[Cdk-commits] SF.net SVN: cdk:[12557] cdk/branches/cdk-1.0.x/src/org/openscience/cdk/ applications/jchempaint/action/CleanupAction.java

[<sh...@us...>]

Revision: 12557
          http://cdk.svn.sourceforge.net/cdk/?rev=12557&view=rev
Author:   shk3
Date:     2008-10-06 12:45:30 +0000 (Mon, 06 Oct 2008)

Log Message:
-----------
the relayout just sets coordinates and does not create new molecules in model (makes undo/redo work and is generally the better solution)

Modified Paths:
--------------
    cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/CleanupAction.java

Modified: cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/CleanupAction.java
===================================================================
--- cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/CleanupAction.java	2008-10-06 12:21:15 UTC (rev 12556)
+++ cdk/branches/cdk-1.0.x/src/org/openscience/cdk/applications/jchempaint/action/CleanupAction.java	2008-10-06 12:45:30 UTC (rev 12557)
@@ -104,14 +104,12 @@
 			{
                 
 				logger.debug("no mols in som: ", som.getMoleculeCount());
-				MoleculeSet newsom = new MoleculeSet();
 				java.util.Iterator mols = som.molecules();
 				while (mols.hasNext())
 				{
                     IMolecule molecule = (IMolecule)mols.next();
                     if (molecule != null && molecule.getAtomCount() > 0) {
                     	IMolecule cleanedMol = relayoutMolecule(molecule);
-                    	newsom.addMolecule(cleanedMol);
                     	for (int j=0; j<molecule.getAtomCount(); j++) {
                     		IAtom atom = molecule.getAtom(j);
                     		IAtom newAtom = cleanedMol.getAtom(j);
@@ -121,42 +119,63 @@
                     			Point2d[] coords = new Point2d[2];
                     			coords[0] = newCoord;
                     			coords[1] = oldCoord;
-                    			atomCoordsMap.put(newAtom, coords);
+                    			atomCoordsMap.put(atom, coords);
                     		}
+                    		jcpmodel.getRendererModel().setRenderingCoordinate(atom, newCoord);
                     	}
                     }
 				}
-				model.setMoleculeSet(newsom);
                 
                 UndoableEdit  edit = new CleanUpEdit(atomCoordsMap,jcpmodel.getRendererModel());
                 jcpPanel.getUndoSupport().postEdit(edit);
-    			GeometryTools.makeRenderingCoordinates(newsom, jcpmodel.getRendererModel().getRenderingCoordinates());
 
 			}
 			org.openscience.cdk.interfaces.IReactionSet reactionSet = model.getReactionSet();
 			if (reactionSet != null)
 			{
-				ReactionSet newSet = new ReactionSet();
-				// FIXME, this does not preserve reactionset properties!
 				java.util.Iterator reactionsIter = reactionSet.reactions();
 				while (reactionsIter.hasNext())
 				{
 					org.openscience.cdk.interfaces.IReaction reaction = (org.openscience.cdk.interfaces.IReaction)reactionsIter.next();
-					Reaction newReaction = new Reaction();
-					// FIXME, this does not preserve reaction properties!
 					java.util.Iterator reactants = reaction.getReactants().molecules();
 					while (reactants.hasNext())
 					{
-						newReaction.addReactant(relayoutMolecule((IMolecule)reactants.next()));
+						IMolecule molecule=(IMolecule)reactants.next();
+                    	IMolecule cleanedMol = relayoutMolecule(molecule);
+                    	for (int j=0; j<molecule.getAtomCount(); j++) {
+                    		IAtom atom = molecule.getAtom(j);
+                    		IAtom newAtom = cleanedMol.getAtom(j);
+                    		Point2d oldCoord =  (Point2d)jcpmodel.getRendererModel().getRenderingCoordinate(atom);
+                    		Point2d newCoord = newAtom.getPoint2d();
+                    		if (!oldCoord.equals(newCoord)) {
+                    			Point2d[] coords = new Point2d[2];
+                    			coords[0] = newCoord;
+                    			coords[1] = oldCoord;
+                    			atomCoordsMap.put(atom, coords);
+                    		}
+                    		jcpmodel.getRendererModel().setRenderingCoordinate(atom, newCoord);
+                    	}
 					}
 					java.util.Iterator products = reaction.getProducts().molecules();
 					while (products.hasNext())
 					{
-						newReaction.addProduct(relayoutMolecule((IMolecule)products.next()));
+						IMolecule molecule=(IMolecule)products.next();
+                    	IMolecule cleanedMol = relayoutMolecule(molecule);
+                    	for (int j=0; j<molecule.getAtomCount(); j++) {
+                    		IAtom atom = molecule.getAtom(j);
+                    		IAtom newAtom = cleanedMol.getAtom(j);
+                    		Point2d oldCoord =  (Point2d)jcpmodel.getRendererModel().getRenderingCoordinate(atom);
+                    		Point2d newCoord = newAtom.getPoint2d();
+                    		if (!oldCoord.equals(newCoord)) {
+                    			Point2d[] coords = new Point2d[2];
+                    			coords[0] = newCoord;
+                    			coords[1] = oldCoord;
+                    			atomCoordsMap.put(atom, coords);
+                    		}
+                    		jcpmodel.getRendererModel().setRenderingCoordinate(atom, newCoord);
+                    	}
 					}
-					newSet.addReaction(newReaction);
 				}
-				model.setReactionSet(newSet);
 			}
 
 			jcpmodel.getRendererModel().setSelectedPart(new AtomContainer());


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