X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=06177f55b72af1a4f8a9190cc43b7bf22d1876e3;hb=451d29e258f764998d1f28272470436fbae3bb1f;hp=30c534b6bba92485945a3c469b6812ef9f49f237;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index 30c534b..06177f5 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -23,27 +23,58 @@ import jalview.util.*; import java.io.*; -public class Matrix { +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Matrix +{ /** * SMJSPUBLIC */ public double[][] value; + + /** DOCUMENT ME!! */ public int rows; + + /** DOCUMENT ME!! */ public int cols; + + /** DOCUMENT ME!! */ public double[] d; // Diagonal + + /** DOCUMENT ME!! */ public double[] e; // off diagonal - public Matrix(double[][] value, int rows, int cols) { + /** + * Creates a new Matrix object. + * + * @param value DOCUMENT ME! + * @param rows DOCUMENT ME! + * @param cols DOCUMENT ME! + */ + public Matrix(double[][] value, int rows, int cols) + { this.rows = rows; this.cols = cols; this.value = value; } - public Matrix transpose() { + /** + * DOCUMENT ME! + * + * @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++) { + for (int i = 0; i < cols; i++) + { + for (int j = 0; j < rows; j++) + { out[i][j] = value[j][i]; } } @@ -51,9 +82,17 @@ public class Matrix { return new Matrix(out, cols, rows); } - public void print(PrintStream ps) { - for (int i = 0; i < rows; i++) { - for (int j = 0; j < cols; j++) { + /** + * 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]); } @@ -61,14 +100,25 @@ public class Matrix { } } - public Matrix preMultiply(Matrix in) { + /** + * DOCUMENT ME! + * + * @param in DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Matrix preMultiply(Matrix in) + { double[][] tmp = new double[in.rows][this.cols]; - for (int i = 0; i < in.rows; i++) { - for (int j = 0; j < this.cols; j++) { + 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++) { + for (int k = 0; k < in.cols; k++) + { tmp[i][j] += (in.value[i][k] * this.value[k][j]); } } @@ -77,13 +127,23 @@ public class Matrix { return new Matrix(tmp, in.rows, this.cols); } - public double[] vectorPostMultiply(double[] in) { + /** + * DOCUMENT ME! + * + * @param in DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public double[] vectorPostMultiply(double[] in) + { double[] out = new double[in.length]; - for (int i = 0; i < in.length; i++) { + for (int i = 0; i < in.length; i++) + { out[i] = 0.0; - for (int k = 0; k < in.length; k++) { + for (int k = 0; k < in.length; k++) + { out[i] += (value[i][k] * in[k]); } } @@ -91,14 +151,25 @@ public class Matrix { return out; } - public Matrix postMultiply(Matrix in) { + /** + * DOCUMENT ME! + * + * @param in DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Matrix postMultiply(Matrix in) + { double[][] out = new double[this.rows][in.cols]; - for (int i = 0; i < this.rows; i++) { - for (int j = 0; j < in.cols; j++) { + for (int i = 0; i < this.rows; i++) + { + for (int j = 0; j < in.cols; j++) + { out[i][j] = 0.0; - for (int k = 0; k < rows; k++) { + for (int k = 0; k < rows; k++) + { out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]); } } @@ -107,11 +178,19 @@ public class Matrix { return new Matrix(out, this.cols, in.rows); } - public Matrix copy() { + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Matrix copy() + { double[][] newmat = new double[rows][cols]; - for (int i = 0; i < rows; i++) { - for (int j = 0; j < cols; j++) { + for (int i = 0; i < rows; i++) + { + for (int j = 0; j < cols; j++) + { newmat[i][j] = value[i][j]; } } @@ -119,7 +198,11 @@ public class Matrix { return new Matrix(newmat, rows, cols); } - public void tred() { + /** + * DOCUMENT ME! + */ + public void tred() + { int n = rows; int l; int k; @@ -135,29 +218,39 @@ public class Matrix { this.d = new double[rows]; this.e = new double[rows]; - for (i = n; i >= 2; i--) { + for (i = n; i >= 2; i--) + { l = i - 1; h = 0.0; scale = 0.0; - if (l > 1) { - for (k = 1; k <= l; k++) { + if (l > 1) + { + for (k = 1; k <= l; k++) + { scale += Math.abs(value[i - 1][k - 1]); } - if (scale == 0.0) { + if (scale == 0.0) + { e[i - 1] = value[i - 1][l - 1]; - } else { - for (k = 1; k <= l; k++) { + } + 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) { + if (f > 0) + { g = -1.0 * Math.sqrt(h); - } else { + } + else + { g = Math.sqrt(h); } @@ -166,15 +259,18 @@ public class Matrix { value[i - 1][l - 1] = f - g; f = 0.0; - for (j = 1; j <= l; j++) { + 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++) { + for (k = 1; k <= j; k++) + { g += (value[j - 1][k - 1] * value[i - 1][k - 1]); } - for (k = j + 1; k <= l; k++) { + for (k = j + 1; k <= l; k++) + { g += (value[k - 1][j - 1] * value[i - 1][k - 1]); } @@ -184,18 +280,22 @@ public class Matrix { hh = f / (h + h); - for (j = 1; j <= l; j++) { + 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++) { + for (k = 1; k <= j; k++) + { value[j - 1][k - 1] -= ((f * e[k - 1]) + (g * value[i - 1][k - 1])); } } } - } else { + } + else + { e[i - 1] = value[i - 1][l - 1]; } @@ -205,18 +305,23 @@ public class Matrix { d[0] = 0.0; e[0] = 0.0; - for (i = 1; i <= n; i++) { + for (i = 1; i <= n; i++) + { l = i - 1; - if (d[i - 1] != 0.0) { - for (j = 1; j <= l; j++) { + if (d[i - 1] != 0.0) + { + for (j = 1; j <= l; j++) + { g = 0.0; - for (k = 1; k <= l; k++) { + for (k = 1; k <= l; k++) + { g += (value[i - 1][k - 1] * value[k - 1][j - 1]); } - for (k = 1; k <= l; k++) { + for (k = 1; k <= l; k++) + { value[k - 1][j - 1] -= (g * value[k - 1][i - 1]); } } @@ -225,14 +330,19 @@ public class Matrix { d[i - 1] = value[i - 1][i - 1]; value[i - 1][i - 1] = 1.0; - for (j = 1; j <= l; j++) { + for (j = 1; j <= l; j++) + { value[j - 1][i - 1] = 0.0; value[i - 1][j - 1] = 0.0; } } } - public void tqli() { + /** + * DOCUMENT ME! + */ + public void tqli() + { int n = rows; int m; @@ -251,31 +361,40 @@ public class Matrix { double c; double b; - for (i = 2; i <= n; i++) { + for (i = 2; i <= n; i++) + { e[i - 2] = e[i - 1]; } e[n - 1] = 0.0; - for (l = 1; l <= n; l++) { + for (l = 1; l <= n; l++) + { iter = 0; - do { - for (m = l; m <= (n - 1); m++) { + 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) { + if ((Math.abs(e[m - 1]) + dd) == dd) + { break; } } - if (m != l) { + if (m != l) + { iter++; - if (iter == 30) { + if (iter == 30) + { System.err.print("Too many iterations in tqli"); System.exit(0); // JBPNote - should this really be here ??? - } else { + } + else + { // System.out.println("Iteration " + iter); } @@ -286,17 +405,21 @@ public class Matrix { s = c; p = 0.0; - for (i = m - 1; i >= l; i--) { + for (i = m - 1; i >= l; i--) + { f = s * e[i - 1]; b = c * e[i - 1]; - if (Math.abs(f) >= Math.abs(g)) { + 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 { + } + else + { s = f / g; r = Math.sqrt((s * s) + 1.0); e[i] = g * r; @@ -310,7 +433,8 @@ public class Matrix { d[i] = g + p; g = (c * r) - b; - for (k = 1; k <= n; k++) { + for (k = 1; k <= n; k++) + { f = value[k - 1][i]; value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f); @@ -323,11 +447,16 @@ public class Matrix { e[l - 1] = g; e[m - 1] = 0.0; } - } while (m != l); + } + while (m != l); } } - public void tred2() { + /** + * DOCUMENT ME! + */ + public void tred2() + { int n = rows; int l; int k; @@ -343,29 +472,39 @@ public class Matrix { this.d = new double[rows]; this.e = new double[rows]; - for (i = n - 1; i >= 1; i--) { + 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++) { + if (l > 0) + { + for (k = 0; k < l; k++) + { scale += Math.abs(value[i][k]); } - if (scale == 0.0) { + if (scale == 0.0) + { e[i] = value[i][l]; - } else { - for (k = 0; k < l; k++) { + } + 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) { + if (f > 0) + { g = -1.0 * Math.sqrt(h); - } else { + } + else + { g = Math.sqrt(h); } @@ -374,15 +513,18 @@ public class Matrix { value[i][l] = f - g; f = 0.0; - for (j = 0; j < l; j++) { + for (j = 0; j < l; j++) + { value[j][i] = value[i][j] / h; g = 0.0; - for (k = 0; k < j; k++) { + for (k = 0; k < j; k++) + { g += (value[j][k] * value[i][k]); } - for (k = j; k < l; k++) { + for (k = j; k < l; k++) + { g += (value[k][j] * value[i][k]); } @@ -392,17 +534,21 @@ public class Matrix { hh = f / (h + h); - for (j = 0; j < l; j++) { + for (j = 0; j < l; j++) + { f = value[i][j]; g = e[j] - (hh * f); e[j] = g; - for (k = 0; k < j; k++) { + for (k = 0; k < j; k++) + { value[j][k] -= ((f * e[k]) + (g * value[i][k])); } } } - } else { + } + else + { e[i] = value[i][l]; } @@ -412,18 +558,23 @@ public class Matrix { d[0] = 0.0; e[0] = 0.0; - for (i = 0; i < n; i++) { + for (i = 0; i < n; i++) + { l = i - 1; - if (d[i] != 0.0) { - for (j = 0; j < l; j++) { + if (d[i] != 0.0) + { + for (j = 0; j < l; j++) + { g = 0.0; - for (k = 0; k < l; k++) { + for (k = 0; k < l; k++) + { g += (value[i][k] * value[k][j]); } - for (k = 0; k < l; k++) { + for (k = 0; k < l; k++) + { value[k][j] -= (g * value[k][i]); } } @@ -432,14 +583,19 @@ public class Matrix { d[i] = value[i][i]; value[i][i] = 1.0; - for (j = 0; j < l; j++) { + for (j = 0; j < l; j++) + { value[j][i] = 0.0; value[i][j] = 0.0; } } } - public void tqli2() { + /** + * DOCUMENT ME! + */ + public void tqli2() + { int n = rows; int m; @@ -458,31 +614,40 @@ public class Matrix { double c; double b; - for (i = 2; i <= n; i++) { + for (i = 2; i <= n; i++) + { e[i - 2] = e[i - 1]; } e[n - 1] = 0.0; - for (l = 1; l <= n; l++) { + for (l = 1; l <= n; l++) + { iter = 0; - do { - for (m = l; m <= (n - 1); m++) { + 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) { + if ((Math.abs(e[m - 1]) + dd) == dd) + { break; } } - if (m != l) { + if (m != l) + { iter++; - if (iter == 30) { + if (iter == 30) + { System.err.print("Too many iterations in tqli"); System.exit(0); // JBPNote - same as above - not a graceful exit! - } else { + } + else + { // System.out.println("Iteration " + iter); } @@ -493,17 +658,21 @@ public class Matrix { s = c; p = 0.0; - for (i = m - 1; i >= l; i--) { + for (i = m - 1; i >= l; i--) + { f = s * e[i - 1]; b = c * e[i - 1]; - if (Math.abs(f) >= Math.abs(g)) { + 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 { + } + else + { s = f / g; r = Math.sqrt((s * s) + 1.0); e[i] = g * r; @@ -517,7 +686,8 @@ public class Matrix { d[i] = g + p; g = (c * r) - b; - for (k = 1; k <= n; k++) { + for (k = 1; k <= n; k++) + { f = value[k - 1][i]; value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f); @@ -530,46 +700,90 @@ public class Matrix { e[l - 1] = g; e[m - 1] = 0.0; } - } while (m != l); + } + while (m != l); } } - public double sign(double a, double b) { - if (b < 0) { + /** + * 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 { + } + else + { return Math.abs(a); } } - public double[] getColumn(int n) { + /** + * DOCUMENT ME! + * + * @param n DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public double[] getColumn(int n) + { double[] out = new double[rows]; - for (int i = 0; i < rows; i++) { + for (int i = 0; i < rows; i++) + { out[i] = value[i][n]; } return out; } - public void printD(PrintStream ps) { - for (int j = 0; j < rows; j++) { + /** + * 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]); } } - public void printE(PrintStream ps) { - for (int j = 0; j < rows; 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]); } } - public static void main(String[] args) { + /** + * DOCUMENT ME! + * + * @param args DOCUMENT ME! + */ + public static void main(String[] args) + { int n = Integer.parseInt(args[0]); double[][] in = new double[n][n]; - for (int i = 0; i < n; i++) { - for (int j = 0; j < n; j++) { + for (int i = 0; i < n; i++) + { + for (int j = 0; j < n; j++) + { in[i][j] = (double) Math.random(); } } @@ -590,13 +804,13 @@ public class Matrix { //symm.print(System.out); //System.out.println(); // Copy the symmetric matrix for later - Matrix origsymm = symm.copy(); + //Matrix origsymm = symm.copy(); // This produces the tridiagonal transformation matrix - long tstart = System.currentTimeMillis(); + //long tstart = System.currentTimeMillis(); symm.tred(); - long tend = System.currentTimeMillis(); + //long tend = System.currentTimeMillis(); //System.out.println("Time take for tred = " + (tend-tstart) + "ms"); //System.out.println(" ---Tridiag transform matrix ---"); @@ -609,9 +823,9 @@ public class Matrix { //symm.printE(System.out); //System.out.println(); // Now produce the diagonalization matrix - tstart = System.currentTimeMillis(); + //tstart = System.currentTimeMillis(); symm.tqli(); - tend = System.currentTimeMillis(); + //tend = System.currentTimeMillis(); //System.out.println("Time take for tqli = " + (tend-tstart) + " ms"); //System.out.println(" --- New diagonalization matrix ---");