Added unit tests for bugs 1270 (removalAllElements should remove ster…

…eo elements) and 1273 (double bond stereo chemistry constructor should throw an exception on wrong input). Added @cdk.bug tag for bug 1264 (stereo element cloning)

Change-Id: I71ebc95fe2fead344c305b7b505573378892c155
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

src/test/org/openscience/cdk/interfaces/AbstractAtomContainerTest.java

@@ -354,7 +354,7 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
      * Unit test to ensure that the stereo elements remain intact on cloning a
      * container. This test ensures tetrahedral chirality is preserved
      *
-     * @cdk.bug 1###
+     * @cdk.bug 1264
      * @throws Exception
      */
     @Test public void testClone_IStereoElement_Tetrahedral() throws Exception {
@@ -430,7 +430,7 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
      * Unit test to ensure that the stereo elements remain intact on cloning a
      * container. This test ensures DoubleBondStereochemistry is preserved
      *
-     * @cdk.bug 1###
+     * @cdk.bug 1264
      * @throws Exception
      */
     @Test public void testClone_IStereoElement_DoubleBond() throws Exception {
@@ -496,7 +496,7 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
      * Unit test to ensure that the stereo elements remain intact on cloning a
      * container. This test ensures AtomParity is preserved
      *
-     * @cdk.bug 1###
+     * @cdk.bug 1264
      * @throws Exception
      */
     @Test public void testClone_IStereoElement_AtomParity() throws Exception {
@@ -821,7 +821,40 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
         Assert.assertEquals(0, container.getAtomCount());
         Assert.assertEquals(0, container.getBondCount());
     }
-
+
+    /**
+     * Unit test ensures that stereo-elements are removed from a container
+     * when {@link IAtomContainer#removeAllElements()} is invoked.
+     * @cdk.bug 1270
+     */
+    @Test public void testRemoveAllElements_StereoElements() {
+
+        IAtomContainer container = (IAtomContainer)newChemObject();
+        container.addStereoElement(new TetrahedralChirality(container.getBuilder().newInstance(IAtom.class),
+                                                            new IAtom[4],
+                                                            ITetrahedralChirality.Stereo.CLOCKWISE));
+
+        int count = 0;
+        for (IStereoElement element : container.stereoElements()) {
+            count++;
+        }
+
+        assertThat("no stereo elements were added", count, is(1));
+
+        count = 0;
+
+        assertThat("count did not reset", count, is(0));
+
+        container.removeAllElements();
+
+        for (IStereoElement element : container.stereoElements()) {
+            count++;
+        }
+
+        assertThat("stereo elements were not removed", count, is(0));
+
+    }
+
     @Test public void testRemoveAtom_int() {
     	IAtomContainer acetone = (IAtomContainer)newChemObject();
         IAtom c1 = acetone.getBuilder().newInstance(IAtom.class,"C");

src/test/org/openscience/cdk/stereo/DoubleBondStereochemistryTest.java

@@ -72,6 +72,23 @@ public static void setup() throws Exception {
         };
     }
 
+    /**
+     * Unit test ensures an exception is thrown if more the two elements are
+     * passed to the constructor. When IDoubleBondStereoChemistry.getBonds()
+     * is invoked the fixed size array is copied to an array of size 2. If
+     * more then 2 bonds are given they would be truncated.
+     *
+     * @cdk.bug 1273
+     */
+    @Test(expected = IllegalArgumentException.class)
+    public void testConstructor_TooManyBonds() {
+
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+
+        new DoubleBondStereochemistry(builder.newInstance(IBond.class),
+                                      new IBond[3], Conformation.OPPOSITE);
+    }
+
     @Test
     public void testConstructor() {
         DoubleBondStereochemistry stereo = new DoubleBondStereochemistry(