/*
 * Copyright (c) 2005, Stanford University. All rights reserved. 
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 *    contributors may be used to endorse or promote products derived 
 *    from this software without specific prior written permission. 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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/*
 * Created on May 3, 2005
 *
 */
package org.simtk.molecularstructure.nucleicacid;

import org.simtk.molecularstructure.*;
import java.util.*;

/** 
 *  
  * @author Christopher Bruns
  * 
  * Double helix of RNA or DNA
 */
public class Duplex extends SecondaryStructureClass {
    static final long serialVersionUID = 1L;
    // private HashSet residues = new HashSet();
    private List<BasePair> basePairs = new Vector<BasePair>();
    
    // TODO these should be const
    // public Collection residues() {return residues;}
    public List<BasePair> basePairs() {return basePairs;}
    
    public void addBasePair(BasePair bp) {
        basePairs.add(bp);
        this.addResidue(bp.getResidue1());
        this.addResidue(bp.getResidue2());
    }
    
    public String helixString() {
    	Residue res5 = ((BasePair) basePairs.get(0)).getResidue1();
       	Residue res3 = ((BasePair) basePairs.get(basePairs.size()-1)).getResidue2();
       	// String mol5 = res5.getPdbChainId();
       	// String mol3 = res3.getPdbChainId();
       	// return "(("+mol5+", "+res5+"), ("+mol3+", "+res3+"), "+basePairs.size()+")";
        return "(("+res5+"), ("+res3+"), "+basePairs.size()+")";
    }
}