Finally managed to read from rxtx in windows but now I just cannot make it work in Ubuntu.I get the rxtx libs using apt-get ,but when i run the application,i can not see anything,tried a couple of try-catch blocks and i don't even get the exceptions,and since Ubuntu based debugging is not possible for now, i can not pinpoint the problem. (Ubuntu is 12.04 64 bit).
import gnu.io.*;
import java.io.*;
import javax.swing.JOptionPane;
public class ReadComPort {
    public static void main(String[] s) {
        readcomport();
    }
    public static String readcomport() {
        String value = null;
        try {
            // CommPortIdentifier portIdentifier = CommPortIdentifier
            // .getPortIdentifier("COM1");
            // String comportidentifier = "COM1"; //*win
            String comportidentifier = "/dev/ttyS0";
            CommPortIdentifier portIdentifier = null;
            portIdentifier = CommPortIdentifier.getPortIdentifier(comportidentifier);
            if (portIdentifier.isCurrentlyOwned()) {
                JOptionPane.showMessageDialog(null, "port in use");
            } else {
                SerialPort serialPort = (SerialPort) portIdentifier.open("ReadComPort", 500);
                JOptionPane.showMessageDialog(null, serialPort.getBaudRate());
                serialPort.setSerialPortParams(serialPort.getBaudRate(), SerialPort.DATABITS_8, SerialPort.STOPBITS_1,
                        SerialPort.PARITY_NONE);
                // serialPort.setFlowControlMode(SerialPort.FLOWCONTROL_RTSCTS_IN | SerialPort.FLOWCONTROL_RTSCTS_OUT);
                serialPort.setDTR(true);
                serialPort.setRTS(true);
                InputStream mInputFromPort = serialPort.getInputStream();
                Thread.sleep(500);
                byte mBytesIn[] = new byte[32];
                mInputFromPort.read(mBytesIn);
                value = new String(mBytesIn);
                mInputFromPort.close();
                serialPort.close();
            }
        } catch (Exception ex) {
            JOptionPane.showMessageDialog(null, "Exception : " + ex.getMessage());
        }
        return value;
    }
}