X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fmath%2FMatrixTest.java;h=2cde5936b38283191711cb961d40edbbb651d905;hb=refs%2Fheads%2Ffeature%2FJAL-2738GeneLocus;hp=61b98f362a0ae39845954e2e00865acd231fed2d;hpb=df1447b81289138e8bd0caaf7c7117ad71f74f29;p=jalview.git

diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 61b98f3..2cde593 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -1,6 +1,7 @@
 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;
@@ -187,8 +188,23 @@ 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);
   }
 
   /**
@@ -354,7 +370,7 @@ 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 +392,10 @@ 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")
@@ -502,4 +520,31 @@ 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
+  }
 }