/* Copyright (c) 2009 Peter Troshin
 *  
 *  Jalview Web Services @version: 2.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library 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 Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */
package compbio.pipeline._jpred;
import java.io.*;
import java.util.*;

import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;


public class BlastParser {
	
	static class Psiseq {
		String id;
		String seq;
	}
	/**
	 * args[0] is assumed to be the name of a Blast output file
	 * @throws XMLStreamException 
	 * @throws FileNotFoundException 
	 */
	public static void main(String[] args) throws FileNotFoundException, XMLStreamException {
		XMLInputFactory f = XMLInputFactory.newInstance();
		XMLStreamReader r = f.createXMLStreamReader( new BufferedInputStream(new FileInputStream(new File(args[0]))));
		List<Psiseq> pl = new ArrayList<Psiseq>();
		Psiseq psi = null;
		while(r.hasNext()) {
			int idx = r.next(); 
			//System.out.println(idx);

			if(r.isStartElement()) {
				String name = r.getLocalName();
				if(name.equals("Hit") ) {
					psi = new Psiseq();
				}
				if(name.equals("Hit_id") ) {
					//System.out.println(r.getElementText());
					psi.id = r.getElementText();
					System.out.println(psi.id);
				} 
				if(name.equals("Hsp_hseq")) {
					psi.seq = r.getElementText();
					System.out.println(psi.seq);
				} 
			}
			
			if(r.isEndElement()) {
				String name = r.getLocalName();
				if(name.equals("Hit") ) {
					pl.add(psi);
					psi = null;
				}
			}

		} 

	}
}