/* $RCSfile$ * $Author: egonw $ * $Date: 2007-02-16 14:38:49 +0100 (Fri, 16 Feb 2007) $ * $Revision: 7960 $ *  * Copyright (C) 2004-2007  Martin Eklund <martin.eklund@farmbio.uu.se> *  * 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;import org.openscience.cdk.interfaces.IStrand;/** * A Strand is an AtomContainer which stores additional strand specific * informations for a group of Atoms. * * @cdk.module  data * @cdk.created 2004-12-20 * @author      Martin Eklund <martin.eklund@farmbio.uu.se> * @author      Ola Spjuth <ola.spjuth@farmbio.uu.se> */public class Strand extends AtomContainer implements java.io.Serializable, IStrand{	/**     * 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>.	 */	private static final long serialVersionUID = 4200943086350928356L;	/** The list of all Monomers in the Strand.*/	private Hashtable monomers;	/** The name of this strand (e.g. A, B). */	private String strandName;	/** The type of this strand (e.g. PEPTIDE, DNA, RNA). */	private String strandType;		/**	 * Contructs a new Strand.	 */		public Strand () {		super();		// Stand stuff		monomers = new Hashtable();		Monomer oMonomer = new Monomer();		oMonomer.setMonomerName("");		oMonomer.setMonomerType("UNKNOWN");		monomers.put("", oMonomer);                strandName = "";	}		/**	 * Retrieve the strand name.	 *	 * @return The name of the Strand object	 * @see #setStrandName	 */	public String getStrandName() {		return strandName;	}		/**	 * Retrieve the strand type.	 *	 * @return The type of the Strand object	 * @see #setStrandType	 */	public String getStrandType() {		return strandType;	}		/**	 * Set the name of the Strand object.	 *	 * @param cStrandName  The new name for this strand	 * @see #getStrandName	 */	public void setStrandName(String cStrandName) {		strandName = cStrandName;	}		/**	 * Set the type of the Strand object.	 *	 * @param cStrandType  The new type for this strand	 * @see #getStrandType	 */	public void setStrandType(String cStrandType) {		strandType = cStrandType;	}		/**	 *	 * Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the	 * atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN.	 *	 * @param oAtom  The atom to add	 *	 */	public void addAtom(IAtom oAtom) {		addAtom(oAtom, getMonomer(""));	}		/**	 *	 * Adds the atom oAtom to a specific Monomer.	 *	 * @param oAtom  The atom to add	 * @param oMonomer  The monomer the atom belongs to	 *	 */	public void addAtom(IAtom oAtom, IMonomer oMonomer) {				int atomCount = super.getAtomCount();				// Add atom to AtomContainer		super.addAtom(oAtom);		if(atomCount != super.getAtomCount()) { // ok, super did not yet contain the atom						if (oMonomer == null) {				oMonomer = getMonomer("");			}						oMonomer.addAtom(oAtom);			if (! monomers.containsKey(oMonomer.getMonomerName())) {				monomers.put(oMonomer.getMonomerName(), oMonomer);			}		}	}		/**	 *	 * Return the number of monomers present in the Strand.	 *	 * @return number of monomers	 *	 */	public int getMonomerCount() {		return monomers.size() - 1;	}		/**	 *	 * 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	 *	 */	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.	 */	public Collection getMonomerNames() {		return monomers.keySet();	}		/**	 * 	 * Adds a <code>Monomer</code> to this <code>Strand</code>. All atoms and	 * bonds in the Monomer are added. NB: The <code>Monomer</code> will *not*	 * "automatically" be connected to the <code>Strand</code>. That has to be	 * done "manually" (as the "connection point" is not known). 	 * @param monomer	 */	/*public void addMonomer(Monomer monomer)	{		if (! monomers.contains(monomer.getMonomerName())) {			monomers.put(monomer.getMonomerName(), monomer);	// Adderas atomer etc? Nope!		}	}*/		/**	 * Removes a particular monomer, specified by its name.	 * 	 * @param name The name of the monomer to remove	 */	public void removeMonomer(String name)	{		if (monomers.containsKey(name))	{			Monomer monomer = (Monomer)monomers.get(name);			this.remove(monomer);			monomers.remove(name);		}	}		/**	 * Returns a hashtable containing the monomers in the strand.	 *	 * @return hashtable containing the monomers in the strand.	 */	public Hashtable getMonomers()	{		return monomers;	}        public String toString() {        StringBuffer stringContent = new StringBuffer(32);        stringContent.append("Strand(");        stringContent.append(this.hashCode());        stringContent.append(", N:").append(getStrandName());        stringContent.append(", T:").append(getStrandType()).append(", ");        stringContent.append(super.toString());        stringContent.append(')');        return stringContent.toString();    }        public Object clone() throws CloneNotSupportedException {        Strand clone = (Strand)super.clone();        clone.monomers.clear();        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;    }}