X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fmath%2FMatrixTest.java;h=2cde5936b38283191711cb961d40edbbb651d905;hb=55d8ed2824ef1e2f5a8ea30f43d14980119f8c43;hp=795b2fad0dd7a3685e1813b7d13eb923f9c227be;hpb=e06941005a462eff3578ec863630edbc519b560f;p=jalview.git

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 795b2fa..2cde593 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -1,23 +1,30 @@
 package jalview.math;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertNull;
+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 = 0.000001d;
+
   @Test(groups = "Timing")
   public void testPreMultiply_timing()
   {
-    int rows = 500;
-    int cols = 1000;
+    int rows = 50; // increase to stress test timing
+    int cols = 100;
     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;
@@ -28,27 +35,27 @@ 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
      * 2x5 + 3x6 + 4*7 =  56
      */
-    Matrix m3 = m2.preMultiply(m1);
-    assertEquals(m3.rows, 1);
-    assertEquals(m3.cols, 1);
-    assertEquals(m3.value[0][0], 56d);
+    MatrixI m3 = m2.preMultiply(m1);
+    assertEquals(m3.height(), 1);
+    assertEquals(m3.width(), 1);
+    assertEquals(m3.getValue(0, 0), 56d);
 
     /*
      * 3x1 times 1x3 is 3x3
      */
     m3 = m1.preMultiply(m2);
-    assertEquals(m3.rows, 3);
-    assertEquals(m3.cols, 3);
-    assertEquals(Arrays.toString(m3.value[0]), "[10.0, 15.0, 20.0]");
-    assertEquals(Arrays.toString(m3.value[1]), "[12.0, 18.0, 24.0]");
-    assertEquals(Arrays.toString(m3.value[2]), "[14.0, 21.0, 28.0]");
+    assertEquals(m3.height(), 3);
+    assertEquals(m3.width(), 3);
+    assertEquals(Arrays.toString(m3.getRow(0)), "[10.0, 15.0, 20.0]");
+    assertEquals(Arrays.toString(m3.getRow(1)), "[12.0, 18.0, 24.0]");
+    assertEquals(Arrays.toString(m3.getRow(2)), "[14.0, 21.0, 28.0]");
   }
 
   @Test(
@@ -56,8 +63,7 @@ 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 +78,7 @@ 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 - 
@@ -85,7 +90,18 @@ public class MatrixTest
   
   
   private boolean matrixEquals(Matrix m1, Matrix m2) {
-    return Arrays.deepEquals(m1.value, m2.value);
+    if (m1.width() != m2.width() || m1.height() != m2.height())
+    {
+      return false;
+    }
+    for (int i = 0; i < m1.height(); i++)
+    {
+      if (!Arrays.equals(m1.getRow(i), m2.getRow(i)))
+      {
+        return false;
+      }
+    }
+    return true;
   }
 
   @Test(groups = "Functional")
@@ -99,37 +115,36 @@ 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 m3 = m1.postMultiply(m2);
-    assertEquals(Arrays.toString(m3.value[0]), "[3020.0, 30200.0]");
-    assertEquals(Arrays.toString(m3.value[1]), "[5040.0, 50400.0]");
+    MatrixI m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } });
+    MatrixI m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } });
+    MatrixI m3 = m1.postMultiply(m2);
+    assertEquals(Arrays.toString(m3.getRow(0)), "[3020.0, 30200.0]");
+    assertEquals(Arrays.toString(m3.getRow(1)), "[5040.0, 50400.0]");
 
     /*
      * also check m2.preMultiply(m1) - should be same as m1.postMultiply(m2) 
      */
     m3 = m2.preMultiply(m1);
-    assertEquals(Arrays.toString(m3.value[0]), "[3020.0, 30200.0]");
-    assertEquals(Arrays.toString(m3.value[1]), "[5040.0, 50400.0]");
+    assertEquals(Arrays.toString(m3.getRow(0)), "[3020.0, 30200.0]");
+    assertEquals(Arrays.toString(m3.getRow(1)), "[5040.0, 50400.0]");
 
     /*
      * m1 has more rows than columns
      * (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);
-    assertEquals(Arrays.toString(m3.value[0]), "[20.0, 200.0, 2000.0]");
-    assertEquals(Arrays.toString(m3.value[1]), "[30.0, 300.0, 3000.0]");
+    assertEquals(m3.height(), 2);
+    assertEquals(m3.width(), 3);
+    assertEquals(Arrays.toString(m3.getRow(0)), "[20.0, 200.0, 2000.0]");
+    assertEquals(Arrays.toString(m3.getRow(1)), "[30.0, 300.0, 3000.0]");
     m3 = m2.preMultiply(m1);
-    assertEquals(m3.rows, 2);
-    assertEquals(m3.cols, 3);
-    assertEquals(Arrays.toString(m3.value[0]), "[20.0, 200.0, 2000.0]");
-    assertEquals(Arrays.toString(m3.value[1]), "[30.0, 300.0, 3000.0]");
+    assertEquals(m3.height(), 2);
+    assertEquals(m3.width(), 3);
+    assertEquals(Arrays.toString(m3.getRow(0)), "[20.0, 200.0, 2000.0]");
+    assertEquals(Arrays.toString(m3.getRow(1)), "[30.0, 300.0, 3000.0]");
 
     /*
      * m1 has more columns than rows
@@ -139,22 +154,57 @@ 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);
-    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);
 
     /*
      * 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 = (Matrix) m1.copy();
+    assertNotSame(m1, m2);
+    assertTrue(matrixEquals(m1, m2));
+    assertNull(m2.d);
+    assertNull(m2.e);
+
+    /*
+     * now add d and e vectors and recopy
+     */
+    m1.d = Arrays.copyOf(in[2], in[2].length);
+    m1.e = Arrays.copyOf(in[4], in[4].length);
+    m2 = (Matrix) m1.copy();
+    assertNotSame(m2.d, m1.d);
+    assertNotSame(m2.e, m1.e);
+    assertEquals(m2.d, m1.d);
+    assertEquals(m2.e, m1.e);
   }
 
   /**
@@ -175,18 +225,18 @@ public class MatrixTest
       }
     }
   
-    Matrix origmat = new Matrix(in, n, n);
+    Matrix origmat = new Matrix(in);
   
     // System.out.println(" --- Original matrix ---- ");
     // / origmat.print(System.out);
     // System.out.println();
     // System.out.println(" --- transpose matrix ---- ");
-    Matrix trans = origmat.transpose();
+    MatrixI trans = origmat.transpose();
   
     // trans.print(System.out);
     // System.out.println();
     // System.out.println(" --- OrigT * Orig ---- ");
-    Matrix symm = trans.postMultiply(origmat);
+    MatrixI symm = trans.postMultiply(origmat);
   
     // symm.print(System.out);
     // System.out.println();
@@ -236,4 +286,265 @@ public class MatrixTest
     // }
     // System.out.println();
   }
+
+  @Test(groups = "Timing")
+  public void testSign()
+  {
+    assertEquals(Matrix.sign(-1, -2), -1d);
+    assertEquals(Matrix.sign(-1, 2), 1d);
+    assertEquals(Matrix.sign(-1, 0), 1d);
+    assertEquals(Matrix.sign(1, -2), -1d);
+    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);
+  }
+
+  public static 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("D vector", m1.getD(), m2.getD(),
+            0.00001d);
+    ArrayAsserts.assertArrayEquals("E vector", m1.getE(), m2.getE(),
+            0.00001d);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindMinMax()
+  {
+    /*
+     * empty matrix case
+     */
+    Matrix m = new Matrix(new double[][] { {} });
+    assertNull(m.findMinMax());
+
+    /*
+     * normal case
+     */
+    double[][] vals = new double[2][];
+    vals[0] = new double[] {7d, 1d, -2.3d};
+    vals[1] = new double[] {-12d, 94.3d, -102.34d};
+    m = new Matrix(vals);
+    double[] minMax = m.findMinMax();
+    assertEquals(minMax[0], -102.34d);
+    assertEquals(minMax[1], 94.3d);
+  }
+
+  @Test(groups = { "Functional", "Timing" })
+  public void testFindMinMax_timing()
+  {
+    Random r = new Random();
+    int size = 1000; // increase to stress test timing
+    double[][] vals = new double[size][size];
+    double max = -Double.MAX_VALUE;
+    double min = Double.MAX_VALUE;
+    for (int i = 0; i < size; i++)
+    {
+      vals[i] = new double[size];
+      for (int j = 0; j < size; j++)
+      {
+        // use nextLong rather than nextDouble to include negative values
+        double d = r.nextLong();
+        if (d > max)
+        {
+          max = d;
+        }
+        if (d < min)
+        {
+          min = d;
+        }
+        vals[i][j] = d;
+      }
+    }
+    Matrix m = new Matrix(vals);
+    long now = System.currentTimeMillis();
+    double[] minMax = m.findMinMax();
+    System.out.println(String.format("findMinMax for %d x %d took %dms",
+            size, size, (System.currentTimeMillis() - now)));
+    assertEquals(minMax[0], min);
+    assertEquals(minMax[1], max);
+  }
+
+  /**
+   * Test range reversal with maximum value becoming zero
+   */
+  @Test(groups = "Functional")
+  public void testReverseRange_maxToZero()
+  {
+    Matrix m1 = new Matrix(
+            new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+
+    /*
+     * subtract all from max: range -3.4 to 15 becomes 18.4 to 0
+     */
+    m1.reverseRange(true);
+    assertEquals(m1.getValue(0, 0), 13d, DELTA);
+    assertEquals(m1.getValue(0, 1), 11.5d, DELTA);
+    assertEquals(m1.getValue(0, 2), 11d, DELTA);
+    assertEquals(m1.getValue(1, 0), 18.4d, DELTA);
+    assertEquals(m1.getValue(1, 1), 11d, DELTA);
+    assertEquals(m1.getValue(1, 2), 0d, DELTA);
+
+    /*
+     * repeat operation - range is now 0 to 18.4
+     */
+    m1.reverseRange(true);
+    assertEquals(m1.getValue(0, 0), 5.4d, DELTA);
+    assertEquals(m1.getValue(0, 1), 6.9d, DELTA);
+    assertEquals(m1.getValue(0, 2), 7.4d, DELTA);
+    assertEquals(m1.getValue(1, 0), 0d, DELTA);
+    assertEquals(m1.getValue(1, 1), 7.4d, DELTA);
+    assertEquals(m1.getValue(1, 2), 18.4d, DELTA);
+  }
+
+  /**
+   * Test range reversal with minimum and maximum values swapped
+   */
+  @Test(groups = "Functional")
+  public void testReverseRange_swapMinMax()
+  {
+    Matrix m1 = new Matrix(
+            new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+  
+    /*
+     * swap all values in min-max range
+     * = subtract from (min + max = 11.6) 
+     * range -3.4 to 15 becomes 18.4 to -3.4
+     */
+    m1.reverseRange(false);
+    assertEquals(m1.getValue(0, 0), 9.6d, DELTA);
+    assertEquals(m1.getValue(0, 1), 8.1d, DELTA);
+    assertEquals(m1.getValue(0, 2), 7.6d, DELTA);
+    assertEquals(m1.getValue(1, 0), 15d, DELTA);
+    assertEquals(m1.getValue(1, 1), 7.6d, DELTA);
+    assertEquals(m1.getValue(1, 2), -3.4d, DELTA);
+  
+    /*
+     * repeat operation - original values restored
+     */
+    m1.reverseRange(false);
+    assertEquals(m1.getValue(0, 0), 2d, DELTA);
+    assertEquals(m1.getValue(0, 1), 3.5d, DELTA);
+    assertEquals(m1.getValue(0, 2), 4d, DELTA);
+    assertEquals(m1.getValue(1, 0), -3.4d, DELTA);
+    assertEquals(m1.getValue(1, 1), 4d, DELTA);
+    assertEquals(m1.getValue(1, 2), 15d, DELTA);
+  }
+
+  @Test(groups = "Functional")
+  public void testMultiply()
+  {
+    Matrix m = new Matrix(new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+    m.multiply(2d);
+    assertEquals(m.getValue(0, 0), 4d, DELTA);
+    assertEquals(m.getValue(0, 1), 7d, DELTA);
+    assertEquals(m.getValue(0, 2), 8d, DELTA);
+    assertEquals(m.getValue(1, 0), -6.8d, DELTA);
+    assertEquals(m.getValue(1, 1), 8d, DELTA);
+    assertEquals(m.getValue(1, 2), 30d, DELTA);
+  }
+
+  @Test(groups = "Functional")
+  public void testConstructor()
+  {
+    double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+    Matrix m = new Matrix(values);
+    assertEquals(m.getValue(0, 0), 1d, DELTA);
+
+    /*
+     * verify the matrix has a copy of the original array
+     */
+    assertNotSame(values[0], m.getRow(0));
+    values[0][0] = -1d;
+    assertEquals(m.getValue(0, 0), 1d, DELTA); // unchanged
+  }
 }