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 a 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 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);
}