// ******************************************************************************
   //
   // 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.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.utilities.Keyword;
  import java.io.File;
  import java.io.Serial;
  import java.util.Hashtable;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.apache.commons.io.FilenameUtils;
  
  /**
   * The FFXSystem class contains extensions to the generic MolecularAssembly class.
   *
   * @author Michael J. Schnieders
   */
  public class FFXSystem extends MolecularAssembly {
  
    @Serial
    private static final long serialVersionUID = 1L;
  
    /** Constant <code>MultiScaleLevel=4</code> */
    public static final int MultiScaleLevel = 4;
    // Log file being used for modeling commands
    private File logFile;
    // Key file for this system
    private File keyFile;
    private Hashtable<String, Keyword> keywords = new Hashtable<String, Keyword>();
    private final CompositeConfiguration properties;
    private String commandDescription;
    // Archive
    private Trajectory trajectory = null;
    // Flag to indicate this System is being closed
    private boolean closing = false;
  
    /**
     * Constructor.
     *
     * @param file Coordinate file.
     * @param description Short description of the command that created this system.
     * @param properties Properties controlling operations on this system.
     */
    public FFXSystem(File file, String description, CompositeConfiguration properties) {
      super(FilenameUtils.getBaseName(file.getName()));
      setFile(file);
      commandDescription = description;
      this.properties = properties;
    }
  
    /**
     * addKeyword
     *
     * @param k a {@link ffx.utilities.Keyword} object.
     */
    public void addKeyword(Keyword k) {
      if (keywords.containsKey(k.getKeyword())) {
        return;
      }
      keywords.put(k.getKeyword(), k);
    }
  
    /** {@inheritDoc} */
   @Override
   public boolean destroy() {
     setClosing(true);
     return super.destroy();
   }
 
   /**
    * Getter for the field <code>keyFile</code>.
    *
    * @return a {@link java.io.File} object.
    */
   public File getKeyFile() {
     return keyFile;
   }
 
   /**
    * Setter for the field <code>keyFile</code>.
    *
    * @param f a {@link java.io.File} object.
    */
   public void setKeyFile(File f) {
     keyFile = f;
   }
 
   /**
    * getKeyword
    *
    * @param k a {@link java.lang.String} object.
    * @return a {@link ffx.utilities.Keyword} object.
    */
   public Keyword getKeyword(String k) {
     return keywords.get(k);
   }
 
   /**
    * Getter for the field <code>keywords</code>.
    *
    * @return a {@link java.util.Hashtable} object.
    */
   public Hashtable<String, Keyword> getKeywords() {
     return keywords;
   }
 
   /**
    * Setter for the field <code>keywords</code>.
    *
    * @param k a {@link java.util.Hashtable} object.
    */
   public void setKeywords(Hashtable<String, Keyword> k) {
     keywords = k;
   }
 
   /**
    * Getter for the field <code>logFile</code>.
    *
    * @return a {@link java.io.File} object.
    */
   public File getLogFile() {
     if (logFile == null) {
       if (getFile() == null) {
         return null;
       }
       String fileName = getFile().getName();
       int dot = fileName.lastIndexOf(".");
       fileName = fileName.subSequence(0, dot) + ".log";
       logFile = new File(fileName);
     }
     return logFile;
   }
 
   /**
    * Setter for the field <code>logFile</code>.
    *
    * @param f a {@link java.io.File} object.
    */
   public void setLogFile(File f) {
     logFile = f;
   }
 
   /**
    * Getter for the field <code>properties</code>.
    *
    * @return a {@link org.apache.commons.configuration2.CompositeConfiguration} object.
    */
   @Override
   public CompositeConfiguration getProperties() {
     return properties;
   }
 
   /**
    * Getter for the field <code>trajectory</code>.
    *
    * @return a {@link ffx.ui.Trajectory} object.
    */
   public Trajectory getTrajectory() {
     return trajectory;
   }
 
   /**
    * Setter for the field <code>trajectory</code>.
    *
    * @param t a {@link ffx.ui.Trajectory} object.
    */
   public void setTrajectory(Trajectory t) {
     trajectory = t;
   }
 
   /**
    * isClosing
    *
    * @return a boolean.
    */
   public boolean isClosing() {
     return closing;
   }
 
   /**
    * Setter for the field <code>closing</code>.
    *
    * @param b a boolean.
    */
   public void setClosing(boolean b) {
     closing = b;
   }
 
   /**
    * isStale
    *
    * @return a boolean.
    */
   public boolean isStale() {
     for (Atom a : getAtomList()) {
       if (a.isStale()) {
         return true;
       }
     }
     return false;
   }
 
   /**
    * removeKeyword
    *
    * @param kd a {@link ffx.utilities.Keyword} object.
    */
   public void removeKeyword(Keyword kd) {
     if (keywords.containsKey(kd.getKeyword())) {
       keywords.remove(kd.getKeyword());
     }
   }
 
   /**
    * Setter for the field <code>commandDescription</code>.
    *
    * @param command a {@link java.lang.String} object.
    */
   public void setCommandDescription(String command) {
     commandDescription = command;
   }
 
   /**
    * toFFString
    *
    * @return a {@link java.lang.String} object.
    */
   public String toFFString() {
     StringBuilder sb = new StringBuilder(toString());
     if (forceField != null) {
       String ff = forceField.toString("forcefield");
       if (ff != null) {
         ff = ff.substring(10).trim();
         sb.append(" (");
         sb.append(ff);
         sb.append(")");
       }
     }
     return sb.toString();
   }
 
   /**
    * toFileString
    *
    * @return a {@link java.lang.String} object.
    */
   public String toFileString() {
     if (getFile() == null) {
       return toFFString();
     }
     StringBuilder sb = new StringBuilder(getFile().getAbsolutePath());
     if (forceField != null) {
       String ff = forceField.toString("forcefield");
       if (ff != null) {
         ff = ff.substring(10).trim();
         sb.append(" (");
         sb.append(ff);
         sb.append(")");
       }
     }
     return sb.toString();
   }
 
   /** {@inheritDoc} */
   @Override
   public String toString() {
     if (getFile() != null) {
       if (commandDescription != null) {
         return getFile().getName() + " (" + commandDescription + ")";
       }
       return getFile().getName();
     }
     if (getName() != null) {
       if (commandDescription != null) {
         return getName() + commandDescription;
       }
       return getName();
     }
     return "FFX System";
   }
 }