vis-rails 0.0.1

data/vendor/assets/vis/graph/ClusterMixin.js

@@ -0,0 +1,1019 @@
+/**
+ * Creation of the ClusterMixin var.
+ *
+ * This contains all the functions the Graph object can use to employ clustering
+ *
+ * Alex de Mulder
+ * 21-01-2013
+ */
+var ClusterMixin = {
+
+/**
+ * This is only called in the constructor of the graph object
+ * */
+ startWithClustering : function() {
+    // cluster if the data set is big
+    this.clusterToFit(this.constants.clustering.initialMaxNodes, true);
+
+    // updates the lables after clustering
+    this.updateLabels();
+
+    // this is called here because if clusterin is disabled, the start and stabilize are called in
+    // the setData function.
+    if (this.stabilize) {
+      this._doStabilize();
+    }
+    this.start();
+  },
+
+  /**
+   * This function clusters until the initialMaxNodes has been reached
+   *
+   * @param {Number}  maxNumberOfNodes
+   * @param {Boolean} reposition
+   */
+  clusterToFit : function(maxNumberOfNodes, reposition) {
+    var numberOfNodes = this.nodeIndices.length;
+
+    var maxLevels = 50;
+    var level = 0;
+
+    // we first cluster the hubs, then we pull in the outliers, repeat
+    while (numberOfNodes > maxNumberOfNodes && level < maxLevels) {
+      if (level % 3 == 0) {
+        this.forceAggregateHubs();
+      }
+      else {
+        this.increaseClusterLevel();
+      }
+      numberOfNodes = this.nodeIndices.length;
+      level += 1;
+    }
+
+    // after the clustering we reposition the nodes to reduce the initial chaos
+    if (level > 1 && reposition == true) {
+      this.repositionNodes();
+    }
+   },
+
+  /**
+   * This function can be called to open up a specific cluster. It is only called by
+   * It will unpack the cluster back one level.
+   *
+   * @param node    | Node object: cluster to open.
+   */
+  openCluster : function(node) {
+    var isMovingBeforeClustering = this.moving;
+    if (node.clusterSize > this.constants.clustering.sectorThreshold && this._nodeInActiveArea(node) &&
+      !(this._sector() == "default" && this.nodeIndices.length == 1)) {
+      this._addSector(node);
+      var level = 0;
+      while ((this.nodeIndices.length < this.constants.clustering.initialMaxNodes) && (level < 10)) {
+        this.decreaseClusterLevel();
+        level += 1;
+      }
+    }
+    else {
+      this._expandClusterNode(node,false,true);
+
+      // update the index list, dynamic edges and labels
+      this._updateNodeIndexList();
+      this._updateDynamicEdges();
+      this.updateLabels();
+    }
+
+    // if the simulation was settled, we restart the simulation if a cluster has been formed or expanded
+    if (this.moving != isMovingBeforeClustering) {
+      this.start();
+    }
+   },
+
+  /**
+   * This calls the updateClustes with default arguments
+   */
+  updateClustersDefault : function() {
+    if (this.constants.clustering.enabled == true) {
+      this.updateClusters(0,false,false);
+    }
+  },
+
+  /**
+   * This function can be called to increase the cluster level. This means that the nodes with only one edge connection will
+   * be clustered with their connected node. This can be repeated as many times as needed.
+   * This can be called externally (by a keybind for instance) to reduce the complexity of big datasets.
+   */
+  increaseClusterLevel : function() {
+    this.updateClusters(-1,false,true);
+   },
+
+
+
+  /**
+   * This function can be called to decrease the cluster level. This means that the nodes with only one edge connection will
+   * be unpacked if they are a cluster. This can be repeated as many times as needed.
+   * This can be called externally (by a key-bind for instance) to look into clusters without zooming.
+   */
+  decreaseClusterLevel : function() {
+    this.updateClusters(1,false,true);
+   },
+
+
+  /**
+   * This is the main clustering function. It clusters and declusters on zoom or forced
+   * This function clusters on zoom, it can be called with a predefined zoom direction
+   * If out, check if we can form clusters, if in, check if we can open clusters.
+   * This function is only called from _zoom()
+   *
+   * @param {Number} zoomDirection  | -1 / 0 / +1   for  zoomOut / determineByZoom / zoomIn
+   * @param {Boolean} recursive     | enabled or disable recursive calling of the opening of clusters
+   * @param {Boolean} force         | enabled or disable forcing
+   *
+   */
+  updateClusters : function(zoomDirection,recursive,force) {
+    var isMovingBeforeClustering = this.moving;
+    var amountOfNodes = this.nodeIndices.length;
+
+    // on zoom out collapse the sector if the scale is at the level the sector was made
+    if (this.previousScale > this.scale && zoomDirection == 0) {
+      this._collapseSector();
+    }
+
+    // check if we zoom in or out
+    if (this.previousScale > this.scale || zoomDirection == -1) { // zoom out
+      // forming clusters when forced pulls outliers in. When not forced, the edge length of the
+      // outer nodes determines if it is being clustered
+      this._formClusters(force);
+    }
+    else if (this.previousScale < this.scale || zoomDirection == 1) { // zoom in
+      if (force == true) {
+        // _openClusters checks for each node if the formationScale of the cluster is smaller than
+        // the current scale and if so, declusters. When forced, all clusters are reduced by one step
+        this._openClusters(recursive,force);
+      }
+      else {
+        // if a cluster takes up a set percentage of the active window
+        this._openClustersBySize();
+      }
+    }
+    this._updateNodeIndexList();
+
+    // if a cluster was NOT formed and the user zoomed out, we try clustering by hubs
+    if (this.nodeIndices.length == amountOfNodes && (this.previousScale > this.scale || zoomDirection == -1))  {
+      this._aggregateHubs(force);
+      this._updateNodeIndexList();
+    }
+
+    // we now reduce chains.
+    if (this.previousScale > this.scale || zoomDirection == -1) { // zoom out
+      this.handleChains();
+      this._updateNodeIndexList();
+    }
+
+    this.previousScale = this.scale;
+
+    // rest of the update the index list, dynamic edges and labels
+    this._updateDynamicEdges();
+    this.updateLabels();
+
+    // if a cluster was formed, we increase the clusterSession
+    if (this.nodeIndices.length < amountOfNodes) { // this means a clustering operation has taken place
+      this.clusterSession += 1;
+    }
+
+    // if the simulation was settled, we restart the simulation if a cluster has been formed or expanded
+    if (this.moving != isMovingBeforeClustering) {
+      this.start();
+    }
+   },
+
+  /**
+   * This function handles the chains. It is called on every updateClusters().
+   */
+  handleChains : function() {
+    // after clustering we check how many chains there are
+    var chainPercentage = this._getChainFraction();
+    if (chainPercentage > this.constants.clustering.chainThreshold) {
+      this._reduceAmountOfChains(1 - this.constants.clustering.chainThreshold / chainPercentage)
+
+    }
+   },
+
+  /**
+   * this functions starts clustering by hubs
+   * The minimum hub threshold is set globally
+   *
+   * @private
+   */
+  _aggregateHubs : function(force) {
+    this._getHubSize();
+    this._formClustersByHub(force,false);
+   },
+
+
+  /**
+   * This function is fired by keypress. It forces hubs to form.
+   *
+   */
+  forceAggregateHubs : function() {
+    var isMovingBeforeClustering = this.moving;
+    var amountOfNodes = this.nodeIndices.length;
+
+    this._aggregateHubs(true);
+
+    // update the index list, dynamic edges and labels
+    this._updateNodeIndexList();
+    this._updateDynamicEdges();
+    this.updateLabels();
+
+    // if a cluster was formed, we increase the clusterSession
+    if (this.nodeIndices.length != amountOfNodes) {
+      this.clusterSession += 1;
+    }
+
+    // if the simulation was settled, we restart the simulation if a cluster has been formed or expanded
+    if (this.moving != isMovingBeforeClustering) {
+      this.start();
+    }
+   },
+
+  /**
+   * If a cluster takes up more than a set percentage of the screen, open the cluster
+   *
+   * @private
+   */
+  _openClustersBySize : function() {
+    for (var nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        var node = this.nodes[nodeId];
+        if (node.inView() == true) {
+          if ((node.width*this.scale > this.constants.clustering.screenSizeThreshold * this.frame.canvas.clientWidth) ||
+              (node.height*this.scale > this.constants.clustering.screenSizeThreshold * this.frame.canvas.clientHeight)) {
+            this.openCluster(node);
+          }
+        }
+      }
+    }
+   },
+
+
+  /**
+   * This function loops over all nodes in the nodeIndices list. For each node it checks if it is a cluster and if it
+   * has to be opened based on the current zoom level.
+   *
+   * @private
+   */
+  _openClusters : function(recursive,force) {
+    for (var i = 0; i < this.nodeIndices.length; i++) {
+      var node = this.nodes[this.nodeIndices[i]];
+      this._expandClusterNode(node,recursive,force);
+    }
+   },
+
+  /**
+   * This function checks if a node has to be opened. This is done by checking the zoom level.
+   * If the node contains child nodes, this function is recursively called on the child nodes as well.
+   * This recursive behaviour is optional and can be set by the recursive argument.
+   *
+   * @param {Node}    parentNode    | to check for cluster and expand
+   * @param {Boolean} recursive     | enabled or disable recursive calling
+   * @param {Boolean} force         | enabled or disable forcing
+   * @param {Boolean} [openAll]     | This will recursively force all nodes in the parent to be released
+   * @private
+   */
+  _expandClusterNode : function(parentNode, recursive, force, openAll) {
+    // first check if node is a cluster
+    if (parentNode.clusterSize > 1) {
+      // this means that on a double tap event or a zoom event, the cluster fully unpacks if it is smaller than 20
+      if (parentNode.clusterSize < this.constants.clustering.sectorThreshold) {
+        openAll = true;
+      }
+      recursive = openAll ? true : recursive;
+
+      // if the last child has been added on a smaller scale than current scale decluster
+      if (parentNode.formationScale < this.scale || force == true) {
+        // we will check if any of the contained child nodes should be removed from the cluster
+        for (var containedNodeId in parentNode.containedNodes) {
+          if (parentNode.containedNodes.hasOwnProperty(containedNodeId)) {
+            var childNode = parentNode.containedNodes[containedNodeId];
+
+            // force expand will expand the largest cluster size clusters. Since we cluster from outside in, we assume that
+            // the largest cluster is the one that comes from outside
+            if (force == true) {
+              if (childNode.clusterSession == parentNode.clusterSessions[parentNode.clusterSessions.length-1]
+                  || openAll) {
+                this._expelChildFromParent(parentNode,containedNodeId,recursive,force,openAll);
+              }
+            }
+            else {
+              if (this._nodeInActiveArea(parentNode)) {
+                this._expelChildFromParent(parentNode,containedNodeId,recursive,force,openAll);
+              }
+            }
+          }
+        }
+      }
+    }
+   },
+
+  /**
+   * ONLY CALLED FROM _expandClusterNode
+   *
+   * This function will expel a child_node from a parent_node. This is to de-cluster the node. This function will remove
+   * the child node from the parent contained_node object and put it back into the global nodes object.
+   * The same holds for the edge that was connected to the child node. It is moved back into the global edges object.
+   *
+   * @param {Node}    parentNode        | the parent node
+   * @param {String}  containedNodeId   | child_node id as it is contained in the containedNodes object of the parent node
+   * @param {Boolean} recursive         | This will also check if the child needs to be expanded.
+   *                                      With force and recursive both true, the entire cluster is unpacked
+   * @param {Boolean} force             | This will disregard the zoom level and will expel this child from the parent
+   * @param {Boolean} openAll           | This will recursively force all nodes in the parent to be released
+   * @private
+   */
+  _expelChildFromParent : function(parentNode, containedNodeId, recursive, force, openAll) {
+    var childNode = parentNode.containedNodes[containedNodeId];
+
+    // if child node has been added on smaller scale than current, kick out
+    if (childNode.formationScale < this.scale || force == true) {
+      // put the child node back in the global nodes object
+      this.nodes[containedNodeId] = childNode;
+
+      // release the contained edges from this childNode back into the global edges
+      this._releaseContainedEdges(parentNode,childNode);
+
+      // reconnect rerouted edges to the childNode
+      this._connectEdgeBackToChild(parentNode,childNode);
+
+      // validate all edges in dynamicEdges
+      this._validateEdges(parentNode);
+
+      // undo the changes from the clustering operation on the parent node
+      parentNode.mass -= this.constants.clustering.massTransferCoefficient * childNode.mass;
+      parentNode.fontSize -= this.constants.clustering.fontSizeMultiplier * childNode.clusterSize;
+      parentNode.clusterSize -= childNode.clusterSize;
+      parentNode.dynamicEdgesLength = parentNode.dynamicEdges.length;
+
+      // place the child node near the parent, not at the exact same location to avoid chaos in the system
+      childNode.x = parentNode.x + this.constants.edges.length * 0.3 * (0.5 - Math.random()) * parentNode.clusterSize;
+      childNode.y = parentNode.y + this.constants.edges.length * 0.3 * (0.5 - Math.random()) * parentNode.clusterSize;
+
+      // remove node from the list
+      delete parentNode.containedNodes[containedNodeId];
+
+      // check if there are other childs with this clusterSession in the parent.
+      var othersPresent = false;
+      for (var childNodeId in parentNode.containedNodes) {
+        if (parentNode.containedNodes.hasOwnProperty(childNodeId)) {
+          if (parentNode.containedNodes[childNodeId].clusterSession == childNode.clusterSession) {
+            othersPresent = true;
+            break;
+          }
+        }
+      }
+      // if there are no others, remove the cluster session from the list
+      if (othersPresent == false) {
+        parentNode.clusterSessions.pop();
+      }
+
+      // remove the clusterSession from the child node
+      childNode.clusterSession = 0;
+
+      // restart the simulation to reorganise all nodes
+      this.moving = true;
+
+      // recalculate the size of the node on the next time the node is rendered
+      parentNode.clearSizeCache();
+    }
+
+    // check if a further expansion step is possible if recursivity is enabled
+    if (recursive == true) {
+      this._expandClusterNode(childNode,recursive,force,openAll);
+    }
+   },
+
+
+  /**
+   * This function checks if any nodes at the end of their trees have edges below a threshold length
+   * This function is called only from updateClusters()
+   * forceLevelCollapse ignores the length of the edge and collapses one level
+   * This means that a node with only one edge will be clustered with its connected node
+   *
+   * @private
+   * @param {Boolean} force
+   */
+  _formClusters : function(force) {
+    if (force == false) {
+      this._formClustersByZoom();
+    }
+    else {
+      this._forceClustersByZoom();
+    }
+   },
+
+  /**
+   * This function handles the clustering by zooming out, this is based on a minimum edge distance
+   *
+   * @private
+   */
+  _formClustersByZoom : function() {
+    var dx,dy,length,
+        minLength = this.constants.clustering.clusterEdgeThreshold/this.scale;
+
+    // check if any edges are shorter than minLength and start the clustering
+    // the clustering favours the node with the larger mass
+    for (var edgeId in this.edges) {
+      if (this.edges.hasOwnProperty(edgeId)) {
+        var edge = this.edges[edgeId];
+        if (edge.connected) {
+          if (edge.toId != edge.fromId) {
+            dx = (edge.to.x - edge.from.x);
+            dy = (edge.to.y - edge.from.y);
+            length = Math.sqrt(dx * dx + dy * dy);
+
+
+            if (length < minLength) {
+              // first check which node is larger
+              var parentNode = edge.from;
+              var childNode = edge.to;
+              if (edge.to.mass > edge.from.mass) {
+                parentNode = edge.to;
+                childNode = edge.from;
+              }
+
+              if (childNode.dynamicEdgesLength == 1) {
+                this._addToCluster(parentNode,childNode,false);
+              }
+              else if (parentNode.dynamicEdgesLength == 1) {
+                this._addToCluster(childNode,parentNode,false);
+              }
+            }
+          }
+        }
+      }
+    }
+   },
+
+  /**
+   * This function forces the graph to cluster all nodes with only one connecting edge to their
+   * connected node.
+   *
+   * @private
+   */
+  _forceClustersByZoom : function() {
+    for (var nodeId in this.nodes) {
+      // another node could have absorbed this child.
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        var childNode = this.nodes[nodeId];
+
+        // the edges can be swallowed by another decrease
+        if (childNode.dynamicEdgesLength == 1 && childNode.dynamicEdges.length != 0) {
+          var edge = childNode.dynamicEdges[0];
+          var parentNode = (edge.toId == childNode.id) ? this.nodes[edge.fromId] : this.nodes[edge.toId];
+
+          // group to the largest node
+          if (childNode.id != parentNode.id) {
+            if (parentNode.mass > childNode.mass) {
+              this._addToCluster(parentNode,childNode,true);
+            }
+            else {
+              this._addToCluster(childNode,parentNode,true);
+            }
+          }
+        }
+      }
+    }
+   },
+
+
+
+  /**
+   * This function forms clusters from hubs, it loops over all nodes
+   *
+   * @param {Boolean} force         |   Disregard zoom level
+   * @param {Boolean} onlyEqual     |   This only clusters a hub with a specific number of edges
+   * @private
+   */
+  _formClustersByHub : function(force, onlyEqual) {
+    // we loop over all nodes in the list
+    for (var nodeId in this.nodes) {
+      // we check if it is still available since it can be used by the clustering in this loop
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        this._formClusterFromHub(this.nodes[nodeId],force,onlyEqual);
+      }
+    }
+   },
+
+  /**
+   * This function forms a cluster from a specific preselected hub node
+   *
+   * @param {Node}    hubNode       |   the node we will cluster as a hub
+   * @param {Boolean} force         |   Disregard zoom level
+   * @param {Boolean} onlyEqual     |   This only clusters a hub with a specific number of edges
+   * @param {Number} [absorptionSizeOffset] |
+   * @private
+   */
+  _formClusterFromHub : function(hubNode, force, onlyEqual, absorptionSizeOffset) {
+    if (absorptionSizeOffset === undefined) {
+      absorptionSizeOffset = 0;
+    }
+    // we decide if the node is a hub
+    if ((hubNode.dynamicEdgesLength >= this.hubThreshold && onlyEqual == false) ||
+      (hubNode.dynamicEdgesLength == this.hubThreshold && onlyEqual == true)) {
+      // initialize variables
+      var dx,dy,length;
+      var minLength = this.constants.clustering.clusterEdgeThreshold/this.scale;
+      var allowCluster = false;
+
+      // we create a list of edges because the dynamicEdges change over the course of this loop
+      var edgesIdarray = [];
+      var amountOfInitialEdges = hubNode.dynamicEdges.length;
+      for (var j = 0; j < amountOfInitialEdges; j++) {
+        edgesIdarray.push(hubNode.dynamicEdges[j].id);
+      }
+
+      // if the hub clustering is not forces, we check if one of the edges connected
+      // to a cluster is small enough based on the constants.clustering.clusterEdgeThreshold
+      if (force == false) {
+        allowCluster = false;
+        for (j = 0; j < amountOfInitialEdges; j++) {
+          var edge = this.edges[edgesIdarray[j]];
+          if (edge !== undefined) {
+            if (edge.connected) {
+              if (edge.toId != edge.fromId) {
+                dx = (edge.to.x - edge.from.x);
+                dy = (edge.to.y - edge.from.y);
+                length = Math.sqrt(dx * dx + dy * dy);
+
+                if (length < minLength) {
+                  allowCluster = true;
+                  break;
+                }
+              }
+            }
+          }
+        }
+      }
+
+      // start the clustering if allowed
+      if ((!force && allowCluster) || force) {
+        // we loop over all edges INITIALLY connected to this hub
+        for (j = 0; j < amountOfInitialEdges; j++) {
+          edge = this.edges[edgesIdarray[j]];
+          // the edge can be clustered by this function in a previous loop
+          if (edge !== undefined) {
+            var childNode = this.nodes[(edge.fromId == hubNode.id) ? edge.toId : edge.fromId];
+            // we do not want hubs to merge with other hubs nor do we want to cluster itself.
+            if ((childNode.dynamicEdges.length <= (this.hubThreshold + absorptionSizeOffset)) &&
+                (childNode.id != hubNode.id)) {
+              this._addToCluster(hubNode,childNode,force);
+            }
+          }
+        }
+      }
+    }
+   },
+
+
+
+  /**
+   * This function adds the child node to the parent node, creating a cluster if it is not already.
+   *
+   * @param {Node} parentNode           | this is the node that will house the child node
+   * @param {Node} childNode            | this node will be deleted from the global this.nodes and stored in the parent node
+   * @param {Boolean} force             | true will only update the remainingEdges at the very end of the clustering, ensuring single level collapse
+   * @private
+   */
+  _addToCluster : function(parentNode, childNode, force) {
+    // join child node in the parent node
+    parentNode.containedNodes[childNode.id] = childNode;
+
+    // manage all the edges connected to the child and parent nodes
+    for (var i = 0; i < childNode.dynamicEdges.length; i++) {
+      var edge = childNode.dynamicEdges[i];
+      if (edge.toId == parentNode.id || edge.fromId == parentNode.id) { // edge connected to parentNode
+        this._addToContainedEdges(parentNode,childNode,edge);
+      }
+      else {
+        this._connectEdgeToCluster(parentNode,childNode,edge);
+      }
+    }
+    // a contained node has no dynamic edges.
+    childNode.dynamicEdges = [];
+
+    // remove circular edges from clusters
+    this._containCircularEdgesFromNode(parentNode,childNode);
+
+
+    // remove the childNode from the global nodes object
+    delete this.nodes[childNode.id];
+
+    // update the properties of the child and parent
+    var massBefore = parentNode.mass;
+    childNode.clusterSession = this.clusterSession;
+    parentNode.mass += this.constants.clustering.massTransferCoefficient * childNode.mass;
+    parentNode.clusterSize += childNode.clusterSize;
+    parentNode.fontSize += this.constants.clustering.fontSizeMultiplier * childNode.clusterSize;
+
+    // keep track of the clustersessions so we can open the cluster up as it has been formed.
+    if (parentNode.clusterSessions[parentNode.clusterSessions.length - 1] != this.clusterSession) {
+      parentNode.clusterSessions.push(this.clusterSession);
+    }
+
+    // forced clusters only open from screen size and double tap
+    if (force == true) {
+      // parentNode.formationScale = Math.pow(1 - (1.0/11.0),this.clusterSession+3);
+      parentNode.formationScale = 0;
+    }
+    else {
+      parentNode.formationScale = this.scale; // The latest child has been added on this scale
+    }
+
+    // recalculate the size of the node on the next time the node is rendered
+    parentNode.clearSizeCache();
+
+    // set the pop-out scale for the childnode
+    parentNode.containedNodes[childNode.id].formationScale = parentNode.formationScale;
+
+    // nullify the movement velocity of the child, this is to avoid hectic behaviour
+    childNode.clearVelocity();
+
+    // the mass has altered, preservation of energy dictates the velocity to be updated
+    parentNode.updateVelocity(massBefore);
+
+    // restart the simulation to reorganise all nodes
+    this.moving = true;
+   },
+
+
+  /**
+   * This function will apply the changes made to the remainingEdges during the formation of the clusters.
+   * This is a seperate function to allow for level-wise collapsing of the node tree.
+   * It has to be called if a level is collapsed. It is called by _formClusters().
+   * @private
+   */
+  _updateDynamicEdges : function() {
+    for (var i = 0; i < this.nodeIndices.length; i++) {
+      var node = this.nodes[this.nodeIndices[i]];
+      node.dynamicEdgesLength = node.dynamicEdges.length;
+
+      // this corrects for multiple edges pointing at the same other node
+      var correction = 0;
+      if (node.dynamicEdgesLength > 1) {
+        for (var j = 0; j < node.dynamicEdgesLength - 1; j++) {
+          var edgeToId = node.dynamicEdges[j].toId;
+          var edgeFromId = node.dynamicEdges[j].fromId;
+          for (var k = j+1; k < node.dynamicEdgesLength; k++) {
+            if ((node.dynamicEdges[k].toId == edgeToId && node.dynamicEdges[k].fromId == edgeFromId) ||
+                (node.dynamicEdges[k].fromId == edgeToId && node.dynamicEdges[k].toId == edgeFromId)) {
+              correction += 1;
+            }
+          }
+        }
+      }
+      node.dynamicEdgesLength -= correction;
+    }
+   },
+
+
+  /**
+   * This adds an edge from the childNode to the contained edges of the parent node
+   *
+   * @param parentNode    | Node object
+   * @param childNode     | Node object
+   * @param edge          | Edge object
+   * @private
+   */
+  _addToContainedEdges : function(parentNode, childNode, edge) {
+    // create an array object if it does not yet exist for this childNode
+    if (!(parentNode.containedEdges.hasOwnProperty(childNode.id))) {
+      parentNode.containedEdges[childNode.id] = []
+    }
+    // add this edge to the list
+    parentNode.containedEdges[childNode.id].push(edge);
+
+    // remove the edge from the global edges object
+    delete this.edges[edge.id];
+
+    // remove the edge from the parent object
+    for (var i = 0; i < parentNode.dynamicEdges.length; i++) {
+      if (parentNode.dynamicEdges[i].id == edge.id) {
+        parentNode.dynamicEdges.splice(i,1);
+        break;
+      }
+    }
+   },
+
+  /**
+   * This function connects an edge that was connected to a child node to the parent node.
+   * It keeps track of which nodes it has been connected to with the originalId array.
+   *
+   * @param {Node} parentNode    | Node object
+   * @param {Node} childNode     | Node object
+   * @param {Edge} edge          | Edge object
+   * @private
+   */
+  _connectEdgeToCluster : function(parentNode, childNode, edge) {
+    // handle circular edges
+    if (edge.toId == edge.fromId) {
+      this._addToContainedEdges(parentNode, childNode, edge);
+    }
+    else {
+      if (edge.toId == childNode.id) {    // edge connected to other node on the "to" side
+        edge.originalToId.push(childNode.id);
+        edge.to = parentNode;
+        edge.toId = parentNode.id;
+      }
+      else {          // edge connected to other node with the "from" side
+
+        edge.originalFromId.push(childNode.id);
+        edge.from = parentNode;
+        edge.fromId = parentNode.id;
+      }
+
+      this._addToReroutedEdges(parentNode,childNode,edge);
+    }
+   },
+
+
+  _containCircularEdgesFromNode : function(parentNode, childNode) {
+    // manage all the edges connected to the child and parent nodes
+    for (var i = 0; i < parentNode.dynamicEdges.length; i++) {
+      var edge = parentNode.dynamicEdges[i];
+      // handle circular edges
+      if (edge.toId == edge.fromId) {
+        this._addToContainedEdges(parentNode, childNode, edge);
+      }
+    }
+  },
+
+
+  /**
+   * This adds an edge from the childNode to the rerouted edges of the parent node
+   *
+   * @param parentNode    | Node object
+   * @param childNode     | Node object
+   * @param edge          | Edge object
+   * @private
+   */
+  _addToReroutedEdges : function(parentNode, childNode, edge) {
+    // create an array object if it does not yet exist for this childNode
+    // we store the edge in the rerouted edges so we can restore it when the cluster pops open
+    if (!(parentNode.reroutedEdges.hasOwnProperty(childNode.id))) {
+      parentNode.reroutedEdges[childNode.id] = [];
+    }
+    parentNode.reroutedEdges[childNode.id].push(edge);
+
+    // this edge becomes part of the dynamicEdges of the cluster node
+    parentNode.dynamicEdges.push(edge);
+   },
+
+
+
+  /**
+   * This function connects an edge that was connected to a cluster node back to the child node.
+   *
+   * @param parentNode    | Node object
+   * @param childNode     | Node object
+   * @private
+   */
+  _connectEdgeBackToChild : function(parentNode, childNode) {
+    if (parentNode.reroutedEdges.hasOwnProperty(childNode.id)) {
+      for (var i = 0; i < parentNode.reroutedEdges[childNode.id].length; i++) {
+        var edge = parentNode.reroutedEdges[childNode.id][i];
+        if (edge.originalFromId[edge.originalFromId.length-1] == childNode.id) {
+          edge.originalFromId.pop();
+          edge.fromId = childNode.id;
+          edge.from = childNode;
+        }
+        else {
+          edge.originalToId.pop();
+          edge.toId = childNode.id;
+          edge.to = childNode;
+        }
+
+        // append this edge to the list of edges connecting to the childnode
+        childNode.dynamicEdges.push(edge);
+
+        // remove the edge from the parent object
+        for (var j = 0; j < parentNode.dynamicEdges.length; j++) {
+          if (parentNode.dynamicEdges[j].id == edge.id) {
+            parentNode.dynamicEdges.splice(j,1);
+            break;
+          }
+        }
+      }
+      // remove the entry from the rerouted edges
+      delete parentNode.reroutedEdges[childNode.id];
+    }
+   },
+
+
+  /**
+   * When loops are clustered, an edge can be both in the rerouted array and the contained array.
+   * This function is called last to verify that all edges in dynamicEdges are in fact connected to the
+   * parentNode
+   *
+   * @param parentNode    | Node object
+   * @private
+   */
+  _validateEdges : function(parentNode) {
+    for (var i = 0; i < parentNode.dynamicEdges.length; i++) {
+      var edge = parentNode.dynamicEdges[i];
+      if (parentNode.id != edge.toId && parentNode.id != edge.fromId) {
+        parentNode.dynamicEdges.splice(i,1);
+      }
+    }
+   },
+
+
+  /**
+   * This function released the contained edges back into the global domain and puts them back into the
+   * dynamic edges of both parent and child.
+   *
+   * @param {Node} parentNode    |
+   * @param {Node} childNode     |
+   * @private
+   */
+  _releaseContainedEdges : function(parentNode, childNode) {
+    for (var i = 0; i < parentNode.containedEdges[childNode.id].length; i++) {
+      var edge = parentNode.containedEdges[childNode.id][i];
+
+      // put the edge back in the global edges object
+      this.edges[edge.id] = edge;
+
+      // put the edge back in the dynamic edges of the child and parent
+      childNode.dynamicEdges.push(edge);
+      parentNode.dynamicEdges.push(edge);
+    }
+    // remove the entry from the contained edges
+    delete parentNode.containedEdges[childNode.id];
+
+   },
+
+
+
+
+  // ------------------- UTILITY FUNCTIONS ---------------------------- //
+
+
+  /**
+   * This updates the node labels for all nodes (for debugging purposes)
+   */
+  updateLabels : function() {
+    var nodeId;
+    // update node labels
+    for (nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        var node = this.nodes[nodeId];
+        if (node.clusterSize > 1) {
+          node.label = "[".concat(String(node.clusterSize),"]");
+        }
+      }
+    }
+
+    // update node labels
+    for (nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        node = this.nodes[nodeId];
+        if (node.clusterSize == 1) {
+          if (node.originalLabel !== undefined) {
+            node.label = node.originalLabel;
+          }
+          else {
+            node.label = String(node.id);
+          }
+        }
+      }
+    }
+
+    /* Debug Override */
+  //  for (nodeId in this.nodes) {
+  //    if (this.nodes.hasOwnProperty(nodeId)) {
+  //      node = this.nodes[nodeId];
+  //      node.label = String(Math.round(node.width)).concat(":",Math.round(node.width*this.scale));
+  //    }
+  //  }
+
+   },
+
+
+  /**
+   * This function determines if the cluster we want to decluster is in the active area
+   * this means around the zoom center
+   *
+   * @param {Node} node
+   * @returns {boolean}
+   * @private
+   */
+  _nodeInActiveArea : function(node) {
+    return (
+      Math.abs(node.x - this.areaCenter.x) <= this.constants.clustering.activeAreaBoxSize/this.scale
+        &&
+      Math.abs(node.y - this.areaCenter.y) <= this.constants.clustering.activeAreaBoxSize/this.scale
+      )
+   },
+
+
+  /**
+   * This is an adaptation of the original repositioning function. This is called if the system is clustered initially
+   * It puts large clusters away from the center and randomizes the order.
+   *
+   */
+  repositionNodes : function() {
+    for (var i = 0; i < this.nodeIndices.length; i++) {
+      var node = this.nodes[this.nodeIndices[i]];
+      if (!node.isFixed()) {
+        var radius = this.constants.edges.length * (1 + 0.6*node.clusterSize);
+        var angle = 2 * Math.PI * Math.random();
+        node.x = radius * Math.cos(angle);
+        node.y = radius * Math.sin(angle);
+      }
+    }
+   },
+
+
+
+
+
+  /**
+   * We determine how many connections denote an important hub.
+   * We take the mean + 2*std as the important hub size. (Assuming a normal distribution of data, ~2.2%)
+   *
+   * @private
+   */
+  _getHubSize : function() {
+    var average = 0;
+    var averageSquared = 0;
+    var hubCounter = 0;
+    var largestHub = 0;
+
+    for (var i = 0; i < this.nodeIndices.length; i++) {
+      var node = this.nodes[this.nodeIndices[i]];
+      if (node.dynamicEdgesLength > largestHub) {
+        largestHub = node.dynamicEdgesLength;
+      }
+      average += node.dynamicEdgesLength;
+      averageSquared += Math.pow(node.dynamicEdgesLength,2);
+      hubCounter += 1;
+    }
+    average = average / hubCounter;
+    averageSquared = averageSquared / hubCounter;
+
+    var variance = averageSquared - Math.pow(average,2);
+
+    var standardDeviation = Math.sqrt(variance);
+
+    this.hubThreshold = Math.floor(average + 2*standardDeviation);
+
+    // always have at least one to cluster
+    if (this.hubThreshold > largestHub) {
+      this.hubThreshold = largestHub;
+    }
+
+  //  console.log("average",average,"averageSQ",averageSquared,"var",variance,"std",standardDeviation);
+  //  console.log("hubThreshold:",this.hubThreshold);
+   },
+
+
+  /**
+   * We reduce the amount of "extension nodes" or chains. These are not quickly clustered with the outliers and hubs methods
+   * with this amount we can cluster specifically on these chains.
+   *
+   * @param   {Number} fraction     | between 0 and 1, the percentage of chains to reduce
+   * @private
+   */
+  _reduceAmountOfChains : function(fraction) {
+    this.hubThreshold = 2;
+    var reduceAmount = Math.floor(this.nodeIndices.length * fraction);
+    for (var nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        if (this.nodes[nodeId].dynamicEdgesLength == 2 && this.nodes[nodeId].dynamicEdges.length >= 2) {
+          if (reduceAmount > 0) {
+            this._formClusterFromHub(this.nodes[nodeId],true,true,1);
+            reduceAmount -= 1;
+          }
+        }
+      }
+    }
+   },
+
+  /**
+   * We get the amount of "extension nodes" or chains. These are not quickly clustered with the outliers and hubs methods
+   * with this amount we can cluster specifically on these chains.
+   *
+   * @private
+   */
+  _getChainFraction : function() {
+    var chains = 0;
+    var total = 0;
+    for (var nodeId in this.nodes) {
+      if (this.nodes.hasOwnProperty(nodeId)) {
+        if (this.nodes[nodeId].dynamicEdgesLength == 2 && this.nodes[nodeId].dynamicEdges.length >= 2) {
+          chains += 1;
+        }
+        total += 1;
+      }
+    }
+    return chains/total;
+   }
+};