Use interfaces instead of implementations

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · Nov 7, 2011 · 76dcdf7 · 76dcdf7
1 parent 5bef796
commit 76dcdf7
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Showing 2 changed files with 12 additions and 13 deletions.
diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -32,7 +32,6 @@
 import org.openscience.cdk.ChemModel;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
-import org.openscience.cdk.PseudoAtom;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.geometry.GeometryTools;
 import org.openscience.cdk.interfaces.IAtom;
@@ -398,7 +397,7 @@ public class MDLV2000ReaderTest extends SimpleChemObjectReaderTest {
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         Molecule mol = reader.read(new Molecule());
-        Assert.assertEquals("R2",((PseudoAtom)mol.getAtom(19)).getLabel());
+        Assert.assertEquals("R2",((IPseudoAtom)mol.getAtom(19)).getLabel());
     }
 
     @Test public void testAliasPropertyGroup() throws Exception {
@@ -408,8 +407,8 @@ public class MDLV2000ReaderTest extends SimpleChemObjectReaderTest {
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         Molecule mol = reader.read(new Molecule());
         IAtom atom = mol.getAtom(3);
-        Assert.assertTrue(atom instanceof PseudoAtom);
-        Assert.assertEquals("R1", ((PseudoAtom)atom).getLabel());
+        Assert.assertTrue(atom instanceof IPseudoAtom);
+        Assert.assertEquals("R1", ((IPseudoAtom)atom).getLabel());
     }
 
     /**
@@ -711,15 +710,15 @@ public void testQueryBondTypes() throws Exception {
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         Molecule mol = (Molecule)reader.read(new Molecule());
         for(IBond bond: mol.bonds() ) {
-            PseudoAtom rGroup = null;
+            IPseudoAtom rGroup = null;
             IAtom partner=null;
-            if (bond.getAtom(0) instanceof PseudoAtom )  {
-                rGroup = (PseudoAtom)bond.getAtom(0);
+            if (bond.getAtom(0) instanceof IPseudoAtom )  {
+                rGroup = (IPseudoAtom)bond.getAtom(0);
                 partner = bond.getAtom(1);
             }
             else {
                 partner = bond.getAtom(0);
-                rGroup = (PseudoAtom)bond.getAtom(1);
+                rGroup = (IPseudoAtom)bond.getAtom(1);
             }
             if (partner.getSymbol().equals("N"))  {
                 Assert.assertEquals(rGroup.getLabel(),"R4");
@@ -753,11 +752,11 @@ public void testQueryBondTypes() throws Exception {
         MDLV2000Reader reader = new MDLV2000Reader(ins);
         Molecule mol = (Molecule)reader.read(new Molecule());
         for(IBond bond: mol.bonds() ) {
-            PseudoAtom rGroup = null;
-            if (bond.getAtom(0) instanceof PseudoAtom )  
-                rGroup = (PseudoAtom)bond.getAtom(0);
+            IPseudoAtom rGroup = null;
+            if (bond.getAtom(0) instanceof IPseudoAtom )  
+                rGroup = (IPseudoAtom)bond.getAtom(0);
             else 
-                rGroup = (PseudoAtom)bond.getAtom(1);
+                rGroup = (IPseudoAtom)bond.getAtom(1);
 
             if (bond.getOrder()== IBond.Order.DOUBLE)  {
                 Assert.assertEquals(rGroup.getLabel(),"R32");

diff --git a/src/test/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java b/src/test/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java
@@ -329,7 +329,7 @@ public void testModel3D_bug_1610997() throws Exception{
 		for (Iterator iter = inputList.iterator(); iter.hasNext();) {
 			IAtomContainer molecules = (IAtomContainer) iter.next();
 			for (Iterator atom = molecules.atoms().iterator(); atom.hasNext();){
-				Atom last = (Atom) atom.next();
+				IAtom last = (IAtom) atom.next();
 				last.setPoint2d(null);
 			}
 		}