// ******************************************************************************
   //
   // 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.potential.parsers;
  
  import ffx.numerics.math.RunningStatistics;
  
  import java.io.BufferedReader;
  import java.io.BufferedWriter;
  import java.io.File;
  import java.io.FileReader;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.List;
  import java.util.logging.Logger;
  
  import static java.lang.Double.parseDouble;
  import static java.lang.String.format;
  import static java.lang.System.arraycopy;
  
  /**
   * The DistanceMatrixFilter class parses a Distance Matrix (*.DST) files.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class DistanceMatrixFilter {
  
    private static final Logger logger = Logger.getLogger(DistanceMatrixFilter.class.getName());
  
    /**
     * No public constructor for DistanceMatrixFilter.
     */
    public DistanceMatrixFilter() {
    }
  
    private int nRows = 0;
    private int nColumns = 0;
    private boolean fillDistanceMatrix = false;
    private double[][] distanceMatrix = null;
  
    /**
     * Get the number of rows read in.
     *
     * @return The number of rows read in.
     */
    public int getRestartRow() {
      return nRows;
    }
  
    /**
     * Get the number of columns in the last row that was read in.
     *
     * @return The number of columns in the last row that was read in.
     */
    public int getRestartColumn() {
      return nColumns;
    }
  
    /**
     * Read in the distance matrix from a file. This method is used from the Clustering code, where the
     * size of the distance matrix is unknown, and the full N^2 matrix is needed.
     *
    * @param filename The filename to read from.
    * @param distanceList The distance matrix (if null, only the last row is returned).
    * @return Statistics for the parsed values.
    */
   public RunningStatistics readDistanceMatrix(String filename, List<double[]> distanceList) {
     fillDistanceMatrix = true;
     RunningStatistics runningStatistics = readDistanceMatrix(filename, -1, -1);
     if (distanceMatrix != null) {
       int size = distanceMatrix[0].length;
       boolean square = true;
       for (int i = 0; i < size; i++) {
         if (distanceMatrix[i] == null || distanceMatrix[i].length != size) {
           square = false;
           break;
         }
       }
       // The full NxN matrix has been read in.
       if (square) {
         // Add all rows of the distanceMatrix into the list
         Collections.addAll(distanceList, distanceMatrix);
       } else {
         // Assume only the upper triangle has been read in.
         for (int i = 0; i < size; i++) {
           double[] row = new double[size];
           // Fill the lower triangle from previous rows.
           for (int j = 0; j < i; j++) {
             double[] previousRow = distanceList.get(j);
             row[j] = previousRow[i];
           }
           // Fill the upper triangle using the current row of the distanceMatrix.
           arraycopy(distanceMatrix[i], 0, row, i, size - i);
           distanceList.add(row);
         }
       }
     }
 
     // Reset the DistanceMatrixFilter for reuse.
     distanceMatrix = null;
     fillDistanceMatrix = false;
     return runningStatistics;
   }
 
   /**
    * Read in the distance matrix from a file.
    *
    * @param filename The filename to read from.
    * @param expectedRows The number of rows to expect.
    * @param expectedColumns The number of columns to expect.
    * @return Statistics for the parsed values.
    */
   public RunningStatistics readDistanceMatrix(String filename, int expectedRows,
       int expectedColumns) {
 
     if (filename == null) {
       return null;
     }
 
     File distanceMatrixFile = new File(filename);
     if (!distanceMatrixFile.exists() || !distanceMatrixFile.canRead()) {
       return null;
     }
 
     // Read in the RMSD matrix.
     try (FileReader fr = new FileReader(distanceMatrixFile); BufferedReader br = new BufferedReader(
         fr)) {
 
       String data = br.readLine();
 
       // Check for blank lines at the top of the file
       while (data != null && data.trim().isEmpty()) {
         data = br.readLine();
       }
 
       if (data == null) {
         logger.info(format("\n No data in RMSD file %s.", distanceMatrixFile));
         return null;
       }
 
       String[] tokens = data.trim().split(" +");
       nColumns = tokens.length;
 
       // If the expectedRows is unknown (i.e. this is called from the Cluster script), set
       // the number of rows to the initial number of parsed tokens.
       if (expectedRows == -1) {
         expectedRows = nColumns;
       }
       if (expectedColumns == -1) {
         expectedColumns = nColumns;
       }
 
       if (nColumns != expectedColumns) {
         logger.info(
             format("\n Unexpected number of entries (%d) in the first row of the RMSD file %s.",
                 nColumns, distanceMatrixFile));
         return null;
       }
 
       if (fillDistanceMatrix) {
         distanceMatrix = new double[expectedRows][];
       }
 
       RunningStatistics runningStatistics = new RunningStatistics();
 
       // Loop over the number of expected rows.
       for (int i = 0; i < expectedRows; i++) {
         double[] row = new double[nColumns];
         for (int j = 0; j < nColumns; j++) {
           row[j] = parseDouble(tokens[j]);
           runningStatistics.addValue(row[j]);
         }
 
         // Are we storing all rows?
         if (distanceMatrix != null && distanceMatrix.length > i) {
           distanceMatrix[i] = row;
         }
 
         nRows = i + 1;
 
         // Read the next line.
         data = br.readLine();
         if (data != null) {
           tokens = data.trim().split(" +");
         } else {
           break;
         }
 
         nColumns = tokens.length;
       }
       return runningStatistics;
 
     } catch (IOException e) {
       logger.info(format(" Exception reading %s:\n %s", distanceMatrixFile, e));
       return null;
     }
   }
 
   /**
    * Convert a distance matrix to a String.
    *
    * @param distanceMatrix The distance matrix.
    * @return Return a String representation (or null if the distanceMatrix is null).
    */
   public static String toDistanceMatrixString(List<double[]> distanceMatrix) {
 
     if (distanceMatrix == null) {
       return null;
     }
 
     StringBuilder sb = new StringBuilder("\n Distance Matrix:\n");
     for (double[] row : distanceMatrix) {
       sb.append("  ");
       for (int j = 0; j < row.length; j++) {
         if (row[j] == -2.0) {
           sb.append(format("%6.4f", Double.NaN));
         } else {
           sb.append(format("%6.4f", row[j]));
         }
         if (j == row.length - 1) {
           sb.append("\n");
         } else {
           sb.append(" ");
         }
       }
     }
 
     return sb.toString();
   }
 
   /**
    * Convert a distance matrix to a String.
    *
    * @param distanceMatrix The distance matrix.
    * @return Return a String representation (or null if the distanceMatrix is null).
    */
   public static String toDistanceMatrixString(double[][] distanceMatrix) {
     return toDistanceMatrixString(Arrays.asList(distanceMatrix));
   }
 
   /**
    * Write the distance matrix to a file.
    *
    * @param filename The filename to write to.
    * @param distanceMatrix a list containing rows of the distance matrix.
    * @return a boolean.
    */
   public static boolean writeDistanceMatrix(String filename, List<double[]> distanceMatrix) {
     // Check for null arguments.
     if (distanceMatrix == null) {
       return false;
     }
 
     for (double[] row : distanceMatrix) {
       boolean success = writeDistanceMatrixRow(filename, row, 0);
       if (!success) {
         return false;
       }
     }
 
     return true;
   }
 
   /**
    * Write the distance matrix to a file.
    *
    * @param filename The filename to write to.
    * @param distanceMatrixRow A row of the distance matrix.
    * @param firstColumn The first column of the distance matrix row to write.
    * @return a boolean.
    */
   public static boolean writeDistanceMatrixRow(String filename, double[] distanceMatrixRow,
       int firstColumn) {
 
     if (filename == null) {
       return false;
     }
 
     File distanceMatrixFile = new File(filename);
 
     // Check for null arguments.
     if (distanceMatrixFile == null || distanceMatrixRow == null) {
       return false;
     }
 
     // Write one row.
     try (FileWriter fw = new FileWriter(distanceMatrixFile,
         true); BufferedWriter bw = new BufferedWriter(fw)) {
       int nColumn = distanceMatrixRow.length;
       for (int column = firstColumn; column < nColumn; column++) {
         bw.write(format("%16.14f", distanceMatrixRow[column]));
         if (column < nColumn - 1) {
           bw.write(" ");
         }
       }
       bw.write("\n");
     } catch (Exception e) {
       logger.info(format(" Exception writing to %s:\n %s", distanceMatrixFile, e));
       return false;
     }
 
     return true;
   }
 }