Java - programa parace corriendo aun despues de haber terminado

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package com.mps.dao;

import com.mps.modelo.Aplicacion;

import com.mps.modelo.Menu;

import com.mps.modelo.PerfilPrograma;

import com.mps.modelo.Programa;

import java.util.ArrayList;

import java.util.Collection;

import java.util.LinkedHashSet;

import java.util.Set;

import javax.swing.JOptionPane;

import org.hibernate.Criteria;

import org.hibernate.Hibernate;

import org.hibernate.Query;

import org.hibernate.Session;

import org.hibernate.SessionFactory;

import org.hibernate.Transaction;

import org.hibernate.criterion.Restrictions;

/**

 *

 * @author MMENDINUETA

 */

public class MenuDao implements InterfaceMenu {

    private ArrayList<Aplicacion> lstAplicacion = new ArrayList();

    private ArrayList<PerfilPrograma> lstPerfilPrograma = new ArrayList();

    private ArrayList<Menu> lstMenu = new ArrayList();

    private ArrayList<Programa> lstPrograma = new ArrayList();

    public MenuDao() {setMenuAcordeon();

    }

    public ArrayList<Aplicacion> getLstAplicacion() {

        return lstAplicacion;

    }

    public ArrayList<PerfilPrograma> getLstPerfilPrograma() {

        return lstPerfilPrograma;

    }

    public ArrayList<Menu> getLstMenu() {

        return lstMenu;

    }

    public ArrayList<Programa> getLstPrograma() {

        return lstPrograma;

    }

    @Override

    public ArrayList<Menu> lista() {

        SessionFactory sessionFactory = HibernateUtil.getSessionFactory();

        Session session = sessionFactory.openSession();

        Transaction tx;

        ArrayList<Menu> lista = new ArrayList();

        tx = session.beginTransaction();

        String sqlString = new String();

        sqlString = "SELECT NEW com.mps.modelo.Menu(f.menuId,f.menuNombre,f.menuOrden,f.programas) FROM Menu f  ";

        Query cmdSql = session.createQuery(sqlString);

        // Query cmdSql = session.createQuery("From Menu f inner join fetch f.programas");

        //cmdSql.setParameter("codigo","100");

        lista.addAll(cmdSql.list());

        tx.commit();

        session.close();

        sessionFactory.close();

        return lista;

    }

    @Override

    public void setMenuAcordeon() {

        SessionFactory sessionFactory =  HibernateUtil.getSessionFactory();

        Session session = sessionFactory.openSession();

        Transaction tx = session.beginTransaction();

        Integer codigoAplicacion = 2;

        Integer codigoPerfil = 1;

        String cmdSql = new String();

        ///

        cmdSql = "Select prfprg "

                + "FROM PerfilPrograma prfprg "

                + "LEFT JOIN  prfprg.programa prg "

                + "LEFT JOIN  prfprg.programa.menu mnu "

                + "LEFT JOIN  prfprg.programa.aplicacion apl "

                + "LEFT JOIN  prfprg.perfil prf "

                + "Where apl.aplicacionId=:codigoAplicacion and prf.perfilId=:codigoPerfil "

                + "Order By apl.aplicacionOrden,mnu.menuOrden,prfprg.perfilProgramaOrden ";

        Query jQuery = session.createQuery(cmdSql);

        jQuery.setParameter("codigoAplicacion", codigoAplicacion);

        jQuery.setParameter("codigoPerfil", codigoPerfil);

        if (lstPerfilPrograma == null || lstPerfilPrograma.size()==0) {

            lstPerfilPrograma.addAll(jQuery.list());

            for (PerfilPrograma prf : lstPerfilPrograma) {

                if (!Hibernate.isInitialized(prf.getPrograma())) {

                    Hibernate.initialize(prf.getPrograma());

                }

                lstPrograma.add(prf.getPrograma()); //Llenamos los programas de la opcion del menu

                if (!Hibernate.isInitialized(prf.getPrograma().getMenu())){

                    Hibernate.initialize(prf.getPrograma().getMenu());

                }

                lstMenu.add(prf.getPrograma().getMenu()); //Llenamos el menu

                if (!Hibernate.isInitialized(prf.getPrograma().getAplicacion())){

                    Hibernate.initialize(prf.getPrograma().getAplicacion());

                }

                lstAplicacion.add(prf.getPrograma().getAplicacion()); //Llenamos la aplicacion

            }

            /*Borramos las aplicaciones que estan repetidas */

            Set<Aplicacion> apl_new = new LinkedHashSet<Aplicacion>(lstAplicacion);

            lstAplicacion.clear();

            lstAplicacion.addAll(apl_new);

            /*Borramos las opciones del menu que estan repetidas */

            Set<Menu> mnu_new = new LinkedHashSet<Menu>(lstMenu);

            lstMenu.clear();

            lstMenu.addAll(mnu_new);

            //

        }

        tx.commit();

        session.close();

        sessionFactory.close();

    }

}

/*

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package com.mps.dao;

/*

 * To change this license header, choose License Headers in Project Properties.

 * To change this template file, choose Tools | Templates

 * and open the template in the editor.

 */

import org.hibernate.HibernateException;

import org.hibernate.SessionFactory;

import org.hibernate.boot.registry.StandardServiceRegistry;

import org.hibernate.boot.registry.StandardServiceRegistryBuilder;

import org.hibernate.cfg.Configuration;

import org.hibernate.service.ServiceRegistry;

public class HibernateUtil {

private static SessionFactory sessionFactory;

    public static SessionFactory getSessionFactory() {

        try {

            if (sessionFactory == null) {

                //Configuration configuration = new Configuration().configure(HibernateUtil.class.getResource("/hibernate.cfg.xml"));

                Configuration configuration = new Configuration().configure();

                ServiceRegistry serviceRegistry = new StandardServiceRegistryBuilder().applySettings(configuration.getProperties()).build();

                //StandardServiceRegistry serviceRegistry = new StandardServiceRegistryBuilder().applySettings(configuration.getProperties()).build();

                sessionFactory = configuration.buildSessionFactory(serviceRegistry);

            }

        } catch (HibernateException he) {

            //System.err.println("Error creating Session: " + he);

            throw new ExceptionInInitializerError("Error al crear la session "+ he);

        }

        return sessionFactory;

    }

    public static void closeSessionFactory() {

        sessionFactory.close();

    }

}