// Create and start the thread
MyThread thread = new MyThread();
thread.start();

while (true) {
    // Do work

    // Pause the thread
    synchronized (thread) {
        thread.pleaseWait = true;
    }

    // Do work

    // Resume the thread
    synchronized (thread) {
        thread.pleaseWait = false;
        thread.notify();
    }

    // Do work
}

class MyThread extends Thread {
    boolean pleaseWait = false;

    // This method is called when the thread runs
    public void run() {
        while (true) {
            // Do work

            // Check if should wait
            synchronized (this) {
                while (pleaseWait) {
                    try {
                        wait();
                    } catch (Exception e) {
                    }
                }
            }

            // Do work
        }
    }
}