/* Copyright (c) 2011 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @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.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;

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

public class BlastParser {

    Map<Integer, Set<Hit>> iters;

    public BlastParser(String file) throws FileNotFoundException,
	    XMLStreamException {
	XMLInputFactory f = XMLInputFactory.newInstance();
	XMLStreamReader r = f.createXMLStreamReader(new BufferedInputStream(
		new FileInputStream(new File(file))));
	Set<Hit> pl = new HashSet<Hit>();
	Hit psi = null;
	this.iters = new HashMap<Integer, Set<Hit>>();
	Integer iternum = null;
	while (r.hasNext()) {
	    int idx = r.next();
	    if (r.isStartElement()) {
		String name = r.getLocalName();
		if (name.equals("Iteration_iter-num")) {
		    iternum = Integer.parseInt(r.getElementText().trim());
		    System.out.println("Iter " + iternum);
		}
		if (name.equals("Hit")) {
		    psi = new Hit();
		}
		if (name.equals("Hit_num")) {
		    psi.number = r.getElementText();
		}
		if (name.equals("Hit_accession")) {
		    psi.accession = r.getElementText();
		    // System.out.println(psi.id);
		}
		if (name.equals("Hit_def")) {
		    // System.out.println(r.getElementText());
		    psi.name = r.getElementText().split("\\s+")[0].trim();
		    // System.out.println(psi.id);
		}
		if (name.equals("Hsp_hseq")) {
		    psi.seq = r.getElementText();
		    // System.out.println(psi.seq);
		}
		if (name.equals("Hsp_evalue")) {
		    psi.evalue = r.getElementText();
		    // System.out.println(psi.seq);
		}

	    }

	    if (r.isEndElement()) {
		String name = r.getLocalName();
		if (name.equals("Hit")) {
		    boolean replaced = pl.add(psi);
		    assert replaced : "Expect unique elements only!";
		    psi = null;
		}
		if (name.equals("Iteration")) {
		    iters.put(iternum, pl);
		    pl = new HashSet<Hit>();
		}
	    }
	}

    }

    /**
     * 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 {
	BlastParser parser = new BlastParser(args[0]);
	printHits(parser.iters);
    }

    static final void printHits(Map<Integer, Set<Hit>> iterNumPsiSeqs) {
	for (Integer iterNum : iterNumPsiSeqs.keySet()) {
	    System.out.println("Iteration " + iterNum);
	    printHits(iterNumPsiSeqs.get(iterNum));
	}
    }

    static final void printHits(Collection<Hit> psiseqs) {
	assert psiseqs != null;
	System.out.println("Total hits: " + psiseqs.size());
	for (Hit pseq : psiseqs) {
	    System.out.println("Hit: " + pseq.number + " Accession: "
		    + pseq.accession + " name " + pseq.name);
	}
    }

    static final void printNames(Collection<Hit> psiseqs) {
	assert psiseqs != null;
	System.out.println("Total hits: " + psiseqs.size());
	for (Hit pseq : psiseqs) {
	    System.out.print(pseq.number + "     ");
	    System.out.println(pseq.name);
	}
    }

}