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 2b2314b..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;
   }
 
@@ -275,7 +267,6 @@ 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;
         }
@@ -372,7 +363,7 @@ public class Matrix implements MatrixI
 
           for (k = 1; k <= l; k++)
           {
-            double x = addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1)));
+            addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1)));
           }
         }
       }
@@ -521,9 +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));