public void linkRemoved(MycoNode a, MycoNode b) {
   MycoEdge edge = graph.findEdge(a, b);
   while (edge != null) {
     graph.removeEdge(edge);
     edge = graph.findEdge(a, b);
   }
 }
 public void nodeStateChanged(MycoNode n, HyphaType t, HyphaType oldState) {
   if (t != HyphaType.DEAD) {
     if (!graph.containsVertex(n)) {
       graph.addVertex(n);
     }
   } else {
     if (graph.containsVertex(n)) {
       graph.removeVertex(n);
     }
   }
 }
  public boolean execute() {
    if (CDState.getCycle() % period != 0) return false;

    MycoCast mycocast = (MycoCast) Network.get(0).getProtocol(mycocastPid);

    int bio = mycocast.countBiomass();
    int ext = mycocast.countExtending();
    int bra = mycocast.countBranching();
    int imm = mycocast.countImmobile();

    // Update vertices
    Set<MycoNode> activeNodes = new HashSet<MycoNode>();
    for (int i = 0; i < Network.size(); i++) {
      MycoNode n = (MycoNode) Network.get(i);
      activeNodes.add(n);
      HyphaData data = n.getHyphaData();
      // if (data.isBiomass()) { continue; }
      if (graph.containsVertex(n)) {
        graph.removeVertex(n);
      }
      if (!graph.containsVertex(n)) {
        graph.addVertex(n);
      }
    }
    Set<MycoNode> jungNodes = new HashSet<MycoNode>(graph.getVertices());
    jungNodes.removeAll(activeNodes);

    for (MycoNode n : jungNodes) {
      graph.removeVertex(n);
    }

    // Update edges
    for (int i = 0; i < Network.size(); i++) {
      MycoNode n = (MycoNode) Network.get(i);
      HyphaData data = n.getHyphaData();
      HyphaLink link = n.getHyphaLink();

      synchronized (graph) {

        // We now add in all links and tune out display in Visualizer
        java.util.List<MycoNode> neighbors = (java.util.List<MycoNode>) link.getNeighbors();

        //// Adding only links to hypha thins out links to biomass
        //    (java.util.List<MycoNode>) link.getHyphae();

        Collection<MycoNode> jungNeighbors = graph.getNeighbors(n);

        // Remove edges from Jung graph that are not in peersim graph
        for (MycoNode o : jungNeighbors) {
          if (!neighbors.contains(o)) {
            MycoEdge edge = graph.findEdge(n, o);
            while (edge != null) {
              graph.removeEdge(edge);
              edge = graph.findEdge(n, o);
            }
          }
        }

        // Add missing edges to Jung graph that are in peersim graph
        for (MycoNode o : neighbors) {
          if (graph.findEdge(n, o) == null) {
            MycoEdge edge = new MycoEdge();
            graph.addEdge(edge, n, o, EdgeType.DIRECTED);
          }
        }
      }

      // log.finest("VERTICES: " + graph.getVertices());
      // log.finest("EDGES: " + graph.getEdges());
    }

    for (ChangeListener cl : changeListeners) {
      cl.stateChanged(new ChangeEvent(graph));
    }
    if (walking) {
      try {
        Thread.sleep(walkDelay);
      } catch (InterruptedException e) {
      }
      stepBlocked = false;
    }

    try {
      while (stepBlocked && !noBlock) {
        synchronized (JungGraphObserver.class) {
          JungGraphObserver.class.wait();
        }
      }
    } catch (InterruptedException e) {
      stepBlocked = true;
    }
    stepBlocked = true;
    // System.out.println(graph.toString());
    return false;
  }
 public void linkAdded(MycoNode a, MycoNode b) {
   if (graph.findEdge(a, b) == null) {
     MycoEdge edge = new MycoEdge();
     graph.addEdge(edge, a, b, EdgeType.DIRECTED);
   }
 }