JAL-2379 more realistic matrices for unit tests

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 1500dc6..bd5614f 100644 (file)
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -4,11 +4,15 @@ import static org.testng.Assert.assertEquals;
 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()
   {
@@ -255,4 +259,102 @@ 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);
+  }
 }

diff --git a/test/jalview/math/SparseMatrixTest.java b/test/jalview/math/SparseMatrixTest.java
index 607d415..5e32e18 100644 (file)
--- a/test/jalview/math/SparseMatrixTest.java
+++ b/test/jalview/math/SparseMatrixTest.java
@@ -200,10 +200,9 @@ public class SparseMatrixTest
   {
     /*
      * make a pseudo-random symmetric matrix as required for tred/tqli
-     * note: test fails for matrices larger than 6x6 due to double value
-     * rounding only (random values result in very small values)
      */
-    int rows = 6;
+    // TODO why does this fail for rows > 9??
+    int rows = 9;
     int cols = rows;
     double[][] d = getSparseValues(rows, cols, 3);
 
@@ -316,25 +315,29 @@ public class SparseMatrixTest
    * 
    * @param rows
    * @param cols
-   * @param fraction
-   *          one n fraction entries will be non-zero
+   * @param occupancy
+   *          one in 'occupancy' entries will be non-zero
    * @return
    */
-  public double[][] getSparseValues(int rows, int cols, int fraction)
+  public double[][] getSparseValues(int rows, int cols, int occupancy)
   {
+    /*
+     * 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 % fraction == 0)
+      if (++m % occupancy == 0)
       {
-        d[i][i] = r.nextDouble(); // diagonal
+        d[i][i] = r.nextInt() % 13; // diagonal
       }
       for (int j = 0; j < i; j++)
       {
-        if (++m % fraction == 0)
+        if (++m % occupancy == 0)
         {
-          d[i][j] = r.nextDouble();
+          d[i][j] = r.nextInt() % 13;
           d[j][i] = d[i][j];
         }
       }
@@ -377,4 +380,38 @@ public class SparseMatrixTest
     { 0, 6, 0, 0, 0 } });
     assertEquals(m1.getFillRatio(), 0.4f);
   }
+
+  /**
+   * 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 SparseMatrix(d);
+    Matrix m2 = new SparseMatrix(d1);
+    assertMatricesMatch(m1, m2); // sanity check
+    m1.tred();
+    m2.tred();
+    assertMatricesMatch(m1, m2);
+  }
 }
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