/* 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.BufferedReader;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Scanner;
import java.util.Set;

/**
 * Parser for the following files:
 * 
 * @author pvtroshin
 * 
 */
public class JackHmmerHitParser {
    //#                                                                      --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
    //# target name          accession  query name                accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
    //#  ------------------- ----------      -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
    //tr|Q6TVU2|Q6TVU2_ORFV  -          gi_74230740_gb_ABA00545.1 -           4.5e-271  910.4   0.0  5.1e-271  910.2   0.0   1.0   1   0   0   1   1   1   1 Putative uncharacterized protein OS=Orf virus PE=4 SV=1

    Set<Hit> hits;

    public JackHmmerHitParser(String file) throws IOException {

	BufferedReader bfr = new BufferedReader(new InputStreamReader(
		new FileInputStream(file), "ISO-8859-1"), 64000);
	// throw away first three lines; 
	this.hits = new HashSet<Hit>();
	String line = bfr.readLine();
	bfr.readLine();
	bfr.readLine();
	int hitc = 0;
	while ((line = bfr.readLine()) != null) {
	    hitc++;
	    Scanner scan = new Scanner(line);
	    scan.useDelimiter("\\s+");
	    extractData(scan, hitc);
	}
	List<Hit> lhits = new ArrayList<Hit>(hits);
	Collections.sort(lhits, new Hit.NumberComporator());
    }

    void extractData(Scanner scan, int hitcounter) {
	Hit pseq = new Hit();

	String tname = scan.next();
	pseq.name = tname;
	//System.out.println(tname);

	String tacc = scan.next();
	pseq.accession = tacc;
	//System.out.println(tacc);
	String qname = scan.next();
	//System.out.println(qname);
	String qacc = scan.next();
	//System.out.println(qacc);

	Double evalue = scan.nextDouble();
	//System.out.println(evalue);
	pseq.evalue = evalue.toString();

	Double score = scan.nextDouble();
	//System.out.println(score);
	pseq.evalue = evalue.toString();
	pseq.number = new Integer(hitcounter).toString();
	boolean unique = hits.add(pseq);
	assert unique : "Unique hits are expected!";
    }

    public static void main(String[] args) throws IOException {
	assert args[0] != null;
	JackHmmerHitParser parser = new JackHmmerHitParser(args[0]);
	BlastParser.printHits(parser.hits);
    }
}