public class Runner implements Runnable {

	 private boolean timeToQuit=false;

	 public void run() {
		 while ( ! timeToQuit ) {
			 ...
		 }
	 	
		// clean up before run() ends
	 }

	 public void stopRunning() {
		 timeToQuit=true;
	 }
  }

  public class ThreadController {
	 private Runner r = new Runner();
	 private Thread t = new Thread(r);

	 public void startThread() {
		 t.start();
	 }

	 public void stopThread() {
		 // use specific instance of Runner
		 r.stopRunning();
	 }
 }