indexOf, so we define
-// it here in that case.
-// http://soledadpenades.com/2007/05/17/arrayindexof-in-internet-explorer/
-if(!Array.prototype.indexOf) {
-  Array.prototype.indexOf = function(obj){
-    for(var i = 0; i < this.length; i++){
-      if(this[i] == obj){
-        return i;
-      }
-    }
-    return -1;
-  };
-
-  try {
-    console.log("Warning: Ancient browser detected. Please update your browser");
-  }
-  catch (err) {
-  }
-}
-
-// Internet Explorer 8 and older does not support Array.forEach, so we define
-// it here in that case.
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Array/forEach
-if (!Array.prototype.forEach) {
-  Array.prototype.forEach = function(fn, scope) {
-    for(var i = 0, len = this.length; i < len; ++i) {
-      fn.call(scope || this, this[i], i, this);
-    }
-  }
-}
-
-// Internet Explorer 8 and older does not support Array.map, so we define it
-// here in that case.
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Array/map
-// Production steps of ECMA-262, Edition 5, 15.4.4.19
-// Reference: http://es5.github.com/#x15.4.4.19
-if (!Array.prototype.map) {
-  Array.prototype.map = function(callback, thisArg) {
-
-    var T, A, k;
-
-    if (this == null) {
-      throw new TypeError(" this is null or not defined");
-    }
-
-    // 1. Let O be the result of calling ToObject passing the |this| value as the argument.
-    var O = Object(this);
-
-    // 2. Let lenValue be the result of calling the Get internal method of O with the argument "length".
-    // 3. Let len be ToUint32(lenValue).
-    var len = O.length >>> 0;
-
-    // 4. If IsCallable(callback) is false, throw a TypeError exception.
-    // See: http://es5.github.com/#x9.11
-    if (typeof callback !== "function") {
-      throw new TypeError(callback + " is not a function");
-    }
-
-    // 5. If thisArg was supplied, let T be thisArg; else let T be undefined.
-    if (thisArg) {
-      T = thisArg;
-    }
-
-    // 6. Let A be a new array created as if by the expression new Array(len) where Array is
-    // the standard built-in constructor with that name and len is the value of len.
-    A = new Array(len);
-
-    // 7. Let k be 0
-    k = 0;
-
-    // 8. Repeat, while k < len
-    while(k < len) {
-
-      var kValue, mappedValue;
-
-      // a. Let Pk be ToString(k).
-      //   This is implicit for LHS operands of the in operator
-      // b. Let kPresent be the result of calling the HasProperty internal method of O with argument Pk.
-      //   This step can be combined with c
-      // c. If kPresent is true, then
-      if (k in O) {
-
-        // i. Let kValue be the result of calling the Get internal method of O with argument Pk.
-        kValue = O[ k ];
-
-        // ii. Let mappedValue be the result of calling the Call internal method of callback
-        // with T as the this value and argument list containing kValue, k, and O.
-        mappedValue = callback.call(T, kValue, k, O);
-
-        // iii. Call the DefineOwnProperty internal method of A with arguments
-        // Pk, Property Descriptor {Value: mappedValue, : true, Enumerable: true, Configurable: true},
-        // and false.
-
-        // In browsers that support Object.defineProperty, use the following:
-        // Object.defineProperty(A, Pk, { value: mappedValue, writable: true, enumerable: true, configurable: true });
-
-        // For best browser support, use the following:
-        A[ k ] = mappedValue;
-      }
-      // d. Increase k by 1.
-      k++;
-    }
-
-    // 9. return A
-    return A;
-  };
-}
-
-// Internet Explorer 8 and older does not support Array.filter, so we define it
-// here in that case.
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Array/filter
-if (!Array.prototype.filter) {
-  Array.prototype.filter = function(fun /*, thisp */) {
-    "use strict";
-
-    if (this == null) {
-      throw new TypeError();
-    }
-
-    var t = Object(this);
-    var len = t.length >>> 0;
-    if (typeof fun != "function") {
-      throw new TypeError();
-    }
-
-    var res = [];
-    var thisp = arguments[1];
-    for (var i = 0; i < len; i++) {
-      if (i in t) {
-        var val = t[i]; // in case fun mutates this
-        if (fun.call(thisp, val, i, t))
-          res.push(val);
-      }
-    }
-
-    return res;
-  };
-}
-
-
-// Internet Explorer 8 and older does not support Object.keys, so we define it
-// here in that case.
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Object/keys
-if (!Object.keys) {
-  Object.keys = (function () {
-    var hasOwnProperty = Object.prototype.hasOwnProperty,
-        hasDontEnumBug = !({toString: null}).propertyIsEnumerable('toString'),
-        dontEnums = [
-          'toString',
-          'toLocaleString',
-          'valueOf',
-          'hasOwnProperty',
-          'isPrototypeOf',
-          'propertyIsEnumerable',
-          'constructor'
-        ],
-        dontEnumsLength = dontEnums.length;
-
-    return function (obj) {
-      if (typeof obj !== 'object' && typeof obj !== 'function' || obj === null) {
-        throw new TypeError('Object.keys called on non-object');
-      }
-
-      var result = [];
-
-      for (var prop in obj) {
-        if (hasOwnProperty.call(obj, prop)) result.push(prop);
-      }
-
-      if (hasDontEnumBug) {
-        for (var i=0; i < dontEnumsLength; i++) {
-          if (hasOwnProperty.call(obj, dontEnums[i])) result.push(dontEnums[i]);
-        }
-      }
-      return result;
-    }
-  })()
-}
-
-// Internet Explorer 8 and older does not support Array.isArray,
-// so we define it here in that case.
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Array/isArray
-if(!Array.isArray) {
-  Array.isArray = function (vArg) {
-    return Object.prototype.toString.call(vArg) === "[object Array]";
-  };
-}
-
-// Internet Explorer 8 and older does not support Function.bind,
-// so we define it here in that case.
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Function/bind
-if (!Function.prototype.bind) {
-  Function.prototype.bind = function (oThis) {
-    if (typeof this !== "function") {
-      // closest thing possible to the ECMAScript 5 internal IsCallable function
-      throw new TypeError("Function.prototype.bind - what is trying to be bound is not callable");
-    }
-
-    var aArgs = Array.prototype.slice.call(arguments, 1),
-        fToBind = this,
-        fNOP = function () {},
-        fBound = function () {
-          return fToBind.apply(this instanceof fNOP && oThis
-              ? this
-              : oThis,
-              aArgs.concat(Array.prototype.slice.call(arguments)));
-        };
-
-    fNOP.prototype = this.prototype;
-    fBound.prototype = new fNOP();
-
-    return fBound;
-  };
-}
-
-// https://developer.mozilla.org/en-US/docs/JavaScript/Reference/Global_Objects/Object/create
-if (!Object.create) {
-  Object.create = function (o) {
-    if (arguments.length > 1) {
-      throw new Error('Object.create implementation only accepts the first parameter.');
-    }
-    function F() {}
-    F.prototype = o;
-    return new F();
-  };
-}
-
-// https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Function/bind
-if (!Function.prototype.bind) {
-  Function.prototype.bind = function (oThis) {
-    if (typeof this !== "function") {
-      // closest thing possible to the ECMAScript 5 internal IsCallable function
-      throw new TypeError("Function.prototype.bind - what is trying to be bound is not callable");
-    }
-
-    var aArgs = Array.prototype.slice.call(arguments, 1),
-        fToBind = this,
-        fNOP = function () {},
-        fBound = function () {
-          return fToBind.apply(this instanceof fNOP && oThis
-              ? this
-              : oThis,
-              aArgs.concat(Array.prototype.slice.call(arguments)));
-        };
-
-    fNOP.prototype = this.prototype;
-    fBound.prototype = new fNOP();
-
-    return fBound;
-  };
-}

lib/timeline/DataStep.js

@@ -172,7 +172,7 @@ DataStep.prototype.previous = function() {
 
 /**
  * Get the current datetime
- * @return {Number}  current The current date
+ * @return {String}  current The current date
  */
 DataStep.prototype.getCurrent = function() {
   var toPrecision = '' + Number(this.current).toPrecision(5);
@@ -189,7 +189,6 @@ DataStep.prototype.getCurrent = function() {
     }
   }
 
-
   return toPrecision;
 };
 
@@ -213,3 +212,5 @@ DataStep.prototype.snap = function(date) {
 DataStep.prototype.isMajor = function() {
   return (this.current % (this.scale * this.majorSteps[this.stepIndex]) == 0);
 };
+
+module.exports = DataStep;

lib/timeline/Graph2d.js

@@ -1,3 +1,14 @@
+var Emitter = require('emitter-component');
+var Hammer = require('hammerjs');
+var util = require('../util');
+var DataSet = require('../DataSet');
+var DataView = require('../DataView');
+var Range = require('./Range');
+var TimeAxis = require('./component/TimeAxis');
+var CurrentTime = require('./component/CurrentTime');
+var CustomTime = require('./component/CustomTime');
+var LineGraph = require('./component/LineGraph');
+
 /**
  * Create a timeline visualization
  * @param {HTMLElement} container
@@ -868,3 +879,5 @@ Graph2d.prototype._updateScrollTop = function () {
 Graph2d.prototype._getScrollTop = function () {
   return this.props.scrollTop;
 };
+
+module.exports = Graph2d;

lib/timeline/Range.js

@@ -1,3 +1,7 @@
+var util = require('../util');
+var moment = require('../module/moment');
+var Component = require('./component/Component');
+
 /**
  * @constructor Range
  * A Range controls a numeric range with a start and end value.
@@ -525,3 +529,5 @@ Range.prototype.moveTo = function(moveTo) {
 
   this.setRange(newStart, newEnd);
 };
+
+module.exports = Range;

lib/timeline/Stack.js

@@ -1,13 +1,10 @@
-/**
- * Utility functions for ordering and stacking of items
- */
-var stack = {};
+// Utility functions for ordering and stacking of items
 
 /**
  * Order items by their start data
  * @param {Item[]} items
  */
-stack.orderByStart = function(items) {
+exports.orderByStart = function(items) {
   items.sort(function (a, b) {
     return a.data.start - b.data.start;
   });
@@ -18,7 +15,7 @@ stack.orderByStart = function(items) {
  * is used.
  * @param {Item[]} items
  */
-stack.orderByEnd = function(items) {
+exports.orderByEnd = function(items) {
   items.sort(function (a, b) {
     var aTime = ('end' in a.data) ? a.data.end : a.data.start,
         bTime = ('end' in b.data) ? b.data.end : b.data.start;
@@ -38,7 +35,7 @@ stack.orderByEnd = function(items) {
  *            If true, all items will be repositioned. If false (default), only
  *            items having a top===null will be re-stacked
  */
-stack.stack = function(items, margin, force) {
+exports.stack = function(items, margin, force) {
   var i, iMax;
 
   if (force) {
@@ -61,7 +58,7 @@ stack.stack = function(items, margin, force) {
         var collidingItem = null;
         for (var j = 0, jj = items.length; j < jj; j++) {
           var other = items[j];
-          if (other.top !== null && other !== item && stack.collision(item, other, margin.item)) {
+          if (other.top !== null && other !== item && exports.collision(item, other, margin.item)) {
             collidingItem = other;
             break;
           }
@@ -83,7 +80,7 @@ stack.stack = function(items, margin, force) {
  * @param {{item: number, axis: number}} margin
  *            Margins between items and between items and the axis.
  */
-stack.nostack = function(items, margin) {
+exports.nostack = function(items, margin) {
   var i, iMax;
 
   // reset top position of all items
@@ -104,7 +101,7 @@ stack.nostack = function(items, margin) {
  *                          the requested margin.
  * @return {boolean}        true if a and b collide, else false
  */
-stack.collision = function(a, b, margin) {
+exports.collision = function(a, b, margin) {
   return ((a.left - margin) < (b.left + b.width) &&
       (a.left + a.width + margin) > b.left &&
       (a.top - margin) < (b.top + b.height) &&

lib/timeline/TimeStep.js

@@ -1,3 +1,5 @@
+var moment = require('../module/moment');
+
 /**
  * @constructor  TimeStep
  * The class TimeStep is an iterator for dates. You provide a start date and an
@@ -464,3 +466,5 @@ TimeStep.prototype.getLabelMajor = function(date) {
     default:                        return '';
   }
 };
+
+module.exports = TimeStep;

lib/timeline/Timeline.js

@@ -1,3 +1,14 @@
+var Emitter = require('emitter-component');
+var Hammer = require('hammerjs');
+var util = require('../util');
+var DataSet = require('../DataSet');
+var DataView = require('../DataView');
+var Range = require('./Range');
+var TimeAxis = require('./component/TimeAxis');
+var CurrentTime = require('./component/CurrentTime');
+var CustomTime = require('./component/CustomTime');
+var ItemSet = require('./component/ItemSet');
+
 /**
  * Create a timeline visualization
  * @param {HTMLElement} container
@@ -885,3 +896,5 @@ Timeline.prototype._updateScrollTop = function () {
 Timeline.prototype._getScrollTop = function () {
   return this.props.scrollTop;
 };
+
+module.exports = Timeline;

lib/timeline/component/Component.js

@@ -50,3 +50,5 @@ Component.prototype._isResized = function() {
 
   return resized;
 };
+
+module.exports = Component;

lib/timeline/component/CurrentTime.js

@@ -1,3 +1,6 @@
+var util = require('../../util');
+var Component = require('./Component');
+
 /**
  * A current time bar
  * @param {{range: Range, dom: Object, domProps: Object}} body
@@ -6,7 +9,6 @@
  * @constructor CurrentTime
  * @extends Component
  */
-
 function CurrentTime (body, options) {
   this.body = body;
 
@@ -126,3 +128,5 @@ CurrentTime.prototype.stop = function() {
     delete this.currentTimeTimer;
   }
 };
+
+module.exports = CurrentTime;

lib/timeline/component/CustomTime.js

@@ -1,3 +1,7 @@
+var Hammer = require('hammerjs');
+var util = require('../../util');
+var Component = require('./Component');
+
 /**
  * A custom time bar
  * @param {{range: Range, dom: Object}} body
@@ -180,3 +184,5 @@ CustomTime.prototype._onDragEnd = function (event) {
   event.stopPropagation();
   event.preventDefault();
 };
+
+module.exports = CustomTime;

lib/timeline/component/DataAxis.js

@@ -1,3 +1,8 @@
+var util = require('../../util');
+var DOMutil = require('../../DOMutil');
+var Component = require('./Component');
+var DataStep = require('../DataStep');
+
 /**
  * A horizontal time axis
  * @param {Object} [options]        See DataAxis.setOptions for the available
@@ -466,3 +471,5 @@ DataAxis.prototype._calculateCharSize = function () {
 DataAxis.prototype.snap = function(date) {
   return this.step.snap(date);
 };
+
+module.exports = DataAxis;

lib/timeline/component/GraphGroup.js

@@ -1,3 +1,6 @@
+var util = require('../../util');
+var DOMutil = require('../../DOMutil');
+
 /**
  * @constructor Group
  * @param {Number | String} groupId
@@ -28,11 +31,11 @@ GraphGroup.prototype.setItems = function(items) {
   else {
     this.itemsData = [];
   }
-}
+};
 
 GraphGroup.prototype.setZeroPosition = function(pos) {
   this.zeroPosition = pos;
-}
+};
 
 GraphGroup.prototype.setOptions = function(options) {
   if (options !== undefined) {
@@ -113,4 +116,6 @@ GraphGroup.prototype.drawIcon = function(x, y, JSONcontainer, SVGcontainer, icon
     DOMutil.drawBar(x + 0.5*barWidth + offset    , y + fillHeight - bar1Height - 1, barWidth, bar1Height, this.className + ' bar', JSONcontainer, SVGcontainer);
     DOMutil.drawBar(x + 1.5*barWidth + offset + 2, y + fillHeight - bar2Height - 1, barWidth, bar2Height, this.className + ' bar', JSONcontainer, SVGcontainer);
   }
-}
+};
+
+module.exports = GraphGroup;

lib/timeline/component/Group.js

@@ -1,3 +1,7 @@
+var util = require('../../util');
+var stack = require('../Stack');
+var ItemRange = require('./item/ItemRange');
+
 /**
  * @constructor Group
  * @param {Number | String} groupId
@@ -415,3 +419,5 @@ Group.prototype._checkIfVisible = function(item, visibleItems, range) {
     if (item.displayed) item.hide();
   }
 };
+
+module.exports = Group;

lib/timeline/component/ItemSet.js

@@ -1,3 +1,14 @@
+var Hammer = require('hammerjs');
+var util = require('../../util');
+var DataSet = require('../../DataSet');
+var DataView = require('../../DataView');
+var Component = require('./Component');
+var Group = require('./Group');
+var ItemBox = require('./item/ItemBox');
+var ItemPoint = require('./item/ItemPoint');
+var ItemRange = require('./item/ItemRange');
+
+
 var UNGROUPED = '__ungrouped__'; // reserved group id for ungrouped items
 
 /**
@@ -1318,3 +1329,4 @@ ItemSet.itemSetFromTarget = function(event) {
   return null;
 };
 
+module.exports = ItemSet;

lib/timeline/component/Legend.js

@@ -1,5 +1,9 @@
+var util = require('../../util');
+var DOMutil = require('../../DOMutil');
+var Component = require('./Component');
+
 /**
- * Created by Alex on 6/17/14.
+ * Legend for Graph2d
  */
 function Legend(body, options, side) {
   this.body = body;
@@ -27,7 +31,7 @@ function Legend(body, options, side) {
   this._create();
 
   this.setOptions(options);
-};
+}
 
 Legend.prototype = new Component();
 
@@ -69,7 +73,7 @@ Legend.prototype._create = function() {
 
   this.dom.frame.appendChild(this.svg);
   this.dom.frame.appendChild(this.dom.textArea);
-}
+};
 
 /**
  * Hide the component from the DOM
@@ -95,7 +99,7 @@ Legend.prototype.show = function() {
 Legend.prototype.setOptions = function(options) {
   var fields = ['enabled','orientation','icons','left','right'];
   util.selectiveDeepExtend(fields, this.options, options);
-}
+};
 
 Legend.prototype.redraw = function() {
   if (this.options[this.side].visible == false || this.amountOfGroups == 0 || this.options.enabled == false) {
@@ -142,7 +146,7 @@ Legend.prototype.redraw = function() {
       this.drawLegendIcons();
     }
 
-    var content = "";
+    var content = '';
     for (var groupId in this.groups) {
       if (this.groups.hasOwnProperty(groupId)) {
         content += this.groups[groupId].content + '<br />';
@@ -151,13 +155,13 @@ Legend.prototype.redraw = function() {
     this.dom.textArea.innerHTML = content;
     this.dom.textArea.style.lineHeight = ((0.75 * this.options.iconSize) + this.options.iconSpacing) + 'px';
   }
-}
+};
 
 Legend.prototype.drawLegendIcons = function() {
   if (this.dom.frame.parentNode) {
     DOMutil.prepareElements(this.svgElements);
     var padding = window.getComputedStyle(this.dom.frame).paddingTop;
-    var iconOffset = Number(padding.replace("px",''));
+    var iconOffset = Number(padding.replace('px',''));
     var x = iconOffset;
     var iconWidth = this.options.iconSize;
     var iconHeight = 0.75 * this.options.iconSize;
@@ -174,4 +178,6 @@ Legend.prototype.drawLegendIcons = function() {
 
     DOMutil.cleanupElements(this.svgElements);
   }
-}
+};
+
+module.exports = Legend;

lib/timeline/component/LineGraph.js

@@ -1,3 +1,12 @@
+var util = require('../../util');
+var DOMutil = require('../../DOMutil');
+var DataSet = require('../../DataSet');
+var DataView = require('../../DataView');
+var Component = require('./Component');
+var DataAxis = require('./DataAxis');
+var GraphGroup = require('./GraphGroup');
+var Legend = require('./Legend');
+
 var UNGROUPED = '__ungrouped__'; // reserved group id for ungrouped items
 
 /**
@@ -1059,7 +1068,4 @@ LineGraph.prototype._linear = function(data) {
   return d;
 };
 
-
-
-
-
+module.exports = LineGraph;

lib/timeline/component/TimeAxis.js

@@ -1,3 +1,7 @@
+var util = require('../../util');
+var Component = require('./Component');
+var TimeStep = require('../TimeStep');
+
 /**
  * A horizontal time axis
  * @param {{dom: Object, domProps: Object, emitter: Emitter, range: Range}} body
@@ -387,3 +391,5 @@ TimeAxis.prototype._calculateCharSize = function () {
 TimeAxis.prototype.snap = function(date) {
   return this.step.snap(date);
 };
+
+module.exports = TimeAxis;

lib/timeline/component/item/Item.js

@@ -1,3 +1,5 @@
+var Hammer = require('hammerjs');
+
 /**
  * @constructor Item
  * @param {Object} data             Object containing (optional) parameters type,
@@ -137,3 +139,5 @@ Item.prototype._repaintDeleteButton = function (anchor) {
     this.dom.deleteButton = null;
   }
 };
+
+module.exports = Item;

lib/timeline/component/item/ItemBox.js

@@ -1,3 +1,5 @@
+var Item = require('./Item');
+
 /**
  * @constructor ItemBox
  * @extends Item
@@ -234,3 +236,5 @@ ItemBox.prototype.repositionY = function() {
 
   dot.style.top = (-this.props.dot.height / 2) + 'px';
 };
+
+module.exports = ItemBox;

lib/timeline/component/item/ItemPoint.js

@@ -1,3 +1,5 @@
+var Item = require('./Item');
+
 /**
  * @constructor ItemPoint
  * @extends Item
@@ -194,3 +196,5 @@ ItemPoint.prototype.repositionY = function() {
     point.style.top = (this.parent.height - this.top - this.height) + 'px';
   }
 };
+
+module.exports = ItemPoint;

lib/timeline/component/item/ItemRange.js

@@ -1,3 +1,6 @@
+var Hammer = require('hammerjs');
+var Item = require('./Item');
+
 /**
  * @constructor ItemRange
  * @extends Item
@@ -284,3 +287,5 @@ ItemRange.prototype._repaintDragRight = function () {
     this.dom.dragRight = null;
   }
 };
+
+module.exports = ItemRange;

lib/util.js

@@ -1,14 +1,16 @@
-/**
- * utility functions
- */
-var util = {};
+// utility functions
+
+// first check if moment.js is already loaded in the browser window, if so,
+// use this instance. Else, load via commonjs.
+var Hammer = require('./module/hammer');
+var moment = require('./module/moment');
 
 /**
  * Test whether given object is a number
  * @param {*} object
  * @return {Boolean} isNumber
  */
-util.isNumber = function(object) {
+exports.isNumber = function(object) {
   return (object instanceof Number || typeof object == 'number');
 };
 
@@ -17,7 +19,7 @@ util.isNumber = function(object) {
  * @param {*} object
  * @return {Boolean} isString
  */
-util.isString = function(object) {
+exports.isString = function(object) {
   return (object instanceof String || typeof object == 'string');
 };
 
@@ -26,11 +28,11 @@ util.isString = function(object) {
  * @param {Date | String} object
  * @return {Boolean} isDate
  */
-util.isDate = function(object) {
+exports.isDate = function(object) {
   if (object instanceof Date) {
     return true;
   }
-  else if (util.isString(object)) {
+  else if (exports.isString(object)) {
     // test whether this string contains a date
     var match = ASPDateRegex.exec(object);
     if (match) {
@@ -49,7 +51,7 @@ util.isDate = function(object) {
  * @param {*} object
  * @return {Boolean} isDataTable
  */
-util.isDataTable = function(object) {
+exports.isDataTable = function(object) {
   return (typeof (google) !== 'undefined') &&
       (google.visualization) &&
       (google.visualization.DataTable) &&
@@ -61,7 +63,7 @@ util.isDataTable = function(object) {
  * source: http://stackoverflow.com/a/105074/1262753
  * @return {String} uuid
  */
-util.randomUUID = function() {
+exports.randomUUID = function() {
   var S4 = function () {
     return Math.floor(
         Math.random() * 0x10000 /* 65536 */
@@ -84,7 +86,7 @@ util.randomUUID = function() {
  * @param {... Object} b
  * @return {Object} a
  */
-util.extend = function (a, b) {
+exports.extend = function (a, b) {
   for (var i = 1, len = arguments.length; i < len; i++) {
     var other = arguments[i];
     for (var prop in other) {
@@ -105,7 +107,7 @@ util.extend = function (a, b) {
  * @param {... Object} b
  * @return {Object} a
  */
-util.selectiveExtend = function (props, a, b) {
+exports.selectiveExtend = function (props, a, b) {
   if (!Array.isArray(props)) {
     throw new Error('Array with property names expected as first argument');
   }
@@ -131,7 +133,7 @@ util.selectiveExtend = function (props, a, b) {
  * @param {... Object} b
  * @return {Object} a
  */
-util.selectiveDeepExtend = function (props, a, b) {
+exports.selectiveDeepExtend = function (props, a, b) {
   // TODO: add support for Arrays to deepExtend
   if (Array.isArray(b)) {
     throw new TypeError('Arrays are not supported by deepExtend');
@@ -146,7 +148,7 @@ util.selectiveDeepExtend = function (props, a, b) {
             a[prop] = {};
           }
           if (a[prop].constructor === Object) {
-            util.deepExtend(a[prop], b[prop]);
+            exports.deepExtend(a[prop], b[prop]);
           }
           else {
             a[prop] = b[prop];
@@ -169,7 +171,7 @@ util.selectiveDeepExtend = function (props, a, b) {
  * @param {Object} b
  * @returns {Object}
  */
-util.deepExtend = function(a, b) {
+exports.deepExtend = function(a, b) {
   // TODO: add support for Arrays to deepExtend
   if (Array.isArray(b)) {
     throw new TypeError('Arrays are not supported by deepExtend');
@@ -182,7 +184,7 @@ util.deepExtend = function(a, b) {
           a[prop] = {};
         }
         if (a[prop].constructor === Object) {
-          util.deepExtend(a[prop], b[prop]);
+          exports.deepExtend(a[prop], b[prop]);
         }
         else {
           a[prop] = b[prop];
@@ -204,7 +206,7 @@ util.deepExtend = function(a, b) {
  * @return {boolean} Returns true if both arrays have the same length and same
  *                   elements.
  */
-util.equalArray = function (a, b) {
+exports.equalArray = function (a, b) {
   if (a.length != b.length) return false;
 
   for (var i = 0, len = a.length; i < len; i++) {
@@ -223,7 +225,7 @@ util.equalArray = function (a, b) {
  * @return {*} object
  * @throws Error
  */
-util.convert = function(object, type) {
+exports.convert = function(object, type) {
   var match;
 
   if (object === undefined) {
@@ -255,7 +257,7 @@ util.convert = function(object, type) {
       return String(object);
 
     case 'Date':
-      if (util.isNumber(object)) {
+      if (exports.isNumber(object)) {
         return new Date(object);
       }
       if (object instanceof Date) {
@@ -264,7 +266,7 @@ util.convert = function(object, type) {
       else if (moment.isMoment(object)) {
         return new Date(object.valueOf());
       }
-      if (util.isString(object)) {
+      if (exports.isString(object)) {
         match = ASPDateRegex.exec(object);
         if (match) {
           // object is an ASP date
@@ -276,12 +278,12 @@ util.convert = function(object, type) {
       }
       else {
         throw new Error(
-            'Cannot convert object of type ' + util.getType(object) +
+            'Cannot convert object of type ' + exports.getType(object) +
                 ' to type Date');
       }
 
     case 'Moment':
-      if (util.isNumber(object)) {
+      if (exports.isNumber(object)) {
         return moment(object);
       }
       if (object instanceof Date) {
@@ -290,7 +292,7 @@ util.convert = function(object, type) {
       else if (moment.isMoment(object)) {
         return moment(object);
       }
-      if (util.isString(object)) {
+      if (exports.isString(object)) {
         match = ASPDateRegex.exec(object);
         if (match) {
           // object is an ASP date
@@ -302,12 +304,12 @@ util.convert = function(object, type) {
       }
       else {
         throw new Error(
-            'Cannot convert object of type ' + util.getType(object) +
+            'Cannot convert object of type ' + exports.getType(object) +
                 ' to type Date');
       }
 
     case 'ISODate':
-      if (util.isNumber(object)) {
+      if (exports.isNumber(object)) {
         return new Date(object);
       }
       else if (object instanceof Date) {
@@ -316,7 +318,7 @@ util.convert = function(object, type) {
       else if (moment.isMoment(object)) {
         return object.toDate().toISOString();
       }
-      else if (util.isString(object)) {
+      else if (exports.isString(object)) {
         match = ASPDateRegex.exec(object);
         if (match) {
           // object is an ASP date
@@ -328,18 +330,18 @@ util.convert = function(object, type) {
       }
       else {
         throw new Error(
-            'Cannot convert object of type ' + util.getType(object) +
+            'Cannot convert object of type ' + exports.getType(object) +
                 ' to type ISODate');
       }
 
     case 'ASPDate':
-      if (util.isNumber(object)) {
+      if (exports.isNumber(object)) {
         return '/Date(' + object + ')/';
       }
       else if (object instanceof Date) {
         return '/Date(' + object.valueOf() + ')/';
       }
-      else if (util.isString(object)) {
+      else if (exports.isString(object)) {
         match = ASPDateRegex.exec(object);
         var value;
         if (match) {
@@ -353,7 +355,7 @@ util.convert = function(object, type) {
       }
       else {
         throw new Error(
-            'Cannot convert object of type ' + util.getType(object) +
+            'Cannot convert object of type ' + exports.getType(object) +
                 ' to type ASPDate');
       }
 
@@ -368,11 +370,11 @@ util.convert = function(object, type) {
 var ASPDateRegex = /^\/?Date\((\-?\d+)/i;
 
 /**
- * Get the type of an object, for example util.getType([]) returns 'Array'
+ * Get the type of an object, for example exports.getType([]) returns 'Array'
  * @param {*} object
  * @return {String} type
  */
-util.getType = function(object) {
+exports.getType = function(object) {
   var type = typeof object;
 
   if (type == 'object') {
@@ -415,7 +417,7 @@ util.getType = function(object) {
  * @return {number} left        The absolute left position of this element
  *                              in the browser page.
  */
-util.getAbsoluteLeft = function(elem) {
+exports.getAbsoluteLeft = function(elem) {
   var doc = document.documentElement;
   var body = document.body;
 
@@ -435,7 +437,7 @@ util.getAbsoluteLeft = function(elem) {
  * @return {number} top        The absolute top position of this element
  *                              in the browser page.
  */
-util.getAbsoluteTop = function(elem) {
+exports.getAbsoluteTop = function(elem) {
   var doc = document.documentElement;
   var body = document.body;
 
@@ -454,7 +456,7 @@ util.getAbsoluteTop = function(elem) {
  * @param {Event} event
  * @return {Number} pageY
  */
-util.getPageY = function(event) {
+exports.getPageY = function(event) {
   if ('pageY' in event) {
     return event.pageY;
   }
@@ -480,7 +482,7 @@ util.getPageY = function(event) {
  * @param {Event} event
  * @return {Number} pageX
  */
-util.getPageX = function(event) {
+exports.getPageX = function(event) {
   if ('pageY' in event) {
     return event.pageX;
   }
@@ -506,7 +508,7 @@ util.getPageX = function(event) {
  * @param {Element} elem
  * @param {String} className
  */
-util.addClassName = function(elem, className) {
+exports.addClassName = function(elem, className) {
   var classes = elem.className.split(' ');
   if (classes.indexOf(className) == -1) {
     classes.push(className); // add the class to the array
@@ -519,7 +521,7 @@ util.addClassName = function(elem, className) {
  * @param {Element} elem
  * @param {String} className
  */
-util.removeClassName = function(elem, className) {
+exports.removeClassName = function(elem, className) {
   var classes = elem.className.split(' ');
   var index = classes.indexOf(className);
   if (index != -1) {
@@ -537,7 +539,7 @@ util.removeClassName = function(elem, className) {
  *                                  the object or array with three parameters:
  *                                  callback(value, index, object)
  */
-util.forEach = function(object, callback) {
+exports.forEach = function(object, callback) {
   var i,
       len;
   if (object instanceof Array) {
@@ -562,7 +564,7 @@ util.forEach = function(object, callback) {
  * @param {Object} object
  * @param {Array} array
  */
-util.toArray = function(object) {
+exports.toArray = function(object) {
   var array = [];
 
   for (var prop in object) {
@@ -579,7 +581,7 @@ util.toArray = function(object) {
  * @param {*} value
  * @return {Boolean} changed
  */
-util.updateProperty = function(object, key, value) {
+exports.updateProperty = function(object, key, value) {
   if (object[key] !== value) {
     object[key] = value;
     return true;
@@ -597,7 +599,7 @@ util.updateProperty = function(object, key, value) {
  * @param {function}    listener   The callback function to be executed
  * @param {boolean}     [useCapture]
  */
-util.addEventListener = function(element, action, listener, useCapture) {
+exports.addEventListener = function(element, action, listener, useCapture) {
   if (element.addEventListener) {
     if (useCapture === undefined)
       useCapture = false;
@@ -619,7 +621,7 @@ util.addEventListener = function(element, action, listener, useCapture) {
  * @param {function}    listener        The listener function
  * @param {boolean}     [useCapture]
  */
-util.removeEventListener = function(element, action, listener, useCapture) {
+exports.removeEventListener = function(element, action, listener, useCapture) {
   if (element.removeEventListener) {
     // non-IE browsers
     if (useCapture === undefined)
@@ -642,7 +644,7 @@ util.removeEventListener = function(element, action, listener, useCapture) {
  * @param {Event} event
  * @return {Element} target element
  */
-util.getTarget = function(event) {
+exports.getTarget = function(event) {
   // code from http://www.quirksmode.org/js/events_properties.html
   if (!event) {
     event = window.event;
@@ -670,7 +672,7 @@ util.getTarget = function(event) {
  * @param {Element} element
  * @param {Event} event
  */
-util.fakeGesture = function(element, event) {
+exports.fakeGesture = function(element, event) {
   var eventType = null;
 
   // for hammer.js 1.0.5
@@ -692,7 +694,7 @@ util.fakeGesture = function(element, event) {
   return gesture;
 };
 
-util.option = {};
+exports.option = {};
 
 /**
  * Convert a value into a boolean
@@ -700,7 +702,7 @@ util.option = {};
  * @param {Boolean} [defaultValue]
  * @returns {Boolean} bool
  */
-util.option.asBoolean = function (value, defaultValue) {
+exports.option.asBoolean = function (value, defaultValue) {
   if (typeof value == 'function') {
     value = value();
   }
@@ -718,7 +720,7 @@ util.option.asBoolean = function (value, defaultValue) {
  * @param {Number} [defaultValue]
  * @returns {Number} number
  */
-util.option.asNumber = function (value, defaultValue) {
+exports.option.asNumber = function (value, defaultValue) {
   if (typeof value == 'function') {
     value = value();
   }
@@ -736,7 +738,7 @@ util.option.asNumber = function (value, defaultValue) {
  * @param {String} [defaultValue]
  * @returns {String} str
  */
-util.option.asString = function (value, defaultValue) {
+exports.option.asString = function (value, defaultValue) {
   if (typeof value == 'function') {
     value = value();
   }
@@ -754,15 +756,15 @@ util.option.asString = function (value, defaultValue) {
  * @param {String} [defaultValue]
  * @returns {String} size
  */
-util.option.asSize = function (value, defaultValue) {
+exports.option.asSize = function (value, defaultValue) {
   if (typeof value == 'function') {
     value = value();
   }
 
-  if (util.isString(value)) {
+  if (exports.isString(value)) {
     return value;
   }
-  else if (util.isNumber(value)) {
+  else if (exports.isNumber(value)) {
     return value + 'px';
   }
   else {
@@ -776,7 +778,7 @@ util.option.asSize = function (value, defaultValue) {
  * @param {HTMLElement} [defaultValue]
  * @returns {HTMLElement | null} dom
  */
-util.option.asElement = function (value, defaultValue) {
+exports.option.asElement = function (value, defaultValue) {
   if (typeof value == 'function') {
     value = value();
   }
@@ -786,7 +788,7 @@ util.option.asElement = function (value, defaultValue) {
 
 
 
-util.GiveDec = function(Hex) {
+exports.GiveDec = function(Hex) {
   var Value;
 
   if (Hex == "A")
@@ -807,7 +809,7 @@ util.GiveDec = function(Hex) {
   return Value;
 };
 
-util.GiveHex = function(Dec) {
+exports.GiveHex = function(Dec) {
   var Value;
 
   if(Dec == 10)
@@ -834,15 +836,15 @@ util.GiveHex = function(Dec) {
  * @param {Object | String} color
  * @return {Object} colorObject
  */
-util.parseColor = function(color) {
+exports.parseColor = function(color) {
   var c;
-  if (util.isString(color)) {
-    if (util.isValidHex(color)) {
-      var hsv = util.hexToHSV(color);
+  if (exports.isString(color)) {
+    if (exports.isValidHex(color)) {
+      var hsv = exports.hexToHSV(color);
       var lighterColorHSV = {h:hsv.h,s:hsv.s * 0.45,v:Math.min(1,hsv.v * 1.05)};
       var darkerColorHSV  = {h:hsv.h,s:Math.min(1,hsv.v * 1.25),v:hsv.v*0.6};
-      var darkerColorHex  = util.HSVToHex(darkerColorHSV.h ,darkerColorHSV.h ,darkerColorHSV.v);
-      var lighterColorHex = util.HSVToHex(lighterColorHSV.h,lighterColorHSV.s,lighterColorHSV.v);
+      var darkerColorHex  = exports.HSVToHex(darkerColorHSV.h ,darkerColorHSV.h ,darkerColorHSV.v);
+      var lighterColorHex = exports.HSVToHex(lighterColorHSV.h,lighterColorHSV.s,lighterColorHSV.v);
 
       c = {
         background: color,
@@ -877,7 +879,7 @@ util.parseColor = function(color) {
     c.background = color.background || 'white';
     c.border = color.border || c.background;
 
-    if (util.isString(color.highlight)) {
+    if (exports.isString(color.highlight)) {
       c.highlight = {
         border: color.highlight,
         background: color.highlight
@@ -889,7 +891,7 @@ util.parseColor = function(color) {
       c.highlight.border = color.highlight && color.highlight.border || c.border;
     }
 
-    if (util.isString(color.hover)) {
+    if (exports.isString(color.hover)) {
       c.hover = {
         border: color.hover,
         background: color.hover
@@ -911,15 +913,15 @@ util.parseColor = function(color) {
  * @param {String} hex
  * @returns {{r: *, g: *, b: *}}
  */
-util.hexToRGB = function(hex) {
+exports.hexToRGB = function(hex) {
   hex = hex.replace("#","").toUpperCase();
 
-  var a = util.GiveDec(hex.substring(0, 1));
-  var b = util.GiveDec(hex.substring(1, 2));
-  var c = util.GiveDec(hex.substring(2, 3));
-  var d = util.GiveDec(hex.substring(3, 4));
-  var e = util.GiveDec(hex.substring(4, 5));
-  var f = util.GiveDec(hex.substring(5, 6));
+  var a = exports.GiveDec(hex.substring(0, 1));
+  var b = exports.GiveDec(hex.substring(1, 2));
+  var c = exports.GiveDec(hex.substring(2, 3));
+  var d = exports.GiveDec(hex.substring(3, 4));
+  var e = exports.GiveDec(hex.substring(4, 5));
+  var f = exports.GiveDec(hex.substring(5, 6));
 
   var r = (a * 16) + b;
   var g = (c * 16) + d;
@@ -928,13 +930,13 @@ util.hexToRGB = function(hex) {
   return {r:r,g:g,b:b};
 };
 
-util.RGBToHex = function(red,green,blue) {
-  var a = util.GiveHex(Math.floor(red / 16));
-  var b = util.GiveHex(red % 16);
-  var c = util.GiveHex(Math.floor(green / 16));
-  var d = util.GiveHex(green % 16);
-  var e = util.GiveHex(Math.floor(blue / 16));
-  var f = util.GiveHex(blue % 16);
+exports.RGBToHex = function(red,green,blue) {
+  var a = exports.GiveHex(Math.floor(red / 16));
+  var b = exports.GiveHex(red % 16);
+  var c = exports.GiveHex(Math.floor(green / 16));
+  var d = exports.GiveHex(green % 16);
+  var e = exports.GiveHex(Math.floor(blue / 16));
+  var f = exports.GiveHex(blue % 16);
 
   var hex = a + b + c + d + e + f;
   return "#" + hex;
@@ -950,7 +952,7 @@ util.RGBToHex = function(red,green,blue) {
  * @returns {*}
  * @constructor
  */
-util.RGBToHSV = function(red,green,blue) {
+exports.RGBToHSV = function(red,green,blue) {
   red=red/255; green=green/255; blue=blue/255;
   var minRGB = Math.min(red,Math.min(green,blue));
   var maxRGB = Math.max(red,Math.max(green,blue));
@@ -978,7 +980,7 @@ util.RGBToHSV = function(red,green,blue) {
  * @returns {{r: number, g: number, b: number}}
  * @constructor
  */
-util.HSVToRGB = function(h, s, v) {
+exports.HSVToRGB = function(h, s, v) {
   var r, g, b;
 
   var i = Math.floor(h * 6);
@@ -999,17 +1001,17 @@ util.HSVToRGB = function(h, s, v) {
   return {r:Math.floor(r * 255), g:Math.floor(g * 255), b:Math.floor(b * 255) };
 };
 
-util.HSVToHex = function(h, s, v) {
-  var rgb = util.HSVToRGB(h, s, v);
-  return util.RGBToHex(rgb.r, rgb.g, rgb.b);
+exports.HSVToHex = function(h, s, v) {
+  var rgb = exports.HSVToRGB(h, s, v);
+  return exports.RGBToHex(rgb.r, rgb.g, rgb.b);
 };
 
-util.hexToHSV = function(hex) {
-  var rgb = util.hexToRGB(hex);
-  return util.RGBToHSV(rgb.r, rgb.g, rgb.b);
+exports.hexToHSV = function(hex) {
+  var rgb = exports.hexToRGB(hex);
+  return exports.RGBToHSV(rgb.r, rgb.g, rgb.b);
 };
 
-util.isValidHex = function(hex) {
+exports.isValidHex = function(hex) {
   var isOk = /(^#[0-9A-F]{6}$)|(^#[0-9A-F]{3}$)/i.test(hex);
   return isOk;
 };
@@ -1022,13 +1024,13 @@ util.isValidHex = function(hex) {
  * @param referenceObject
  * @returns {*}
  */
-util.selectiveBridgeObject = function(fields, referenceObject) {
+exports.selectiveBridgeObject = function(fields, referenceObject) {
   if (typeof referenceObject == "object") {
     var objectTo = Object.create(referenceObject);
     for (var i = 0; i < fields.length; i++) {
       if (referenceObject.hasOwnProperty(fields[i])) {
         if (typeof referenceObject[fields[i]] == "object") {
-          objectTo[fields[i]] = util.bridgeObject(referenceObject[fields[i]]);
+          objectTo[fields[i]] = exports.bridgeObject(referenceObject[fields[i]]);
         }
       }
     }
@@ -1046,13 +1048,13 @@ util.selectiveBridgeObject = function(fields, referenceObject) {
  * @param referenceObject
  * @returns {*}
  */
-util.bridgeObject = function(referenceObject) {
+exports.bridgeObject = function(referenceObject) {
   if (typeof referenceObject == "object") {
     var objectTo = Object.create(referenceObject);
     for (var i in referenceObject) {
       if (referenceObject.hasOwnProperty(i)) {
         if (typeof referenceObject[i] == "object") {
-          objectTo[i] = util.bridgeObject(referenceObject[i]);
+          objectTo[i] = exports.bridgeObject(referenceObject[i]);
         }
       }
     }
@@ -1073,7 +1075,7 @@ util.bridgeObject = function(referenceObject) {
  * @param [String] option      | this is the option key in the options argument
  * @private
  */
-util.mergeOptions = function (mergeTarget, options, option) {
+exports.mergeOptions = function (mergeTarget, options, option) {
   if (options[option] !== undefined) {
     if (typeof options[option] == 'boolean') {
       mergeTarget[option].enabled = options[option];
@@ -1099,7 +1101,7 @@ util.mergeOptions = function (mergeTarget, options, option) {
  * @param [String] option      | this is the option key in the options argument
  * @private
  */
-util.mergeOptions = function (mergeTarget, options, option) {
+exports.mergeOptions = function (mergeTarget, options, option) {
   if (options[option] !== undefined) {
     if (typeof options[option] == 'boolean') {
       mergeTarget[option].enabled = options[option];
@@ -1134,7 +1136,7 @@ util.mergeOptions = function (mergeTarget, options, option) {
  * @returns {number}
  * @private
  */
-util.binarySearch = function(orderedItems, range, field, field2) {
+exports.binarySearch = function(orderedItems, range, field, field2) {
   var array = orderedItems;
   var interval = range.end - range.start;
 
@@ -1200,7 +1202,7 @@ util.binarySearch = function(orderedItems, range, field, field2) {
  * @returns {number}
  * @private
  */
-util.binarySearchGeneric = function(orderedItems, target, field, sidePreference) {
+exports.binarySearchGeneric = function(orderedItems, target, field, sidePreference) {
   var array = orderedItems;
   var found = false;
   var low = 0;

package.json

@@ -20,21 +20,29 @@
     "network",
     "browser"
   ],
+  "main": "./index",
   "scripts": {
-    "test": "jake test --trace",
-    "build": "jake --trace"
+    "test": "mocha",
+    "build": "build"
+  },
+  "dependencies": {
+    "emitter-component": "^1.1.1",
+    "hammerjs": "1.0.5",
+    "moment": "^2.7.0",
+    "mousetrap": "0.0.1"
   },
-  "dependencies": {},
   "devDependencies": {
-    "jake": "latest",
-    "jake-utils": "latest",
     "clean-css": "latest",
-    "browserify": "3.22",
-    "wrench": "latest",
-    "moment": "latest",
-    "hammerjs": "1.0.5",
-    "mousetrap": "latest",
-    "emitter-component": "latest",
-    "node-watch": "latest"
+    "gulp": "^3.8.5",
+    "gulp-concat": "^2.2.0",
+    "gulp-minify-css": "^0.3.6",
+    "gulp-rename": "^1.2.0",
+    "gulp-util": "^2.2.19",
+    "merge-stream": "^0.1.5",
+    "mocha": "^1.20.1",
+    "rimraf": "^2.2.8",
+    "uglify-js": "^2.4.14",
+    "webpack": "^1.3.1-beta7",
+    "wrench": "latest"
   }
 }

test/dataset.js

@@ -1,7 +1,6 @@
-var assert = require('assert'),
-    moment = require('moment'),
-    vis = require('../dist/vis.js'),
-    DataSet = vis.DataSet;
+var assert = require('assert');
+var moment = require('moment');
+var DataSet = require('../lib/DataSet');
 
 var now = new Date();
 
@@ -103,7 +102,7 @@ assert.equal(data.get().length, 0);
 
 
 // test filtering and sorting
-data = new vis.DataSet();
+data = new DataSet();
 data.add([
   {id:1, age: 30, group: 2},
   {id:2, age: 25, group: 4},

test/dataview.js

@@ -1,9 +1,7 @@
-var assert = require('assert'),
-    moment = require('moment'),
-    vis = require('../dist/vis.js'),
-    DataSet = vis.DataSet,
-    DataView = vis.DataView;
-
+var assert = require('assert');
+var moment = require('moment');
+var DataSet = require('../lib/DataSet');
+var DataView = require('../lib/DataView');
 
 var groups = new DataSet();