/* * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.math; import jalview.util.Format; import jalview.util.MessageManager; import java.io.PrintStream; /** * A class to model rectangular matrices of double values and operations on them */ public class Matrix { /* * the cell values in row-major order */ public double[][] value; /* * the number of rows */ public int rows; /* * the number of columns */ public int cols; /** DOCUMENT ME!! */ public double[] d; // Diagonal /** DOCUMENT ME!! */ public double[] e; // off diagonal /** * maximum number of iterations for tqli * */ int maxIter = 45; // fudge - add 15 iterations, just in case /** * Creates a new Matrix object. For example * *
   *   new Matrix(new double[][] {{2, 3, 4}, {5, 6, 7})
   * constructs
   *   (2 3 4)
   *   (5 6 7)
   * 
* * Note that ragged arrays (with not all rows, or columns, of the same * length), are not supported by this class. They can be constructed, but * results of operations on them are undefined and may throw exceptions. * * @param values * the matrix values in row-major order */ public Matrix(double[][] values) { this.rows = values.length; this.cols = this.rows == 0 ? 0 : values[0].length; this.value = values; } /** * Returns a new matrix which is the transposes of this one * * @return DOCUMENT ME! */ public Matrix transpose() { double[][] out = new double[cols][rows]; for (int i = 0; i < cols; i++) { for (int j = 0; j < rows; j++) { out[i][j] = value[j][i]; } } return new Matrix(out); } /** * DOCUMENT ME! * * @param ps * DOCUMENT ME! */ public void print(PrintStream ps) { for (int i = 0; i < rows; i++) { for (int j = 0; j < cols; j++) { Format.print(ps, "%8.2f", value[i][j]); } ps.println(); } } /** * Returns a new matrix which is the result of premultiplying this matrix by * the supplied argument. If this of size AxB (A rows and B columns), and the * argument is CxA (C rows and A columns), the result is of size CxB. * * @param in * * @return * @throws IllegalArgumentException * if the number of columns in the pre-multiplier is not equal to * the number of rows in the multiplicand (this) */ public Matrix preMultiply(Matrix in) { if (in.cols != this.rows) { throw new IllegalArgumentException("Can't pre-multiply " + this.rows + " rows by " + in.cols + " columns"); } double[][] tmp = new double[in.rows][this.cols]; for (int i = 0; i < in.rows; i++) { for (int j = 0; j < this.cols; j++) { tmp[i][j] = 0.0; for (int k = 0; k < in.cols; k++) { tmp[i][j] += (in.value[i][k] * this.value[k][j]); } } } return new Matrix(tmp); } /** * * @param in * * @return */ public double[] vectorPostMultiply(double[] in) { double[] out = new double[in.length]; for (int i = 0; i < in.length; i++) { out[i] = 0.0; for (int k = 0; k < in.length; k++) { out[i] += (value[i][k] * in[k]); } } return out; } /** * Returns a new matrix which is the result of postmultiplying this matrix by * the supplied argument. If this of size AxB (A rows and B columns), and the * argument is BxC (B rows and C columns), the result is of size AxC. *

* This method simply returns the result of in.preMultiply(this) * * @param in * * @return * @throws IllegalArgumentException * if the number of rows in the post-multiplier is not equal to the * number of columns in the multiplicand (this) * @see #preMultiply(Matrix) */ public Matrix postMultiply(Matrix in) { if (in.rows != this.cols) { throw new IllegalArgumentException("Can't post-multiply " + this.cols + " columns by " + in.rows + " rows"); } return in.preMultiply(this); } /** * Answers a new matrix with a copy of the values in this one * * @return */ public Matrix copy() { double[][] newmat = new double[rows][cols]; for (int i = 0; i < rows; i++) { System.arraycopy(value[i], 0, newmat[i], 0, value[i].length); } return new Matrix(newmat); } /** * DOCUMENT ME! */ public void tred() { int n = rows; int l; int k; int j; int i; double scale; double hh; double h; double g; double f; this.d = new double[rows]; this.e = new double[rows]; for (i = n; i >= 2; i--) { l = i - 1; h = 0.0; scale = 0.0; if (l > 1) { for (k = 1; k <= l; k++) { scale += Math.abs(value[i - 1][k - 1]); } if (scale == 0.0) { e[i - 1] = value[i - 1][l - 1]; } else { for (k = 1; k <= l; k++) { value[i - 1][k - 1] /= scale; h += (value[i - 1][k - 1] * value[i - 1][k - 1]); } f = value[i - 1][l - 1]; if (f > 0) { g = -1.0 * Math.sqrt(h); } else { g = Math.sqrt(h); } e[i - 1] = scale * g; h -= (f * g); value[i - 1][l - 1] = f - g; f = 0.0; for (j = 1; j <= l; j++) { value[j - 1][i - 1] = value[i - 1][j - 1] / h; g = 0.0; for (k = 1; k <= j; k++) { g += (value[j - 1][k - 1] * value[i - 1][k - 1]); } for (k = j + 1; k <= l; k++) { g += (value[k - 1][j - 1] * value[i - 1][k - 1]); } e[j - 1] = g / h; f += (e[j - 1] * value[i - 1][j - 1]); } hh = f / (h + h); for (j = 1; j <= l; j++) { f = value[i - 1][j - 1]; g = e[j - 1] - (hh * f); e[j - 1] = g; for (k = 1; k <= j; k++) { value[j - 1][k - 1] -= ((f * e[k - 1]) + (g * value[i - 1][k - 1])); } } } } else { e[i - 1] = value[i - 1][l - 1]; } d[i - 1] = h; } d[0] = 0.0; e[0] = 0.0; for (i = 1; i <= n; i++) { l = i - 1; if (d[i - 1] != 0.0) { for (j = 1; j <= l; j++) { g = 0.0; for (k = 1; k <= l; k++) { g += (value[i - 1][k - 1] * value[k - 1][j - 1]); } for (k = 1; k <= l; k++) { value[k - 1][j - 1] -= (g * value[k - 1][i - 1]); } } } d[i - 1] = value[i - 1][i - 1]; value[i - 1][i - 1] = 1.0; for (j = 1; j <= l; j++) { value[j - 1][i - 1] = 0.0; value[i - 1][j - 1] = 0.0; } } } /** * DOCUMENT ME! */ public void tqli() throws Exception { int n = rows; int m; int l; int iter; int i; int k; double s; double r; double p; ; double g; double f; double dd; double c; double b; for (i = 2; i <= n; i++) { e[i - 2] = e[i - 1]; } e[n - 1] = 0.0; for (l = 1; l <= n; l++) { iter = 0; do { for (m = l; m <= (n - 1); m++) { dd = Math.abs(d[m - 1]) + Math.abs(d[m]); if ((Math.abs(e[m - 1]) + dd) == dd) { break; } } if (m != l) { iter++; if (iter == maxIter) { throw new Exception(MessageManager.formatMessage( "exception.matrix_too_many_iteration", new String[] { "tqli", Integer.valueOf(maxIter).toString() })); } else { // System.out.println("Iteration " + iter); } g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]); r = Math.sqrt((g * g) + 1.0); g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g))); c = 1.0; s = c; p = 0.0; for (i = m - 1; i >= l; i--) { f = s * e[i - 1]; b = c * e[i - 1]; if (Math.abs(f) >= Math.abs(g)) { c = g / f; r = Math.sqrt((c * c) + 1.0); e[i] = f * r; s = 1.0 / r; c *= s; } else { s = f / g; r = Math.sqrt((s * s) + 1.0); e[i] = g * r; c = 1.0 / r; s *= c; } g = d[i] - p; r = ((d[i - 1] - g) * s) + (2.0 * c * b); p = s * r; d[i] = g + p; g = (c * r) - b; for (k = 1; k <= n; k++) { f = value[k - 1][i]; value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f); value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f); } } d[l - 1] = d[l - 1] - p; e[l - 1] = g; e[m - 1] = 0.0; } } while (m != l); } } /** * DOCUMENT ME! */ public void tred2() { int n = rows; int l; int k; int j; int i; double scale; double hh; double h; double g; double f; this.d = new double[rows]; this.e = new double[rows]; for (i = n - 1; i >= 1; i--) { l = i - 1; h = 0.0; scale = 0.0; if (l > 0) { for (k = 0; k < l; k++) { scale += Math.abs(value[i][k]); } if (scale == 0.0) { e[i] = value[i][l]; } else { for (k = 0; k < l; k++) { value[i][k] /= scale; h += (value[i][k] * value[i][k]); } f = value[i][l]; if (f > 0) { g = -1.0 * Math.sqrt(h); } else { g = Math.sqrt(h); } e[i] = scale * g; h -= (f * g); value[i][l] = f - g; f = 0.0; for (j = 0; j < l; j++) { value[j][i] = value[i][j] / h; g = 0.0; for (k = 0; k < j; k++) { g += (value[j][k] * value[i][k]); } for (k = j; k < l; k++) { g += (value[k][j] * value[i][k]); } e[j] = g / h; f += (e[j] * value[i][j]); } hh = f / (h + h); for (j = 0; j < l; j++) { f = value[i][j]; g = e[j] - (hh * f); e[j] = g; for (k = 0; k < j; k++) { value[j][k] -= ((f * e[k]) + (g * value[i][k])); } } } } else { e[i] = value[i][l]; } d[i] = h; } d[0] = 0.0; e[0] = 0.0; for (i = 0; i < n; i++) { l = i - 1; if (d[i] != 0.0) { for (j = 0; j < l; j++) { g = 0.0; for (k = 0; k < l; k++) { g += (value[i][k] * value[k][j]); } for (k = 0; k < l; k++) { value[k][j] -= (g * value[k][i]); } } } d[i] = value[i][i]; value[i][i] = 1.0; for (j = 0; j < l; j++) { value[j][i] = 0.0; value[i][j] = 0.0; } } } /** * DOCUMENT ME! */ public void tqli2() throws Exception { int n = rows; int m; int l; int iter; int i; int k; double s; double r; double p; ; double g; double f; double dd; double c; double b; for (i = 2; i <= n; i++) { e[i - 2] = e[i - 1]; } e[n - 1] = 0.0; for (l = 1; l <= n; l++) { iter = 0; do { for (m = l; m <= (n - 1); m++) { dd = Math.abs(d[m - 1]) + Math.abs(d[m]); if ((Math.abs(e[m - 1]) + dd) == dd) { break; } } if (m != l) { iter++; if (iter == maxIter) { throw new Exception(MessageManager.formatMessage( "exception.matrix_too_many_iteration", new String[] { "tqli2", Integer.valueOf(maxIter).toString() })); } else { // System.out.println("Iteration " + iter); } g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]); r = Math.sqrt((g * g) + 1.0); g = d[m - 1] - d[l - 1] + (e[l - 1] / (g + sign(r, g))); c = 1.0; s = c; p = 0.0; for (i = m - 1; i >= l; i--) { f = s * e[i - 1]; b = c * e[i - 1]; if (Math.abs(f) >= Math.abs(g)) { c = g / f; r = Math.sqrt((c * c) + 1.0); e[i] = f * r; s = 1.0 / r; c *= s; } else { s = f / g; r = Math.sqrt((s * s) + 1.0); e[i] = g * r; c = 1.0 / r; s *= c; } g = d[i] - p; r = ((d[i - 1] - g) * s) + (2.0 * c * b); p = s * r; d[i] = g + p; g = (c * r) - b; for (k = 1; k <= n; k++) { f = value[k - 1][i]; value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f); value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f); } } d[l - 1] = d[l - 1] - p; e[l - 1] = g; e[m - 1] = 0.0; } } while (m != l); } } /** * DOCUMENT ME! * * @param a * DOCUMENT ME! * @param b * DOCUMENT ME! * * @return DOCUMENT ME! */ public double sign(double a, double b) { if (b < 0) { return -Math.abs(a); } else { return Math.abs(a); } } /** * Returns an array containing the values in the specified column * * @param col * * @return */ public double[] getColumn(int col) { double[] out = new double[rows]; for (int i = 0; i < rows; i++) { out[i] = value[i][col]; } return out; } /** * DOCUMENT ME! * * @param ps * DOCUMENT ME! */ public void printD(PrintStream ps) { for (int j = 0; j < rows; j++) { Format.print(ps, "%15.4e", d[j]); } } /** * DOCUMENT ME! * * @param ps * DOCUMENT ME! */ public void printE(PrintStream ps) { for (int j = 0; j < rows; j++) { Format.print(ps, "%15.4e", e[j]); } } }