/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * 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 WARRANTIES 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.
 */

package org.broad.igv.tools.sort;

import net.sf.samtools.util.AsciiLineReader;
import org.broad.igv.util.ParsingUtils;

/**
 * @author: nazaire
 */
public class Parser {

    private int chrCol;
    private int startCol;
    private String[] fields;

    public Parser(int chrCol, int startCol) {
        this.chrCol = chrCol;
        this.startCol = startCol;
        fields = new String[this.startCol + 1];
    }

    public SortableRecord readNextRecord(AsciiLineReader reader) {
        String nextLine = reader.readLine();
        if (nextLine == null) {
            return null;
        }

        return createRecord(nextLine);
    }

    public SortableRecord createRecord(String nextLine) {
        int nTokens = ParsingUtils.split(nextLine, fields, '\t');
        // TODO -- what to do if nTokens < startCol?

        String chr = fields[chrCol];

        int start ;
        try {
            start = Integer.parseInt(fields[startCol].trim());
        }
        catch(NumberFormatException e) {
            start = Integer.MAX_VALUE;
        }
        String text = nextLine;

        return new SortableRecord(chr, start, text);
    }
}
