/*
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
 * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
 * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
 * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
 * OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
 * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
 * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
 * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
 * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
 * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
 */

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package org.broad.igv.tools.sort;

import htsjdk.tribble.readers.AsciiLineReader;

import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;

/**
 * @author jrobinso
 */
public class BedSorter extends Sorter {
    private int chrCol;
    private int startCol;


    public BedSorter(File inputFile, File outputFile) {
        super(inputFile, outputFile);
        if (inputFile.getName().endsWith(".psl") || inputFile.getName().endsWith(".pslx")) {
            chrCol = 13;
            startCol = 15;
        } else {
            chrCol = 0;
            startCol = 1;
        }
    }

    @Override
    Parser getParser() {
        return new Parser(chrCol, startCol);
    }

    @Override
    String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {

        String nextLine = reader.readLine();

        if (nextLine.startsWith("psLayout")) {
            do {
                writer.println(nextLine);
                nextLine = reader.readLine();
            } while (!nextLine.startsWith("-"));
            nextLine = reader.readLine();
        }
        // TODO -- check "browser" line syntax,  is it a multi-line directive?
        while (nextLine.startsWith("#") ||
                nextLine.startsWith("browser") ||
                nextLine.startsWith("track") ||
                nextLine.trim().length() == 0) {
            writer.println(nextLine);
            nextLine = reader.readLine();
        }

        return nextLine;


    }
}
