public static void drawImage(int[][][] pixels, int startX, int startY) {
// Key idea: draw a bunch (lots of rectangles) with the appropriate color
DrawObject R = new DrawObject();
R.pixels = pixels;
R.startX = startX;
R.startY = startY;
R.sequenceNum = currentSequenceNum;
images.add(R);
// Rescale if needed.
int leftX = startX;
int rightX = startX + pixels.length;
int lowY = startY;
int highY = startY + pixels[0].length;
if (minX > leftX) {
minX = leftX;
}
if (maxX < rightX) {
maxX = rightX;
}
if (minY > lowY) {
minY = lowY;
}
if (maxY < highY) {
maxY = highY;
}
drawArea.repaint();
}
static void handleMouseDragged(MouseEvent e) {
DrawObject L = new DrawObject();
L.scribbleX = e.getX();
L.scribbleY = e.getY();
L.scribbleNum = currentScribbleNum;
scribbles.add(L);
drawArea.repaint();
}
public static void drawLabel(double x, double y, String str) {
DrawObject L = new DrawObject();
L.color = labelColor;
L.x = x;
L.y = y;
L.str = str;
L.sequenceNum = currentSequenceNum;
if (animationMode) {
synchronized (animLabels) {
animLabels.add(L);
}
} else {
synchronized (labels) {
labels.add(L);
}
}
drawArea.repaint();
}
public static void drawPoint(double x, double y) {
DrawObject p = new DrawObject();
p.color = pointColor;
p.x = x;
p.y = y;
p.diameter = pointDiameter;
p.sequenceNum = currentSequenceNum;
if (animationMode) {
synchronized (animPoints) {
animPoints.add(p);
}
} else {
synchronized (points) {
points.add(p);
}
}
drawArea.repaint();
}
public static void drawRectangle(double x1, double y1, double width, double height) {
DrawObject R = new DrawObject();
R.color = rectangleColor;
R.x = x1;
R.y = y1;
R.width = width;
R.height = height;
R.sequenceNum = currentSequenceNum;
R.drawStroke = drawStroke;
if (animationMode) {
synchronized (animRectangles) {
animRectangles.add(R);
}
} else {
synchronized (rectangles) {
rectangles.add(R);
}
}
drawArea.repaint();
}
public static void animationPause(int pauseTime) {
if ((pauseTime < 1) || (pauseTime > 1000)) {
pauseTime = 100;
}
try {
Thread.sleep(pauseTime);
synchronized (animPoints) {
animPoints.clear();
}
synchronized (animLines) {
animLines.clear();
}
synchronized (animOvals) {
animOvals.clear();
}
synchronized (animRectangles) {
animRectangles.clear();
}
} catch (InterruptedException e) {
}
}
/**
* parses the segment string and initializes this segment properties
*
* @param segmentString the string representation of a segment
*/
protected void parseString(String segmentString) {
segmentString = segmentString.trim();
// whether the command is a relative one
boolean isRelative = isRelativeCommand(segmentString);
// getting the list of the points corresponding to the segment string
java.util.List<Point2D> pointsList =
getPoints(segmentString.substring(1, segmentString.length()));
if (pointsList.size() > 0) {
point = pointsList.get(0);
// if the segment is relative, it is transformed into an absolute one
if (isRelative && previousSegment != null) {
point = computeAbsolute(point, previousSegment.getEndPoint());
}
}
}
public static void drawLineFromEquation(double a, double b, double c) {
// Draw the equation ax+by+c=0 in the available range.
DrawObject L = new DrawObject();
L.color = lineEqnColor;
L.a = a;
L.b = b;
L.c = c;
L.sequenceNum = currentSequenceNum;
L.drawStroke = drawStroke;
synchronized (eqnLines) {
eqnLines.add(L);
}
drawArea.repaint();
}
void drawScribbles(Graphics g) {
if ((scribbles == null) || (scribbles.size() == 0)) {
return;
}
DrawObject L = (DrawObject) scribbles.get(0);
int scribbleCounter = L.scribbleNum;
g.setColor(scribbleColor);
((Graphics2D) g).setStroke(new BasicStroke(2f));
int prevX = L.scribbleX;
int prevY = L.scribbleY;
for (int i = 1; i < scribbles.size(); i++) {
L = (DrawObject) scribbles.get(i);
if (L.scribbleNum == scribbleCounter) {
// Keep drawing.
g.drawLine(prevX, prevY, L.scribbleX, L.scribbleY);
prevX = L.scribbleX;
prevY = L.scribbleY;
} else {
scribbleCounter = L.scribbleNum;
prevX = L.scribbleX;
prevY = L.scribbleY;
}
}
}
public static void drawLine(double x1, double y1, double x2, double y2, boolean isArrow) {
DrawObject L = new DrawObject();
L.color = lineColor;
L.x = x1;
L.y = y1;
L.x2 = x2;
L.y2 = y2;
if (isArrow) {
L.color = arrowColor;
L.isArrow = true;
}
L.sequenceNum = currentSequenceNum;
L.drawStroke = drawStroke;
if (animationMode) {
synchronized (animLines) {
animLines.add(L);
}
} else {
synchronized (lines) {
lines.add(L);
}
}
drawArea.repaint();
}
public void moveKnot(int index, double x, double y) {
java.util.List knotlist = getControlPoints();
knotlist.set(index, new Point2D.Double(x, y));
updateLookupTable();
}
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;
}
