X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fmath%2FMatrixTest.java;h=71050c1dc8c8bedd79bafac472ce3fd0c6fd63f7;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=61b98f362a0ae39845954e2e00865acd231fed2d;hpb=df1447b81289138e8bd0caaf7c7117ad71f74f29;p=jalview.git

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 61b98f3..71050c1 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -1,6 +1,8 @@
 package jalview.math;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
@@ -59,7 +61,8 @@ public class MatrixTest
 
   @Test(
     groups = "Functional",
-    expectedExceptions = { IllegalArgumentException.class })
+    expectedExceptions =
+    { IllegalArgumentException.class })
   public void testPreMultiply_tooManyColumns()
   {
     Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
@@ -74,7 +77,8 @@ public class MatrixTest
 
   @Test(
     groups = "Functional",
-    expectedExceptions = { IllegalArgumentException.class })
+    expectedExceptions =
+    { IllegalArgumentException.class })
   public void testPreMultiply_tooFewColumns()
   {
     Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
@@ -86,9 +90,9 @@ public class MatrixTest
     m1.preMultiply(m1);
     fail("Expected exception");
   }
-  
-  
-  private boolean matrixEquals(Matrix m1, Matrix m2) {
+
+  private boolean matrixEquals(Matrix m1, Matrix m2)
+  {
     if (m1.width() != m2.width() || m1.height() != m2.height())
     {
       return false;
@@ -115,7 +119,9 @@ public class MatrixTest
      * (5040 50400)
      */
     MatrixI m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } });
-    MatrixI m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } });
+    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]");
@@ -187,8 +193,23 @@ public class MatrixTest
       }
     }
     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);
   }
 
   /**
@@ -200,7 +221,7 @@ public class MatrixTest
   {
     int n = Integer.parseInt(args[0]);
     double[][] in = new double[n][n];
-  
+
     for (int i = 0; i < n; i++)
     {
       for (int j = 0; j < n; j++)
@@ -208,31 +229,31 @@ public class MatrixTest
         in[i][j] = Math.random();
       }
     }
-  
+
     Matrix origmat = new Matrix(in);
-  
+
     // System.out.println(" --- Original matrix ---- ");
     // / origmat.print(System.out);
     // System.out.println();
     // System.out.println(" --- transpose matrix ---- ");
     MatrixI trans = origmat.transpose();
-  
+
     // trans.print(System.out);
     // System.out.println();
     // System.out.println(" --- OrigT * Orig ---- ");
     MatrixI symm = trans.postMultiply(origmat);
-  
+
     // symm.print(System.out);
     // System.out.println();
     // Copy the symmetric matrix for later
     // Matrix origsymm = symm.copy();
-  
+
     // This produces the tridiagonal transformation matrix
     // long tstart = System.currentTimeMillis();
     symm.tred();
-  
+
     // long tend = System.currentTimeMillis();
-  
+
     // System.out.println("Time take for tred = " + (tend-tstart) + "ms");
     // System.out.println(" ---Tridiag transform matrix ---");
     // symm.print(System.out);
@@ -247,7 +268,7 @@ public class MatrixTest
     // tstart = System.currentTimeMillis();
     symm.tqli();
     // tend = System.currentTimeMillis();
-  
+
     // System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
     // System.out.println(" --- New diagonalization matrix ---");
     // symm.print(System.out);
@@ -317,7 +338,7 @@ public class MatrixTest
       }
     }
     return d;
-  
+
   }
 
   /**
@@ -333,7 +354,7 @@ public class MatrixTest
     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!
@@ -354,7 +375,7 @@ public class MatrixTest
     assertMatricesMatch(m1, m2);
   }
 
-  private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+  public static void assertMatricesMatch(MatrixI m1, MatrixI m2)
   {
     if (m1.height() != m2.height())
     {
@@ -376,8 +397,10 @@ public class MatrixTest
         }
       }
     }
-    ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
-    ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
+    ArrayAsserts.assertArrayEquals("D vector", m1.getD(), m2.getD(),
+            0.00001d);
+    ArrayAsserts.assertArrayEquals("E vector", m1.getE(), m2.getE(),
+            0.00001d);
   }
 
   @Test(groups = "Functional")
@@ -393,8 +416,8 @@ public class MatrixTest
      * normal case
      */
     double[][] vals = new double[2][];
-    vals[0] = new double[] {7d, 1d, -2.3d};
-    vals[1] = new double[] {-12d, 94.3d, -102.34d};
+    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);
@@ -443,7 +466,8 @@ public class MatrixTest
   public void testReverseRange_maxToZero()
   {
     Matrix m1 = new Matrix(
-            new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+            new double[][]
+            { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
 
     /*
      * subtract all from max: range -3.4 to 15 becomes 18.4 to 0
@@ -475,8 +499,9 @@ public class MatrixTest
   public void testReverseRange_swapMinMax()
   {
     Matrix m1 = new Matrix(
-            new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
-  
+            new double[][]
+            { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+
     /*
      * swap all values in min-max range
      * = subtract from (min + max = 11.6) 
@@ -489,7 +514,7 @@ public class MatrixTest
     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
      */
@@ -502,4 +527,59 @@ public class MatrixTest
     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
+  }
+
+  @Test(groups = "Functional")
+  public void testEquals()
+  {
+    double[][] values = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+    Matrix m1 = new Matrix(values);
+    double[][] values2 = new double[][] { { 1, 2, 3 }, { 4, 5, 6 } };
+    Matrix m2 = new Matrix(values2);
+
+    double delta = 0.0001d;
+    assertTrue(m1.equals(m1, delta));
+    assertTrue(m1.equals(m2, delta));
+    assertTrue(m2.equals(m1, delta));
+
+    double[][] values3 = new double[][] { { 1, 2, 3 }, { 4, 5, 7 } };
+    m2 = new Matrix(values3);
+    assertFalse(m1.equals(m2, delta));
+    assertFalse(m2.equals(m1, delta));
+
+    // must be same shape
+    values2 = new double[][] { { 1, 2, 3 } };
+    m2 = new Matrix(values2);
+    assertFalse(m2.equals(m1, delta));
+
+    assertFalse(m1.equals(null, delta));
+  }
 }