X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fmath%2FMatrixTest.java;fp=test%2Fjalview%2Fmath%2FMatrixTest.java;h=961602d142a0572604564d555fdbf23a8e66b604;hb=d5bcc3830eab04e6db816e1c2ad8fce1dc189612;hp=a4acbd00c335ad5176deaf5805b9aaaca95b40a7;hpb=3ebdd4e28382e38a181aae1eed71549f603f9025;p=jalview.git

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index a4acbd0..961602d 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -8,9 +8,12 @@ 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()
   {
@@ -37,20 +40,20 @@ public class MatrixTest
      * 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(
@@ -85,7 +88,18 @@ 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")
@@ -99,18 +113,18 @@ public class MatrixTest
      * (3020 30200)
      * (5040 50400)
      */
-    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]");
+    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
@@ -120,15 +134,15 @@ public class MatrixTest
     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
@@ -141,19 +155,19 @@ public class MatrixTest
     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")
@@ -172,7 +186,7 @@ public class MatrixTest
       }
     }
     Matrix m1 = new Matrix(in);
-    Matrix m2 = m1.copy();
+    Matrix m2 = (Matrix) m1.copy();
     assertTrue(matrixEquals(m1, m2));
   }
 
@@ -200,12 +214,12 @@ public class MatrixTest
     // / 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();
@@ -255,4 +269,113 @@ 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);
+  }
+
+  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);
+  }
 }