Merge branch 'develop' into features/JAL-2379pcaMemory

Conflicts:
	src/jalview/analysis/PCA.java
	src/jalview/math/Matrix.java
	test/jalview/math/MatrixTest.java

diff --cc src/jalview/analysis/PCA.java
index 9fc6027,eaea7bf..7d6b822
--- 1/src/jalview/analysis/PCA.java
--- 2/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@@ -151,10 -152,10 +151,10 @@@ public class PCA implements Runnabl
    /**
     * Returns the matrix used in PCA calculation
     * 
--   * @return java.math.Matrix object
++   * @return
     */
  
 -  public Matrix getM()
 +  public MatrixI getM()
    {
      return m;
    }

diff --cc src/jalview/math/Matrix.java
index 2b2314b,647fc3a..ee74b9b
--- 1/src/jalview/math/Matrix.java
--- 2/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@@ -26,17 -26,14 +26,14 @@@ 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
 +public class Matrix implements MatrixI
  {
    /*
-    * the [row][column] values in the matrix
+    * the cell values in row-major order
     */
 -  public double[][] value;
 +  private double[][] value;
  
    /*
     * the number of rows
@@@ -46,13 -43,13 +43,11 @@@
    /*
     * the number of columns
     */
 -  public int cols;
 +  protected int cols;
  
--  /** DOCUMENT ME!! */
 -  public double[] d; // Diagonal
 +  protected double[] d; // Diagonal
  
--  /** DOCUMENT ME!! */
 -  public double[] e; // off diagonal
 +  protected double[] e; // off diagonal
  
    /**
     * maximum number of iterations for tqli
@@@ -372,7 -345,7 +364,7 @@@
  
            for (k = 1; k <= l; k++)
            {
-             double x = addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1)));
 -            value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
++            addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1)));
            }
          }
        }

diff --cc test/jalview/math/MatrixTest.java
index bd5614f,a4acbd0..961602d
--- 1/test/jalview/math/MatrixTest.java
--- 2/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@@ -163,12 -150,32 +164,32 @@@ public class MatrixTes
       * and check premultiply equivalent
       */
      m3 = m2.preMultiply(m1);
 -    assertEquals(m3.rows, 1);
 -    assertEquals(m3.cols, 2);
 -    assertEquals(m3.value[0][0], 56d);
 -    assertEquals(m3.value[0][1], 25d);
 +    assertEquals(m3.height(), 1);
 +    assertEquals(m3.width(), 2);
 +    assertEquals(m3.getRow(0)[0], 56d);
 +    assertEquals(m3.getRow(0)[1], 25d);
    }
  
+   @Test(groups = "Functional")
+   public void testCopy()
+   {
+     Random r = new Random();
+     int rows = 5;
+     int cols = 11;
+     double[][] in = new double[rows][cols];
+ 
+     for (int i = 0; i < rows; i++)
+     {
+       for (int j = 0; j < cols; j++)
+       {
+         in[i][j] = r.nextDouble();
+       }
+     }
+     Matrix m1 = new Matrix(in);
 -    Matrix m2 = m1.copy();
++    Matrix m2 = (Matrix) m1.copy();
+     assertTrue(matrixEquals(m1, m2));
+   }
+ 
    /**
     * main method extracted from Matrix
     *