/* Copyright (c) 2005 Stanford University and Christopher Bruns
 * 
 * Permission is hereby granted, free of charge, to any person obtaining
 * a copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including 
 * without limitation the rights to use, copy, modify, merge, publish, 
 * distribute, sublicense, and/or sell copies of the Software, and to
 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included 
 * in all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
 * CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 * TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 * SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

/*
 * Created on Dec 7, 2005
 * Original author: Christopher Bruns
 */
package org.simtk.isimsu;

import java.io.*;
import java.text.*;
import java.util.*;
import org.simtk.gui.*;

/**
 *  
  * @author Christopher Bruns
  * 
  * Combine RunAPBSThread and RunISIMThread into one
 */
public class SimulateIonsThread extends JarDefinedExecutableThread 
implements MonitoredProcess
{
    APBSParameters apbsParameters;
    ISIMStepParameters stepParameters;
    ISIMWrapper isimWrapper;

    // Constructor
    SimulateIonsThread(ISIMStepParameters s, APBSParameters p, ISIMWrapper isimWrapper) {
        stepParameters = s;
        apbsParameters = p;
        this.isimWrapper = isimWrapper;
    }

    public void run() {
        RunAPBSThread apbsThread = new RunAPBSThread(stepParameters, apbsParameters, isimWrapper);
        apbsThread.start();

        // And another process to monitor the process
        ProgressDialog progressDialog = isimWrapper.simulateRow;
        ProgressManager  progressManager = new ProgressManager(apbsThread, progressDialog);
        progressManager.start();

        try {
            apbsThread.join();
        } catch (InterruptedException exc) {return;}

        RunISIMThread isimThread = new RunISIMThread(stepParameters, apbsParameters, isimWrapper);
        isimThread.start();
        
        // And another process to monitor the process
        progressManager = new ProgressManager(isimThread, progressDialog);
        progressManager.start();
    }
    
}