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

[jalview.git] / test / jalview / math / MatrixTest.java

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 1500dc6..961602d 100644 (file)
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -1,14 +1,19 @@
 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;
+import org.testng.internal.junit.ArrayAsserts;
 
 public class MatrixTest
 {
+  final static double DELTA = 0.0001d;
+
   @Test(groups = "Timing")
   public void testPreMultiply_timing()
   {
@@ -28,8 +33,8 @@ public class MatrixTest
   @Test(groups = "Functional")
   public void testPreMultiply()
   {
-    MatrixI m1 = new Matrix(new double[][] { { 2, 3, 4 } }); // 1x3
-    MatrixI m2 = new Matrix(new double[][] { { 5 }, { 6 }, { 7 } }); // 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
@@ -165,6 +170,26 @@ public class MatrixTest
     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 = (Matrix) m1.copy();
+    assertTrue(matrixEquals(m1, m2));
+  }
+
   /**
    * main method extracted from Matrix
    * 
@@ -255,4 +280,102 @@ public class MatrixTest
     assertEquals(Matrix.sign(1, 2), 1d);
     assertEquals(Matrix.sign(1, 0), 1d);
   }
+
+  /**
+   * Helper method to make values for a sparse, pseudo-random symmetric matrix
+   * 
+   * @param rows
+   * @param cols
+   * @param occupancy
+   *          one in 'occupancy' entries will be non-zero
+   * @return
+   */
+  public double[][] getSparseValues(int rows, int cols, int occupancy)
+  {
+    Random r = new Random(1729);
+
+    /*
+     * generate whole number values between -12 and +12
+     * (to mimic score matrices used in Jalview)
+     */
+    double[][] d = new double[rows][cols];
+    int m = 0;
+    for (int i = 0; i < rows; i++)
+    {
+      if (++m % occupancy == 0)
+      {
+        d[i][i] = r.nextInt() % 13; // diagonal
+      }
+      for (int j = 0; j < i; j++)
+      {
+        if (++m % occupancy == 0)
+        {
+          d[i][j] = r.nextInt() % 13;
+          d[j][i] = d[i][j];
+        }
+      }
+    }
+    return d;
+  
+  }
+
+  /**
+   * Verify that the results of method tred() are the same if the calculation is
+   * redone
+   */
+  @Test(groups = "Functional")
+  public void testTred_reproducible()
+  {
+    /*
+     * make a pseudo-random symmetric matrix as required for tred/tqli
+     */
+    int rows = 10;
+    int cols = rows;
+    double[][] d = getSparseValues(rows, cols, 3);
+  
+    /*
+     * make a copy of the values so m1, m2 are not
+     * sharing arrays!
+     */
+    double[][] d1 = new double[rows][cols];
+    for (int row = 0; row < rows; row++)
+    {
+      for (int col = 0; col < cols; col++)
+      {
+        d1[row][col] = d[row][col];
+      }
+    }
+    Matrix m1 = new Matrix(d);
+    Matrix m2 = new Matrix(d1);
+    assertMatricesMatch(m1, m2); // sanity check
+    m1.tred();
+    m2.tred();
+    assertMatricesMatch(m1, m2);
+  }
+
+  private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+  {
+    if (m1.height() != m2.height())
+    {
+      fail("height mismatch");
+    }
+    if (m1.width() != m2.width())
+    {
+      fail("width mismatch");
+    }
+    for (int row = 0; row < m1.height(); row++)
+    {
+      for (int col = 0; col < m1.width(); col++)
+      {
+        double v2 = m2.getValue(row, col);
+        double v1 = m1.getValue(row, col);
+        if (Math.abs(v1 - v2) > DELTA)
+        {
+          fail(String.format("At [%d, %d] %f != %f", row, col, v1, v2));
+        }
+      }
+    }
+    ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
+    ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
+  }
 }