Resolved NoNotify fails on AtomParity. Error was due to subclassing o…

…f AtomParity. Also the assertEquals params were swapped as the assertion was the wrong way. Change-Id: Idebf543ef01e1f81f9bdb1264a1dea0088c8d752 Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Nov 4, 2012 · 46ffbb4 · 46ffbb4
1 parent 938306a
commit 46ffbb4
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Showing 3 changed files with 177 additions and 3 deletions.
diff --git a/src/main/org/openscience/cdk/nonotify/NNAtomParity.java b/src/main/org/openscience/cdk/nonotify/NNAtomParity.java
@@ -29,7 +29,12 @@
 package org.openscience.cdk.nonotify;
 
 import org.openscience.cdk.AtomParity;
+import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomParity;
+import org.openscience.cdk.interfaces.IBond;
+
+import java.util.Map;
 
 /**
  * @cdk.module nonotify
@@ -49,6 +54,31 @@ public NNAtomParity(
     		int parity) {
     	super(centralAtom, first, second, third, fourth, parity);
     }
+
+    /**
+     * @inheritDoc
+     */
+    @TestMethod("testMap_Map_Map,testMap_Null_Map,testMap_Map_Map_NullElement,testMap_Map_Map_EmptyMapping")
+    @Override
+    public IAtomParity map(Map<IAtom, IAtom> atoms, Map<IBond, IBond> bonds) {
+
+        if(atoms == null) // not using bond mapping
+            throw new IllegalArgumentException("null atom mapping provided");
+
+        IAtom[] neighbors = getSurroundingAtoms();
+
+        // could map neighbours with a for loop but we need to pull individuals
+        // atoms for the constructor
+        return new NNAtomParity(
+                getAtom()  != null ? atoms.get(getAtom()) : null,
+                neighbors[0] != null ? atoms.get(neighbors[0]) : null,
+                neighbors[1] != null ? atoms.get(neighbors[1]) : null,
+                neighbors[2] != null ? atoms.get(neighbors[2]) : null,
+                neighbors[3] != null ? atoms.get(neighbors[3]) : null,
+                getParity()
+        );
+
+    }
 
 }
 

diff --git a/src/test/org/openscience/cdk/interfaces/AbstractAtomContainerTest.java b/src/test/org/openscience/cdk/interfaces/AbstractAtomContainerTest.java
@@ -404,7 +404,7 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
 
         IStereoElement element = elements.next();
 
-        Assert.assertEquals("cloned element was incorrect class", element.getClass(), chirality.getClass());
+        Assert.assertEquals("cloned element was incorrect class", chirality.getClass(), element.getClass());
         assertThat("too many stereo elements", elements.hasNext(), is(not(true)));
 
         // we've tested the class already  - cast is okay
@@ -472,7 +472,7 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
 
         IStereoElement element = elements.next();
 
-        Assert.assertEquals("cloned element was incorrect class", element.getClass(), dbStereo.getClass());
+        Assert.assertEquals("cloned element was incorrect class", dbStereo.getClass(), element.getClass());
         assertThat("too many stereo elements", elements.hasNext(), is(not(true)));
 
         // we've tested the class already - cast is okay
@@ -546,7 +546,7 @@ public abstract class AbstractAtomContainerTest extends AbstractChemObjectTest {
 
         IStereoElement element = elements.next();
 
-        Assert.assertEquals("cloned element was incorrect class", element.getClass(), chirality.getClass());
+        Assert.assertEquals("cloned element was incorrect class", chirality.getClass(), element.getClass());
         assertThat("too many stereo elements", elements.hasNext(), is(not(true)));
 
         // we've tested the class already  - cast is okay

diff --git a/src/test/org/openscience/cdk/nonotify/NNAtomParityTest.java b/src/test/org/openscience/cdk/nonotify/NNAtomParityTest.java
@@ -31,6 +31,15 @@
 import org.openscience.cdk.interfaces.AbstractAtomParityTest;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomParity;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.CoreMatchers.not;
+import static org.hamcrest.CoreMatchers.sameInstance;
 
 /**
  * Checks the functionality of the {@link NNAtomParity}.
@@ -74,4 +83,139 @@ public class NNAtomParityTest extends AbstractAtomParityTest {
         Assert.assertNotNull(parity);
     }
 
+
+    @Test public void testMap_Map_Map() throws CloneNotSupportedException {
+
+        IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
+
+        IAtom c1 = builder.newInstance(IAtom.class, "C");
+        IAtom o2 = builder.newInstance(IAtom.class, "O");
+        IAtom n3 = builder.newInstance(IAtom.class, "N");
+        IAtom c4 = builder.newInstance(IAtom.class, "C");
+        IAtom h5 = builder.newInstance(IAtom.class, "H");
+
+        // new stereo element
+        IAtomParity original = new AtomParity(c1,
+                                              o2,n3,c4,h5,
+                                              2);
+
+        // clone the atoms and place in a map
+        Map<IAtom,IAtom> mapping = new HashMap<IAtom,IAtom>();
+        IAtom c1clone = (IAtom) c1.clone(); mapping.put(c1, c1clone);
+        IAtom o2clone = (IAtom) o2.clone(); mapping.put(o2, o2clone);
+        IAtom n3clone = (IAtom) n3.clone(); mapping.put(n3, n3clone);
+        IAtom c4clone = (IAtom) c4.clone(); mapping.put(c4, c4clone);
+        IAtom h5clone = (IAtom) h5.clone(); mapping.put(h5, h5clone);
+
+        // map the existing element a new element
+        IAtomParity mapped = original.map(mapping, Collections.EMPTY_MAP);
+
+        Assert.assertThat("mapped chiral atom was the same as the original",
+                          mapped.getAtom(), is(not(sameInstance(original.getAtom()))));
+        Assert.assertThat("mapped chiral atom was not the clone",
+                          mapped.getAtom(), is(sameInstance(c1clone)));
+
+        IAtom[] originalLigands = original.getSurroundingAtoms();
+        IAtom[] mappedLigands   = mapped.getSurroundingAtoms();
+
+        Assert.assertThat("first ligand was te same as the original",
+                          mappedLigands[0], is(not(sameInstance(originalLigands[0]))));
+        Assert.assertThat("first mapped ligand was not the clone",
+                          mappedLigands[0], is(sameInstance(o2clone)));
+        Assert.assertThat("second ligand was te same as the original",
+                          mappedLigands[1], is(not(sameInstance(originalLigands[1]))));
+        Assert.assertThat("second mapped ligand was not the clone",
+                          mappedLigands[1], is(sameInstance(n3clone)));
+        Assert.assertThat("third ligand was te same as the original",
+                          mappedLigands[2], is(not(sameInstance(originalLigands[2]))));
+        Assert.assertThat("third mapped ligand was not the clone",
+                          mappedLigands[2], is(sameInstance(c4clone)));
+        Assert.assertThat("forth ligand was te same as the original",
+                          mappedLigands[3], is(not(sameInstance(originalLigands[3]))));
+        Assert.assertThat("forth mapped ligand was not the clone",
+                          mappedLigands[3], is(sameInstance(h5clone)));
+
+        Assert.assertThat("stereo was not mapped",
+                          mapped.getParity(), is(original.getParity()));
+
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testMap_Null_Map() throws CloneNotSupportedException {
+
+        IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
+
+        IAtom c1 = builder.newInstance(IAtom.class, "C");
+        IAtom o2 = builder.newInstance(IAtom.class, "O");
+        IAtom n3 = builder.newInstance(IAtom.class, "N");
+        IAtom c4 = builder.newInstance(IAtom.class, "C");
+        IAtom h5 = builder.newInstance(IAtom.class, "H");
+
+        // new stereo element
+        IAtomParity original = new AtomParity(c1,
+                                              o2,n3,c4,h5,
+                                              2);
+
+
+        // map the existing element a new element - should through an IllegalArgumentException
+        IAtomParity mapped = original.map(null, Collections.EMPTY_MAP);
+
+    }
+
+    @Test
+    public void testMap_Map_Map_NullElement() throws CloneNotSupportedException {
+
+        IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
+
+        IAtom c1 = builder.newInstance(IAtom.class, "C");
+        IAtom o2 = builder.newInstance(IAtom.class, "O");
+        IAtom n3 = builder.newInstance(IAtom.class, "N");
+        IAtom c4 = builder.newInstance(IAtom.class, "C");
+        IAtom h5 = builder.newInstance(IAtom.class, "H");
+
+        // new stereo element
+        IAtomParity original = new NNAtomParity(null,
+                                               null, null, null, null,
+                                               0);
+
+
+        // map the existing element a new element
+        IAtomParity mapped = original.map(Collections.EMPTY_MAP, Collections.EMPTY_MAP);
+
+        Assert.assertNull(mapped.getAtom());
+        Assert.assertNull(mapped.getSurroundingAtoms()[0]);
+        Assert.assertNull(mapped.getSurroundingAtoms()[1]);
+        Assert.assertNull(mapped.getSurroundingAtoms()[2]);
+        Assert.assertNull(mapped.getSurroundingAtoms()[3]);
+
+    }
+
+    @Test
+    public void testMap_Map_Map_EmptyMapping() throws CloneNotSupportedException {
+
+        IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance();
+
+        IAtom c1 = builder.newInstance(IAtom.class, "C");
+        IAtom o2 = builder.newInstance(IAtom.class, "O");
+        IAtom n3 = builder.newInstance(IAtom.class, "N");
+        IAtom c4 = builder.newInstance(IAtom.class, "C");
+        IAtom h5 = builder.newInstance(IAtom.class, "H");
+
+        // new stereo element
+        IAtomParity original = new NNAtomParity(c1,
+                                               o2,n3,c4,h5,
+                                               2);
+
+
+        // map the existing element a new element - should through an IllegalArgumentException
+        IAtomParity mapped = original.map(Collections.EMPTY_MAP, Collections.EMPTY_MAP);
+
+        Assert.assertNull(mapped.getAtom());
+        Assert.assertNull(mapped.getSurroundingAtoms()[0]);
+        Assert.assertNull(mapped.getSurroundingAtoms()[1]);
+        Assert.assertNull(mapped.getSurroundingAtoms()[2]);
+        Assert.assertNull(mapped.getSurroundingAtoms()[3]);
+        Assert.assertNotNull(mapped.getParity());
+
+    }
 }