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The protein structure modules of BioJava.

There is a newer version: 7.2.2

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on May 10, 2010
 * Author: Andreas Prlic
 *
 */

package org.biojava.nbio.structure.align.xml;

import org.biojava.nbio.core.util.PrettyXMLWriter;
import org.w3c.dom.Document;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringReader;
import java.io.StringWriter;

public class PositionInQueueXMLConverter
{

	public String toXML(int position) throws IOException{
		StringWriter swriter = new StringWriter();

		PrintWriter writer = new PrintWriter(swriter);
		PrettyXMLWriter xml = new PrettyXMLWriter(writer);

		xml.openTag("queue");
		xml.attribute("position", position+"");
		xml.closeTag("queue");
		xml.close();
		return swriter.toString();
	}

	public int fromXML(String xml){
		int position = Integer.MIN_VALUE;

		try
		{
			//Convert string to XML document
			DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
			DocumentBuilder db = factory.newDocumentBuilder();
			InputSource inStream = new InputSource();
			inStream.setCharacterStream(new StringReader(xml));
			Document doc = db.parse(inStream);

			// normalize text representation
			doc.getDocumentElement().normalize();


			//Element rootElement = doc.getDocumentElement();

			NodeList listOfAlignments = doc.getElementsByTagName("queue");
			//int numArrays = listOfAlignments.getLength();
			//System.out.println("got " + numArrays + " alignment results.");
			// go over the blocks


			for(int afpPos=0; afpPos