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AddAtomsAndBondsEdit.java

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-05-01 21:15:34 +0200 (Tue, 01 May 2007) $
 * $Revision: 8292 $
 *
 * Copyright (C) 2005-2007  The Chemistry Development Kit (CDK) project
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.applications.undoredo;

import java.util.Iterator;

import javax.swing.undo.AbstractUndoableEdit;
import javax.swing.undo.CannotRedoException;
import javax.swing.undo.CannotUndoException;

import org.openscience.cdk.controller.Controller2DModel;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

/**
 * @author tohel
 * @cdk.module control
 */
00047 public class AddAtomsAndBondsEdit extends AbstractUndoableEdit {

    private static final long serialVersionUID = -7667903450980188402L;

    private IChemModel chemModel;

      private IAtomContainer undoRedoContainer;

      private String type;
      
      private HydrogenAdder hydrogenAdder = new HydrogenAdder("org.openscience.cdk.tools.ValencyChecker");
      
      private Controller2DModel c2dm=null;

      /**
       * @param chemModel
       * @param undoRedoContainer
       * @param c2dm The controller model; if none, set to null
       */
00066       public AddAtomsAndBondsEdit(IChemModel chemModel,
                  IAtomContainer undoRedoContainer, String type, Controller2DModel c2dm) {
            this.chemModel = chemModel;
            this.undoRedoContainer = undoRedoContainer;
            this.type = type;
            this.c2dm=c2dm;
      }

      /*
       * (non-Javadoc)
       * 
       * @see javax.swing.undo.UndoableEdit#redo()
       */
      public void redo() throws CannotRedoException {
            IAtomContainer container = chemModel.getBuilder().newAtomContainer();
            Iterator containers = ChemModelManipulator.getAllAtomContainers(chemModel).iterator();
      while (containers.hasNext()) {
            container.add((IAtomContainer)containers.next());
      }
            for (int i = 0; i < undoRedoContainer.getBondCount(); i++) {
                  IBond bond = undoRedoContainer.getBond(i);
                  container.addBond(bond);
            }
            for (int i = 0; i < undoRedoContainer.getAtomCount(); i++) {
                  IAtom atom = undoRedoContainer.getAtom(i);
                  container.addAtom(atom);
            }
            for (int i = 0; i < container.getAtomCount(); i++) {
                  this.updateAtom(container,container.getAtom(i));
            }
            IMolecule molecule = container.getBuilder().newMolecule(container);
            IMoleculeSet moleculeSet = ConnectivityChecker
                        .partitionIntoMolecules(molecule);
            chemModel.setMoleculeSet(moleculeSet);
      }

      /*
       * (non-Javadoc)
       * 
       * @see javax.swing.undo.UndoableEdit#undo()
       */
      public void undo() throws CannotUndoException {
            for (int i = 0; i < undoRedoContainer.getBondCount(); i++) {
                  IBond bond = undoRedoContainer.getBond(i);
                  ChemModelManipulator.getRelevantAtomContainer(chemModel, bond).removeBond(bond);
            }
            for (int i = 0; i < undoRedoContainer.getAtomCount(); i++) {
                  IAtom atom = undoRedoContainer.getAtom(i);
                  ChemModelManipulator.getRelevantAtomContainer(chemModel, atom).removeAtom(atom);
            }
            Iterator containers = ChemModelManipulator.getAllAtomContainers(chemModel).iterator();
      while (containers.hasNext()) {
            IAtomContainer container = (IAtomContainer)containers.next();
            for (int i = 0; i < container.getAtomCount(); i++) {
                  this.updateAtom(container,container.getAtom(i));
            }
      }
      }

      /*
       * (non-Javadoc)
       * 
       * @see javax.swing.undo.UndoableEdit#canRedo()
       */
      public boolean canRedo() {
            return true;
      }

      /*
       * (non-Javadoc)
       * 
       * @see javax.swing.undo.UndoableEdit#canUndo()
       */
      public boolean canUndo() {
            return true;
      }

      /*
       * (non-Javadoc)
       * 
       * @see javax.swing.undo.UndoableEdit#getPresentationName()
       */
      public String getPresentationName() {
            return type;
      }
      
      
      /**
       *  Updates an atom with respect to its hydrogen count
       *
       *@param  container  The AtomContainer to work on
       *@param  atom       The Atom to update
       */
00159       public void updateAtom(IAtomContainer container, IAtom atom)
      {
            if (c2dm!=null && c2dm.getAutoUpdateImplicitHydrogens())
            {
                  atom.setHydrogenCount(0);
                  try
                  {
                        hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atom);
                  } catch (Exception exception)
                  {
                        //we fail silently, when the handling of implicit Hs can't done
                  }
            }
      }
}

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