Serial Communication between java and Arduino

my goal is to send an input from the user using java and send it to the arduino via serial. But arduino isn't behaving like I want it to. I send the data and simply nothing happens! The arduino Rx led blinks when I input something indicating that it's reading, but I don't know why isn't it lighting up LED 13.

Java code:

import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.OutputStreamWriter;

import gnu.io.CommPortIdentifier; 
import gnu.io.PortInUseException;
import gnu.io.SerialPort;
import gnu.io.SerialPortEvent; 
import gnu.io.SerialPortEventListener; 
import java.util.Enumeration;
import java.util.Scanner;


public class SerialTest implements SerialPortEventListener {
	SerialPort serialPort;
        /** The port we're normally going to use. */
	private static final String PORT_NAMES[] = { 
			"/dev/tty.usbserial-A9007UX1", // Mac OS X
			"/dev/ttyUSB0", // Linux
			"COM7", // Windows
	};
	/**
	* A BufferedReader which will be fed by a InputStreamReader 
	* converting the bytes into characters 
	* making the displayed results codepage independent
	*/
	private DataInputStream input;
	/** The output stream to the port */
	private DataOutputStream output;
	/** Milliseconds to block while waiting for port open */
	private static final int TIME_OUT = 2000;
	/** Default bits per second for COM port. */
	private static final int DATA_RATE = 9600;

	public void initialize() {
		CommPortIdentifier portId = null;
		Enumeration portEnum = CommPortIdentifier.getPortIdentifiers();


		//First, Find an instance of serial port as set in PORT_NAMES.
		while (portEnum.hasMoreElements()) {
			CommPortIdentifier currPortId = (CommPortIdentifier) portEnum.nextElement();
			for (String portName : PORT_NAMES) {
				if (currPortId.getName().equals(portName)) {
					portId = currPortId;
					break;
				}
			}
		}
		if (portId == null) {
			System.out.println("Could not find COM port.");
			return;
		}

		try {
			// open serial port, and use class name for the appName.
			serialPort = (SerialPort) portId.open(this.getClass().getName(),
					TIME_OUT);

			// set port parameters
			serialPort.setSerialPortParams(DATA_RATE,
					SerialPort.DATABITS_8,
					SerialPort.STOPBITS_1,
					SerialPort.PARITY_NONE);
			
			input = new DataInputStream (serialPort.getInputStream());
			output = new DataOutputStream (serialPort.getOutputStream());
			
			serialPort.addEventListener(this);
			serialPort.notifyOnDataAvailable(true);
		}catch (Exception e) {
			System.err.println(e.toString());
		}
		
		while(true)
		{
			// open the streams
			System.out.print("Input something: ");
			Scanner sc = new Scanner(System.in);
			short x = sc.nextShort();
			System.out.println("short is " + x);

			//output = new OutputStreamWriter(serialPort.getOutputStream());*/
			byte upper = (byte) (x >> 8); //Get the upper 8 bits
			byte lower = (byte) (x & 0xFF); //Get the lower 8bits
			try{
			output.write(upper);
			output.write(lower);
			}
			catch(Exception ex)
			{}
			
			// add event listeners
		}
		}

	/**
	 * This should be called when you stop using the port.
	 * This will prevent port locking on platforms like Linux.
	 */
	public synchronized void close() {
		if (serialPort != null) {
			serialPort.removeEventListener();
			serialPort.close();
		}
	}

	/**
	 * Handle an event on the serial port. Read the data and print it.
	 */
	public synchronized void serialEvent(SerialPortEvent oEvent) {
		if (oEvent.getEventType() == SerialPortEvent.DATA_AVAILABLE) {
			try {
				int inputLine=input.read();
				System.out.println(inputLine);
			} catch (Exception e) {
				System.err.println(e.toString());
			}
		}
		// Ignore all the other eventTypes, but you should consider the other ones.
	}

	public static void main(String[] args) throws Exception {
		SerialTest main = new SerialTest();
		main.initialize();
	
		
	}
}

Arduino Code:

void setup(){
  Serial.begin(9600);
  pinMode(13,OUTPUT);
}

void loop(){
  if (Serial.available() > 0){
  byte upper = Serial.read();
  byte lower = Serial.read();
  int x = (upper<<8) | lower;
  if(x==1200){
    digitalWrite(13,HIGH);
  }
  else{
    digitalWrite(13,HIGH);
    delay(1000);
    digitalWrite(13,LOW);
    delay(1000);
  }
  }
}
  if (Serial.available() > 0){
  byte upper = Serial.read();
  byte lower = Serial.read();

If there is at least one byte, read both of them. Ummm, no.

i read somewhere on these forums to use this method, but before that I was simply using a switch case:

switch (inByte) {
    case '1':    
      digitalWrite(13, HIGH);
      break;
    case '2':    
        digitalWrite(13,HIGH);
        delay(1000);
        digitalWrite(13,LOW);
        delay(1000);
      break;

in both ways i got the same result.

I was able to send/receive data using rxtx serial lib and even upload sketch using stk500 protocol. Thouht i have problems with uploading from android as is has specific USB API