// ******************************************************************************
   //
   // 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.xray.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.Logger;
  
  /**
   * DiffractionFile class.
   *
   * @author Timothy D. Fenn
   * @since 1.0
   */
  public class DiffractionFile {
  
    private static final Logger logger = Logger.getLogger(DiffractionFile.class.getName());
  
    private final String fileName;
    private final double weight;
    private final boolean neutron;
    private final DiffractionFileFilter diffractionFilter;
  
    /**
     * read in a diffraction file, weight set to 1.0 and neutron value of false
     *
     * @param filename file name to read in
     */
    public DiffractionFile(String filename) {
      this(filename, 1.0, false);
    }
  
    /**
     * read in a diffraction file, neutron value set to false
     *
     * @param filename file name to read in
     * @param weight the weight of the data
     */
    public DiffractionFile(String filename, double weight) {
      this(filename, weight, false);
    }
  
    /**
     * read in a diffraction file
     *
     * @param filename file name to read in
     * @param weight the weight of the data
     * @param neutron if true, this is a neutron data set
     */
    public DiffractionFile(String filename, double weight, boolean neutron) {
      File tmp = new File(filename);
      if (!tmp.exists()) {
        logger.severe(" Data file: " + filename + " not found!");
      }
  
      if (isExtension(filename, "mtz")) {
        diffractionFilter = new MTZFilter();
      } else if (isExtension(filename, new String[] {"cif", "ent", "sf"})) {
       diffractionFilter = new CIFFilter();
     } else if (isExtension(filename, new String[] {"cns", "hkl"})) {
       diffractionFilter = new CNSFilter();
     } else {
       diffractionFilter = null;
     }
 
     if (diffractionFilter == null) {
       logger.severe(
           "input data file format not recognized!\n Please use an appropriate file extension: [MTZ: mtz] [CIF: cif, ent, sf] [CNS: cns, hkl] to identify your data file type!");
     }
 
     this.fileName = filename;
     this.weight = weight;
     this.neutron = neutron;
   }
 
   /**
    * read in a diffraction 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 DiffractionFile(MolecularAssembly[] assembly) {
     this(assembly[0], 1.0, false);
   }
 
   /**
    * Constructor for DiffractionFile.
    *
    * @param assembly an array of {@link ffx.potential.MolecularAssembly} objects.
    * @param weight a double.
    */
   public DiffractionFile(MolecularAssembly[] assembly, double weight) {
     this(assembly[0], weight, false);
   }
 
   /**
    * Constructor for DiffractionFile.
    *
    * @param assembly an array of {@link ffx.potential.MolecularAssembly} objects.
    * @param weight a double.
    * @param neutron a boolean.
    */
   public DiffractionFile(MolecularAssembly[] assembly, double weight, boolean neutron) {
     this(assembly[0], weight, neutron);
   }
 
   /**
    * read in a diffraction 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 DiffractionFile(MolecularAssembly assembly) {
     this(assembly, 1.0, false);
   }
 
   /**
    * read in a diffraction file based on the molecular assembly fileName, using a neutron value of
    * false
    *
    * @param assembly {@link ffx.potential.MolecularAssembly} from which a fileName will be
    *     determined
    * @param weight the weight of the data
    */
   public DiffractionFile(MolecularAssembly assembly, double weight) {
     this(assembly, weight, false);
   }
 
   /**
    * read in a diffraction 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
    * @param weight the weight of the data
    * @param neutron if true, this is a neutron data set
    */
   public DiffractionFile(MolecularAssembly assembly, double weight, boolean neutron) {
     String name = removeExtension(assembly.getFile().getPath());
 
     File tmp = new File(name + ".mtz");
     if (tmp.exists()) {
       // logger.info("\n Data file: " + tmp.getName());
       diffractionFilter = new MTZFilter();
     } else {
       tmp = new File(name + ".cif");
       if (tmp.exists()) {
         // logger.info("\n Data file: " + tmp.getName());
         diffractionFilter = new CIFFilter();
       } else {
         tmp = new File(name + ".ent");
         if (tmp.exists()) {
           // logger.info("\n Data file: " + tmp.getName());
           diffractionFilter = new CIFFilter();
         } else {
           tmp = new File(name + ".sf");
           if (tmp.exists()) {
             // logger.info("\n Data file: " + tmp.getName());
             diffractionFilter = new CIFFilter();
           } else {
             tmp = new File(name + ".cns");
             if (tmp.exists()) {
               // logger.info("\n Data file: " + tmp.getName());
               diffractionFilter = new CNSFilter();
             } else {
               tmp = new File(name + ".hkl");
               if (tmp.exists()) {
                 // logger.info("\n Data file: " + tmp.getName());
                 diffractionFilter = new CNSFilter();
               } else {
                 logger.severe("no input data found!");
                 diffractionFilter = null;
               }
             }
           }
         }
       }
     }
     String filenameHolder; // Compiler complains if I set this.fileName directly.
     try {
       Path filepath = Paths.get(tmp.getCanonicalPath());
       Path pwdPath = Paths.get(new File("").getCanonicalPath());
       filenameHolder = pwdPath.relativize(filepath).toString();
     } catch (IOException ex) {
       logger.warning(
           " Relative path to provided data file could not be resolved: using data file name instead.");
       filenameHolder = tmp.getName();
     }
     this.fileName = filenameHolder;
     this.weight = weight;
     this.neutron = neutron;
   }
 
   /**
    * getDiffractionfilter.
    *
    * @return the diffractionFilter
    */
   public DiffractionFileFilter getDiffractionfilter() {
     return diffractionFilter;
   }
 
   /**
    * getFilename.
    *
    * @return the fileName
    */
   public String getFilename() {
     return fileName;
   }
 
   /**
    * return the weight of this dataset
    *
    * @return weight wA
    */
   public double getWeight() {
     return weight;
   }
 
   /**
    * is this a neutron dataset?
    *
    * @return true if neutron
    */
   public boolean isNeutron() {
     return neutron;
   }
 }