Fixes for the pseudo atom patch backporting: allow reading of IAtomCo…

…ntainer where IMolecule was already supported, fixed imports. Also removes an redundant, incorrect accepts() method Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
cdk · Jan 22, 2012 · 7dc949f · 7dc949f
1 parent e59d204
commit 7dc949f
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Showing 4 changed files with 17 additions and 18 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -29,6 +29,7 @@
 import org.openscience.cdk.config.IsotopeFactory;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemFile;
 import org.openscience.cdk.interfaces.IChemModel;
@@ -164,6 +165,7 @@ public boolean accepts(Class<? extends IChemObject> classObject) {
 			if (IChemFile.class.equals(interfaces[i])) return true;
 			if (IChemModel.class.equals(interfaces[i])) return true;
 			if (IMolecule.class.equals(interfaces[i])) return true;
+			if (IAtomContainer.class.equals(interfaces[i])) return true;
 		}
     Class superClass = classObject.getSuperclass();
     if (superClass != null) return this.accepts(superClass);
@@ -187,6 +189,8 @@ public <T extends IChemObject> T read(T object) throws CDKException {
             return (T)readChemModel((IChemModel)object);
 		} else if (object instanceof IMolecule) {
 			return (T)readMolecule((IMolecule)object);
+		} else if (object instanceof IAtomContainer) {
+			return (T)readMolecule(object.getBuilder().newInstance(IMolecule.class, object));
 		} else {
 			throw new CDKException("Only supported are ChemFile and Molecule.");
 		}

diff --git a/src/main/org/openscience/cdk/io/MDLV3000Reader.java b/src/main/org/openscience/cdk/io/MDLV3000Reader.java
@@ -128,14 +128,15 @@ public boolean accepts(Class classObject) {
 		Class[] interfaces = classObject.getInterfaces();
 		for (int i=0; i<interfaces.length; i++) {
 			if (IMolecule.class.equals(interfaces[i])) return true;
+			if (IAtomContainer.class.equals(interfaces[i])) return true;
 		}
     Class superClass = classObject.getSuperclass();
     if (superClass != null) return this.accepts(superClass);
 		return false;
 	}
 
 	public <T extends IChemObject> T read(T object) throws CDKException {
-        if (object instanceof IMolecule) {
+        if (object instanceof IAtomContainer) {
             return (T)readMolecule(object.getBuilder());
         }
         return null;
@@ -585,14 +586,6 @@ public boolean isReady() throws CDKException {
         }
     }
 
-    @TestMethod("testAccepts")
-    public boolean accepts(IChemObject object) {
-        if (object instanceof IMolecule) {
-            return true;
-        }
-        return false;
-    }
-
     @TestMethod("testClose")
     public void close() throws IOException {
         input.close();

diff --git a/src/test/org/openscience/cdk/io/MDLV2000WriterTest.java b/src/test/org/openscience/cdk/io/MDLV2000WriterTest.java
@@ -24,10 +24,16 @@
 package org.openscience.cdk.io;
 
 
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.Properties;
+
+import javax.vecmath.Point2d;
+import javax.vecmath.Point3d;
+
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
-
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.Bond;
@@ -39,6 +45,7 @@
 import org.openscience.cdk.PseudoAtom;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemModel;
@@ -51,12 +58,6 @@
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.templates.MoleculeFactory;
 
-import javax.vecmath.Point2d;
-import javax.vecmath.Point3d;
-import java.io.StringWriter;
-import java.io.InputStream;
-import java.util.Properties;
-
 
 /**
  * TestCase for the writer MDL mol files using one test file.

diff --git a/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java
@@ -30,15 +30,16 @@
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.nonotify.NNMolecule;
 import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.nonotify.NNMolecule;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
-import org.openscience.cdk.DefaultChemObjectBuilder;
 
 /**
  * TestCase for the reading MDL V3000 mol files using one test file.