Moved TetrahedralChirality from data to core.

egonw · egonw · commit 0e41b055507c · 2012-10-31T19:14:10.000+01:00
- added missing TestMethod/-Class annotation
- made TetrahedralChirality getBuilder() settable via a setBuilder()
- updated the IChemObjectBuilder implementations to instantiate this
  class via that builder
- added a unit test in AbstractChemObjectBuilderTest to test that
  the properly build TetrahedralChirality instances

Signed-off-by: Rajarshi  Guha &lt;rajarshi.guha@gmail.com&gt;

Conflicts:
	src/test/org/openscience/cdk/AbstractChemObjectBuilderTest.java
	src/test/org/openscience/cdk/modulesuites/McoreTests.java

Change-Id: Iae7ed5dfc75d902d4cde5fc80bdea9de84379884
Signed-off-by: John May &lt;john.wilkinsonmay@gmail.com&gt;
diff --git a/src/main/org/openscience/cdk/DefaultChemObjectBuilder.java b/src/main/org/openscience/cdk/DefaultChemObjectBuilder.java
@@ -68,10 +68,13 @@
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.interfaces.IStrand;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
 import org.openscience.cdk.protein.data.PDBAtom;
 import org.openscience.cdk.protein.data.PDBMonomer;
 import org.openscience.cdk.protein.data.PDBPolymer;
 import org.openscience.cdk.protein.data.PDBStructure;
+import org.openscience.cdk.stereo.TetrahedralChirality;
 
 /**
  * A helper class to instantiate a {@link ICDKObject} for the original CDK
@@ -167,6 +170,18 @@ public <T extends ICDKObject>T newInstance(
             if (params.length == 0) return (T)new PDBStructure();
         } else if (clazz.isAssignableFrom(IMolecularFormula.class)) {
             if (params.length == 0) return (T)new MolecularFormula();
+        } else if (clazz.isAssignableFrom(ITetrahedralChirality.class)) {
+            System.out.println(params.length);
+            if (params.length == 3 &&
+                params[0] instanceof IAtom &&
+                params[1] instanceof IAtom[] &&
+                params[2] instanceof Stereo) {
+                TetrahedralChirality chirality = new TetrahedralChirality(
+                    (IAtom)params[0], (IAtom[])params[1], (Stereo)params[2]
+                );
+                chirality.setBuilder(this);
+                return (T)chirality;
+            }
         } else if (clazz.isAssignableFrom(IMolecularFormulaSet.class)) {
             if (params.length == 0) return (T)new MolecularFormulaSet();
             if (params.length == 1 &&
diff --git a/src/main/org/openscience/cdk/debug/DebugChemObjectBuilder.java b/src/main/org/openscience/cdk/debug/DebugChemObjectBuilder.java
@@ -65,6 +65,9 @@
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.interfaces.IStrand;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
+import org.openscience.cdk.stereo.TetrahedralChirality;
 
 /**
  * A helper class to instantiate a {@link IChemObject} for the original CDK
@@ -371,6 +374,18 @@ public <T extends ICDKObject>T newInstance(
             if (params.length == 1 &&
                     params[0] instanceof IMolecularFormula)
                 return (T)new DebugAdductFormula((IMolecularFormula)params[0]);
+        } else if (clazz.isAssignableFrom(ITetrahedralChirality.class)) {
+            System.out.println(params.length);
+            if (params.length == 3 &&
+                params[0] instanceof IAtom &&
+                params[1] instanceof IAtom[] &&
+                params[2] instanceof Stereo) {
+                TetrahedralChirality chirality = new TetrahedralChirality(
+                    (IAtom)params[0], (IAtom[])params[1], (Stereo)params[2]
+                );
+                chirality.setBuilder(this);
+                return (T)chirality;
+            }
         }
 
 	    throw new IllegalArgumentException(getNoConstructorFoundMessage(clazz));
diff --git a/src/main/org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java b/src/main/org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java
@@ -65,6 +65,9 @@
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.interfaces.IStrand;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
+import org.openscience.cdk.stereo.TetrahedralChirality;
 
 /**
  * A helper class to instantiate a {@link IChemObject} for the original CDK
@@ -371,6 +374,18 @@ public <T extends ICDKObject>T newInstance(
             if (params.length == 1 &&
                     params[0] instanceof IMolecularFormula)
                 return (T)new NNMolecularFormulaSet((IMolecularFormula)params[0]);
+        } else if (clazz.isAssignableFrom(ITetrahedralChirality.class)) {
+            System.out.println(params.length);
+            if (params.length == 3 &&
+                params[0] instanceof IAtom &&
+                params[1] instanceof IAtom[] &&
+                params[2] instanceof Stereo) {
+                TetrahedralChirality chirality = new TetrahedralChirality(
+                    (IAtom)params[0], (IAtom[])params[1], (Stereo)params[2]
+                );
+                chirality.setBuilder(this);
+                return (T)chirality;
+            }
         } else if (clazz.isAssignableFrom(IAdductFormula.class)) {
             if (params.length == 0) return (T)new NNAdductFormula();
             if (params.length == 1 &&
diff --git a/src/main/org/openscience/cdk/silent/SilentChemObjectBuilder.java b/src/main/org/openscience/cdk/silent/SilentChemObjectBuilder.java
@@ -38,6 +38,7 @@
 import org.openscience.cdk.interfaces.IChemFile;
 import org.openscience.cdk.interfaces.IChemModel;
 import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IChemSequence;
 import org.openscience.cdk.interfaces.ICrystal;
 import org.openscience.cdk.interfaces.IElectronContainer;
@@ -51,7 +52,6 @@
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.interfaces.IMoleculeSet;
 import org.openscience.cdk.interfaces.IMonomer;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IPDBAtom;
 import org.openscience.cdk.interfaces.IPDBMonomer;
 import org.openscience.cdk.interfaces.IPDBPolymer;
@@ -65,6 +65,9 @@
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.interfaces.IStrand;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
+import org.openscience.cdk.stereo.TetrahedralChirality;
 
 /**
  * A helper class to instantiate a {@link ICDKObject} for the original CDK
@@ -170,6 +173,18 @@ public <T extends ICDKObject>T newInstance(
             if (params.length == 1 &&
                 params[0] instanceof IMolecularFormula)
                 return (T)new AdductFormula((IMolecularFormula)params[0]);
+        } else if (clazz.isAssignableFrom(ITetrahedralChirality.class)) {
+            System.out.println(params.length);
+            if (params.length == 3 &&
+                params[0] instanceof IAtom &&
+                params[1] instanceof IAtom[] &&
+                params[2] instanceof Stereo) {
+                TetrahedralChirality chirality = new TetrahedralChirality(
+                    (IAtom)params[0], (IAtom[])params[1], (Stereo)params[2]
+                );
+                chirality.setBuilder(this);
+                return (T)chirality;
+            }
         }
 
 	    throw new IllegalArgumentException(getNoConstructorFoundMessage(clazz));
diff --git a/src/main/org/openscience/cdk/stereo/TetrahedralChirality.java b/src/main/org/openscience/cdk/stereo/TetrahedralChirality.java
@@ -22,7 +22,8 @@
  */
 package org.openscience.cdk.stereo;
 
-import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.ITetrahedralChirality;
@@ -31,16 +32,26 @@
  * Stereochemistry specification for quadrivalent atoms. See {@link ITetrahedralChirality} for
  * further details.
  *
- * @cdk.module data
+ * @cdk.module core
  *
  * @see org.openscience.cdk.interfaces.ITetrahedralChirality
  */
+@TestClass("org.openscience.cdk.stereo.TetrahedralChiralityTest")
 public class TetrahedralChirality implements ITetrahedralChirality {
 
     private IAtom chiralAtom;
     private IAtom[] ligandAtoms;
     private Stereo stereo;
+    private IChemObjectBuilder builder;
 
+    /**
+     * Constructor to create a new {@link ITetrahedralChirality} implementation instance.
+     * 
+     * @param chiralAtom  The chiral {@link IAtom}.
+     * @param ligandAtoms The ligand atoms around the chiral atom.
+     * @param chirality   The {@link Stereo} chirality.
+     */
+    @TestMethod("testTetrahedralChirality_IAtom_arrayIAtom_ITetrahedralChirality_Stereo")
     public TetrahedralChirality(IAtom chiralAtom, IAtom[] ligandAtoms, Stereo chirality) {
         this.chiralAtom = chiralAtom;
         this.ligandAtoms = ligandAtoms;
@@ -52,6 +63,7 @@ public TetrahedralChirality(IAtom chiralAtom, IAtom[] ligandAtoms, Stereo chiral
      *
      * @return an array of four {@link IAtom}s.
      */
+    @TestMethod("testGetLigands")
     public IAtom[] getLigands() {
         IAtom[] arrayCopy = new IAtom[4];
         System.arraycopy(ligandAtoms, 0, arrayCopy, 0, 4);
@@ -63,6 +75,7 @@ public IAtom[] getLigands() {
      *
      * @return the chiral {@link IAtom}.
      */
+    @TestMethod("testGetChiralAtom")
     public IAtom getChiralAtom() {
         return chiralAtom;
     }
@@ -72,14 +85,34 @@ public IAtom getChiralAtom() {
      *
      * @return the {@link ITetrahedralChirality.Stereo} for this stereo element.
      */
+    @TestMethod("testGetStereo")
     public Stereo getStereo() {
         return stereo;
     }
 
+    /**
+     * Sets a new {@link IChemObjectBuilder}.
+     *
+     * @param builder the new {@link IChemObjectBuilder} to be returned
+     * @see #getBuilder()
+     */
+    @TestMethod("testBuilder")
+    public void setBuilder(IChemObjectBuilder builder) {
+        this.builder = builder;
+    }
+
+    /** {@inheritDoc} */
+    @TestMethod("testBuilder")
     public IChemObjectBuilder getBuilder() {
-        return DefaultChemObjectBuilder.getInstance();
+        return builder;
     }
 
+    /**
+     * Returns a {@link String} representation of this chiral element.
+     * 
+     * @return the String representation
+     */
+    @TestMethod("testToString")
     public String toString() {
         StringBuilder builder = new StringBuilder();
         builder.append("Tetrahedral{").append(this.hashCode()).append(", ");
diff --git a/src/test/org/openscience/cdk/AbstractChemObjectBuilderTest.java b/src/test/org/openscience/cdk/AbstractChemObjectBuilderTest.java
@@ -62,6 +62,9 @@
 import org.openscience.cdk.interfaces.IRingSet;
 import org.openscience.cdk.interfaces.ISingleElectron;
 import org.openscience.cdk.interfaces.IStrand;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.IBond.Order;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
 
 /**
  * Checks the functionality of {@link IChemObjectBuilder} implementations.
@@ -689,4 +692,30 @@ public void testNewBond_IAtom_IMolecule() {
     		Assert.assertTrue("But got this message instead: " + message, message.contains("Candidates are"));
     	}
     }
+
+    @Test public void testNewTetrahedralChirality() {
+        IChemObjectBuilder builder = rootObject.getBuilder();
+        IMolecule molecule = builder.newInstance(IMolecule.class);
+        molecule.addAtom(builder.newInstance(IAtom.class, "Cl"));
+        molecule.addAtom(builder.newInstance(IAtom.class, "C"));
+        molecule.addAtom(builder.newInstance(IAtom.class, "Br"));
+        molecule.addAtom(builder.newInstance(IAtom.class, "I"));
+        molecule.addAtom(builder.newInstance(IAtom.class, "H"));
+        molecule.addBond(0, 1, Order.SINGLE);
+        molecule.addBond(1, 2, Order.SINGLE);
+        molecule.addBond(1, 3, Order.SINGLE);
+        molecule.addBond(1, 4, Order.SINGLE);
+        IAtom[] ligands = new IAtom[] {
+            molecule.getAtom(4),
+            molecule.getAtom(3),
+            molecule.getAtom(2),
+            molecule.getAtom(0)
+        };
+        ITetrahedralChirality chirality = builder.newInstance(
+            ITetrahedralChirality.class,
+            molecule.getAtom(1), ligands, Stereo.CLOCKWISE
+        );
+        Assert.assertNotNull(chirality);
+        Assert.assertEquals(builder, chirality.getBuilder());
+    }
 }
diff --git a/src/test/org/openscience/cdk/modulesuites/McoreTests.java b/src/test/org/openscience/cdk/modulesuites/McoreTests.java
@@ -48,6 +48,7 @@
 import org.openscience.cdk.graph.SpanningTreeTest;
 import org.openscience.cdk.graph.matrix.AdjacencyMatrixTest;
 import org.openscience.cdk.stereo.DoubleBondStereochemistryTest;
+import org.openscience.cdk.stereo.TetrahedralChiralityTest;
 import org.openscience.cdk.tools.DataFeaturesTest;
 import org.openscience.cdk.tools.LoggingToolFactoryTest;
 import org.openscience.cdk.tools.SystemOutLoggingToolTest;
@@ -106,6 +107,7 @@
     AdjacencyMatrixTest.class,
     PathToolsTest.class,
     DoubleBondStereochemistryTest.class,
+    TetrahedralChiralityTest.class,
     SpanningTreeTest.class
 })
 public class McoreTests {}
diff --git a/src/test/org/openscience/cdk/modulesuites/MdataTests.java b/src/test/org/openscience/cdk/modulesuites/MdataTests.java
@@ -69,7 +69,6 @@
 import org.openscience.cdk.protein.data.PDBMonomerTest;
 import org.openscience.cdk.protein.data.PDBPolymerTest;
 import org.openscience.cdk.protein.data.PDBStructureTest;
-import org.openscience.cdk.stereo.TetrahedralChiralityTest;
 
 /**
  * TestSuite that runs all the sample tests.
@@ -119,8 +118,6 @@
     AdductFormulaTest.class,
     MolecularFormulaSetTest.class,
     MolecularFormulaTest.class,
-    
-    TetrahedralChiralityTest.class,
 
     // test from test.event
     ChemObjectChangeEventTest.class,
diff --git a/src/test/org/openscience/cdk/stereo/TetrahedralChiralityTest.java b/src/test/org/openscience/cdk/stereo/TetrahedralChiralityTest.java
@@ -35,7 +35,7 @@
 import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
 
 /**
- * @cdk.module test-data
+ * @cdk.module test-core
  */
 public class TetrahedralChiralityTest extends CDKTestCase {
 
@@ -71,10 +71,12 @@ public void testTetrahedralChirality_IAtom_arrayIAtom_ITetrahedralChirality_Ster
     }
 
     @Test
-    public void testGetBuilder() {
+    public void testBuilder() {
         TetrahedralChirality chirality = new TetrahedralChirality(
             molecule.getAtom(1), ligands, Stereo.CLOCKWISE
         );
+        Assert.assertNull(chirality.getBuilder());
+        chirality.setBuilder(DefaultChemObjectBuilder.getInstance());
         Assert.assertEquals(
             DefaultChemObjectBuilder.getInstance(),
             chirality.getBuilder()
