Updated casting to remove usage of Molecule

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Dec 11, 2011 · 04b1542 · 04b1542
1 parent 6e6cf8e
commit 04b1542
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Showing 14 changed files with 171 additions and 183 deletions.
diff --git a/src/test/org/openscience/cdk/CloneAtomContainerTest.java b/src/test/org/openscience/cdk/CloneAtomContainerTest.java
@@ -45,7 +45,7 @@ public class CloneAtomContainerTest extends CDKTestCase {
 	@Test public void testClone() throws Exception  
 	{
 	    IAtomContainer molecule = MoleculeFactory.makeAlphaPinene();
-		Molecule clonedMol = (Molecule)molecule.clone();
+		IAtomContainer clonedMol = (IAtomContainer)molecule.clone();
 		Assert.assertTrue(molecule.getAtomCount() == clonedMol.getAtomCount());
 		for (int f = 0; f < molecule.getAtomCount(); f++)
 		{

diff --git a/src/test/org/openscience/cdk/geometry/GeometryToolsTest.java b/src/test/org/openscience/cdk/geometry/GeometryToolsTest.java
@@ -18,14 +18,6 @@
  */
 package org.openscience.cdk.geometry;
 
-import java.awt.geom.Rectangle2D;
-import java.io.InputStream;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.vecmath.Point2d;
-import javax.vecmath.Point3d;
-
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.Atom;
@@ -49,6 +41,13 @@
 import org.openscience.cdk.isomorphism.AtomMappingTools;
 import org.openscience.cdk.tools.diff.AtomContainerDiff;
 
+import javax.vecmath.Point2d;
+import javax.vecmath.Point3d;
+import java.awt.geom.Rectangle2D;
+import java.io.InputStream;
+import java.util.HashMap;
+import java.util.Map;
+
 /**
  * This class defines regression tests that should ensure that the source code
  * of the {@link GeometryTools} is not broken.
@@ -123,15 +122,15 @@ public class GeometryToolsTest extends CDKTestCase {
 		String filenameMolTwo = "data/mdl/murckoTest6_3d.mol";
     	//String filenameMolTwo = "data/mdl/murckoTest6_3d_2.mol";
 	    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMolOne);
-	    Molecule molOne=null;
+	    IAtomContainer molOne;
-	    Molecule molTwo=null;
+	    IAtomContainer molTwo;
 	    Map mappedAtoms=new HashMap();
 	    MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-	    molOne = (Molecule)reader.read(new Molecule());
+	    molOne = reader.read(new Molecule());
 
 	    ins = this.getClass().getClassLoader().getResourceAsStream(filenameMolTwo);
 	    reader = new MDLV2000Reader(ins, Mode.STRICT);
-	    molTwo = (Molecule)reader.read(new Molecule());
+	    molTwo = reader.read(new Molecule());
 
 	    mappedAtoms=AtomMappingTools.mapAtomsOfAlignedStructures(molOne, molTwo, mappedAtoms);
 	    //logger.debug("mappedAtoms:"+mappedAtoms.toString());

diff --git a/src/test/org/openscience/cdk/graph/invariant/CanonicalLabelerTest.java b/src/test/org/openscience/cdk/graph/invariant/CanonicalLabelerTest.java
@@ -21,18 +21,13 @@
  */
 package org.openscience.cdk.graph.invariant;
 
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.util.Iterator;
-
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.ChemFile;
-import org.openscience.cdk.Molecule;
 import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.Molecule;
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -42,13 +37,18 @@
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.io.CMLReader;
 import org.openscience.cdk.io.CMLWriter;
-import org.openscience.cdk.io.MDLReader;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
+import org.openscience.cdk.io.MDLReader;
 import org.openscience.cdk.smiles.InvPair;
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.Iterator;
+
 /**
  * Checks the functionality of the CanonicalLabeler.
  *
@@ -126,7 +126,7 @@ public void testSomeMoleculeWithDifferentStartingOrder() throws Exception {
         String filename = "data/mdl/bug1014344-1.mol";
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
         MDLReader reader = new MDLReader(ins, Mode.STRICT);
-        Molecule mol1 = (Molecule) reader.read(new Molecule());
+        IAtomContainer mol1 = reader.read(new Molecule());
         addImplicitHydrogens(mol1);
         StringWriter output=new StringWriter();
         CMLWriter cmlWriter = new CMLWriter(output);

diff --git a/src/test/org/openscience/cdk/gui/smiles/SmilesGeneratorTest.java b/src/test/org/openscience/cdk/gui/smiles/SmilesGeneratorTest.java
@@ -20,12 +20,6 @@
  */
 package org.openscience.cdk.gui.smiles;
 
-import java.io.IOException;
-import java.io.InputStream;
-
-import javax.vecmath.Point2d;
-import javax.vecmath.Vector2d;
-
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.Atom;
@@ -44,7 +38,6 @@
 import org.openscience.cdk.interfaces.IAtomType.Hybridization;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemFile;
-import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.io.CMLReader;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
 import org.openscience.cdk.io.MDLReader;
@@ -58,6 +51,11 @@
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
 
+import javax.vecmath.Point2d;
+import javax.vecmath.Vector2d;
+import java.io.IOException;
+import java.io.InputStream;
+
 /**
  *@author         steinbeck
  *@cdk.created    February 9, 2004
@@ -239,7 +237,7 @@ public void setStandAlone(boolean standAlone)
 	@Test public void testCisResorcinol() throws Exception
 	{
 		HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
-        Molecule mol1 = new Molecule();
+        IAtomContainer mol1 = new Molecule();
 		SmilesGenerator sg = new SmilesGenerator();
 		mol1.addAtom(new Atom("O", new Point2d(3, 1)));
 		// 1
@@ -314,7 +312,7 @@ public void setStandAlone(boolean standAlone)
 		}
 		Assert.assertNotNull(smiles1);
 		Assert.assertEquals("[H]O[C@]1(C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]1(O[H])([H]))([H])", smiles1);
-		mol1 = (Molecule) AtomContainerManipulator.removeHydrogens(mol1);
+		mol1 = AtomContainerManipulator.removeHydrogens(mol1);
 		try
 		{
 			smiles1 = sg.createSMILES(mol1);
@@ -832,13 +830,13 @@ private void fixCarbonHCount(IAtomContainer mol)
 			String filename = "data/mdl/l-ala.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLReader reader = new MDLReader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
 			addExplicitHydrogens(mol1);
 			new HydrogenPlacer().placeHydrogens2D(mol1, 1.0);
 			filename = "data/mdl/d-ala.mol";
 			ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			reader = new MDLReader(ins, Mode.STRICT);
-			Molecule mol2 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol2 = reader.read(new Molecule());
 			addExplicitHydrogens(mol2);
 			new HydrogenPlacer().placeHydrogens2D(mol2, 1.0);
 			SmilesGenerator sg = new SmilesGenerator();
@@ -862,13 +860,13 @@ private void fixCarbonHCount(IAtomContainer mol)
 			String filename = "data/mdl/D-mannose.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLReader reader = new MDLReader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
 			addExplicitHydrogens(mol1);
 			new HydrogenPlacer().placeHydrogens2D(mol1, 1.0);
 			filename = "data/mdl/D+-glucose.mol";
 			ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			reader = new MDLReader(ins, Mode.STRICT);
-			Molecule mol2 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol2 = reader.read(new Molecule());
 			addExplicitHydrogens(mol2);
 			new HydrogenPlacer().placeHydrogens2D(mol2, 1.0);
 			SmilesGenerator sg = new SmilesGenerator();
@@ -907,7 +905,7 @@ private void display(IAtomContainer molecule)
 			String filename = "data/mdl/cyclooctan.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
             SmilesGenerator sg = new SmilesGenerator();
 			String moleculeSmile = sg.createSMILES(mol1);
 			Assert.assertEquals(moleculeSmile, "C1=CCCCCCC1");
@@ -930,7 +928,7 @@ private void display(IAtomContainer molecule)
 			String filename = "data/mdl/cycloocten.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
             SmilesGenerator sg = new SmilesGenerator();
 			String moleculeSmile = sg.createSMILES(mol1);
 			Assert.assertEquals(moleculeSmile, "C1C=CCCCCC1");
@@ -953,7 +951,7 @@ private void display(IAtomContainer molecule)
 			String filename = "data/mdl/cyclooctadien.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
             SmilesGenerator sg = new SmilesGenerator();
 			String moleculeSmile = sg.createSMILES(mol1);
 			Assert.assertEquals(moleculeSmile, "C=1CCC=CCCC=1");
@@ -977,7 +975,7 @@ private void display(IAtomContainer molecule)
 			String filename = "data/mdl/bug1089770-1.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
             SmilesGenerator sg = new SmilesGenerator();
 			String moleculeSmile = sg.createSMILES(mol1);
 			//logger.debug(filename + " -> " + moleculeSmile);
@@ -1002,7 +1000,7 @@ private void display(IAtomContainer molecule)
 			String filename = "data/mdl/bug1089770-2.mol";
 			InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
 			MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-			Molecule mol1 = (Molecule) reader.read(new Molecule());
+			IAtomContainer mol1 = reader.read(new Molecule());
             SmilesGenerator sg = new SmilesGenerator();
 			String moleculeSmile = sg.createSMILES(mol1);
 			//logger.debug(filename + " -> " + moleculeSmile);
@@ -1025,7 +1023,7 @@ private void display(IAtomContainer molecule)
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
         SmilesGenerator sg = new SmilesGenerator();
         sg.setUseAromaticityFlag(true);
-        String s1 = sg.createSMILES((IMolecule) mol);
+        String s1 = sg.createSMILES(mol);
 
         String filename = "data/cml/bug1535055.cml";
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
@@ -1037,7 +1035,7 @@ private void display(IAtomContainer molecule)
         IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
         CDKHueckelAromaticityDetector.detectAromaticity(mol2);
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
-        String s2 = sg.createSMILES((IMolecule) mol2);
+        String s2 = sg.createSMILES(mol2);
 
         Assert.assertTrue(s1.contains("[nH]"));
         Assert.assertTrue(s2.contains("[nH]"));

diff --git a/src/test/org/openscience/cdk/io/MDLCMLRoundtripTest.java b/src/test/org/openscience/cdk/io/MDLCMLRoundtripTest.java
@@ -27,16 +27,17 @@
  *  */
 package org.openscience.cdk.io;
 
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.io.StringWriter;
-
 import org.junit.Assert;
 import org.junit.Test;
-import org.openscience.cdk.Molecule;
 import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.Molecule;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IChemFile;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.StringWriter;
+
 /**
  * Combined TestCase for the reading/writing of mdl and cml files.
  *
@@ -60,7 +61,7 @@ public void testBug1649526() throws Exception{
     	String filename = "data/mdl/bug-1649526.mol";
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
         MDLReader reader = new MDLReader(ins);
-        Molecule mol = (Molecule)reader.read(new Molecule());
+        IAtomContainer mol = reader.read(new Molecule());
         //Write it as cml
 		StringWriter writer = new StringWriter();
         CMLWriter cmlWriter = new CMLWriter(writer);        

diff --git a/src/test/org/openscience/cdk/io/MDLReaderTest.java b/src/test/org/openscience/cdk/io/MDLReaderTest.java
@@ -141,7 +141,7 @@ public class MDLReaderTest extends SimpleChemObjectReaderTest {
             "  1  0  0  0  0                 1\n" +
             "   -0.0073   -0.5272    0.9655 H   0  3  0  0  0\n";
     	MDLReader reader = new MDLReader(new StringReader(mdl), Mode.STRICT);
-    	Molecule mol = (Molecule)reader.read(new Molecule());
+    	IAtomContainer mol = reader.read(new Molecule());
     	Assert.assertNotNull(mol);
     	Assert.assertEquals(1, mol.getAtomCount());
     	Assert.assertEquals(0, mol.getBondCount());
@@ -227,9 +227,9 @@ public class MDLReaderTest extends SimpleChemObjectReaderTest {
     public void testHas2DCoordinates_With000() throws CDKException {
         String filenameMol = "data/mdl/with000coordinate.mol";
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMol);
-        Molecule molOne=null;
+        IAtomContainer molOne=null;
         MDLReader reader = new MDLReader(ins, Mode.RELAXED);
-        molOne = (Molecule)reader.read(new Molecule());
+        molOne = reader.read(new Molecule());
         Assert.assertNotNull(molOne.getAtom(0).getPoint2d());
     }
 }
diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -701,7 +701,7 @@ public class MDLV2000ReaderTest extends SimpleChemObjectReaderTest {
         logger.info("Testing: " + filename);
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
-        Molecule mol = (Molecule)reader.read(new Molecule());
+        IAtomContainer mol = reader.read(new Molecule());
         for(IBond bond: mol.bonds() ) {
             IPseudoAtom rGroup = null;
             IAtom partner=null;
@@ -743,9 +743,9 @@ public class MDLV2000ReaderTest extends SimpleChemObjectReaderTest {
         logger.info("Testing: " + filename);
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
-        Molecule mol = (Molecule)reader.read(new Molecule());
+        IAtomContainer mol = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
         for(IBond bond: mol.bonds() ) {
-            IPseudoAtom rGroup = null;
+            IPseudoAtom rGroup;
             if (bond.getAtom(0) instanceof IPseudoAtom )  
                 rGroup = (IPseudoAtom)bond.getAtom(0);
             else 
@@ -816,9 +816,9 @@ private void testShortLinesForMode (IChemObjectReader.Mode mode) throws Exceptio
     @Test public void testHas2DCoordinates_With000() throws CDKException {
         String filenameMol = "data/mdl/with000coordinate.mol";
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMol);
-        Molecule molOne=null;
+        IAtomContainer molOne=null;
         MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
-        molOne = (Molecule)reader.read(new Molecule());
+        molOne = reader.read(new Molecule());
         Assert.assertNotNull(molOne.getAtom(0).getPoint2d());
         Assert.assertNotNull(molOne.getAtom(0).getPoint3d());
     }
@@ -827,8 +827,8 @@ private void testShortLinesForMode (IChemObjectReader.Mode mode) throws Exceptio
     	String filename = "data/mdl/atomValueLines.mol";
     	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
     	MDLV2000Reader reader = new MDLV2000Reader(ins);
-    	Molecule testMolecule = new Molecule();
+    	IAtomContainer testMolecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
-    	Molecule result = reader.read(testMolecule);
+    	IAtomContainer result = reader.read(testMolecule);
     	IAtom oxygen = result.getAtom(0);
     	Assert.assertTrue(oxygen.getSymbol().equals("O"));
     	Assert.assertEquals(oxygen.getProperty(CDKConstants.COMMENT), "Oxygen comment");

diff --git a/src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java b/src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java
@@ -32,7 +32,6 @@
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.DefaultChemObjectBuilder;
-import org.openscience.cdk.Molecule;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.geometry.GeometryTools;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -122,7 +121,7 @@ public boolean ready() throws IOException {
         Object object = reader.next();
         Assert.assertNotNull(object);
         Assert.assertTrue(object instanceof IAtomContainer);
-        Assert.assertEquals("2-methylbenzo-1,4-quinone", ((Molecule) object).getProperty(CDKConstants.TITLE));
+        Assert.assertEquals("2-methylbenzo-1,4-quinone", ((IAtomContainer) object).getProperty(CDKConstants.TITLE));
         Assert.assertEquals(MDLV2000Format.getInstance(), reader.getFormat());
     }
 
@@ -139,7 +138,7 @@ public boolean ready() throws IOException {
         Object object = reader.next();
         Assert.assertNotNull(object);
         Assert.assertTrue(object instanceof IAtomContainer);
-        Molecule m = (Molecule) object;
+        IAtomContainer m = (IAtomContainer) object;
         Assert.assertEquals("1", m.getProperty("E_NSC"));
         Assert.assertEquals("553-97-9", m.getProperty("E_CAS"));
     }