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BioPolymer.java

/* $RCSfile$
 * $Author: egonw $    
 * $Date: 2007-04-22 22:49:31 +0200 (Sun, 22 Apr 2007) $    
 * $Revision: 8242 $
 * 
 * Copyright (C) 1997-2007  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.Enumeration;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;

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

/**
 * A BioPolymer is a subclass of a Polymer which is supposed to store
 * additional informations about the Polymer which are connected to BioPolymers.
 *
 * @cdk.module  data
 *
 * @author      Edgar Luttmann <edgar@uni-paderborn.de>
 * @author      Martin Eklund
 * @cdk.created 2001-08-06 
 *
 * @cdk.keyword polymer
 * @cdk.keyword biopolymer
 */
00054 public class BioPolymer extends Polymer implements java.io.Serializable, IBioPolymer
{

      /**
     * 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>.
       */
00065       private static final long serialVersionUID = -5001873073769634393L;

      private Hashtable strands;    // the list of all the contained Strands.
      
      /**
       * Contructs a new Polymer to store the Strands.
       */   
00072       public BioPolymer() {
            super();
            // Strand stuff
            strands = new Hashtable();
      }
      
      /**
       * Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence
       * the atom will be added to a Monomer of type UNKNOWN in the specified Strand.
       *
       * @param oAtom   The atom to add
       * @param oStrand The strand the atom belongs to
       */
00085       public void addAtom(IAtom oAtom, IStrand oStrand) {
            
            int atomCount = super.getAtomCount();
            
            // Add atom to AtomContainer
            super.addAtom(oAtom);

            if (atomCount != super.getAtomCount() && 
                oStrand != null) {  // Maybe better to throw nullpointer exception here, so user realises that
                                                // Strand == null and Atom only gets added to this BioPolymer, but not to a Strand.
                  oStrand.addAtom(oAtom); 
                  if (!strands.containsKey(oStrand.getStrandName())) {
                        strands.put(oStrand.getStrandName(), oStrand);
                  }
            }
            /* notifyChanged() is called by addAtom in
             AtomContainer */
      }
      
      /**
       * Adds the atom to a specified Strand and a specified Monomer.
       * 
       * @param oAtom
       * @param oMonomer
       * @param oStrand
       */
00111       public void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)    {
            
            int atomCount = super.getAtomCount();
            
            // Add atom to AtomContainer
            super.addAtom(oAtom);

            if(atomCount != super.getAtomCount() && // ok, super did not yet contain the atom
                     // Add atom to Strand (also adds the atom to the monomer).
                   oStrand != null) {
                  oStrand.addAtom(oAtom, oMonomer);   // Same problem as above: better to throw nullpointer exception?
                  if (!strands.containsKey(oStrand.getStrandName())) {
                        strands.put(oStrand.getStrandName(), oStrand);
                  }
            }
            /* The reasoning above is: 
             * All Monomers have to belong to a Strand and all atoms belonging to strands have to belong to a Monomer =>
             * ? oMonomer != null and oStrand != null, oAtom is added to BioPolymer and to oMonomer in oStrand
             * ? oMonomer == null and oStrand != null, oAtom is added to BioPolymer and default Monomer in oStrand
             * ? oMonomer != null and oStrand == null, oAtom is added to BioPolymer, but not to a Monomer or Strand (especially good to maybe throw exception in this case)
             * ? oMonomer == null and oStrand == null, oAtom is added to BioPolymer, but not to a Monomer or Strand
             * */
      }
      
      /**
       * Return the number of monomers present in BioPolymer.
       *
       * @return number of monomers
       *
       */
00141       public int getMonomerCount() {
            Enumeration keys = strands.keys();
            int number = 0;
            
            while(keys.hasMoreElements()) {
                  Strand tmp = (Strand)strands.get(keys.nextElement()); // Cast exception?!
                  number += (tmp.getMonomers()).size() - 1;
            }
            return number;
      }
      
      /**
       * Retrieve a Monomer object by specifying its name. [You have to specify the strand to enable
       * monomers with the same name in different strands. There is at least one such case: every
       * strand contains a monomer called "".]
       *
       * @param monName  The name of the monomer to look for
       * @return The Monomer object which was asked for
       *
       */
00161       public IMonomer getMonomer(String monName, String strandName) {
          Strand strand = (Strand)strands.get(strandName); 
          
          if(strand != null)  {
              return (Monomer)strand.getMonomer(monName);
          }
          else    {
              return null;
          } 
      }
      
      /*    Could look like this if you ensured individual name giving for ALL monomers:
       *    
       public Monomer getMonomer(String cName) {
       Enumeration keys = strands.keys();
       Monomer oMonomer = null;
       
       while(keys.hasMoreElements())      {
       
       if(((Strand)strands.get(keys.nextElement())).getMonomers().containsKey(cName))     {
       Strand oStrand = (Strand)strands.get(keys.nextElement());
       oMonomer = oStrand.getMonomer(cName);
       break;
       }
       }
       return oMonomer;
       }
       */   
      
      /**
       * Returns a collection of the names of all <code>Monomer</code>s in this
       * BioPolymer.
       *
       * @return a <code>Collection</code> of all the monomer names.
       */
00196       public Collection getMonomerNames() {
            Enumeration keys = strands.keys();
            Hashtable monomers = new Hashtable();
            
            while(keys.hasMoreElements()) {
                  Strand oStrand = (Strand)strands.get(keys.nextElement());
                  monomers.putAll(oStrand.getMonomers());
            }           
            return monomers.keySet();
      }
      
      /**
       *
       * Return the number of strands present in the BioPolymer.
       *
       * @return number of strands
       *
       */
00214       public int getStrandCount() {
            return strands.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
       *
       */
00226       public IStrand getStrand(String cName) {
            return (Strand)strands.get(cName);
      }
      
      /**
       * Returns a collection of the names of all <code>Strand</code>s in this
       * BioPolymer.
       *
       * @return a <code>Collection</code> of all the strand names.
       */
00236       public Collection getStrandNames() {
            return strands.keySet();
      }
      
      /**
       * Removes a particular strand, specified by its name.
       * 
       * @param name name of the strand to remove
       */
00245       public void removeStrand(String name)     {
            if (strands.containsKey(name))      {
                  Strand strand = (Strand)strands.get(name);
                  this.remove(strand);
                  strands.remove(name);
            }
      }
      
      /**
       * @return hashtable containing the monomers in the strand.
       */
00256       public Map getStrands() {
            return strands;
      }
      
00260       public String toString() {
        StringBuffer stringContent = new StringBuffer();
        stringContent.append("BioPolymer(");
        stringContent.append(this.hashCode()).append(", ");
        stringContent.append(super.toString());
        stringContent.append(')');
        return stringContent.toString();
    }

00269     public Object clone() throws CloneNotSupportedException {
      BioPolymer clone = (BioPolymer)super.clone();
        clone.strands.clear();
        for (Iterator strands = clone.getStrandNames().iterator(); strands.hasNext();) {
            Strand strand = (Strand)clone.getStrand(strands.next().toString()).clone();
            for (Iterator iter = strand.getMonomerNames().iterator(); iter.hasNext();) {
                  IMonomer monomer = strand.getMonomer(iter.next().toString());
                  java.util.Iterator atoms = monomer.atoms();
                  while (atoms.hasNext()) {
                    clone.addAtom((IAtom)atoms.next(), monomer, strand);
                } 
            }
        }
        return clone;
    }
}

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