/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.math;

import java.io.PrintStream;

public interface MatrixI
{
  /**
   * Answers the number of columns
   * 
   * @return
   */
  int width();

  /**
   * Answers the number of rows
   * 
   * @return
   */
  int height();

  /**
   * Answers the value at row i, column j
   * 
   * @param i
   * @param j
   * @return
   */
  double getValue(int i, int j);

  /**
   * Sets the value at row i, colum j
   * 
   * @param i
   * @param j
   * @param d
   */
  void setValue(int i, int j, double d);

  /**
   * Answers a copy of the values in the i'th row
   * 
   * @return
   */
  double[] getRow(int i);

  MatrixI copy();

  MatrixI transpose();

  MatrixI preMultiply(MatrixI m);

  MatrixI postMultiply(MatrixI m);

  double[] getD();

  double[] getE();

  void print(PrintStream ps, String format);

  void printD(PrintStream ps, String format);

  void printE(PrintStream ps, String format);

  void tqli() throws Exception;

  void tred();

  /**
   * Reverses the range of the matrix values, so that the smallest values become
   * the largest, and the largest become the smallest. This operation supports
   * using a distance measure as a similarity measure, or vice versa.
   * <p>
   * If parameter <code>maxToZero</code> is true, then the maximum value becomes
   * zero, i.e. all values are subtracted from the maximum. This is consistent
   * with converting an identity similarity score to a distance score - the most
   * similar (identity) corresponds to zero distance. However note that the
   * operation is not reversible (unless the original minimum value is zero).
   * For example a range of 10-40 would become 30-0, which would reverse a
   * second time to 0-30. Also note that a general similarity measure (such as
   * BLOSUM) may give different 'identity' scores for different sequences, so
   * they cannot all convert to zero distance.
   * <p>
   * If parameter <code>maxToZero</code> is false, then the values are reflected
   * about the average of {min, max} (effectively swapping min and max). This
   * operation <em>is</em> reversible.
   * 
   * @param maxToZero
   */
  void reverseRange(boolean maxToZero);

  /**
   * Multiply all entries by the given value
   * 
   * @param d
   */
  void multiply(double d);
}