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CreateReactionAction.java

/*
 *  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-04-16 10:40:19 +0200 (Mon, 16 Apr 2007) $
 *  $Revision: 8201 $
 *
 *  Copyright (C) 1997-2007  The JChemPaint project
 *
 *  Contact: jchempaint-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.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  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.jchempaint.action;

import java.awt.event.ActionEvent;

import javax.swing.JOptionPane;
import javax.vecmath.Point2d;

import org.openscience.cdk.applications.jchempaint.JChemPaintModel;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;


/**
 * Creates a reaction object
 *
 * @cdk.module jchempaint
 *@author     steinbeck
 */
00052 public class CreateReactionAction extends JCPAction
{

      private static final long serialVersionUID = -7625810885316702776L;

00057       public void actionPerformed(ActionEvent event)
      {
            IChemObject object = getSource(event);

            logger.debug("CreateReaction action");
            JChemPaintModel jcpmodel = jcpPanel.getJChemPaintModel();
            IChemModel model = jcpmodel.getChemModel();
            IReactionSet reactionSet = model.getReactionSet();
            if (reactionSet == null)
            {
                  reactionSet = model.getBuilder().newReactionSet();
            }
            IAtomContainer container = null;
            if (object instanceof IAtom)
            {
                  container = ChemModelManipulator.getRelevantAtomContainer(model, (IAtom) object);
            } else
            {
                  logger.error("Cannot add to reaction object of type: " + object.getClass().getName());
            }
            if (container == null)
            {
                  logger.error("Cannot find container to add object to!");
            } else
            {
                  IAtomContainer newContainer;
                  try {
                        newContainer = (IAtomContainer) container.clone();
                  } catch (CloneNotSupportedException e) {
                        logger.error("Could not clone IAtomContainer: ", e.getMessage());
                        logger.debug(e);
                        return;
                  }
                  // delete atoms in current model
                  java.util.Iterator atoms = container.atoms();
                  while (atoms.hasNext())
                  {
                        ChemModelManipulator.removeAtomAndConnectedElectronContainers(model, (IAtom)atoms.next());
                  }
                  logger.debug("Deleted atom from old container...");

                  // add reaction
                  IReaction reaction = model.getBuilder().newReaction();
                  reaction.setID("reaction-" + System.currentTimeMillis());
                  logger.debug("type: ", type);
                  if ("addReactantToNew".equals(type))
                  {
                        reaction.addReactant(model.getBuilder().newMolecule(newContainer));
                        reactionSet.addReaction(reaction);
                  } else if ("addReactantToExisting".equals(type))
                  {
                        if (reactionSet.getReactionCount() == 0)
                        {
                              logger.warn("Cannot add to reaction if no one exists");
                              // FIXME: give feedback to user
                              return;
                        } else
                        {
//                            XXX needs fixing
                              Object[] ids = getReactionIDs(reactionSet);
                              
                              String s = (String) JOptionPane.showInputDialog(
                                          //jcpPanel.getFrame(),
                            null,
                                          "Reaction Chooser",
                                          "Choose reaction to add reaction to",
                                          JOptionPane.PLAIN_MESSAGE,
                                          null,
                                          ids,
                                          ids[0]
                                          );
                              //String s2 = "";

                              if ((s != null) && (s.length() > 0))
                              {
                                    String selectedReactionID = s;
                                    reaction = getReaction(reactionSet, selectedReactionID);
                                    reaction.addReactant(model.getBuilder().newMolecule(newContainer));
                              } else
                              {
                                    logger.error("No reaction selected");
                              }
                        }
                  } else if ("addProductToNew".equals(type))
                  {
                        reaction.addProduct(model.getBuilder().newMolecule(newContainer));
                        reactionSet.addReaction(reaction);
                  } else if ("addProductToExisting".equals(type))
                  {
                        if (reactionSet.getReactionCount() == 0)
                        {
                              logger.warn("Cannot add to reaction if no one exists");
                              // FIXME: give feedback to user
                              return;
                        } else
                        {
                              //XXX needs fixing
                              
                              Object[] ids = getReactionIDs(reactionSet);
                              String s = (String) JOptionPane.showInputDialog(
                            //jcpPanel.getFrame(),
                                          null,
                            "Reaction Chooser",
                                          "Choose reaction to add reaction to",
                                          JOptionPane.PLAIN_MESSAGE,
                                          null,
                                          ids,
                                          ids[0]
                                          );
                              //String s2 = "";

                              if ((s != null) && (s.length() > 0))
                              {
                                    String selectedReactionID = s;
                                    reaction = getReaction(reactionSet, selectedReactionID);
                                    reaction.addProduct(model.getBuilder().newMolecule(newContainer));
                              } else
                              {
                                    logger.error("No reaction selected");
                              }
                        }
                  } else
                  {
                        logger.warn("Don't know about this action type: " + type);
                        return;
                  }
            }
            model.setReactionSet(reactionSet);
            
            for(int i=0;i<reactionSet.getReactionCount();i++){
                  for(int k=0;k<reactionSet.getReaction(i).getProductCount();k++){
                        for(int l=0;l<reactionSet.getReaction(i).getProducts().getAtomContainer(k).getAtomCount();l++){
                              if(jcpmodel.getRendererModel().getRenderingCoordinates().get(reactionSet.getReaction(i).getProducts().getAtomContainer(k).getAtom(l))==null)
                                    jcpmodel.getRendererModel().getRenderingCoordinates().put(reactionSet.getReaction(i).getProducts().getAtomContainer(k).getAtom(l),new Point2d(reactionSet.getReaction(i).getProducts().getAtomContainer(k).getAtom(l).getPoint2d()));
                        }
                  }
                  for(int k=0;k<reactionSet.getReaction(i).getReactantCount();k++){
                        for(int l=0;l<reactionSet.getReaction(i).getReactants().getAtomContainer(k).getAtomCount();l++){
                              if(jcpmodel.getRendererModel().getRenderingCoordinates().get(reactionSet.getReaction(i).getReactants().getAtomContainer(k).getAtom(l))==null)
                                    jcpmodel.getRendererModel().getRenderingCoordinates().put(reactionSet.getReaction(i).getReactants().getAtomContainer(k).getAtom(l),new Point2d(reactionSet.getReaction(i).getReactants().getAtomContainer(k).getAtom(l).getPoint2d()));
                        }
                  }
            }
      }


      /**
       *  Gets the reactionIDs attribute of the CreateReactionAction object
       *
       *@param  reactionSet  Description of the Parameter
       *@return              The reactionIDs value
       */
00209       private Object[] getReactionIDs(IReactionSet reactionSet)
      {
            if (reactionSet != null)
            {
                  
                  String[] ids = new String[reactionSet.getReactionCount()];
                  for (int i = 0; i < reactionSet.getReactionCount(); i++)
                  {
                        ids[i] = reactionSet.getReaction(i).getID();
                  }
                  return ids;
            } else
            {
                  return new String[0];
            }
      }


      /**
       *  Gets the reaction attribute of the CreateReactionAction object
       *
       *@param  reactionSet  Description of the Parameter
       *@param  id           Description of the Parameter
       *@return              The reaction value
       */
00234       private org.openscience.cdk.interfaces.IReaction getReaction(org.openscience.cdk.interfaces.IReactionSet reactionSet, String id)
      {
            java.util.Iterator reactionIter = reactionSet.reactions();
            while (reactionIter.hasNext())
            {
                  IReaction reaction = (IReaction)reactionIter.next();
                  if (reaction.getID().equals(id))
                  {
                        return reaction;
                  }
            }
            return null;
      }
}


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