//******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // 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.xray.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.numerics.Potential;
  import ffx.utilities.FFXBinding;
  import ffx.xray.parsers.MTZFilter;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.util.Collections;
  import java.util.List;
  
  /**
   * Use AverageMTZ to provide two MTZ files and an iteration for a cumulative moving average.
   * <br>
   * Usage:
   * <br>
   * ffxc xray.AverageMTZ &lt;filename1&gt; &lt;filename2&gt;
   */
  @Command(description = " Average two MTZ files.", name = "xray.AverageMTZ")
  public class AverageMTZ extends AlgorithmsCommand {
  
    /**
     * -i or --iteration the current moving average iteration
     */
    @Option(names = {"-i", "--iterations"}, paramLabel = "1",
        description = "The current moving average iteration (use 1 for a \"normal\" average of two files).")
    private int iteration = 1;
  
    /**
     * One or more filenames.
     */
    @Parameters(arity = "2", paramLabel = "MTZ", description = "Two diffraction input files.")
    private List<String> filenames;
  
    /**
     * AverageMTZ constructor.
     */
    public AverageMTZ() {
      super();
    }
  
    /**
     * AverageMTZ constructor that sets the command line arguments.
     *
     * @param args Command line arguments.
     */
    public AverageMTZ(String[] args) {
      super(args);
    }
  
    /**
     * AverageMTZ constructor.
     *
     * @param binding The Binding to use.
     */
    public AverageMTZ(FFXBinding binding) {
      super(binding);
    }
  
   @Override
   public AverageMTZ run() {
 
     if (!init()) {
       return this;
     }
 
     String mtzfile1;
     String mtzfile2;
 
     if (filenames != null && filenames.size() > 1) {
       // Read in command line.
       mtzfile1 = filenames.get(0);
       mtzfile2 = filenames.get(1);
     } else {
       logger.info(helpString());
       return this;
     }
 
     File file1 = new File(mtzfile1);
     if (!file1.exists()) {
       logger.info(mtzfile1 + " not found.");
       return this;
     }
 
     File file2 = new File(mtzfile2);
     if (!file2.exists()) {
       logger.info(mtzfile2 + " not found");
       return this;
     }
 
     MTZFilter mtzfilter = new MTZFilter();
     mtzfilter.averageFcs(file1, file2, mtzfilter.getReflectionList(file1), iteration, null);
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return Collections.emptyList();
   }
 }