// ******************************************************************************
   //
   // 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.realspace.parsers;
  
  import static org.apache.commons.io.FilenameUtils.isExtension;
  import static org.apache.commons.io.FilenameUtils.removeExtension;
  
  import ffx.potential.MolecularAssembly;
  import java.io.File;
  import java.io.IOException;
  import java.nio.file.Path;
  import java.nio.file.Paths;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * RealSpaceFile class.
   *
   * @author Timothy D. Fenn
   * @since 1.0
   */
  public class RealSpaceFile {
  
    private static final Logger logger = Logger.getLogger(RealSpaceFile.class.getName());
  
    private final String filename;
    private final double weight;
    private final RealSpaceFileFilter realSpaceFileFilter;
  
    /**
     * Read in a Real Space density file and set weight set to 1.0.
     *
     * @param filename file name to read in
     */
    public RealSpaceFile(String filename) {
      this(filename, 1.0);
    }
  
    /**
     * Read in a Real Space density file.
     *
     * @param fileName file name to read in
     * @param weight the weight of the data
     */
    public RealSpaceFile(String fileName, double weight) {
      File tmp = new File(fileName);
      if (!tmp.exists()) {
        logger.severe(" Data file: " + fileName + " not found!");
      }
  
      if (isExtension(fileName, "map")) {
        realSpaceFileFilter = new CCP4MapFilter();
      } else {
        realSpaceFileFilter = null;
      }
  
      this.filename = fileName;
      this.weight = weight;
    }
  
    /**
     * Read in a Real Space density file based on the molecular assembly filename, using a weight of
     * 1.0 and neutron value of false.
     *
    * @param assembly {@link ffx.potential.MolecularAssembly} from which a filename will be
    *     determined.
    */
   public RealSpaceFile(MolecularAssembly[] assembly) {
     this(assembly[0], 1.0);
   }
 
   /**
    * Read in a Real Space density file based on the molecular assembly filename, using a weight of
    * 1.0.
    *
    * @param assembly {@link ffx.potential.MolecularAssembly} from which a filename will be
    *     determined.
    */
   public RealSpaceFile(MolecularAssembly assembly) {
     this(assembly, 1.0);
   }
 
   /**
    * Read in a Real Space density file based on the molecular assembly filename, using a weight of
    * 1.0.
    *
    * @param assembly {@link ffx.potential.MolecularAssembly} from which a filename will be
    *     determined
    * @param weight the weight of the data
    */
   public RealSpaceFile(MolecularAssembly assembly, double weight) {
     String name = removeExtension(assembly.getFile().getPath());
 
     File tmp = new File(name + ".map");
     if (tmp.exists()) {
       logger.info(" Data file: " + tmp.getName());
       realSpaceFileFilter = new CCP4MapFilter();
     } else {
       logger.severe(" No input data was found.");
       realSpaceFileFilter = null;
     }
 
     String filenameHolder;
     try {
       Path filePath = Paths.get(tmp.getCanonicalPath());
       Path pwdPath = Paths.get(new File("").getCanonicalPath());
       filenameHolder = pwdPath.relativize(filePath).toString();
     } catch (IOException e) {
       String message =
           " Relative path to provided data file could not be resolved: using map file name instead.";
       logger.log(Level.WARNING, message, e);
       filenameHolder = tmp.getName();
     }
     this.filename = filenameHolder;
     this.weight = weight;
   }
 
   /**
    * Getter for the field <code>filename</code>.
    *
    * @return the filename
    */
   public String getFilename() {
     return filename;
   }
 
   /**
    * Getter for the field <code>realSpaceFileFilter</code>.
    *
    * @return the realSpaceFileFilter
    */
   public RealSpaceFileFilter getRealSpaceFileFilter() {
     return realSpaceFileFilter;
   }
 
   /**
    * Return the weight of this dataset.
    *
    * @return weight The weight (wA).
    */
   public double getWeight() {
     return weight;
   }
 }