code: ///////////////////////////////////////////////////////////////////////////////
  // For information as to what this class does, see the Javadoc, below.       //
  // Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
  // 2007, 2008, 2009, 2010, 2014, 2015 by Peter Spirtes, Richard Scheines, Joseph   //
  // Ramsey, and Clark Glymour.                                                //
  //                                                                           //
  // This program is free software; you can redistribute it and/or modify      //
  // it under the terms of the GNU General Public License as published by      //
  // the Free Software Foundation; either version 2 of the License, or         //
  // (at your option) any later version.                                       //
  //                                                                           //
  // This program 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 this program; if not, write to the Free Software               //
  // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
  ///////////////////////////////////////////////////////////////////////////////
  
  package edu.cmu.tetrad.util;
  
  
  /**
   * @author Joseph Ramsey
   * Returns values of the given square matrix, where the indices are remapped via
   * the given indices array. If the supplied matrix is 6 x 6, for example, and
   * the indices set are [5 4 2 1], then getValue(1, 2) will return element [4][2]
   * of the given matrix.
   */
  public final class IndexedMatrix {
  
      /**
       * A square matrix.
       */
      private final double[][] matrix;
  
      /**
       * Indices into this matrix, implicitly specifying a submatrix.
       */
      private int[] indices;
  
      /**
       * Constructs a new IndexedMatrix for the given matrix.
       *
       * @param matrix The wrapped matrix.
       */
      public IndexedMatrix(double[][] matrix) {
          assert MatrixUtils.isSquare(matrix);
          this.matrix = new TetradMatrix(matrix).toArray();
          setIndices(new int[0]);
      }
  
      /**
       * @return Ibid.
       */
      public final int[] getIndices() {
          return indices;
      }
  
      /**
       * Sets the index array. The index array must be of length <= the order of
       * the matrix, each element of which is distinct and < the order of the
       * matrix.
       *
       * @param indices The indices of the submatrix desired.
       */
      public final void setIndices(int[] indices) {
          if (indices == null) {
              throw new NullPointerException("Permutation must not be null.");
          }
          if (!isLegal(indices)) {
              throw new IllegalArgumentException(
                      "Illegal index array: " + ArrUtils.toString(indices));
          }
          this.indices = ArrUtils.copy(indices);
      }
  
      /**
       * @param i The row value in the remapped indices of the cell desired.
       * @param j The column value in teh remapped indices of the cell desired.
       * @return Ibid.
       */
      public final double getValue(int i, int j) {
          return matrix[indices[i]][indices[j]];
      }
  
      /**
       * @param indices The array indices to check.
       * @return Ibid.
       */
      @SuppressWarnings({"BooleanMethodIsAlwaysInverted"})
      private boolean isLegal(int[] indices) {
          int[] check = new int[matrix.length];
          for (int indice : indices) {
              if (indice < 0 || indice >= matrix.length) {
                  return false;
              }
              check[indice]++;
          }
  
          for (int i = 0; i < matrix.length; i++) {
              if (check[i] > 1) {
                  return false;
              }
          }
  
          return true;
      }
  }
  
  
  
  
  
  