private void simulatePropagation(Molecule molecule, FileWriter... writer) {
String newline = "";
long time = System.nanoTime();
long elapsed = 0;
double runStep = maxSimulationTime;
// boolean reachFlag = false;
boolean onRailFlag = false;
// double distance = distSendReciever!=0?distSendReciever:;
if (maxSimulationStep > 0) {
runStep = maxSimulationStep;
}
try {
Position curpos = molecule.getPosition();
if (probDrail != 0) {
if (!onRailFlag) {
for (MicroTubule mt : listOfMicroTubule) {
Position p = getInitPointOnMicrotubule(mt, curpos);
if (p != null) {
molecule.setCurrentMicrotubule(mt);
molecule.setPosition(p);
onRailFlag = true;
break;
}
}
}
}
while ((elapsed = (maxSimulationStep <= 0) ? (System.nanoTime() - time) : (elapsed + 1))
< (long) runStep) {
curpos = molecule.getPosition();
if (generateOutputFile) {
writer[1].write(newline + curpos.getX() + delim + curpos.getY() + delim + curpos.getZ());
newline = "\n";
}
if (hasReachDestination(curpos)) {
if (maxSimulationStep <= 0) {
molecule.setReachTime(System.nanoTime() - time);
} else {
molecule.setReachTime(elapsed);
}
molecule.setReachFlag(true);
break;
}
if (probDrail != 0) {
if (onRailFlag) {
if (hasDRailed()) {
onRailFlag = false;
System.out.println("off rail");
molecule.setCurrentMicrotubule(null);
Position newPos = new Position();
newPos.setX(
curpos.getX() + molecule.getStepLengthX() * steparr[(int) (Math.random() * 3)]);
newPos.setY(
curpos.getY() + molecule.getStepLengthY() * steparr[(int) (Math.random() * 3)]);
newPos.setZ(
curpos.getZ() + molecule.getStepLengthZ() * steparr[(int) (Math.random() * 3)]);
checkBoundary(newPos);
Position nextPos = checkRailPos(curpos, newPos, molecule);
if (nextPos != null) {
// distance = curpos.getDistance(reciever);
molecule.setPosition(nextPos);
onRailFlag = true;
System.out.println("On Rail");
} else {
molecule.setPosition(newPos);
}
} else {
Position plusend = molecule.getCurrentMicrotubule().getPlusEndCentre();
Position minusend = molecule.getCurrentMicrotubule().getMinusEndCentre();
Position newPos = new Position();
Position perp = new Position();
double x2 = plusend.getX();
double y2 = plusend.getY();
double z2 = plusend.getZ();
double x1 = minusend.getX();
double y1 = minusend.getY();
double z1 = minusend.getZ();
double d = curpos.getX();
double e = curpos.getY();
double f = curpos.getZ();
double t =
((x2 - d) * (x2 - x1) + (y2 - e) * (y2 - y1) + (z2 - f) * (z2 - z1))
/ ((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1) + (z2 - z1) * (z2 - z1));
perp.setX(d + (x2 - x1) * t);
perp.setY(e + (y2 - y1) * t);
perp.setZ(f + (z2 - z1) * t);
double distance = perp.getDistance(curpos);
curpos.setX(
(velRail * perp.getX() + (distance - velRail) * curpos.getX()) / distance);
curpos.setY(
(velRail * perp.getY() + (distance - velRail) * curpos.getY()) / distance);
curpos.setZ(
(velRail * perp.getZ() + (distance - velRail) * curpos.getZ()) / distance);
// System.out.println(curpos.getX()+","+curpos.getY()+","+curpos.getZ());
// molecule.setPosition(curpos);
}
} else {
Position newPos = new Position();
newPos.setX(
curpos.getX() + molecule.getStepLengthX() * steparr[(int) (Math.random() * 3)]);
newPos.setY(
curpos.getY() + molecule.getStepLengthY() * steparr[(int) (Math.random() * 3)]);
newPos.setZ(
curpos.getZ() + molecule.getStepLengthZ() * steparr[(int) (Math.random() * 3)]);
checkBoundary(newPos);
Position nextPos = checkRailPos(curpos, newPos, molecule);
if (nextPos != null) {
// distance = curpos.getDistance(reciever);
molecule.setPosition(nextPos);
onRailFlag = true;
System.out.println("Gets on Rail");
} else {
molecule.setPosition(newPos);
}
}
} else {
curpos.setX(
curpos.getX() + molecule.getStepLengthX() * steparr[(int) (Math.random() * 3)]);
curpos.setY(
curpos.getY() + molecule.getStepLengthY() * steparr[(int) (Math.random() * 3)]);
curpos.setZ(
curpos.getZ() + molecule.getStepLengthZ() * steparr[(int) (Math.random() * 3)]);
checkBoundary(curpos);
}
if (generateOutputFile) {
writer[1].flush();
}
}
if (generateOutputFile) {
writer[1].flush();
writer[1].close();
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (molecule.isReachFlag()) {
System.out.println(":) Hooray this molecule reached to destination");
try {
writer[0].write(molecule.getReachTime() + "\n");
writer[0].flush();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} else System.out.println(":( This molecule couldn't reach its destination");
}
