JAL-1767 minor field tidying prior to functional changes

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

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 8910c67..b910a7e 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -31,37 +31,40 @@ import java.io.PrintStream;
 public class Matrix implements MatrixI
 {
   /*
-   * the cell values in row-major order
+   * maximum number of iterations for tqli
    */
-  private double[][] value;
+  private static final int MAX_ITER = 45;
+  // fudge - add 15 iterations, just in case
 
   /*
    * the number of rows
    */
-  protected int rows;
+  final protected int rows;
 
   /*
    * the number of columns
    */
-  protected int cols;
+  final protected int cols;
+
+  /*
+   * the cell values in row-major order
+   */
+  private double[][] value;
 
   protected double[] d; // Diagonal
 
   protected double[] e; // off diagonal
 
   /**
-   * maximum number of iterations for tqli
+   * Constructor given number of rows and columns
    * 
+   * @param colCount
+   * @param rowCount
    */
-  private static final int maxIter = 45; // fudge - add 15 iterations, just in
-                                         // case
-
-  /**
-   * Default constructor
-   */
-  public Matrix()
+  protected Matrix(int rowCount, int colCount)
   {
-
+    rows = rowCount;
+    cols = colCount;
   }
 
   /**
@@ -103,11 +106,6 @@ public class Matrix implements MatrixI
     }
   }
 
-  /**
-   * Returns a new matrix which is the transpose of this one
-   * 
-   * @return
-   */
   @Override
   public MatrixI transpose()
   {
@@ -145,18 +143,6 @@ public class Matrix implements MatrixI
     }
   }
 
-  /**
-   * Returns a new matrix which is the result of premultiplying this matrix by
-   * the supplied argument. If this of size AxB (A rows and B columns), and the
-   * argument is CxA (C rows and A columns), the result is of size CxB.
-   * 
-   * @param in
-   * 
-   * @return
-   * @throws IllegalArgumentException
-   *           if the number of columns in the pre-multiplier is not equal to
-   *           the number of rows in the multiplicand (this)
-   */
   @Override
   public MatrixI preMultiply(MatrixI in)
   {
@@ -208,21 +194,6 @@ public class Matrix implements MatrixI
     return out;
   }
 
-  /**
-   * Returns a new matrix which is the result of postmultiplying this matrix by
-   * the supplied argument. If this of size AxB (A rows and B columns), and the
-   * argument is BxC (B rows and C columns), the result is of size AxC.
-   * <p>
-   * This method simply returns the result of in.preMultiply(this)
-   * 
-   * @param in
-   * 
-   * @return
-   * @throws IllegalArgumentException
-   *           if the number of rows in the post-multiplier is not equal to the
-   *           number of columns in the multiplicand (this)
-   * @see #preMultiply(Matrix)
-   */
   @Override
   public MatrixI postMultiply(MatrixI in)
   {
@@ -234,11 +205,6 @@ public class Matrix implements MatrixI
     return in.preMultiply(this);
   }
 
-  /**
-   * Answers a new matrix with a copy of the values in this one
-   * 
-   * @return
-   */
   @Override
   public MatrixI copy()
   {
@@ -479,11 +445,11 @@ public class Matrix implements MatrixI
         {
           iter++;
 
-          if (iter == maxIter)
+          if (iter == MAX_ITER)
           {
             throw new Exception(MessageManager.formatMessage(
                     "exception.matrix_too_many_iteration", new String[]
-                    { "tqli", Integer.valueOf(maxIter).toString() }));
+                    { "tqli", Integer.valueOf(MAX_ITER).toString() }));
           }
           else
           {
@@ -743,11 +709,11 @@ public class Matrix implements MatrixI
         {
           iter++;
 
-          if (iter == maxIter)
+          if (iter == MAX_ITER)
           {
             throw new Exception(MessageManager.formatMessage(
                     "exception.matrix_too_many_iteration", new String[]
-                    { "tqli2", Integer.valueOf(maxIter).toString() }));
+                    { "tqli2", Integer.valueOf(MAX_ITER).toString() }));
           }
           else
           {