JSSC & Netbeans & lubuntu

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Linux

I have made an app, that when you click a button, it scans for the serial ports, and tries to connect to each one that contains the string:

"/dev/ttyACM"+i

I am trying to find out to whic port my arduino is connected to. after that I send a byte to it, and wait another byte in response, that way I know it is my arduino.
After that, I turn on/off a led after 1 second, making it blink.
It detects when the arduino is disconnected and starts scanning the ports again, the problem I'm having, is that even though I reconnect the arduino and I know to which port it is connected to, the java app just wont reconnect to the arduino.
Here is my code:

package serialscan;

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
//package TestBatery001;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JLabel;
import javax.swing.JProgressBar;
//import jPicUsb.*;
import java.awt.Color;
import java.awt.Graphics2D;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.concurrent.TimeUnit;
import javax.swing.JTextField;
import javax.swing.Painter;
import javax.swing.UIDefaults;
import javax.swing.UIManager;
import javax.swing.plaf.basic.BasicProgressBarUI;
//import Serialio.*;
import jssc.SerialPort;
import jssc.SerialPortEvent;
import jssc.SerialPortException;
import jssc.SerialPortList;

/**
 *
 * @author Faster
 */
public class Barra extends Thread {

    JLabel com;
    int i = 0;
    SerialPort port;
    byte inBytes;
    boolean state = false;
    String puerto;
    String[] puertos;

    public Barra(JLabel com) throws Exception {

        this.com = com;

    }

    public void run() {
        while (true) {
            try {
                puertos = SerialPortList.getPortNames();
            } catch (Exception ex) {
            }
            if (state == false) {
                chequeo();//Revisa los puertos, si ya se conecto, solo se ejecuta esa vez, hasta que se desconecte el aparato
            } else {        //en ese caso, debe volver a escanear los otros puertos.
                if (port.isOpened()) {
                    try {                        
                        port.writeByte((byte) 49);
                        TimeUnit.SECONDS.sleep(1);
                        port.writeByte((byte) 48);
                        TimeUnit.SECONDS.sleep(1);
                        try{
                            if(!puertos[i].contains(puerto)){
                                port.closePort();
                                state=false;
                                i++;
                            }                                                            
                        }catch(Exception ex){state=false;
                        //i++;
                        }
                        System.out.println("entro al ciclo on/off");
                    } catch (SerialPortException ex) {
                        Logger.getLogger(Barra.class.getName()).log(Level.SEVERE, null, ex);
                    } catch (InterruptedException ex) {
                        Logger.getLogger(Barra.class.getName()).log(Level.SEVERE, null, ex);
                    }
                } else {
                    state = false;
                }
            }

        }
    }

    protected byte getByte() throws jssc.SerialPortException {
        try{
            while (port.getInputBufferBytesCount() < 1) {
                try {
                    Thread.sleep(1);
                    if (Thread.currentThread().isInterrupted()) {
                        return 0;
                    }
                } catch (InterruptedException e) {
                    Thread.currentThread().interrupt();
                    return 0;
                }
            }    
            return (byte) (port.readBytes(1))[0];
        }catch(Exception ex){state=false;}return 0;
}
        
    

    public void chequeo() {
        //String puerto = "/dev/ttyACM" + i;            
        puerto = "/dev/ttyACM" + (i);
        port = new SerialPort(puerto);
        System.setProperty("JSSC_NO_TIOCEXCL", "");
        try {
            if (!port.isOpened()) {
                port.openPort();
                TimeUnit.SECONDS.sleep(10);
                port.writeByte((byte) 1);
                inBytes = getByte();
                //Read
                System.out.println("1. port " + puerto + " is opened");
            }
        } catch (Exception ex) {
            //i++;
            System.out.println("serialexception");           
        }

        if (!port.isOpened()) {
            i++;
            try {
                try{
                port.closePort();
                }catch(Exception ex){state=false;
                }
                System.out.println("3. port " + puerto + " is not opened! NOT ARDUINO");
                System.out.println("b " + getByte());
            } catch (SerialPortException ex) {
                Logger.getLogger(Barra.class.getName()).log(Level.SEVERE, null, ex);
            }
            System.out.println("2. port " + puerto + " is not opened!");
            if (i == 10) {
                i = 0;
            }
        } else if (port.isOpened()) {
            //TimeUnit.SECONDS.sleep(10);
            if (inBytes == (byte) 1) {
                System.out.println("arduino");
                System.out.println("2. port " + puerto + " is opened!");
                state = true;
                try {
                    System.out.println("byte " + getByte());
                } catch (SerialPortException ex) {
                    Logger.getLogger(Barra.class.getName()).log(Level.SEVERE, null, ex);
                }

            }

        }
    }
}

That is the code for the thread and that is what does all the process.
Can someone please help me fix this?
I really need my app to reconnect to the arduino, once it is reconnected to the computer.
Thanks!