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ensure lastSeq is refreshed if new feature added
[jalview.git]
/
src
/
jalview
/
math
/
Matrix.java
diff --git
a/src/jalview/math/Matrix.java
b/src/jalview/math/Matrix.java
index
30c534b
..
06177f5
100755
(executable)
--- a/
src/jalview/math/Matrix.java
+++ b/
src/jalview/math/Matrix.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-23,27
+23,58
@@
import jalview.util.*;
import java.io.*;
\r
\r
\r
import java.io.*;
\r
\r
\r
-public class Matrix {
\r
+/**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @author $author$
\r
+ * @version $Revision$
\r
+ */
\r
+public class Matrix
\r
+{
\r
/**
\r
* SMJSPUBLIC
\r
*/
\r
public double[][] value;
\r
/**
\r
* SMJSPUBLIC
\r
*/
\r
public double[][] value;
\r
+
\r
+ /** DOCUMENT ME!! */
\r
public int rows;
\r
public int rows;
\r
+
\r
+ /** DOCUMENT ME!! */
\r
public int cols;
\r
public int cols;
\r
+
\r
+ /** DOCUMENT ME!! */
\r
public double[] d; // Diagonal
\r
public double[] d; // Diagonal
\r
+
\r
+ /** DOCUMENT ME!! */
\r
public double[] e; // off diagonal
\r
\r
public double[] e; // off diagonal
\r
\r
- public Matrix(double[][] value, int rows, int cols) {
\r
+ /**
\r
+ * Creates a new Matrix object.
\r
+ *
\r
+ * @param value DOCUMENT ME!
\r
+ * @param rows DOCUMENT ME!
\r
+ * @param cols DOCUMENT ME!
\r
+ */
\r
+ public Matrix(double[][] value, int rows, int cols)
\r
+ {
\r
this.rows = rows;
\r
this.cols = cols;
\r
this.value = value;
\r
}
\r
\r
this.rows = rows;
\r
this.cols = cols;
\r
this.value = value;
\r
}
\r
\r
- public Matrix transpose() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public Matrix transpose()
\r
+ {
\r
double[][] out = new double[cols][rows];
\r
\r
double[][] out = new double[cols][rows];
\r
\r
- for (int i = 0; i < cols; i++) {
\r
- for (int j = 0; j < rows; j++) {
\r
+ for (int i = 0; i < cols; i++)
\r
+ {
\r
+ for (int j = 0; j < rows; j++)
\r
+ {
\r
out[i][j] = value[j][i];
\r
}
\r
}
\r
out[i][j] = value[j][i];
\r
}
\r
}
\r
@@
-51,9
+82,17
@@
public class Matrix {
return new Matrix(out, cols, rows);
\r
}
\r
\r
return new Matrix(out, cols, rows);
\r
}
\r
\r
- public void print(PrintStream ps) {
\r
- for (int i = 0; i < rows; i++) {
\r
- for (int j = 0; j < cols; j++) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param ps DOCUMENT ME!
\r
+ */
\r
+ public void print(PrintStream ps)
\r
+ {
\r
+ for (int i = 0; i < rows; i++)
\r
+ {
\r
+ for (int j = 0; j < cols; j++)
\r
+ {
\r
Format.print(ps, "%8.2f", value[i][j]);
\r
}
\r
\r
Format.print(ps, "%8.2f", value[i][j]);
\r
}
\r
\r
@@
-61,14
+100,25
@@
public class Matrix {
}
\r
}
\r
\r
}
\r
}
\r
\r
- public Matrix preMultiply(Matrix in) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param in DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public Matrix preMultiply(Matrix in)
\r
+ {
\r
double[][] tmp = new double[in.rows][this.cols];
\r
\r
double[][] tmp = new double[in.rows][this.cols];
\r
\r
- for (int i = 0; i < in.rows; i++) {
\r
- for (int j = 0; j < this.cols; j++) {
\r
+ for (int i = 0; i < in.rows; i++)
\r
+ {
\r
+ for (int j = 0; j < this.cols; j++)
\r
+ {
\r
tmp[i][j] = 0.0;
\r
\r
tmp[i][j] = 0.0;
\r
\r
- for (int k = 0; k < in.cols; k++) {
\r
+ for (int k = 0; k < in.cols; k++)
\r
+ {
\r
tmp[i][j] += (in.value[i][k] * this.value[k][j]);
\r
}
\r
}
\r
tmp[i][j] += (in.value[i][k] * this.value[k][j]);
\r
}
\r
}
\r
@@
-77,13
+127,23
@@
public class Matrix {
return new Matrix(tmp, in.rows, this.cols);
\r
}
\r
\r
return new Matrix(tmp, in.rows, this.cols);
\r
}
\r
\r
- public double[] vectorPostMultiply(double[] in) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param in DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public double[] vectorPostMultiply(double[] in)
\r
+ {
\r
double[] out = new double[in.length];
\r
\r
double[] out = new double[in.length];
\r
\r
- for (int i = 0; i < in.length; i++) {
\r
+ for (int i = 0; i < in.length; i++)
\r
+ {
\r
out[i] = 0.0;
\r
\r
out[i] = 0.0;
\r
\r
- for (int k = 0; k < in.length; k++) {
\r
+ for (int k = 0; k < in.length; k++)
\r
+ {
\r
out[i] += (value[i][k] * in[k]);
\r
}
\r
}
\r
out[i] += (value[i][k] * in[k]);
\r
}
\r
}
\r
@@
-91,14
+151,25
@@
public class Matrix {
return out;
\r
}
\r
\r
return out;
\r
}
\r
\r
- public Matrix postMultiply(Matrix in) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param in DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public Matrix postMultiply(Matrix in)
\r
+ {
\r
double[][] out = new double[this.rows][in.cols];
\r
\r
double[][] out = new double[this.rows][in.cols];
\r
\r
- for (int i = 0; i < this.rows; i++) {
\r
- for (int j = 0; j < in.cols; j++) {
\r
+ for (int i = 0; i < this.rows; i++)
\r
+ {
\r
+ for (int j = 0; j < in.cols; j++)
\r
+ {
\r
out[i][j] = 0.0;
\r
\r
out[i][j] = 0.0;
\r
\r
- for (int k = 0; k < rows; k++) {
\r
+ for (int k = 0; k < rows; k++)
\r
+ {
\r
out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
\r
}
\r
}
\r
out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
\r
}
\r
}
\r
@@
-107,11
+178,19
@@
public class Matrix {
return new Matrix(out, this.cols, in.rows);
\r
}
\r
\r
return new Matrix(out, this.cols, in.rows);
\r
}
\r
\r
- public Matrix copy() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public Matrix copy()
\r
+ {
\r
double[][] newmat = new double[rows][cols];
\r
\r
double[][] newmat = new double[rows][cols];
\r
\r
- for (int i = 0; i < rows; i++) {
\r
- for (int j = 0; j < cols; j++) {
\r
+ for (int i = 0; i < rows; i++)
\r
+ {
\r
+ for (int j = 0; j < cols; j++)
\r
+ {
\r
newmat[i][j] = value[i][j];
\r
}
\r
}
\r
newmat[i][j] = value[i][j];
\r
}
\r
}
\r
@@
-119,7
+198,11
@@
public class Matrix {
return new Matrix(newmat, rows, cols);
\r
}
\r
\r
return new Matrix(newmat, rows, cols);
\r
}
\r
\r
- public void tred() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ */
\r
+ public void tred()
\r
+ {
\r
int n = rows;
\r
int l;
\r
int k;
\r
int n = rows;
\r
int l;
\r
int k;
\r
@@
-135,29
+218,39
@@
public class Matrix {
this.d = new double[rows];
\r
this.e = new double[rows];
\r
\r
this.d = new double[rows];
\r
this.e = new double[rows];
\r
\r
- for (i = n; i >= 2; i--) {
\r
+ for (i = n; i >= 2; i--)
\r
+ {
\r
l = i - 1;
\r
h = 0.0;
\r
scale = 0.0;
\r
\r
l = i - 1;
\r
h = 0.0;
\r
scale = 0.0;
\r
\r
- if (l > 1) {
\r
- for (k = 1; k <= l; k++) {
\r
+ if (l > 1)
\r
+ {
\r
+ for (k = 1; k <= l; k++)
\r
+ {
\r
scale += Math.abs(value[i - 1][k - 1]);
\r
}
\r
\r
scale += Math.abs(value[i - 1][k - 1]);
\r
}
\r
\r
- if (scale == 0.0) {
\r
+ if (scale == 0.0)
\r
+ {
\r
e[i - 1] = value[i - 1][l - 1];
\r
e[i - 1] = value[i - 1][l - 1];
\r
- } else {
\r
- for (k = 1; k <= l; k++) {
\r
+ }
\r
+ else
\r
+ {
\r
+ for (k = 1; k <= l; k++)
\r
+ {
\r
value[i - 1][k - 1] /= scale;
\r
h += (value[i - 1][k - 1] * value[i - 1][k - 1]);
\r
}
\r
\r
f = value[i - 1][l - 1];
\r
\r
value[i - 1][k - 1] /= scale;
\r
h += (value[i - 1][k - 1] * value[i - 1][k - 1]);
\r
}
\r
\r
f = value[i - 1][l - 1];
\r
\r
- if (f > 0) {
\r
+ if (f > 0)
\r
+ {
\r
g = -1.0 * Math.sqrt(h);
\r
g = -1.0 * Math.sqrt(h);
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
g = Math.sqrt(h);
\r
}
\r
\r
g = Math.sqrt(h);
\r
}
\r
\r
@@
-166,15
+259,18
@@
public class Matrix {
value[i - 1][l - 1] = f - g;
\r
f = 0.0;
\r
\r
value[i - 1][l - 1] = f - g;
\r
f = 0.0;
\r
\r
- for (j = 1; j <= l; j++) {
\r
+ for (j = 1; j <= l; j++)
\r
+ {
\r
value[j - 1][i - 1] = value[i - 1][j - 1] / h;
\r
g = 0.0;
\r
\r
value[j - 1][i - 1] = value[i - 1][j - 1] / h;
\r
g = 0.0;
\r
\r
- for (k = 1; k <= j; k++) {
\r
+ for (k = 1; k <= j; k++)
\r
+ {
\r
g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
\r
}
\r
\r
g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
\r
}
\r
\r
- for (k = j + 1; k <= l; k++) {
\r
+ for (k = j + 1; k <= l; k++)
\r
+ {
\r
g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
\r
}
\r
\r
g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
\r
}
\r
\r
@@
-184,18
+280,22
@@
public class Matrix {
\r
hh = f / (h + h);
\r
\r
\r
hh = f / (h + h);
\r
\r
- for (j = 1; j <= l; j++) {
\r
+ for (j = 1; j <= l; j++)
\r
+ {
\r
f = value[i - 1][j - 1];
\r
g = e[j - 1] - (hh * f);
\r
e[j - 1] = g;
\r
\r
f = value[i - 1][j - 1];
\r
g = e[j - 1] - (hh * f);
\r
e[j - 1] = g;
\r
\r
- for (k = 1; k <= j; k++) {
\r
+ for (k = 1; k <= j; k++)
\r
+ {
\r
value[j - 1][k - 1] -= ((f * e[k - 1]) +
\r
(g * value[i - 1][k - 1]));
\r
}
\r
}
\r
}
\r
value[j - 1][k - 1] -= ((f * e[k - 1]) +
\r
(g * value[i - 1][k - 1]));
\r
}
\r
}
\r
}
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
e[i - 1] = value[i - 1][l - 1];
\r
}
\r
\r
e[i - 1] = value[i - 1][l - 1];
\r
}
\r
\r
@@
-205,18
+305,23
@@
public class Matrix {
d[0] = 0.0;
\r
e[0] = 0.0;
\r
\r
d[0] = 0.0;
\r
e[0] = 0.0;
\r
\r
- for (i = 1; i <= n; i++) {
\r
+ for (i = 1; i <= n; i++)
\r
+ {
\r
l = i - 1;
\r
\r
l = i - 1;
\r
\r
- if (d[i - 1] != 0.0) {
\r
- for (j = 1; j <= l; j++) {
\r
+ if (d[i - 1] != 0.0)
\r
+ {
\r
+ for (j = 1; j <= l; j++)
\r
+ {
\r
g = 0.0;
\r
\r
g = 0.0;
\r
\r
- for (k = 1; k <= l; k++) {
\r
+ for (k = 1; k <= l; k++)
\r
+ {
\r
g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
\r
}
\r
\r
g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
\r
}
\r
\r
- for (k = 1; k <= l; k++) {
\r
+ for (k = 1; k <= l; k++)
\r
+ {
\r
value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
\r
}
\r
}
\r
value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
\r
}
\r
}
\r
@@
-225,14
+330,19
@@
public class Matrix {
d[i - 1] = value[i - 1][i - 1];
\r
value[i - 1][i - 1] = 1.0;
\r
\r
d[i - 1] = value[i - 1][i - 1];
\r
value[i - 1][i - 1] = 1.0;
\r
\r
- for (j = 1; j <= l; j++) {
\r
+ for (j = 1; j <= l; j++)
\r
+ {
\r
value[j - 1][i - 1] = 0.0;
\r
value[i - 1][j - 1] = 0.0;
\r
}
\r
}
\r
}
\r
\r
value[j - 1][i - 1] = 0.0;
\r
value[i - 1][j - 1] = 0.0;
\r
}
\r
}
\r
}
\r
\r
- public void tqli() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ */
\r
+ public void tqli()
\r
+ {
\r
int n = rows;
\r
\r
int m;
\r
int n = rows;
\r
\r
int m;
\r
@@
-251,31
+361,40
@@
public class Matrix {
double c;
\r
double b;
\r
\r
double c;
\r
double b;
\r
\r
- for (i = 2; i <= n; i++) {
\r
+ for (i = 2; i <= n; i++)
\r
+ {
\r
e[i - 2] = e[i - 1];
\r
}
\r
\r
e[n - 1] = 0.0;
\r
\r
e[i - 2] = e[i - 1];
\r
}
\r
\r
e[n - 1] = 0.0;
\r
\r
- for (l = 1; l <= n; l++) {
\r
+ for (l = 1; l <= n; l++)
\r
+ {
\r
iter = 0;
\r
\r
iter = 0;
\r
\r
- do {
\r
- for (m = l; m <= (n - 1); m++) {
\r
+ do
\r
+ {
\r
+ for (m = l; m <= (n - 1); m++)
\r
+ {
\r
dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
\r
\r
dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
\r
\r
- if ((Math.abs(e[m - 1]) + dd) == dd) {
\r
+ if ((Math.abs(e[m - 1]) + dd) == dd)
\r
+ {
\r
break;
\r
}
\r
}
\r
\r
break;
\r
}
\r
}
\r
\r
- if (m != l) {
\r
+ if (m != l)
\r
+ {
\r
iter++;
\r
\r
iter++;
\r
\r
- if (iter == 30) {
\r
+ if (iter == 30)
\r
+ {
\r
System.err.print("Too many iterations in tqli");
\r
System.exit(0); // JBPNote - should this really be here ???
\r
System.err.print("Too many iterations in tqli");
\r
System.exit(0); // JBPNote - should this really be here ???
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
// System.out.println("Iteration " + iter);
\r
}
\r
\r
// System.out.println("Iteration " + iter);
\r
}
\r
\r
@@
-286,17
+405,21
@@
public class Matrix {
s = c;
\r
p = 0.0;
\r
\r
s = c;
\r
p = 0.0;
\r
\r
- for (i = m - 1; i >= l; i--) {
\r
+ for (i = m - 1; i >= l; i--)
\r
+ {
\r
f = s * e[i - 1];
\r
b = c * e[i - 1];
\r
\r
f = s * e[i - 1];
\r
b = c * e[i - 1];
\r
\r
- if (Math.abs(f) >= Math.abs(g)) {
\r
+ if (Math.abs(f) >= Math.abs(g))
\r
+ {
\r
c = g / f;
\r
r = Math.sqrt((c * c) + 1.0);
\r
e[i] = f * r;
\r
s = 1.0 / r;
\r
c *= s;
\r
c = g / f;
\r
r = Math.sqrt((c * c) + 1.0);
\r
e[i] = f * r;
\r
s = 1.0 / r;
\r
c *= s;
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
s = f / g;
\r
r = Math.sqrt((s * s) + 1.0);
\r
e[i] = g * r;
\r
s = f / g;
\r
r = Math.sqrt((s * s) + 1.0);
\r
e[i] = g * r;
\r
@@
-310,7
+433,8
@@
public class Matrix {
d[i] = g + p;
\r
g = (c * r) - b;
\r
\r
d[i] = g + p;
\r
g = (c * r) - b;
\r
\r
- for (k = 1; k <= n; k++) {
\r
+ for (k = 1; k <= n; k++)
\r
+ {
\r
f = value[k - 1][i];
\r
value[k - 1][i] = (s * value[k - 1][i - 1]) +
\r
(c * f);
\r
f = value[k - 1][i];
\r
value[k - 1][i] = (s * value[k - 1][i - 1]) +
\r
(c * f);
\r
@@
-323,11
+447,16
@@
public class Matrix {
e[l - 1] = g;
\r
e[m - 1] = 0.0;
\r
}
\r
e[l - 1] = g;
\r
e[m - 1] = 0.0;
\r
}
\r
- } while (m != l);
\r
+ }
\r
+ while (m != l);
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
- public void tred2() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ */
\r
+ public void tred2()
\r
+ {
\r
int n = rows;
\r
int l;
\r
int k;
\r
int n = rows;
\r
int l;
\r
int k;
\r
@@
-343,29
+472,39
@@
public class Matrix {
this.d = new double[rows];
\r
this.e = new double[rows];
\r
\r
this.d = new double[rows];
\r
this.e = new double[rows];
\r
\r
- for (i = n - 1; i >= 1; i--) {
\r
+ for (i = n - 1; i >= 1; i--)
\r
+ {
\r
l = i - 1;
\r
h = 0.0;
\r
scale = 0.0;
\r
\r
l = i - 1;
\r
h = 0.0;
\r
scale = 0.0;
\r
\r
- if (l > 0) {
\r
- for (k = 0; k < l; k++) {
\r
+ if (l > 0)
\r
+ {
\r
+ for (k = 0; k < l; k++)
\r
+ {
\r
scale += Math.abs(value[i][k]);
\r
}
\r
\r
scale += Math.abs(value[i][k]);
\r
}
\r
\r
- if (scale == 0.0) {
\r
+ if (scale == 0.0)
\r
+ {
\r
e[i] = value[i][l];
\r
e[i] = value[i][l];
\r
- } else {
\r
- for (k = 0; k < l; k++) {
\r
+ }
\r
+ else
\r
+ {
\r
+ for (k = 0; k < l; k++)
\r
+ {
\r
value[i][k] /= scale;
\r
h += (value[i][k] * value[i][k]);
\r
}
\r
\r
f = value[i][l];
\r
\r
value[i][k] /= scale;
\r
h += (value[i][k] * value[i][k]);
\r
}
\r
\r
f = value[i][l];
\r
\r
- if (f > 0) {
\r
+ if (f > 0)
\r
+ {
\r
g = -1.0 * Math.sqrt(h);
\r
g = -1.0 * Math.sqrt(h);
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
g = Math.sqrt(h);
\r
}
\r
\r
g = Math.sqrt(h);
\r
}
\r
\r
@@
-374,15
+513,18
@@
public class Matrix {
value[i][l] = f - g;
\r
f = 0.0;
\r
\r
value[i][l] = f - g;
\r
f = 0.0;
\r
\r
- for (j = 0; j < l; j++) {
\r
+ for (j = 0; j < l; j++)
\r
+ {
\r
value[j][i] = value[i][j] / h;
\r
g = 0.0;
\r
\r
value[j][i] = value[i][j] / h;
\r
g = 0.0;
\r
\r
- for (k = 0; k < j; k++) {
\r
+ for (k = 0; k < j; k++)
\r
+ {
\r
g += (value[j][k] * value[i][k]);
\r
}
\r
\r
g += (value[j][k] * value[i][k]);
\r
}
\r
\r
- for (k = j; k < l; k++) {
\r
+ for (k = j; k < l; k++)
\r
+ {
\r
g += (value[k][j] * value[i][k]);
\r
}
\r
\r
g += (value[k][j] * value[i][k]);
\r
}
\r
\r
@@
-392,17
+534,21
@@
public class Matrix {
\r
hh = f / (h + h);
\r
\r
\r
hh = f / (h + h);
\r
\r
- for (j = 0; j < l; j++) {
\r
+ for (j = 0; j < l; j++)
\r
+ {
\r
f = value[i][j];
\r
g = e[j] - (hh * f);
\r
e[j] = g;
\r
\r
f = value[i][j];
\r
g = e[j] - (hh * f);
\r
e[j] = g;
\r
\r
- for (k = 0; k < j; k++) {
\r
+ for (k = 0; k < j; k++)
\r
+ {
\r
value[j][k] -= ((f * e[k]) + (g * value[i][k]));
\r
}
\r
}
\r
}
\r
value[j][k] -= ((f * e[k]) + (g * value[i][k]));
\r
}
\r
}
\r
}
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
e[i] = value[i][l];
\r
}
\r
\r
e[i] = value[i][l];
\r
}
\r
\r
@@
-412,18
+558,23
@@
public class Matrix {
d[0] = 0.0;
\r
e[0] = 0.0;
\r
\r
d[0] = 0.0;
\r
e[0] = 0.0;
\r
\r
- for (i = 0; i < n; i++) {
\r
+ for (i = 0; i < n; i++)
\r
+ {
\r
l = i - 1;
\r
\r
l = i - 1;
\r
\r
- if (d[i] != 0.0) {
\r
- for (j = 0; j < l; j++) {
\r
+ if (d[i] != 0.0)
\r
+ {
\r
+ for (j = 0; j < l; j++)
\r
+ {
\r
g = 0.0;
\r
\r
g = 0.0;
\r
\r
- for (k = 0; k < l; k++) {
\r
+ for (k = 0; k < l; k++)
\r
+ {
\r
g += (value[i][k] * value[k][j]);
\r
}
\r
\r
g += (value[i][k] * value[k][j]);
\r
}
\r
\r
- for (k = 0; k < l; k++) {
\r
+ for (k = 0; k < l; k++)
\r
+ {
\r
value[k][j] -= (g * value[k][i]);
\r
}
\r
}
\r
value[k][j] -= (g * value[k][i]);
\r
}
\r
}
\r
@@
-432,14
+583,19
@@
public class Matrix {
d[i] = value[i][i];
\r
value[i][i] = 1.0;
\r
\r
d[i] = value[i][i];
\r
value[i][i] = 1.0;
\r
\r
- for (j = 0; j < l; j++) {
\r
+ for (j = 0; j < l; j++)
\r
+ {
\r
value[j][i] = 0.0;
\r
value[i][j] = 0.0;
\r
}
\r
}
\r
}
\r
\r
value[j][i] = 0.0;
\r
value[i][j] = 0.0;
\r
}
\r
}
\r
}
\r
\r
- public void tqli2() {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ */
\r
+ public void tqli2()
\r
+ {
\r
int n = rows;
\r
\r
int m;
\r
int n = rows;
\r
\r
int m;
\r
@@
-458,31
+614,40
@@
public class Matrix {
double c;
\r
double b;
\r
\r
double c;
\r
double b;
\r
\r
- for (i = 2; i <= n; i++) {
\r
+ for (i = 2; i <= n; i++)
\r
+ {
\r
e[i - 2] = e[i - 1];
\r
}
\r
\r
e[n - 1] = 0.0;
\r
\r
e[i - 2] = e[i - 1];
\r
}
\r
\r
e[n - 1] = 0.0;
\r
\r
- for (l = 1; l <= n; l++) {
\r
+ for (l = 1; l <= n; l++)
\r
+ {
\r
iter = 0;
\r
\r
iter = 0;
\r
\r
- do {
\r
- for (m = l; m <= (n - 1); m++) {
\r
+ do
\r
+ {
\r
+ for (m = l; m <= (n - 1); m++)
\r
+ {
\r
dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
\r
\r
dd = Math.abs(d[m - 1]) + Math.abs(d[m]);
\r
\r
- if ((Math.abs(e[m - 1]) + dd) == dd) {
\r
+ if ((Math.abs(e[m - 1]) + dd) == dd)
\r
+ {
\r
break;
\r
}
\r
}
\r
\r
break;
\r
}
\r
}
\r
\r
- if (m != l) {
\r
+ if (m != l)
\r
+ {
\r
iter++;
\r
\r
iter++;
\r
\r
- if (iter == 30) {
\r
+ if (iter == 30)
\r
+ {
\r
System.err.print("Too many iterations in tqli");
\r
System.exit(0); // JBPNote - same as above - not a graceful exit!
\r
System.err.print("Too many iterations in tqli");
\r
System.exit(0); // JBPNote - same as above - not a graceful exit!
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
// System.out.println("Iteration " + iter);
\r
}
\r
\r
// System.out.println("Iteration " + iter);
\r
}
\r
\r
@@
-493,17
+658,21
@@
public class Matrix {
s = c;
\r
p = 0.0;
\r
\r
s = c;
\r
p = 0.0;
\r
\r
- for (i = m - 1; i >= l; i--) {
\r
+ for (i = m - 1; i >= l; i--)
\r
+ {
\r
f = s * e[i - 1];
\r
b = c * e[i - 1];
\r
\r
f = s * e[i - 1];
\r
b = c * e[i - 1];
\r
\r
- if (Math.abs(f) >= Math.abs(g)) {
\r
+ if (Math.abs(f) >= Math.abs(g))
\r
+ {
\r
c = g / f;
\r
r = Math.sqrt((c * c) + 1.0);
\r
e[i] = f * r;
\r
s = 1.0 / r;
\r
c *= s;
\r
c = g / f;
\r
r = Math.sqrt((c * c) + 1.0);
\r
e[i] = f * r;
\r
s = 1.0 / r;
\r
c *= s;
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
s = f / g;
\r
r = Math.sqrt((s * s) + 1.0);
\r
e[i] = g * r;
\r
s = f / g;
\r
r = Math.sqrt((s * s) + 1.0);
\r
e[i] = g * r;
\r
@@
-517,7
+686,8
@@
public class Matrix {
d[i] = g + p;
\r
g = (c * r) - b;
\r
\r
d[i] = g + p;
\r
g = (c * r) - b;
\r
\r
- for (k = 1; k <= n; k++) {
\r
+ for (k = 1; k <= n; k++)
\r
+ {
\r
f = value[k - 1][i];
\r
value[k - 1][i] = (s * value[k - 1][i - 1]) +
\r
(c * f);
\r
f = value[k - 1][i];
\r
value[k - 1][i] = (s * value[k - 1][i - 1]) +
\r
(c * f);
\r
@@
-530,46
+700,90
@@
public class Matrix {
e[l - 1] = g;
\r
e[m - 1] = 0.0;
\r
}
\r
e[l - 1] = g;
\r
e[m - 1] = 0.0;
\r
}
\r
- } while (m != l);
\r
+ }
\r
+ while (m != l);
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
- public double sign(double a, double b) {
\r
- if (b < 0) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param a DOCUMENT ME!
\r
+ * @param b DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public double sign(double a, double b)
\r
+ {
\r
+ if (b < 0)
\r
+ {
\r
return -Math.abs(a);
\r
return -Math.abs(a);
\r
- } else {
\r
+ }
\r
+ else
\r
+ {
\r
return Math.abs(a);
\r
}
\r
}
\r
\r
return Math.abs(a);
\r
}
\r
}
\r
\r
- public double[] getColumn(int n) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param n DOCUMENT ME!
\r
+ *
\r
+ * @return DOCUMENT ME!
\r
+ */
\r
+ public double[] getColumn(int n)
\r
+ {
\r
double[] out = new double[rows];
\r
\r
double[] out = new double[rows];
\r
\r
- for (int i = 0; i < rows; i++) {
\r
+ for (int i = 0; i < rows; i++)
\r
+ {
\r
out[i] = value[i][n];
\r
}
\r
\r
return out;
\r
}
\r
\r
out[i] = value[i][n];
\r
}
\r
\r
return out;
\r
}
\r
\r
- public void printD(PrintStream ps) {
\r
- for (int j = 0; j < rows; j++) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param ps DOCUMENT ME!
\r
+ */
\r
+ public void printD(PrintStream ps)
\r
+ {
\r
+ for (int j = 0; j < rows; j++)
\r
+ {
\r
Format.print(ps, "%15.4e", d[j]);
\r
}
\r
}
\r
\r
Format.print(ps, "%15.4e", d[j]);
\r
}
\r
}
\r
\r
- public void printE(PrintStream ps) {
\r
- for (int j = 0; j < rows; j++) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param ps DOCUMENT ME!
\r
+ */
\r
+ public void printE(PrintStream ps)
\r
+ {
\r
+ for (int j = 0; j < rows; j++)
\r
+ {
\r
Format.print(ps, "%15.4e", e[j]);
\r
}
\r
}
\r
\r
Format.print(ps, "%15.4e", e[j]);
\r
}
\r
}
\r
\r
- public static void main(String[] args) {
\r
+ /**
\r
+ * DOCUMENT ME!
\r
+ *
\r
+ * @param args DOCUMENT ME!
\r
+ */
\r
+ public static void main(String[] args)
\r
+ {
\r
int n = Integer.parseInt(args[0]);
\r
double[][] in = new double[n][n];
\r
\r
int n = Integer.parseInt(args[0]);
\r
double[][] in = new double[n][n];
\r
\r
- for (int i = 0; i < n; i++) {
\r
- for (int j = 0; j < n; j++) {
\r
+ for (int i = 0; i < n; i++)
\r
+ {
\r
+ for (int j = 0; j < n; j++)
\r
+ {
\r
in[i][j] = (double) Math.random();
\r
}
\r
}
\r
in[i][j] = (double) Math.random();
\r
}
\r
}
\r
@@
-590,13
+804,13
@@
public class Matrix {
//symm.print(System.out);
\r
//System.out.println();
\r
// Copy the symmetric matrix for later
\r
//symm.print(System.out);
\r
//System.out.println();
\r
// Copy the symmetric matrix for later
\r
- Matrix origsymm = symm.copy();
\r
+ //Matrix origsymm = symm.copy();
\r
\r
// This produces the tridiagonal transformation matrix
\r
\r
// This produces the tridiagonal transformation matrix
\r
- long tstart = System.currentTimeMillis();
\r
+ //long tstart = System.currentTimeMillis();
\r
symm.tred();
\r
\r
symm.tred();
\r
\r
- long tend = System.currentTimeMillis();
\r
+ //long tend = System.currentTimeMillis();
\r
\r
//System.out.println("Time take for tred = " + (tend-tstart) + "ms");
\r
//System.out.println(" ---Tridiag transform matrix ---");
\r
\r
//System.out.println("Time take for tred = " + (tend-tstart) + "ms");
\r
//System.out.println(" ---Tridiag transform matrix ---");
\r
@@
-609,9
+823,9
@@
public class Matrix {
//symm.printE(System.out);
\r
//System.out.println();
\r
// Now produce the diagonalization matrix
\r
//symm.printE(System.out);
\r
//System.out.println();
\r
// Now produce the diagonalization matrix
\r
- tstart = System.currentTimeMillis();
\r
+ //tstart = System.currentTimeMillis();
\r
symm.tqli();
\r
symm.tqli();
\r
- tend = System.currentTimeMillis();
\r
+ //tend = System.currentTimeMillis();
\r
\r
//System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
\r
//System.out.println(" --- New diagonalization matrix ---");
\r
\r
//System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
\r
//System.out.println(" --- New diagonalization matrix ---");
\r