// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.ui;
  
  import ffx.potential.bonded.Atom;
  import ffx.ui.commands.FFXClient;
  import ffx.ui.commands.SimulationFilter;
  import ffx.ui.commands.SimulationUpdate;
  import ffx.utilities.Keyword;
  import java.awt.event.ActionEvent;
  import java.awt.event.ActionListener;
  import java.io.File;
  import java.net.InetSocketAddress;
  import java.util.List;
  import javax.swing.Timer;
  
  /**
   * This SimulationLoader class oversees loading information from an executing FFX instance program
   * this instance of Force Field X.
   *
   * @author Michael J. Schnieders
   */
  public class SimulationLoader implements ActionListener {
    // The client monitors a socket based connection to an executing TINKER
    // program.
  
    private FFXClient client;
    private SimulationFilter simulationFilter;
    private InetSocketAddress address;
    // If the TINKER program was launched from the GUI,
    // the job Thread will be alive until the program exits.
    private Thread job = null;
    // Once the simulation is finished, this flag will be true.
    private boolean finished = false;
    private MainPanel mainPanel;
    private FFXSystem system;
    private SimulationUpdate ffxUpdate = null;
    private boolean firstUpdate = true;
    private Timer timer;
    private double time = 0.0;
    private int step = 0;
  
    // Constructor
  
    /**
     * Constructor for SimulationLoader.
     *
     * @param s a {@link ffx.ui.FFXSystem} object.
     * @param j a {@link java.lang.Thread} object.
     * @param f a {@link ffx.ui.MainPanel} object.
     * @param a a {@link java.net.InetSocketAddress} object.
     */
    public SimulationLoader(FFXSystem s, Thread j, MainPanel f, InetSocketAddress a) {
      system = s;
      job = j;
      mainPanel = f;
      address = a;
      if (address == null) {
        finished = true;
      }
    }
  
    /** {@inheritDoc} */
    @Override
   public void actionPerformed(ActionEvent e) {
     // Check if we're connected to a TINKER Server.
     if (!connect()) {
       return;
     }
     // Check if we need to initialize the Simulation System.
     if (system == null) {
       ffx.ui.commands.SimulationDefinition sys = client.getSystem();
       if (sys != null) {
         if (simulationFilter == null) {
           if (system == null) {
             system =
                 new FFXSystem(new File("Simulation"), "Simulation", Keyword.loadProperties(null));
           }
           simulationFilter = new SimulationFilter(sys, system);
           UIFileOpener openFile = new UIFileOpener(simulationFilter, mainPanel);
           // The reader thread contains a SimulationFilter instance that will read a
           // simulation into the FFX.
           Thread reader = new Thread(openFile);
           reader.start();
         } else if (simulationFilter.fileRead()) {
           system = (FFXSystem) simulationFilter.getActiveMolecularSystem();
           simulationFilter = null;
         }
       }
     } // A Simulation System exists, attempt to Update it.
     else {
       if (ffxUpdate == null || ffxUpdate.read) {
         ffxUpdate = client.getUpdate();
       }
       if (ffxUpdate != null
           && !ffxUpdate.read
           && !mainPanel.getGraphics3D().isSceneRendering()) {
         update();
       }
     }
   }
 
   /**
    * isConnected
    *
    * @return a boolean.
    */
   public boolean isConnected() {
     return client != null && client.isConnected();
   }
 
   /** release */
   public void release() {
     finished = true;
     if (timer != null) {
       timer.stop();
     }
     if (client != null) {
       client.release();
     }
     mainPanel.getMainMenu().setConnect(true);
   }
 
   /**
    * connect
    *
    * @return a boolean.
    */
   boolean connect() {
     if (isFinished()) {
       return false;
     }
     if (isConnected()) {
       return true;
     }
     // Create a timer to regularly wake up this SimulationLoader.
     int delay = 10;
     if (timer == null) {
       timer = new Timer(delay, this);
       timer.setCoalesce(true);
       timer.setDelay(10);
       timer.start();
     }
     // Create the FFXClient to monitor messages to/from TINKER.
     if (client == null) {
       client = new FFXClient(address);
     }
     // Try to connect.
     client.connect();
     // If connected, change to our "steady-state" timer delay.
     if (client.isConnected()) {
       timer.setDelay(delay);
       return true;
     }
     // The FFXClient and the Timer are set up, but a TINKER simulation
     // has not responded yet. This connect method will be called again
     // through "actionPerformed" when
     // the timer wakes up.
     return false;
   }
 
   /**
    * getFSystem
    *
    * @return a {@link ffx.ui.FFXSystem} object.
    */
   FFXSystem getFSystem() {
     return system;
   }
 
   // Release the simulation
 
   /**
    * isFinished
    *
    * @return a boolean.
    */
   boolean isFinished() {
     if (client != null && client.isClosed()) {
       finished = true;
     }
     if (job != null && !job.isAlive()) {
       finished = true;
     }
     if (finished) {
       if (timer != null) {
         timer.stop();
       }
       update();
       release();
     }
     return finished;
   }
 
   private void update() {
     if (system.isStale()) {
       return;
     }
     if (ffxUpdate == null || ffxUpdate.read) {
       return;
     }
     // Sanity check - FFX and TINKER should agree on the number of atoms.
     List<Atom> atoms = system.getAtomList();
     int n = atoms.size();
     if (ffxUpdate.numatoms != n) {
       finished = true;
       return;
     }
     // This is either an MD Run.
     if (ffxUpdate.type == ffx.ui.commands.SimulationUpdate.SIMULATION) {
       if (ffxUpdate.time == time) {
         ffxUpdate.read = true;
         return;
       }
       time = ffxUpdate.time;
     } else if (ffxUpdate.type == ffx.ui.commands.SimulationUpdate.OPTIMIZATION) {
       if (ffxUpdate.step == step) {
         ffxUpdate.read = true;
         return;
       }
       step = ffxUpdate.step;
     }
     // Reset the Maximum Magnitude Values, such that they will be consistent
     // with this frame of the simulation after the update.
     double[] d = new double[3];
     for (Atom a : atoms) {
       int index = a.getIndex() - 1;
       d[0] = ffxUpdate.coordinates[0][index];
       d[1] = ffxUpdate.coordinates[1][index];
       d[2] = ffxUpdate.coordinates[2][index];
       a.moveTo(d);
     }
     if (firstUpdate) {
       system.center();
       firstUpdate = false;
     }
     mainPanel.getGraphics3D().updateScene(system, true, false, null, false, null);
     mainPanel.getHierarchy().updateStatus();
     mainPanel.getHierarchy().repaint();
     ffxUpdate.read = true;
     ffxUpdate = client.getUpdate();
   }
 }