JAL-2379 commented out code removed

[jalview.git] / src / jalview / math / Matrix.java

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 0f93eb5..de0bf77 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -26,15 +26,12 @@ import jalview.util.MessageManager;
 import java.io.PrintStream;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A class to model rectangular matrices of double values and operations on them
  */
 public class Matrix implements MatrixI
 {
   /*
-   * the [row][column] values in the matrix
+   * the cell values in row-major order
    */
   private double[][] value;
 
@@ -48,10 +45,8 @@ public class Matrix implements MatrixI
    */
   protected int cols;
 
-  /** DOCUMENT ME!! */
   protected double[] d; // Diagonal
 
-  /** DOCUMENT ME!! */
   protected double[] e; // off diagonal
 
   /**
@@ -89,10 +84,7 @@ public class Matrix implements MatrixI
   public Matrix(double[][] values)
   {
     this.rows = values.length;
-    if (rows > 0)
-    {
-      this.cols = values[0].length;
-    }
+    this.cols = this.rows == 0 ? 0 : values[0].length;
     this.value = values;
   }
 
@@ -275,27 +267,22 @@ public class Matrix implements MatrixI
       {
         for (k = 1; k <= l; k++)
         {
-          // double v = Math.abs(value[i - 1][k - 1]);
           double v = Math.abs(getValue(i - 1, k - 1));
           scale += v;
         }
 
         if (scale == 0.0)
         {
-          // e[i - 1] = value[i - 1][l - 1];
           e[i - 1] = getValue(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]);
             double v = divideValue(i - 1, k - 1, scale);
             h += v * v;
           }
 
-          // f = value[i - 1][l - 1];
           f = getValue(i - 1, l - 1);
 
           if (f > 0)
@@ -309,34 +296,26 @@ public class Matrix implements MatrixI
 
           e[i - 1] = scale * g;
           h -= (f * g);
-          // value[i - 1][l - 1] = f - g;
           setValue(i - 1, l - 1, f - g);
-          // System.out.println(String.format("%d %d %f %f %f %f %f %.5e", i,
-          // l,
-          // scale, f, g, h, getValue(i - 1, l - 1), checksum()));
           f = 0.0;
 
           for (j = 1; j <= l; j++)
           {
-            // value[j - 1][i - 1] = value[i - 1][j - 1] / h;
             double val = getValue(i - 1, j - 1) / h;
             setValue(j - 1, i - 1, val);
             g = 0.0;
 
             for (k = 1; k <= j; k++)
             {
-              // g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
               g += (getValue(j - 1, k - 1) * getValue(i - 1, k - 1));
             }
 
             for (k = j + 1; k <= l; k++)
             {
-              // g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
               g += (getValue(k - 1, j - 1) * getValue(i - 1, k - 1));
             }
 
             e[j - 1] = g / h;
-            // f += (e[j - 1] * value[i - 1][j - 1]);
             f += (e[j - 1] * getValue(i - 1, j - 1));
           }
 
@@ -344,15 +323,12 @@ public class Matrix implements MatrixI
 
           for (j = 1; j <= l; j++)
           {
-            // f = value[i - 1][j - 1];
             f = getValue(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]));
               double val = (f * e[k - 1]) + (g * getValue(i - 1, k - 1));
               addValue(j - 1, k - 1, -val);
             }
@@ -361,7 +337,6 @@ public class Matrix implements MatrixI
       }
       else
       {
-        // e[i - 1] = value[i - 1][l - 1];
         e[i - 1] = getValue(i - 1, l - 1);
       }
 
@@ -383,27 +358,21 @@ public class Matrix implements MatrixI
 
           for (k = 1; k <= l; k++)
           {
-            // g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
             g += (getValue(i - 1, k - 1) * getValue(k - 1, j - 1));
           }
 
           for (k = 1; k <= l; k++)
           {
-            // value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
             addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1)));
           }
         }
       }
 
-      // d[i - 1] = value[i - 1][i - 1];
-      // value[i - 1][i - 1] = 1.0;
       d[i - 1] = getValue(i - 1, i - 1);
       setValue(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;
         setValue(j - 1, i - 1, 0.0);
         setValue(i - 1, j - 1, 0.0);
       }
@@ -543,9 +512,6 @@ public class Matrix implements MatrixI
 
             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);
               f = getValue(k - 1, i);
               setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f));
               setValue(k - 1, i - 1, (c * getValue(k - 1, i - 1)) - (s * f));