// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2023.
   //
   // 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.algorithms.thermodynamics;
  
  import static java.lang.Boolean.parseBoolean;
  import static java.lang.Double.parseDouble;
  import static java.lang.Integer.parseInt;
  import static java.lang.String.format;
  
  import ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram;
  
  import javax.annotation.Nullable;
  import java.io.BufferedReader;
  import java.io.IOException;
  import java.io.Reader;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * Read in the Histogram.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class HistogramReader extends BufferedReader {
  
    private static final Logger logger = Logger.getLogger(HistogramReader.class.getName());
    /** Private reference to the Histogram instance, if any. */
    private final Histogram histogram;
  
    private double temperature;
    private double thetaMass;
    private double thetaFriction;
    private double biasMag;
    private int biasCutoff;
    private int countInterval;
    private int lambdaBins;
    private int dUdLBins;
    private double mindUdL;
    private double dUdLBinWidth;
    private double[][] counts;
    private boolean metaDynamics = false;
  
    public HistogramReader(Reader reader) {
      this(null, reader);
    }
  
    /**
     * Constructor.
     *
     * @param histogram The Histogram instance.
     * @param reader The Reader to use.
     */
    public HistogramReader(@Nullable Histogram histogram, Reader reader) {
      super(reader);
      this.histogram = histogram;
    }
  
    public int getBiasCutoff() {
      return biasCutoff;
    }
  
    public double getBiasMag() {
      return biasMag;
   }
 
   public int getCountInterval() {
     return countInterval;
   }
 
   public double getdUdLBinWidth() {
     return dUdLBinWidth;
   }
 
   public int getLambdaBins() {
     return lambdaBins;
   }
 
   public double getTemperature() {
     return temperature;
   }
 
   public double getThetaFriction() {
     return thetaFriction;
   }
 
   public double getThetaMass() {
     return thetaMass;
   }
 
   /** Read the histogram file. */
   public void readHistogramFile() {
     try {
       temperature = parseDouble(readLine().split(" +")[1]);
       thetaMass = parseDouble(readLine().split(" +")[1]);
       thetaFriction = parseDouble(readLine().split(" +")[1]);
       biasMag = parseDouble(readLine().split(" +")[1]);
       biasCutoff = parseInt(readLine().split(" +")[1]);
       countInterval = parseInt(readLine().split(" +")[1]);
       lambdaBins = parseInt(readLine().split(" +")[1]);
       dUdLBins = parseInt(readLine().split(" +")[1]);
       mindUdL = parseDouble(readLine().split(" +")[1]);
       dUdLBinWidth = parseDouble(readLine().split(" +")[1]);
       counts = new double[lambdaBins][dUdLBins];
       int i = 0;
       String[] toks = readLine().split(" +");
       if (toks.length == 2) {
         // Read the flag for the metadynamics.
         metaDynamics = parseBoolean(toks[1]);
       } else {
         // Read the first line of the histogram.
         for (int j = 0; j < dUdLBins; j++) {
           counts[i][j] = parseDouble(toks[j]);
         }
         i++;
       }
 
       for (; i < lambdaBins; i++) {
         String[] countToks = readLine().split(" +");
         for (int j = 0; j < dUdLBins; j++) {
           counts[i][j] = parseDouble(countToks[j]);
         }
       }
 
       if (histogram != null) {
         histogram.dUdLBins = dUdLBins;
         histogram.mindUdL = mindUdL;
         // Allocate memory for the recursion kernel.
         histogram.allocateRecursionKernel();
         // Set the recursion kernel.
         histogram.setRecursionKernel(counts);
         histogram.setMetaDynamics(metaDynamics);
       }
 
     } catch (Exception e) {
       String message = " Invalid OST Histogram file.";
       logger.log(Level.SEVERE, message, e);
     }
     try {
       close();
     } catch (IOException ioe) {
       String histoName = histogram == null ? "unknown file" : histogram.toString();
       logger.warning(format(" Failed to close histogram reader for %s", histoName));
     }
   }
 
 }