Apparently the super.clone() does not clone the pointer to the IAtomC…

…ontainer[], causing a clone() followed by changing containers in the clone to overwrite the original IAtomContainer[]. Fixed by creating a new array. Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
egonw · Apr 7, 2010 · 4e5d6a1 · 4e5d6a1
1 parent 068fb3b
commit 4e5d6a1
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/AtomContainerSet.java b/src/main/org/openscience/cdk/AtomContainerSet.java
@@ -365,9 +365,11 @@ public String toString() {
 	 */
 	public Object clone() throws CloneNotSupportedException {
 		AtomContainerSet clone = (AtomContainerSet)super.clone();
+		clone.atomContainers = new AtomContainer[atomContainerCount];
+		clone.atomContainerCount = 0;
 		for (int i = 0; i < atomContainerCount; i++) {
-        clone.replaceAtomContainer(i, (IAtomContainer)atomContainers[i].clone());
-        clone.setMultiplier(i, getMultiplier(i));
+		    clone.addAtomContainer((IAtomContainer)atomContainers[i].clone());
+		    clone.setMultiplier(i, getMultiplier(i));
 		}
 		return clone;
 	}