Made the AtomContainerPermutors IAtomContainer implementation indepen…

…dent Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
egonw · Nov 15, 2009 · 4748098 · 4748098
1 parent 8a95d93
commit 4748098
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Showing 3 changed files with 24 additions and 21 deletions.
diff --git a/src/main/org/openscience/cdk/graph/AtomContainerAtomPermutor.java b/src/main/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
@@ -29,8 +29,10 @@
  */
 package org.openscience.cdk.graph;
 
+import java.util.Iterator;
+
 import org.openscience.cdk.Atom;
-import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 
 /**
@@ -51,7 +53,7 @@
 public class AtomContainerAtomPermutor extends AtomContainerPermutor
 {
 
-	public AtomContainerAtomPermutor(AtomContainer ac)
+	public AtomContainerAtomPermutor(IAtomContainer ac)
 	{
 		setAtomContainer(ac);
 		N = atomContainer.getAtomCount();
@@ -61,7 +63,7 @@ public AtomContainerAtomPermutor(AtomContainer ac)
 
 	public void initObjectArray()
 	{
-		java.util.Iterator atoms = atomContainer.atoms().iterator();
+		Iterator<IAtom> atoms = atomContainer.atoms().iterator();
 		objects = new Object[atomContainer.getAtomCount()];
 		int count = -1;
 		while (atoms.hasNext())
@@ -70,7 +72,7 @@ public void initObjectArray()
 		}
 	}
 
-	AtomContainer makeResult()
+	IAtomContainer makeResult()
 	{
 		Atom[] atoms = new Atom[objects.length];
 		for (int f = 0; f < objects.length; f++)
@@ -79,9 +81,9 @@ AtomContainer makeResult()
 		}
 		IAtomContainer ac = atomContainer.getBuilder().newAtomContainer(atomContainer);
 		ac.setAtoms(atoms);
-		AtomContainer clone = null;
+		IAtomContainer clone = null;
 		try {
-			clone = (AtomContainer)ac.clone();
+			clone = (IAtomContainer)ac.clone();
 		} catch (CloneNotSupportedException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();

diff --git a/src/main/org/openscience/cdk/graph/AtomContainerBondPermutor.java b/src/main/org/openscience/cdk/graph/AtomContainerBondPermutor.java
@@ -29,11 +29,11 @@
  */
 package org.openscience.cdk.graph;
 
-import org.openscience.cdk.AtomContainer;
-import org.openscience.cdk.interfaces.IBond;
-
 import java.util.Iterator;
 
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+
 
 /**
  * This class allows to iterate trough the set of all possible
@@ -53,7 +53,7 @@
 public class AtomContainerBondPermutor extends AtomContainerPermutor
 {
 
-    public AtomContainerBondPermutor(AtomContainer ac)
+    public AtomContainerBondPermutor(IAtomContainer ac)
     {
         setAtomContainer(ac);
         N = atomContainer.getBondCount();
@@ -71,18 +71,18 @@ public void initObjectArray() {
         }
     }
 
-    AtomContainer makeResult()
+    IAtomContainer makeResult()
     {
         IBond[] bonds = new IBond[objects.length];
         for (int f = 0; f < objects.length; f++)
         {
             bonds[f] = ((IBond)objects[f]);
         }
-        AtomContainer ac = new AtomContainer(atomContainer);
+        IAtomContainer ac = atomContainer.getBuilder().newAtomContainer(atomContainer);
         ac.setBonds(bonds);
-        AtomContainer clone = null;
+        IAtomContainer clone = null;
         try {
-            clone = (AtomContainer)ac.clone();
+            clone = (IAtomContainer)ac.clone();
         } catch (CloneNotSupportedException e) {
             // TODO Auto-generated catch block
             e.printStackTrace();

diff --git a/src/main/org/openscience/cdk/graph/AtomContainerPermutor.java b/src/main/org/openscience/cdk/graph/AtomContainerPermutor.java
@@ -31,7 +31,7 @@
 
 import java.util.Iterator;
 
-import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
@@ -45,8 +45,9 @@
  *@cdk.created    2005-05-04
  *@cdk.keyword    permutation
  */
-public abstract class AtomContainerPermutor implements Iterator
-{
+public abstract class AtomContainerPermutor
+    implements Iterator<IAtomContainer> {
+
 	final static boolean debug = true;
 	static int debugCounter = 0;
 	int N, i, j;
@@ -56,9 +57,9 @@ public abstract class AtomContainerPermutor implements Iterator
 	private static ILoggingTool logger =
         LoggingToolFactory.createLoggingTool(AtomContainerPermutor.class);
 
-	AtomContainer atomContainer;
+	IAtomContainer atomContainer;
 
-	public void setAtomContainer(AtomContainer ac)
+	public void setAtomContainer(IAtomContainer ac)
 	{
 		this.atomContainer = ac;
 	}
@@ -74,7 +75,7 @@ public void initBookkeeping()
 
 	}
 
-	public Object next()
+	public IAtomContainer next()
 	{
 		bookkeeping[i] = bookkeeping[i] - 1;
 		if (isOdd(i)) j = bookkeeping[i];
@@ -113,7 +114,7 @@ void initObjectArray()
 		//
 	}
 
-	AtomContainer makeResult()
+	IAtomContainer makeResult()
 	{
 		return null;
 	}