static void removeFromLayers(Shape shape) {
if (!layerOf.containsKey(shape)) return;
int oldLayer = layerOf.get(shape);
layerContents.get(oldLayer).remove(shape);
if (layerContents.get(oldLayer).isEmpty()) {
layerContents.remove(oldLayer);
layers.remove((Integer) oldLayer);
}
layerOf.remove(shape);
}
/**
* Set the layer that a given shape will be displayed in. Since the shapes in this game are two
* dimensional, it must be decided which will appear "on top" when two shapes overlap. The shape
* in the higher layer will appear on top.
*
* <p>Setting a shape's layer will only affect how it is displayed; a shape's layer has no effect
* on how it interacts with other shapes. (For example, two shapes can touch even if they are in
* different layers. See {@link Shape#isTouching(Shape)}.)
*
* @param shape the shape whose layer is being set.
* @param layer the layer into which this shape will be moved.
*/
static void setLayer(Shape shape, int layer) {
removeFromLayers(shape);
// add new stuff
if (!layerContents.containsKey(layer)) {
layerContents.put(layer, new CopyOnWriteArrayList<Shape>());
int insertionPoint = ~Collections.binarySearch(layers, layer);
layers.add(insertionPoint, layer);
}
layerContents.get(layer).add(shape);
layerOf.put(shape, layer);
}
static void removeCounter(Counter counter) {
counters.remove(counter);
}
static void addCounter(Counter counter) {
counters.add(counter);
}
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;
}