X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fmath%2FSparseMatrixTest.java;h=3c2ccaa21f8aac9f889c34cf1246e11c2b8e44d8;hb=80ff57c095b792b8e8e123ddb0eff4d1780d6cbd;hp=607d415fd15dc63b43ef97ae9158eaa58e2351b4;hpb=ab7ccf4373a27d71bca31bd6356c1390d9a0054c;p=jalview.git

diff --git a/test/jalview/math/SparseMatrixTest.java b/test/jalview/math/SparseMatrixTest.java
index 607d415..3c2ccaa 100644
--- a/test/jalview/math/SparseMatrixTest.java
+++ b/test/jalview/math/SparseMatrixTest.java
@@ -134,7 +134,7 @@ public class SparseMatrixTest
      * also check m2.preMultiply(m1) - should be same as m1.postMultiply(m2) 
      */
     MatrixI m4 = m2.preMultiply(m1);
-    assertMatricesMatch(m3, m4);
+    assertMatricesMatch(m3, m4, 0.00001d);
 
     /*
      * m1 has more rows than columns
@@ -154,7 +154,7 @@ public class SparseMatrixTest
     assertEquals(m3.getValue(1, 2), 3000d);
 
     m4 = m2.preMultiply(m1);
-    assertMatricesMatch(m3, m4);
+    assertMatricesMatch(m3, m4, 0.00001d);
 
     /*
      * m1 has more columns than rows
@@ -176,7 +176,7 @@ public class SparseMatrixTest
      * and check premultiply equivalent
      */
     m4 = m2.preMultiply(m1);
-    assertMatricesMatch(m3, m4);
+    assertMatricesMatch(m3, m4, 0.00001d);
   }
 
   @Test(groups = "Timing")
@@ -200,10 +200,8 @@ 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;
+    int rows = 10;
     int cols = rows;
     double[][] d = getSparseValues(rows, cols, 3);
 
@@ -221,13 +219,13 @@ public class SparseMatrixTest
     }
     Matrix m1 = new Matrix(d);
     Matrix m2 = new SparseMatrix(d1);
-    assertMatricesMatch(m1, m2); // sanity check
+    assertMatricesMatch(m1, m2, 0.00001d); // sanity check
     m1.tred();
     m2.tred();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
   }
 
-  private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+  private void assertMatricesMatch(MatrixI m1, MatrixI m2, double delta)
   {
     if (m1.height() != m2.height())
     {
@@ -249,7 +247,7 @@ public class SparseMatrixTest
         }
       }
     }
-    ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
+    ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), delta);
     ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
   }
 
@@ -304,11 +302,11 @@ public class SparseMatrixTest
     // have to do tred() before doing tqli()
     m1.tred();
     m2.tred();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
 
     m1.tqli();
     m2.tqli();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
   }
 
   /**
@@ -316,25 +314,29 @@ 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 +379,38 @@ 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, 1.0e16); // sanity check
+    m1.tred();
+    m2.tred();
+    assertMatricesMatch(m1, m2, 0.00001d);
+  }
 }
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