JAL-2380 code tidy after review

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 06a139b..eaea7bf 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -144,8 +144,8 @@ public class PCA implements Runnable
     // System.out.println("Created array");
     // printMemory(rt);
     // System.out.println(" --- Original matrix ---- ");
-    m = new Matrix(seqmat, count, bs[0].getDBinary().length);
-    m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);
+    m = new Matrix(seqmat);
+    m2 = new Matrix(seqmat2);
 
   }
 
@@ -252,15 +252,18 @@ public class PCA implements Runnable
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     PrintStream ps = new PrintStream(System.out)
     {
+      @Override
       public void print(String x)
       {
         details.append(x);
       }
 
+      @Override
       public void println()
       {
         details.append("\n");

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 28b9d67..647fc3a 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -26,22 +26,23 @@ 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
 {
-  /**
-   * SMJSPUBLIC
+  /*
+   * the cell values in row-major order
    */
   public double[][] value;
 
-  /** DOCUMENT ME!! */
+  /*
+   * the number of rows
+   */
   public int rows;
 
-  /** DOCUMENT ME!! */
+  /*
+   * the number of columns
+   */
   public int cols;
 
   /** DOCUMENT ME!! */
@@ -60,10 +61,10 @@ public class Matrix
    * Creates a new Matrix object. For example
    * 
    * <pre>
-   *   new Matrix(new double[][] {{2, 3}, {4, 5}, 2, 2)
+   *   new Matrix(new double[][] {{2, 3, 4}, {5, 6, 7})
    * constructs
-   *   (2 3)
-   *   (4 5)
+   *   (2 3 4)
+   *   (5 6 7)
    * </pre>
    * 
    * Note that ragged arrays (with not all rows, or columns, of the same
@@ -72,13 +73,11 @@ public class Matrix
    * 
    * @param values
    *          the matrix values in row-major order
-   * @param rows
-   * @param cols
    */
-  public Matrix(double[][] values, int rows, int cols)
+  public Matrix(double[][] values)
   {
-    this.rows = rows;
-    this.cols = cols;
+    this.rows = values.length;
+    this.cols = this.rows == 0 ? 0 : values[0].length;
     this.value = values;
   }
 
@@ -99,7 +98,7 @@ public class Matrix
       }
     }
 
-    return new Matrix(out, cols, rows);
+    return new Matrix(out);
   }
 
   /**
@@ -155,7 +154,7 @@ public class Matrix
       }
     }
 
-    return new Matrix(tmp, in.rows, this.cols);
+    return new Matrix(tmp);
   }
 
   /**
@@ -218,13 +217,9 @@ public class Matrix
     for (int i = 0; i < rows; i++)
     {
       System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
-      // for (int j = 0; j < cols; j++)
-      // {
-      // newmat[i][j] = value[i][j];
-      // }
     }
 
-    return new Matrix(newmat, rows, cols);
+    return new Matrix(newmat);
   }
 
   /**

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 795b2fa..a4acbd0 100644 (file)
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -1,9 +1,11 @@
 package jalview.math;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
 
 import java.util.Arrays;
+import java.util.Random;
 
 import org.testng.annotations.Test;
 
@@ -16,8 +18,8 @@ public class MatrixTest
     int cols = 1000;
     double[][] d1 = new double[rows][cols];
     double[][] d2 = new double[cols][rows];
-    Matrix m1 = new Matrix(d1, rows, cols);
-    Matrix m2 = new Matrix(d2, cols, rows);
+    Matrix m1 = new Matrix(d1);
+    Matrix m2 = new Matrix(d2);
     long start = System.currentTimeMillis();
     m1.preMultiply(m2);
     long elapsed = System.currentTimeMillis() - start;
@@ -28,8 +30,8 @@ public class MatrixTest
   @Test(groups = "Functional")
   public void testPreMultiply()
   {
-    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 } }, 1, 3); // 1x3
-    Matrix m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }, 3, 1); // 3x1
+    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 } }); // 1x3
+    Matrix m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }); // 3x1
 
     /*
      * 1x3 times 3x1 is 1x1
@@ -56,8 +58,7 @@ public class MatrixTest
     expectedExceptions = { IllegalArgumentException.class })
   public void testPreMultiply_tooManyColumns()
   {
-    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }, 2,
-            3); // 2x3
+    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
 
     /*
      * 2x3 times 2x3 invalid operation - 
@@ -72,8 +73,7 @@ public class MatrixTest
     expectedExceptions = { IllegalArgumentException.class })
   public void testPreMultiply_tooFewColumns()
   {
-    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }, 2,
-            3); // 2x3
+    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
 
     /*
      * 3x2 times 3x2 invalid operation - 
@@ -99,9 +99,8 @@ public class MatrixTest
      * (3020 30200)
      * (5040 50400)
      */
-    Matrix m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } }, 2, 2);
-    Matrix m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } },
-            2, 2);
+    Matrix m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } });
+    Matrix m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } });
     Matrix m3 = m1.postMultiply(m2);
     assertEquals(Arrays.toString(m3.value[0]), "[3020.0, 30200.0]");
     assertEquals(Arrays.toString(m3.value[1]), "[5040.0, 50400.0]");
@@ -118,8 +117,8 @@ public class MatrixTest
      * (2).(10 100 1000) = (20 200 2000)
      * (3)                 (30 300 3000)
      */
-    m1 = new Matrix(new double[][] { { 2 }, { 3 } }, 2, 1);
-    m2 = new Matrix(new double[][] { { 10, 100, 1000 } }, 1, 3);
+    m1 = new Matrix(new double[][] { { 2 }, { 3 } });
+    m2 = new Matrix(new double[][] { { 10, 100, 1000 } });
     m3 = m1.postMultiply(m2);
     assertEquals(m3.rows, 2);
     assertEquals(m3.cols, 3);
@@ -139,8 +138,8 @@ public class MatrixTest
      * [0, 0] = 2*5 + 3*6 + 4*7 = 56
      * [0, 1] = 2*4 + 3*3 + 4*2 = 25  
      */
-    m1 = new Matrix(new double[][] { { 2, 3, 4 } }, 1, 3);
-    m2 = new Matrix(new double[][] { { 5, 4 }, { 6, 3 }, { 7, 2 } }, 3, 2);
+    m1 = new Matrix(new double[][] { { 2, 3, 4 } });
+    m2 = new Matrix(new double[][] { { 5, 4 }, { 6, 3 }, { 7, 2 } });
     m3 = m1.postMultiply(m2);
     assertEquals(m3.rows, 1);
     assertEquals(m3.cols, 2);
@@ -157,6 +156,26 @@ public class MatrixTest
     assertEquals(m3.value[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();
+    assertTrue(matrixEquals(m1, m2));
+  }
+
   /**
    * main method extracted from Matrix
    * 
@@ -175,7 +194,7 @@ public class MatrixTest
       }
     }
   
-    Matrix origmat = new Matrix(in, n, n);
+    Matrix origmat = new Matrix(in);
   
     // System.out.println(" --- Original matrix ---- ");
     // / origmat.print(System.out);