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Polymer.java

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 * $Revision: 7636 $
 * 
 * Copyright (C) 2001-2007  Edgar Luttmann <edgar@uni-paderborn.de>
 * 
 * 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.
 * 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;

import java.util.Collection;
import java.util.Hashtable;
import java.util.Iterator;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IMonomer;

/**
 * Subclass of Molecule to store Polymer specific attributes that a Polymer has.
 *
 * @cdk.module data
 *
 * @author      Edgar Luttmann <edgar@uni-paderborn.de>
 * @author      Martin Eklund <martin.eklund@farmbio.uu.se>
 * @cdk.created 2001-08-06
 * @cdk.keyword polymer
 */
00047 public class Polymer extends Molecule implements java.io.Serializable, org.openscience.cdk.interfaces.IPolymer
{ 
      /**
     * 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>.
       */
00056       private static final long serialVersionUID = -2596790658835319339L;

      private Hashtable monomers;   // the list of all the contained Monomers. 
      
      /**
       * Contructs a new Polymer to store the Monomers.
       */   
00063       public Polymer() {
            super();
            monomers = new Hashtable();
      }
      
      /**
       * Adds the atom oAtom to a specified Monomer.
       *
       * @param oAtom  The atom to add
       * @param oMonomer  The monomer the atom belongs to
       */
00074       public void addAtom(IAtom oAtom, IMonomer oMonomer) {
            
            if(!contains(oAtom))    {
                  super.addAtom(oAtom);
                  
                  if(oMonomer != null)    {     // Not sure what's better here...throw nullpointer exception?
                        oMonomer.addAtom(oAtom);
                        
                        if (! monomers.containsKey(oMonomer.getMonomerName())) {
                              monomers.put(oMonomer.getMonomerName(), oMonomer);
                        }
                  }
            }
            /* notifyChanged() is called by addAtom in
             AtomContainer */
      }
      
      /**
       * Return the number of monomers present in the Polymer.
       *
       * @return number of monomers
       */
00096       public int getMonomerCount() {
            return monomers.size();
      }
      
      /**
       * Retrieve a Monomer object by specifying its name.
       *
       * @param cName  The name of the monomer to look for
       * @return The Monomer object which was asked for
       */
00106       public IMonomer getMonomer(String cName) {
            return (Monomer)monomers.get(cName);
      }
      
      /**
       * Returns a collection of the names of all <code>Monomer</code>s in this
       * polymer.
       *
       * @return a <code>Collection</code> of all the monomer names.
       */
00116       public Collection getMonomerNames() {
            return monomers.keySet();
      }
      
      /**
       * Removes a particular monomer, specified by its name.
       * 
       * @param name The name of the monomer to remove
       */
00125       public void removeMonomer(String name)    {
            if (monomers.containsKey(name))     {
                  Monomer monomer = (Monomer)monomers.get(name);
                  this.remove(monomer);
                  monomers.remove(name);
            }
      }

00133     public String toString() {
        StringBuffer stringContent = new StringBuffer();
        stringContent.append("Polymer(");
        stringContent.append(this.hashCode()).append(", ");
//        stringContent.append("N:").append(getStrandName()).append(", ");
//        stringContent.append("T:").append(getStrandType()).append(", ");
        stringContent.append(super.toString());
        stringContent.append(')');
        return stringContent.toString();
    }

00144     public Object clone() throws CloneNotSupportedException {
      Polymer clone = (Polymer)super.clone();
        clone.removeAllElements();
        for (Iterator iter = clone.getMonomerNames().iterator(); iter.hasNext();) {
            Monomer monomerClone = (Monomer)(clone.getMonomer(iter.next().toString()).clone());
            java.util.Iterator atoms = monomerClone.atoms();
            while (atoms.hasNext()) {
                clone.addAtom((IAtom)atoms.next(), monomerClone);
            }
        }
        return clone;
    }
}

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