// ******************************************************************************
   //
   // 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.utilities;
  
  import java.io.BufferedOutputStream;
  import java.io.File;
  import java.io.FileOutputStream;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.OutputStream;
  import java.nio.file.Files;
  import java.nio.file.Path;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.logging.Logger;
  import java.util.regex.Pattern;
  import java.util.stream.Collectors;
  import java.util.stream.Stream;
  
  import static java.io.File.createTempFile;
  import static java.lang.String.format;
  import static java.nio.file.Paths.get;
  
  /**
   * FileUtils class.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class FileUtils {
  
    private static final Logger logger = Logger.getLogger(FileUtils.class.getName());
  
    /**
     * Private constructor to prevent instantiation.
     */
    private FileUtils() {
      // Empty constructor.
    }
  
    /**
     * Returns the file name of a temporary copy of <code>input</code> content.
     *
     * @param input  The input stream contents are copied to a temporary file.
     * @param prefix Temporary file prefix.
     * @param name   Temporary file name.
     * @param suffix Temporary file suffix.
     * @return The temporary file.
     * @throws java.io.IOException An IOException is thrown if a temporary file could not be created.
     */
    public static String copyInputStreamToTmpFile(
        final InputStream input, String prefix, String name, final String suffix) throws IOException {
      File tmpFile = null;
  
      name = prefix + "." + name + ".";
      try {
        tmpFile = createTempFile(name, "." + suffix);
      } catch (IOException e) {
        System.out.printf(" Could not extract %s.%n", name);
        System.err.println(e.getMessage());
        System.exit(-1);
      }
      tmpFile.deleteOnExit();
 
     try (input;
          OutputStream output = new BufferedOutputStream(new FileOutputStream(tmpFile))) {
       byte[] buffer = new byte[8192];
       int size;
       while ((size = input.read(buffer)) != -1) {
         output.write(buffer, 0, size);
       }
     }
 
     return tmpFile.toString();
   }
 
   /**
    * Constructs a relative path from the present working directory to a file.
    *
    * @param file Construct a relative path to file.
    * @return Relative path to file.
    */
   public static Path relativePathTo(File file) {
     File pwd = new File(".");
     Path pwdPath = get(pwd.getAbsolutePath());
     Path otherPath = get(file.getAbsolutePath());
     return pwdPath.relativize(otherPath);
   }
 
   /**
    * Traverse a directory to find files matching the given regex pattern.
    *
    * @param directory   The directory to traverse.
    * @param maxDepth    Maximum depth to traverse.
    * @param filePattern Regular expression pattern to match file names.
    * @return List of matching files.
    */
   public static List<File> traverseFiles(File directory, int maxDepth, String filePattern) {
     List<File> matchingFiles = new ArrayList<>();
     Pattern pattern = Pattern.compile(filePattern);
 
     try (Stream<Path> paths = Files.walk(directory.toPath(), maxDepth)) {
       matchingFiles = paths
           .filter(Files::isRegularFile)
           .filter(path -> pattern.matcher(path.getFileName().toString()).matches())
           .map(Path::toFile)
           .collect(Collectors.toList());
     } catch (IOException e) {
       logger.warning(format("Error traversing directory %s: %s", directory.getAbsolutePath(), e.getMessage()));
     }
 
     return matchingFiles;
   }
 
   /**
    * Append content to a file.
    *
    * @param file    The file to append content to.
    * @param content The content to append.
    */
   public static void append(File file, String content) {
     try (FileWriter fw = new FileWriter(file, true)) {
       fw.write(content);
     } catch (IOException e) {
       logger.warning(format(" Error appending %s to file %s\n " + e.getMessage(), content, file.getAbsolutePath()));
     }
   }
 }