// ******************************************************************************
   //
   // 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.potential.parsers;
  
  import ffx.utilities.Keyword;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.FileReader;
  import java.io.IOException;
  import java.util.Hashtable;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static java.lang.Integer.parseInt;
  
  /**
   * The KeyFilter class parses Force Field X Keyword (*.KEY) and Property (*.PROPERTIES) files.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class KeyFilter {
  
    private static final Logger logger = Logger.getLogger(KeyFilter.class.getName());
  
    /** Constructor for KeyFilter. */
    public KeyFilter() {
    }
  
    /**
     * open
     *
     * @param keyFile a {@link java.io.File} object.
     * @return a {@link java.util.Hashtable} object.
     */
    public static Hashtable<String, Keyword> open(File keyFile) {
      if (keyFile == null || !keyFile.exists() || !keyFile.canRead()) {
        return null;
      }
      Hashtable<String, Keyword> keywordHash = loadSystemKeywords();
      return open(keyFile, keywordHash);
    }
  
    /**
     * open
     *
     * @param keyFile a {@link java.io.File} object.
     * @param keywordHash a {@link java.util.Hashtable} object.
     * @return a {@link java.util.Hashtable} object.
     */
    public static Hashtable<String, Keyword> open(
        File keyFile, Hashtable<String, Keyword> keywordHash) {
      if (keyFile == null || !keyFile.exists() || !keyFile.canRead()) {
        return null;
      }
      if (keywordHash == null) {
        keywordHash = new Hashtable<>();
      }
      try (BufferedReader br = new BufferedReader(new FileReader(keyFile))) {
        Keyword comments = new Keyword("COMMENTS");
        keywordHash.put("COMMENTS", comments);
        while (br.ready()) {
          String s = br.readLine();
         if (s == null) {
           continue;
         }
         s = s.trim();
         if (s.isEmpty()) {
           continue; // Skip blank lines
         }
         // Store comments together
         if (s.startsWith("#") || s.toUpperCase().startsWith("ECHO")) {
           comments.append(s);
         } else {
           int firstSpace = s.indexOf(" ");
           String keyword, data;
           if (firstSpace == -1) { // no parameters
             keyword = s.trim().toUpperCase();
             // Rattle is special case, because it can be active
             // without being checked
             // Valid Key files can have: RATTLE
             // or RATTLE BONDS
             // or RATTLE & RATTLE BONDS as separate lines
             // Each of these valid cases mean different things...
             if (keyword.equalsIgnoreCase("rattle")) {
               data = "RATTLE";
             } else {
               data = null;
             }
           } else {
             keyword = s.substring(0, firstSpace).toUpperCase();
             data = s.substring(firstSpace).trim();
           }
           Keyword kd = keywordHash.get(keyword);
           if (kd == null) {
             kd = new Keyword(keyword);
             keywordHash.put(keyword, kd);
           }
           if (data != null) {
             kd.append(data);
           }
           /*
            Multipoles and TORTORS are the only keywords that span
            multiple lines. Editing these from within Force Field X
            seems unlikely, so they are treated as comments.
           */
           if (keyword.equalsIgnoreCase("MULTIPOLE")) {
             int[] mnum = {3, 1, 2, 3};
             for (int i = 0; i < 4; i++) {
               if (!br.ready()) {
                 System.out.println("Check for an invalid MULTIPOLE keyword.");
                 return null;
               }
               s = br.readLine();
               if (s == null) {
                 logger.warning("Multipole format error.");
                 return null;
               }
               s = s.trim();
               if (s.split(" +").length != mnum[i]) {
                 logger.warning("Multipole format error.");
                 return null;
               }
               kd.append(s);
             }
           } else if (keyword.equalsIgnoreCase("TORTORS")) {
             String[] res = data.split(" +");
             if (res.length < 7) {
               logger.warning("TORTOR format error.");
               return null;
             }
             int xres = parseInt(res[5]);
             int yres = parseInt(res[6]);
             for (int i = 0; i < xres * yres; i++) {
               if (!br.ready()) {
                 System.out.println("Check for an invalid TORTOR keyword.");
                 return null;
               }
               s = br.readLine();
               if (s == null) {
                 logger.warning("TORTOR format error.");
                 return null;
               }
               s = s.trim();
               if (s.split(" +").length != 3) {
                 logger.warning("TORTOR format error.");
                 return null;
               }
               kd.append(s);
             }
           }
         }
       }
       return keywordHash;
     } catch (IOException e) {
       System.err.println("Error reading Key File: " + e);
       return null;
     }
   }
 
   /**
    * loadSystemKeywords
    *
    * @return a {@link java.util.Hashtable} object.
    */
   private static Hashtable<String, Keyword> loadSystemKeywords() {
     File f = new File("/etc/ffx.conf");
     Hashtable<String, Keyword> systemKeywords = new Hashtable<>();
     if (f.exists() && f.canRead()) {
       logger.info("Reading /etc/ffx.conf");
       systemKeywords = KeyFilter.open(f, systemKeywords);
     }
     String path = System.getProperty("user.home") + File.separator + ".ffx/ffx.conf";
     f = new File(path);
     if (f.exists() && f.canRead()) {
       logger.log(Level.INFO, "Reading {0}", path);
       systemKeywords = KeyFilter.open(f, systemKeywords);
     }
     return systemKeywords;
   }
 }