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ChemSequence.java

/* $RCSfile$
 * $Author: egonw $    
 * $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $    
 * $Revision: 7636 $
 *
 * Copyright (C) 1997-2007  Christoph Steinbeck <steinbeck@users.sf.net>
 * 
 * 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;

import java.io.Serializable;

import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IChemSequence;

/** 
 * A sequence of ChemModels, which can, for example, be used to
 * store the course of a reaction. Each state of the reaction would be
 * stored in one ChemModel.
 *
 * @cdk.module data
 *
 * @cdk.keyword animation
 * @cdk.keyword reaction
 */
00043 public class ChemSequence extends ChemObject implements Serializable, IChemSequence, IChemObjectListener, Cloneable
{

      /**
     * Determines if a de-serialized object is compatible with this class.
     *
     * This value must only be changed if and only if the new version
     * of this class is imcompatible with the old version. See Sun docs
     * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
     * /serialization/spec/version.doc.html>details</a>.
       */
00054       private static final long serialVersionUID = 2199218627455492000L;

      /**
       *  Array of ChemModels.
       */
00059       protected org.openscience.cdk.interfaces.IChemModel[] chemModels;
      
      /**
       *  Number of ChemModels contained by this container.
       */
00064       protected int chemModelCount;
      
      /**
       *  Amount by which the chemModels array grows when elements are added and
       *  the array is not large enough for that. 
       */
00070       protected int growArraySize = 4;



      /**
       *  Constructs an empty ChemSequence.
       */
00077       public ChemSequence()   
      {
            chemModelCount = 0;
            chemModels = new ChemModel[growArraySize];
      }


      
      /**
       *  Adds an chemModel to this container.
       *
       * @param  chemModel  The chemModel to be added to this container
     *
     * @see            #getChemModel
       */
00092       public void addChemModel(org.openscience.cdk.interfaces.IChemModel chemModel)
      {
            if (chemModelCount + 1 >= chemModels.length)
            {
                  growChemModelArray();
            }
            chemModels[chemModelCount] = chemModel;
            chemModelCount++;
            chemModel.addListener(this);
            notifyChanged();
      }

      
      /**
       * Remove a ChemModel from this ChemSequence.
       *
       * @param  pos  The position of the ChemModel to be removed.
       */
00110       public void removeChemModel(int pos) {
            chemModels[pos].removeListener(this);
            for (int i = pos; i < chemModelCount - 1; i++) {
                  chemModels[i] = chemModels[i + 1];
            }
            chemModels[chemModelCount - 1] = null;
            chemModelCount--;
            notifyChanged();
      }

      /**
     * Returns an Iterator to ChemModels in this container.
     *
     * @return    The Iterator to ChemModels in this container
     * @see       #addChemModel
     */
00126      public java.util.Iterator chemModels() {
       return new ChemModelIterator();
     }

     /**
      * The inner Iterator class.
      *
      */
00134      private class ChemModelIterator implements java.util.Iterator {

         private int pointer = 0;
      
         public boolean hasNext() {
             if (pointer < chemModelCount) return true;
          return false;
         }

         public Object next() {
             return chemModels[pointer++];
         }

         public void remove() {
             removeChemModel(--pointer);
         }
      
     }
     
     
      /**
       *
       * Returns the ChemModel at position <code>number</code> in the
       * container.
       *
       * @param  number  The position of the ChemModel to be returned.
       * @return         The ChemModel at position <code>number</code>.
     *
     * @see            #addChemModel
       */
00164       public org.openscience.cdk.interfaces.IChemModel getChemModel(int number)
      {
            return chemModels[number];
      }
      
      /**
       *  Grows the chemModel array by a given size.
       *
       * @see    growArraySize
       */
00174       protected void growChemModelArray()
      {
            ChemModel[] newchemModels = new ChemModel[chemModels.length + growArraySize];
            System.arraycopy(chemModels, 0, newchemModels, 0, chemModels.length);
            chemModels = newchemModels;
      }
      

      /**
       * Returns the number of ChemModels in this Container.
       *
       * @return    The number of ChemModels in this Container
       */
00187       public int getChemModelCount()
      {
            return this.chemModelCount;
      }

00192       public String toString() {
        StringBuffer buffer = new StringBuffer(32);
        buffer.append("ChemSequence(#M=");
        buffer.append(chemModelCount);
        buffer.append(", ");
        for (int i=0; i<chemModelCount; i++) {
            buffer.append(chemModels[i].toString());
        }
        buffer.append(')');
        return buffer.toString();
    }
      
00204       public Object clone() throws CloneNotSupportedException {
            ChemSequence clone = (ChemSequence)super.clone();
        // clone the chemModels
        clone.chemModelCount = getChemModelCount();
            clone.chemModels = new ChemModel[clone.chemModelCount];
            for (int f = 0; f < clone.chemModelCount; f++) {
                  clone.chemModels[f] = (ChemModel)((ChemModel)chemModels[f]).clone();
            }
            return clone;
      }
      
      /**
       *  Called by objects to which this object has
       *  registered as a listener.
       *
       *@param  event  A change event pointing to the source of the change
       */
00221       public void stateChanged(IChemObjectChangeEvent event)
      {
            notifyChanged(event);
      }
}

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