jrtechs-vis/lib/network/networkMixins/ClusterMixin.js

/**
 * Creation of the ClusterMixin var.
 *
 * This contains all the functions the Network object can use to employ clustering
 *
 * Alex de Mulder
 * 21-01-2013
 */
var ClusterMixin = {

 /**
  * This is only called in the constructor of the network 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._stabilize();
   }
   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(true);
        this.normalizeClusterLevels();
      }
      else {
        this.increaseClusterLevel(); // this also includes a cluster normalization
      }

      numberOfNodes = this.nodeIndices.length;
      level += 1;
    }

    // after the clustering we reposition the nodes to reduce the initial chaos
    if (level > 0 && reposition == true) {
      this.repositionNodes();
    }
    this._updateCalculationNodes();
  },

  /**
   * 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 loads a new sector, loads the nodes and edges and nodeIndices of it.
      this._addSector(node);
      var level = 0;

      // we decluster until we reach a decent number of nodes
      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._updateCalculationNodes();
      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
   * @param {Boolean} doNotStart    | if true do not call start
   *
   */
  updateClusters : function(zoomDirection,recursive,force,doNotStart) {
    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 clusters have been made, we normalize the cluster level
      this.normalizeClusterLevels();
    }

    if (doNotStart == false || doNotStart === undefined) {
      // if the simulation was settled, we restart the simulation if a cluster has been formed or expanded
      if (this.moving != isMovingBeforeClustering) {
        this.start();
      }
    }

    this._updateCalculationNodes();
  },

  /**
   * 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(doNotStart) {
    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 (doNotStart == false || doNotStart === undefined) {
      // 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._updateCalculationNodes();
    }
  },

  /**
   * 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) {
      // unselect all selected items
      this._unselectAll();

      // 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 -= childNode.mass;
      parentNode.clusterSize -= childNode.clusterSize;
      parentNode.fontSize = Math.min(this.constants.clustering.maxFontSize, this.constants.nodes.fontSize + this.constants.clustering.fontSizeMultiplier*parentNode.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 + parentNode.growthIndicator * (0.5 - Math.random());
      childNode.y = parentNode.y + parentNode.growthIndicator * (0.5 - Math.random());

      // 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();
      }

      this._repositionBezierNodes(childNode);
//      this._repositionBezierNodes(parentNode);

      // remove the clusterSession from the child node
      childNode.clusterSession = 0;

      // recalculate the size of the node on the next time the node is rendered
      parentNode.clearSizeCache();

      // restart the simulation to reorganise all nodes
      this.moving = true;
    }

    // check if a further expansion step is possible if recursivity is enabled
    if (recursive == true) {
      this._expandClusterNode(childNode,recursive,force,openAll);
    }
  },


  /**
   * position the bezier nodes at the center of the edges
   *
   * @param node
   * @private
   */
  _repositionBezierNodes : function(node) {
    for (var i = 0; i < node.dynamicEdges.length; i++) {
      node.dynamicEdges[i].positionBezierNode();
    }
  },


  /**
   * 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 network 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);
            }
          }
        }
      }
    }
  },


  /**
   * To keep the nodes of roughly equal size we normalize the cluster levels.
   * This function clusters a node to its smallest connected neighbour.
   *
   * @param node
   * @private
   */
  _clusterToSmallestNeighbour : function(node) {
    var smallestNeighbour = -1;
    var smallestNeighbourNode = null;
    for (var i = 0; i < node.dynamicEdges.length; i++) {
      if (node.dynamicEdges[i] !== undefined) {
        var neighbour = null;
        if (node.dynamicEdges[i].fromId != node.id) {
          neighbour = node.dynamicEdges[i].from;
        }
        else if (node.dynamicEdges[i].toId != node.id) {
          neighbour = node.dynamicEdges[i].to;
        }


        if (neighbour != null && smallestNeighbour > neighbour.clusterSessions.length) {
          smallestNeighbour = neighbour.clusterSessions.length;
          smallestNeighbourNode = neighbour;
        }
      }
    }

    if (neighbour != null && this.nodes[neighbour.id] !== undefined) {
      this._addToCluster(neighbour, node, 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 += childNode.mass;
    parentNode.clusterSize += childNode.clusterSize;
    parentNode.fontSize = Math.min(this.constants.clustering.maxFontSize, this.constants.nodes.fontSize + this.constants.clustering.fontSizeMultiplier*parentNode.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 barnesHutTree.
   * 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);
    }
  },


  /**
   * If a node is connected to itself, a circular edge is drawn. When clustering we want to contain
   * these edges inside of the cluster.
   *
   * @param parentNode
   * @param childNode
   * @private
   */
  _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(node.level);
//      }
//    }

  },


  /**
   * We want to keep the cluster level distribution rather small. This means we do not want unclustered nodes
   * if the rest of the nodes are already a few cluster levels in.
   * To fix this we use this function. It determines the min and max cluster level and sends nodes that have not
   * clustered enough to the clusterToSmallestNeighbours function.
   */
  normalizeClusterLevels : function() {
    var maxLevel = 0;
    var minLevel = 1e9;
    var clusterLevel = 0;
    var nodeId;

    // we loop over all nodes in the list
    for (nodeId in this.nodes) {
      if (this.nodes.hasOwnProperty(nodeId)) {
        clusterLevel = this.nodes[nodeId].clusterSessions.length;
        if (maxLevel < clusterLevel) {maxLevel = clusterLevel;}
        if (minLevel > clusterLevel) {minLevel = clusterLevel;}
      }
    }

    if (maxLevel - minLevel > this.constants.clustering.clusterLevelDifference) {
      var amountOfNodes = this.nodeIndices.length;
      var targetLevel = maxLevel - this.constants.clustering.clusterLevelDifference;
      // we loop over all nodes in the list
      for (nodeId in this.nodes) {
        if (this.nodes.hasOwnProperty(nodeId)) {
          if (this.nodes[nodeId].clusterSessions.length < targetLevel) {
            this._clusterToSmallestNeighbour(this.nodes[nodeId]);
          }
        }
      }
      this._updateNodeIndexList();
      this._updateDynamicEdges();
      // if a cluster was formed, we increase the clusterSession
      if (this.nodeIndices.length != amountOfNodes) {
        this.clusterSession += 1;
      }
    }
  },



  /**
   * 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.xFixed == false || node.yFixed == false)) {
        var radius = 10 * 0.1*this.nodeIndices.length * Math.min(100,node.mass);
        var angle = 2 * Math.PI * Math.random();
        if (node.xFixed == false) {node.x = radius * Math.cos(angle);}
        if (node.yFixed == false) {node.y = radius * Math.sin(angle);}
        this._repositionBezierNodes(node);
      }
    }
  },


  /**
   * 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;
  }

};