/*
 * Matrix.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package beast.base.math.matrixalgebra;

/**
 * Class representing matrix
 *
 * @author Didier H. Besset
 */
public class Matrix {
	protected double[][] components;
	protected LUPDecomposition lupDecomposition = null;

	/**
	 * Creates a matrix with given components.
	 * NOTE: the components must not be altered after the definition.
	 *
	 * @param a double[][]
	 */
	public Matrix(double[][] a) {
		components = a;
	}

	/**
	 * Creates a matrix with given components.
	 * NOTE: the components must not be altered after the definition.
	 *
	 * @param a double[]
	 */
	public Matrix(double[] a, int n, int m) {
		if (n <= 0 || m <= 0)
			throw new NegativeArraySizeException(
					"Requested matrix size: " + n + " by " + m);
		if (n * m != a.length) {
			throw new IllegalArgumentException(
					"Requested matrix size: " + n + " by " + m + " doesn't match array size: " + a.length);
		}
		components = new double[n][m];
		int k = 0;
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++) {
				components[i][j] = a[k];
				k++;
			}

		}
	}

	/**
	 * Creates a null matrix of given dimensions.
	 *
	 * @param n int	number of rows
	 * @param m int	number of columns
	 * @throws NegativeArraySizeException
	 */
	public Matrix(int n, int m) throws NegativeArraySizeException {
		if (n <= 0 || m <= 0)
			throw new NegativeArraySizeException(
					"Requested matrix size: " + n + " by " + m);
		components = new double[n][m];
		clear();
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          if the supplied matrix
	 *          does not have the same dimensions.
	 */
	public void accumulate(Matrix a) throws IllegalDimension {
		if (a.rows() != rows() || a.columns() != columns())
			throw new IllegalDimension("Operation error: cannot add a"
					+ a.rows() + " by " + a.columns()
					+ " matrix to a " + rows() + " by "
					+ columns() + " matrix");
		int m = components[0].length;
		for (int i = 0; i < components.length; i++) {
			for (int j = 0; j < m; j++)
				components[i][j] += a.component(i, j);
		}
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix		sum of the receiver with the
	 *         supplied matrix.
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          if the supplied matrix
	 *          does not have the same dimensions.
	 */
	public Matrix add(Matrix a) throws IllegalDimension {
		if (a.rows() != rows() || a.columns() != columns())
			throw new IllegalDimension("Operation error: cannot add a"
					+ a.rows() + " by " + a.columns()
					+ " matrix to a " + rows() + " by "
					+ columns() + " matrix");
		return new Matrix(addComponents(a));
	}

	/**
	 * Computes the components of the sum of the receiver and
	 * a supplied matrix.
	 *
	 * @param a MatrixAlgebra.Matrix
	 * @return double[][]
	 */
	protected double[][] addComponents(Matrix a) {
		int n = this.rows();
		int m = this.columns();
		double[][] newComponents = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < n; j++)
				newComponents[i][j] = components[i][j] + a.components[i][j];
		}
		return newComponents;
	}

	public void clear() {
		int m = components[0].length;
		for (int i = 0; i < components.length; i++) {
			for (int j = 0; j < m; j++) components[i][j] = 0;
		}
	}

	/**
	 * @return int	the number of columns of the matrix
	 */
	public int columns() {
		return components[0].length;
	}

	/**
	 * @param n int
	 * @param m int
	 * @return double
	 */
	public double component(int n, int m) {
		return components[n][m];
	}

	/**
	 * @return double
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          if the supplied
	 *          matrix is not square.
	 */
	public double determinant() throws IllegalDimension {
		return lupDecomposition().determinant();
	}

	public boolean isPD() throws IllegalDimension {
		return lupDecomposition().isPD();
	}


	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return true if the supplied matrix is equal to the receiver.
	 */
	public boolean equals(Matrix a) {
		int n = this.rows();
		if (a.rows() != n)
			return false;
		int m = this.columns();
		if (a.columns() != m)
			return false;
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < n; j++) {
				if (a.components[i][j] != components[i][j])
					return false;
			}
		}
		return true;
	}

	/**
	 * @return MatrixAlgebra.Matrix		inverse of the receiver
	 *         or pseudoinverse if the receiver is not a square matrix.
	 * @throws java.lang.ArithmeticException if the receiver is
	 *                                       a singular matrix.
	 */
	public Matrix inverse() throws ArithmeticException {
		try {
			return new Matrix(
					lupDecomposition().inverseMatrixComponents());
		}
		catch (IllegalDimension e) {
			return new Matrix(
					transposedProduct().inverse()
							.productWithTransposedComponents(this));
		}
	}

	/**
	 * @return boolean
	 */
	public boolean isSquare() {
		return rows() == columns();
	}

	/**
	 * @return LUPDecomposition	the LUP decomposition of the receiver.
	 * @throws IllegalDimension if the receiver is not
	 *                          a square matrix.
	 */
	protected LUPDecomposition lupDecomposition()
			throws IllegalDimension {
		if (lupDecomposition == null)
			lupDecomposition = new LUPDecomposition(this);
		return lupDecomposition;
	}

	/**
	 * @param a double	multiplicand.
	 * @return MatrixAlgebra.Matrix		product of the matrix with
	 *         a supplied number
	 */
	public Matrix product(double a) {
		return new Matrix(productComponents(a));
	}

	/**
	 * Computes the product of the matrix with a vector.
	 *
	 * @param v matrixAlgebra.Vector
	 * @return matrixAlgebra.Vector
	 */
	public Vector product(Vector v) throws IllegalDimension {
		int n = this.rows();
		int m = this.columns();
		if (v.dimension() != m)
			throw new IllegalDimension("Product error: " + n + " by " + m
					+ " matrix cannot by multiplied with vector of dimension "
					+ v.dimension());
		return secureProduct(v);
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix		product of the receiver with the
	 *         supplied matrix
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          If the number of
	 *          columns of the receiver are not equal to the
	 *          number of rows of the supplied matrix.
	 */
	public Matrix product(Matrix a) throws IllegalDimension {
		if (a.rows() != columns())
			throw new IllegalDimension(
					"Operation error: cannot multiply a"
							+ rows() + " by " + columns()
							+ " matrix with a " + a.rows()
							+ " by " + a.columns()
							+ " matrix");
		return new Matrix(productComponents(a));
	}

	/**
	 * @param a double
	 * @return double[][]
	 */
	protected double[][] productComponents(double a) {
		int n = this.rows();
		int m = this.columns();
		double[][] newComponents = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++)
				newComponents[i][j] = a * components[i][j];
		}
		return newComponents;
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return double[][]	the components of the product of the receiver
	 *         with the supplied matrix
	 */
	protected double[][] productComponents(Matrix a) {
		int p = this.columns();
		int n = this.rows();
		int m = a.columns();
		double[][] newComponents = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++) {
				double sum = 0;
				for (int k = 0; k < p; k++)
					sum += components[i][k] * a.components[k][j];
				newComponents[i][j] = sum;
			}
		}
		return newComponents;
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix	product of the receiver with the
	 *         tranpose of the supplied matrix
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          If the number of
	 *          columns of the receiver are not equal to
	 *          the number of columns of the supplied matrix.
	 */
	public Matrix productWithTransposed(Matrix a)
			throws IllegalDimension {
		if (a.columns() != columns())
			throw new IllegalDimension(
					"Operation error: cannot multiply a " + rows()
							+ " by " + columns()
							+ " matrix with the transpose of a "
							+ a.rows() + " by " + a.columns()
							+ " matrix");
		return new Matrix(productWithTransposedComponents(a));
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return double[][]	the components of the product of the receiver
	 *         with the transpose of the supplied matrix
	 */
	protected double[][] productWithTransposedComponents(Matrix a) {
		int p = this.columns();
		int n = this.rows();
		int m = a.rows();
		double[][] newComponents = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++) {
				double sum = 0;
				for (int k = 0; k < p; k++)
					sum += components[i][k] * a.components[j][k];
				newComponents[i][j] = sum;
			}
		}
		return newComponents;
	}

	/**
	 * @return int	the number of rows of the matrix
	 */
	public int rows() {
		return components.length;
	}

	/**
	 * Computes the product of the matrix with a vector.
	 *
	 * @param v matrixAlgebra.Vector
	 * @return matrixAlgebra.Vector
	 */
	protected Vector secureProduct(Vector v) {
		int n = this.rows();
		int m = this.columns();
		double[] vectorComponents = new double[n];
		for (int i = 0; i < n; i++) {
			vectorComponents[i] = 0;
			for (int j = 0; j < m; j++)
				vectorComponents[i] += components[i][j] * v.components[j];
		}
		return new Vector(vectorComponents);
	}

	/**
	 * Same as product(Matrix a), but without dimension checking.
	 *
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix		product of the receiver with the
	 *         supplied matrix
	 */
	protected Matrix secureProduct(Matrix a) {
		return new Matrix(productComponents(a));
	}

	/**
	 * Same as subtract ( Marix a), but without dimension checking.
	 *
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix
	 */
	protected Matrix secureSubtract(Matrix a) {
		return new Matrix(subtractComponents(a));
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix		subtract the supplied matrix to
	 *         the receiver.
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          if the supplied matrix
	 *          does not have the same dimensions.
	 */
	public Matrix subtract(Matrix a) throws IllegalDimension {
		if (a.rows() != rows() || a.columns() != columns())
			throw new IllegalDimension(
					"Product error: cannot subtract a" + a.rows()
							+ " by " + a.columns() + " matrix to a "
							+ rows() + " by " + columns() + " matrix");
		return new Matrix(subtractComponents(a));
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return double[][]
	 */
	protected double[][] subtractComponents(Matrix a) {
		int n = this.rows();
		int m = this.columns();
		double[][] newComponents = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < n; j++)
				newComponents[i][j] = components[i][j] - a.components[i][j];
		}
		return newComponents;
	}

	/**
	 * @return double[][]	a copy of the components of the receiver.
	 */
	public double[][] toComponents() {
		int n = rows();
		int m = columns();
		double[][] answer = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++)
				answer[i][j] = components[i][j];
		}
		return answer;
	}

	/**
	 * Returns a string representation of the system.
	 *
	 * @return java.lang.String
	 */
	public String toString() {
		StringBuffer sb = new StringBuffer();
		char[] separator = {'[', ' '};
		int n = rows();
		int m = columns();
		for (int i = 0; i < n; i++) {
			separator[0] = '{';
			for (int j = 0; j < m; j++) {
				sb.append(separator);
				sb.append(components[i][j]);
				separator[0] = ' ';
			}
			sb.append('}');
			sb.append('\n');
		}
		return sb.toString();
	}

	public String toStringOctave() {
		StringBuffer sb = new StringBuffer();
		int n = rows();
		int m = columns();
		sb.append("[ ");
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++) {
				sb.append(components[i][j]);
				if (j == m - 1) {
					if (i == n - 1)
						sb.append(" ");
					else
						sb.append("; ");
				} else
					sb.append(", ");
			}
		}
		sb.append("]");
		return sb.toString();
	}

	/**
	 * @return MatrixAlgebra.Matrix		transpose of the receiver
	 */
	public Matrix transpose() {
		int n = rows();
		int m = columns();
		double[][] newComponents = new double[m][n];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++)
				newComponents[j][i] = components[i][j];
		}
		return new Matrix(newComponents);
	}

	/**
	 * @return MatrixAlgebra.SymmetricMatrix	the transposed product
	 *         of the receiver with itself.
	 */
	public SymmetricMatrix transposedProduct() {
		return new SymmetricMatrix(transposedProductComponents(this));
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return MatrixAlgebra.Matrix	product of the tranpose of the
	 *         receiver with the supplied matrix
	 * @throws dr.math.matrixAlgebra.IllegalDimension
	 *          If the number of rows
	 *          of the receiver are not equal to
	 *          the number of rows of the supplied matrix.
	 */
	public Matrix transposedProduct(Matrix a) throws IllegalDimension {
		if (a.rows() != rows())
			throw new IllegalDimension(
					"Operation error: cannot multiply a tranposed "
							+ rows() + " by " + columns()
							+ " matrix with a " + a.rows() + " by "
							+ a.columns() + " matrix");
		return new Matrix(transposedProductComponents(a));
	}

	/**
	 * @param a MatrixAlgebra.Matrix
	 * @return double[][]	the components of the product of the
	 *         transpose of the receiver
	 *         with the supplied matrix.
	 */
	protected double[][] transposedProductComponents(Matrix a) {
		int p = this.rows();
		int n = this.columns();
		int m = a.columns();
		double[][] newComponents = new double[n][m];
		for (int i = 0; i < n; i++) {
			for (int j = 0; j < m; j++) {
				double sum = 0;
				for (int k = 0; k < p; k++)
					sum += components[k][i] * a.components[k][j];
				newComponents[i][j] = sum;
			}
		}
		return newComponents;
	}
}