// ******************************************************************************
   //
   // 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.utilities;
  
  import static java.lang.String.format;
  import static org.apache.commons.io.FilenameUtils.removeExtension;
  
  import java.io.File;
  import java.io.IOException;
  import java.util.Arrays;
  import java.util.Iterator;
  import java.util.Vector;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.apache.commons.configuration2.PropertiesConfiguration;
  import org.apache.commons.configuration2.SystemConfiguration;
  import org.apache.commons.configuration2.builder.FileBasedConfigurationBuilder;
  import org.apache.commons.configuration2.builder.fluent.Parameters;
  import org.apache.commons.configuration2.ex.ConfigurationException;
  
  /**
   * The Keyword class holds a single Force Field X keyword entry.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class Keyword {
  
    private static final Logger logger = Logger.getLogger(Keyword.class.getName());
    private final String keyword;
    private final Vector<String> data;
  
    /**
     * Constructor for Keyword.
     *
     * @param k a {@link java.lang.String} object.
     */
    public Keyword(String k) {
      keyword = k;
      data = new Vector<>();
    }
  
    /**
     * Constructor for Keyword.
     *
     * @param k a {@link java.lang.String} object.
     * @param entry a {@link java.lang.String} object.
     */
    public Keyword(String k, String entry) {
      this(k);
      data.add(entry);
    }
  
    /**
     * Constructor for Keyword.
     *
     * @param k a {@link java.lang.String} object.
     * @param entry an array of {@link java.lang.String} objects.
     */
    public Keyword(String k, String[] entry) {
      this(k);
      data.addAll(Arrays.asList(entry));
    }
 
   /**
    * This method sets up configuration properties in the following precedence * order:
    *
    * <p>1.) Structure specific properties (for example pdbname.properties)
    *
    * <p>2.) Java system properties a.) -Dkey=value from the Java command line b.)
    * System.setProperty("key","value") within Java code.
    *
    * <p>3.) User specific properties (~/.ffx/ffx.properties)
    *
    * <p>4.) System wide properties (file defined by environment variable FFX_PROPERTIES)
    *
    * <p>5.) Internal force field definition.
    *
    * @param file a {@link java.io.File} object.
    * @return a {@link org.apache.commons.configuration2.CompositeConfiguration} object.
    * @since 1.0
    */
   public static CompositeConfiguration loadProperties(File file) {
 
     // Command line options take precedence.
     CompositeConfiguration properties = new CompositeConfiguration();
 
     /*
      JVM system properties are read first.
      a.) -Dkey=value from the Java command line
      b.) System.setProperty("key","value") within Java code.
     */
     PropertiesConfiguration systemConfiguration = new PropertiesConfiguration();
     systemConfiguration.append(new SystemConfiguration());
     systemConfiguration.setHeader("JVM system properties (i.e. command line -Dkey=value pairs).");
     properties.addConfiguration(systemConfiguration);
 
     // Structure specific options are 2md.
     // -Dkey=file.key takes precedence over using the structure file name.
     if (properties.containsKey("key")) {
       String keyString = properties.getString("key");
       File keyFile = new File(keyString);
       if (keyFile.exists() && keyFile.canRead()) {
         try {
           FileBasedConfigurationBuilder<PropertiesConfiguration> builder =
               new FileBasedConfigurationBuilder<>(PropertiesConfiguration.class)
                   .configure(
                       new Parameters()
                           .properties()
                           .setFile(keyFile)
                           .setThrowExceptionOnMissing(true)
                           .setIncludesAllowed(false));
           PropertiesConfiguration propertyConfiguration = builder.getConfiguration();
           propertyConfiguration.setHeader(
               "Structure properties from (" + keyString + ").");
           properties.addConfiguration(propertyConfiguration);
           properties.addProperty("propertyFile", keyFile.getCanonicalPath());
         } catch (ConfigurationException | IOException e) {
           logger.log(Level.INFO, " Error loading {0}.", keyFile);
         }
       } else {
         logger.severe(
             format(" Keyword file supplied at the command line does not exist: %s.", keyString));
       }
     } else if (file != null) {
       String structureBasename = removeExtension(file.getAbsolutePath());
       String propertyFilename =
           (new File(structureBasename + ".properties").exists())
               ? structureBasename + ".properties"
               : (new File(structureBasename + ".prop").exists())
                   ? structureBasename + ".prop"
                   : (new File(structureBasename + ".key").exists())
                       ? structureBasename + ".key"
                       : null;
       if (propertyFilename != null) {
         File structurePropFile = new File(propertyFilename);
         if (structurePropFile.canRead()) {
           try {
             FileBasedConfigurationBuilder<PropertiesConfiguration> builder =
                 new FileBasedConfigurationBuilder<>(PropertiesConfiguration.class)
                     .configure(
                         new Parameters()
                             .properties()
                             .setFile(structurePropFile)
                             .setThrowExceptionOnMissing(true)
                             .setIncludesAllowed(false));
             PropertiesConfiguration propertyConfiguration = builder.getConfiguration();
             propertyConfiguration.setHeader(
                 "Structure properties from (" + propertyFilename + ").");
             properties.addConfiguration(propertyConfiguration);
             properties.addProperty("propertyFile", structurePropFile.getCanonicalPath());
           } catch (ConfigurationException | IOException e) {
             logger.log(Level.INFO, " Error loading {0}.", structureBasename);
           }
         }
       }
     }
 
     // User specific options are 3rd.
     String filename = System.getProperty("user.home") + File.separator + ".ffx/ffx.properties";
     File userPropFile = new File(filename);
     if (userPropFile.exists() && userPropFile.canRead()) {
       try {
         FileBasedConfigurationBuilder<PropertiesConfiguration> builder =
             new FileBasedConfigurationBuilder<>(PropertiesConfiguration.class)
                 .configure(
                     new Parameters()
                         .properties()
                         .setFile(userPropFile)
                         .setThrowExceptionOnMissing(true)
                         // .setListDelimiterHandler(new DefaultListDelimiterHandler(','))
                         .setIncludesAllowed(false));
         PropertiesConfiguration ffxConfiguration = builder.getConfiguration();
         ffxConfiguration.setHeader("FFX user property file (" + filename + ").");
         properties.addConfiguration(ffxConfiguration);
       } catch (ConfigurationException e) {
         logger.log(Level.INFO, " Error loading {0}.", filename);
       }
     }
 
     // System-wide options are 2nd to last.
     filename = System.getenv("FFX_PROPERTIES");
     if (filename != null) {
       File systemPropFile = new File(filename);
       if (systemPropFile.exists() && systemPropFile.canRead()) {
         try {
           FileBasedConfigurationBuilder<PropertiesConfiguration> builder =
               new FileBasedConfigurationBuilder<>(PropertiesConfiguration.class)
                   .configure(
                       new Parameters()
                           .properties()
                           .setFile(systemPropFile)
                           .setThrowExceptionOnMissing(true)
                           // .setListDelimiterHandler(new DefaultListDelimiterHandler(','))
                           .setIncludesAllowed(false));
           PropertiesConfiguration envConfiguration = builder.getConfiguration();
           envConfiguration.setHeader("Environment variable FFX_PROPERTIES (" + filename + ").");
           properties.addConfiguration(envConfiguration);
         } catch (ConfigurationException e) {
           logger.log(Level.INFO, " Error loading {0}.", filename);
         }
       }
     }
 
     // Echo the interpolated configuration.
     if (logger.isLoggable(Level.FINE)) {
       Iterator<String> i = properties.getKeys();
       StringBuilder sb = new StringBuilder();
       sb.append(format("\n %-30s %s\n", "Property", "Value"));
       while (i.hasNext()) {
         String s = i.next();
         sb.append(
             format(" %-30s %s\n", s, Arrays.toString(properties.getList(s).toArray())));
       }
       logger.fine(sb.toString());
     }
 
     return properties;
   }
 
   /**
    * append
    *
    * @param entry a {@link java.lang.String} object.
    */
   public void append(String entry) {
     data.add(entry);
   }
 
   /**
    * append
    *
    * @param entry an array of {@link java.lang.String} objects.
    */
   public void append(String[] entry) {
     data.addAll(Arrays.asList(entry));
   }
 
   /**
    * clear
    */
   public void clear() {
     data.clear();
   }
 
   /**
    * getEntries
    *
    * @return a {@link java.util.Vector} object.
    */
   public Vector<String> getEntries() {
     return data;
   }
 
   /**
    * getEntry
    *
    * @param i The index of the entry to return.
    * @return a {@link java.lang.String} object.
    */
   public String getEntry(int i) {
     return data.get(i);
   }
 
   /**
    * Getter for the field <code>keyword</code>.
    *
    * @return a {@link java.lang.String} object.
    */
   public String getKeyword() {
     return keyword;
   }
 
   /**
    * print
    */
   public void print() {
     logger.info(this.toString());
   }
 
   /** {@inheritDoc} */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder(keyword + " ");
     for (String s : data) {
       sb.append(s);
     }
     return sb.toString();
   }
 }