X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=2f79875369e3464cc8fb1a45c271e2805f0dc6ae;hb=cb7652a58feba83df46110a571785ce99be6da99;hp=3b93d6dcb9210b2c8d3f150105f330c61a3d624a;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 3b93d6d..2f79875 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1,123 +1,207 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.math;
 
-import jalview.util.*;
-
 import java.io.*;
 
-public class Matrix {
+import jalview.util.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Matrix
+{
   /**
    * SMJSPUBLIC
    */
   public double[][] value;
+
+  /** DOCUMENT ME!! */
   public int rows;
+
+  /** DOCUMENT ME!! */
   public int cols;
-  public double[] d;  // Diagonal
-  public double[] e;  // off diagonal
 
-  public Matrix(double[][] value, int rows, int cols) {
+  /** DOCUMENT ME!! */
+  public double[] d; // Diagonal
+
+  /** DOCUMENT ME!! */
+  public double[] e; // off diagonal
+
+  /**
+   * 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];
       }
     }
-    return new Matrix(out,cols,rows);
-  }
 
-  public void print(PrintStream ps) {
+    return new Matrix(out, cols, rows);
+  }
 
-    for (int i = 0; i < rows; i++) {
-      for (int j = 0; j < cols; j++) {
-        Format.print(ps,"%8.2f",value[i][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]);
       }
+
       ps.println();
     }
   }
 
-
-  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++) {
-          tmp[i][j] += in.value[i][k]*this.value[k][j];
+        for (int k = 0; k < in.cols; k++)
+        {
+          tmp[i][j] += (in.value[i][k] * this.value[k][j]);
         }
-
       }
     }
 
-    return new Matrix(tmp,in.rows,this.cols);
+    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++) {
-        out[i] += value[i][k] * in[k];
+
+      for (int k = 0; k < in.length; k++)
+      {
+        out[i] += (value[i][k] * in[k]);
       }
     }
+
     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++) {
-          out[i][j] = out[i][j] + value[i][k]*in.value[k][j];
+        for (int k = 0; k < rows; k++)
+        {
+          out[i][j] = out[i][j] + (value[i][k] * in.value[k][j]);
         }
-
       }
     }
-    return new Matrix(out,this.cols,in.rows);
+
+    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];
       }
     }
-    return new Matrix(newmat,rows,cols);
+
+    return new Matrix(newmat, rows, cols);
   }
 
-  public void tred() {
+  /**
+   * DOCUMENT ME!
+   */
+  public void tred()
+  {
     int n = rows;
     int l;
     int k;
@@ -133,84 +217,131 @@ public class Matrix {
     this.d = new double[rows];
     this.e = new double[rows];
 
-    for (i=n; i >= 2;i--) {
-      l=i-1;
+    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 (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];
         }
-        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];
+        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 {
+
+          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];
+
+          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];
+
+            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];
+
+            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]);
+
+          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;
+      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 (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];
+
+          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;
+
+      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;
       }
     }
   }
 
-  public void tqli() {
+  /**
+   * DOCUMENT ME!
+   */
+  public void tqli()
+  {
     int n = rows;
 
     int m;
@@ -222,73 +353,109 @@ public class Matrix {
     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];
+    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)
+
+    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) {
+
+        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);
           }
-          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));
+
+          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;
+          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;
+            }
+            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;
+
+            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;
+            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;
+
+          d[l - 1] = d[l - 1] - p;
+          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;
@@ -304,84 +471,130 @@ public class Matrix {
     this.d = new double[rows];
     this.e = new double[rows];
 
-    for (i=n-1; i >= 1;i--) {
-      l=i-1;
+    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];
+            h += (value[i][k] * value[i][k]);
           }
+
           f = value[i][l];
-          if (f>0) {
-            g = -1.0*Math.sqrt(h);
-          } else {
+
+          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];
+
+          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];
+
+            for (k = j; k < l; k++)
+            {
+              g += (value[k][j] * value[i][k]);
             }
-            e[j] = g/h;
-            f+=e[j]*value[i][j];
+
+            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;
+
+          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]);
+
+            for (k = 0; k < j; k++)
+            {
+              value[j][k] -= ( (f * e[k]) + (g * value[i][k]));
             }
           }
         }
-      } else {
+      }
+      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 (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];
+
+          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++) {
+
+      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;
@@ -393,199 +606,246 @@ public class Matrix {
     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];
+    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)
+
+    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) {
+
+        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);
           }
-          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));
+
+          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;
+          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;
+            }
+            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;
+
+            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;
+            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;
+
+          d[l - 1] = d[l - 1] - p;
+          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) {
-    double[] out  = new double[rows];
-    for (int i=0;i<rows;i++) {
+  /**
+   * 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++)
+    {
       out[i] = value[i][n];
     }
+
     return out;
   }
 
-
-  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 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++) {
-      Format.print(ps,"%15.4e",e[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++) {
-        in[i][j] = (double)Math.random();
+    for (int i = 0; i < n; i++)
+    {
+      for (int j = 0; j < n; j++)
+      {
+        in[i][j] = (double) Math.random();
       }
     }
 
-    Matrix origmat = new Matrix(in,n,n);
+    Matrix origmat = new Matrix(in, n, n);
+
     //    System.out.println(" --- Original matrix ---- ");
     ///    origmat.print(System.out);
     //System.out.println();
-
     //System.out.println(" --- transpose matrix ---- ");
     Matrix trans = origmat.transpose();
+
     //trans.print(System.out);
     //System.out.println();
-
     //System.out.println(" --- OrigT * Orig ---- ");
-
     Matrix symm = trans.postMultiply(origmat);
+
     //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 ---");
     //symm.print(System.out);
     //System.out.println();
-
     //System.out.println(" --- D vector ---");
     //symm.printD(System.out);
     //System.out.println();
     //System.out.println(" --- E vector ---");
     //symm.printE(System.out);
     //System.out.println();
-
-
     // Now produce the diagonalization matrix
-    tstart = System.currentTimeMillis();
+    //tstart = System.currentTimeMillis();
     symm.tqli();
-    tend = System.currentTimeMillis();
-    //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
+    //tend = System.currentTimeMillis();
 
+    //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
     //System.out.println(" --- New diagonalization matrix ---");
     //symm.print(System.out);
     //System.out.println();
-
     //System.out.println(" --- D vector ---");
     //symm.printD(System.out);
     //System.out.println();
     //System.out.println(" --- E vector ---");
     //symm.printE(System.out);
     //System.out.println();
-
     //System.out.println(" --- First eigenvector --- ");
     //double[] eigenv = symm.getColumn(0);
     //for (int i=0; i < eigenv.length;i++) {
     //  Format.print(System.out,"%15.4f",eigenv[i]);
     // }
     //System.out.println();
-
     //double[] neigenv = origsymm.vectorPostMultiply(eigenv);
-
     //for (int i=0; i < neigenv.length;i++) {
     //  Format.print(System.out,"%15.4f",neigenv[i]/symm.d[0]);
     //}
-
     //System.out.println();
   }
-
 }
-
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