content: /*
  * Copyright (c) 1997 - 2016
  * Actelion Pharmaceuticals Ltd.
  * Gewerbestrasse 16
  * CH-4123 Allschwil, Switzerland
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  *
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  * 3. Neither the name of the the copyright holder nor the
  *    names of its 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 LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
  * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
  */
  
  package com.actelion.research.chem.properties.complexity;
  
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.List;
  
  import javax.xml.parsers.ParserConfigurationException;
  
  import org.w3c.dom.DOMException;
  import org.w3c.dom.Document;
  import org.w3c.dom.Element;
  import org.w3c.dom.Node;
  import org.w3c.dom.NodeList;
  
  import com.actelion.research.chem.Canonizer;
  import com.actelion.research.chem.IDCodeParser;
  import com.actelion.research.chem.StereoMolecule;
  
  public class ResultFragmentsStatistic {
  	
  	public static final String TAG_ResultFragmentsStatistic = "ResultFragmentsStatistic";
  	
  	private static final String TAG_ATTR_NAME = "Name";
  	
  	private static final String TAG_ATTR_IDCODE = "IdCode";
  	
  	private static final String TAG_ATTR_COORD = "Coordinates"; 
  	
  	private static final String TAG_LIST_ModelExhaustiveStatistics = "ListModelExhaustiveStatistics";
  			
  	private String name;
  	
  	private StereoMolecule mol;
  	
  	private List<ModelExhaustiveStatistics> liModelExhaustiveStatistics;
  	
  	/**
  	 * @param liModelExhaustiveStatistics
  	 */
  	public ResultFragmentsStatistic(StereoMolecule mol,	List<ModelExhaustiveStatistics> liModelExhaustiveStatistics) {
  		super();
  		
  		
  		this.mol = mol;
  		this.liModelExhaustiveStatistics = liModelExhaustiveStatistics;
  	}
  
  
  	/**
  	 * @return the nAtomsMolecule
  	 */
  	public int getAtoms() {
  		return mol.getAtoms();
  	}
  
  
  	/**
  	 * @return the nBondsMolecule
  	 */
  	public int getBonds() {
  		return mol.getBonds();
  	}
  
  
  	/**
  	 * @return the liModelExhaustiveStatistics
  	 */
  	public List<ModelExhaustiveStatistics> getExhaustiveStatistics() {
  		return liModelExhaustiveStatistics;
  	}
  	
  	/**
  	 * @return the name
  	 */
  	public String getName() {
  		return name;
  	}
  
  
  	/**
  	 * @param name the name to set
  	 */
  	public void setName(String name) {
  		this.name = name;
  	}
  
  
  	public String toString() {
  		StringBuilder sb = new StringBuilder();
  		
  		if(name!=null){
  			sb.append("Name " + name);
  			sb.append("\n");
  		}
  		
  		sb.append("Atoms " + getAtoms() + ", bonds " + getBonds() + ".");
  		
  		sb.append("\n");
  		
  		sb.append(ModelExhaustiveStatistics.toString(this));
  		
  		
  		return sb.toString();
  	}
  	
  	public Element getXMLElement(Document doc) throws ParserConfigurationException, DOMException, IOException{
  		
          Element nodeRoot  = doc.createElement(TAG_ResultFragmentsStatistic);
          
          nodeRoot.setAttribute(TAG_ATTR_NAME, name);
          
          Canonizer can = new Canonizer(mol);
          
          nodeRoot.setAttribute(TAG_ATTR_IDCODE, can.getIDCode());
          
          nodeRoot.setAttribute(TAG_ATTR_COORD, can.getEncodedCoordinates());
                                  
          Element nodeListModelExhaustiveStatistics  = doc.createElement(TAG_LIST_ModelExhaustiveStatistics);
  
          for (ModelExhaustiveStatistics model : liModelExhaustiveStatistics) {
  			
              Element nodeModelExhaustiveStatistics  = model.getXMLElement(doc);
              
              
  
              nodeListModelExhaustiveStatistics.appendChild(nodeModelExhaustiveStatistics);
  		}
                          
          nodeRoot.appendChild(nodeListModelExhaustiveStatistics);
          
  		return nodeRoot;
  	}
  	
  	/**
  	 * @return the mol
  	 */
  	public StereoMolecule getMol() {
  		return mol;
  	}
  
  
  	public static ResultFragmentsStatistic readXMLElement(Element root) throws ParserConfigurationException, DOMException, IOException{
  				
  		String name = root.getAttribute(TAG_ATTR_NAME);
  		
  		String idcode = root.getAttribute(TAG_ATTR_IDCODE);
  		
  		String coord = root.getAttribute(TAG_ATTR_COORD);
  		
  		
  		NodeList nl = root.getChildNodes();
  		
  		int len = nl.getLength();
  		
  		Element nodeListModelExhaustiveStatistics = null; 
  		
  		for (int i = 0; i < len; i++) {
  			Node node = nl.item(i);
  			
  			String nodeName = node.getNodeName();
  			
  			if(TAG_LIST_ModelExhaustiveStatistics.equals(nodeName)){
  				nodeListModelExhaustiveStatistics = (Element)node;
  				break;
  			}
  			
  		}
  		
  		
  		NodeList nlModelExhaustiveStatistics = nodeListModelExhaustiveStatistics.getChildNodes();
  		
  		List<ModelExhaustiveStatistics> liModelExhaustiveStatistics = new ArrayList<ModelExhaustiveStatistics>();
  
  		for (int i = 0; i < nlModelExhaustiveStatistics.getLength(); i++) {
  			Node node = nlModelExhaustiveStatistics.item(i);
  			
  			String nodeName = node.getNodeName();
  			
  			if(ModelExhaustiveStatistics.TAG_ModelExhaustiveStatistics.equals(nodeName)){
  				Element nodeModelExhaustiveStatistics = (Element)node;
  				
  				ModelExhaustiveStatistics modelExhaustiveStatistics = ModelExhaustiveStatistics.readXMLElement(nodeModelExhaustiveStatistics);
  				
  				liModelExhaustiveStatistics.add(modelExhaustiveStatistics);
  				
  			}
  			
  		}
  		
  		IDCodeParser parser = new IDCodeParser(false);
  		
  		StereoMolecule mol = parser.getCompactMolecule(idcode, coord);
  		
  		ResultFragmentsStatistic resultFragmentsStatistic = new ResultFragmentsStatistic(mol, liModelExhaustiveStatistics);
  		
  		resultFragmentsStatistic.setName(name);
  		
  
  		return resultFragmentsStatistic;
  	}
  
  
  }
  