/*
 * 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.
 */

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

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

/**
 * @author jrobinso
 */
public class DotAlignedParser implements AlignmentParser {

    public static int CHROMOSOME_COLUMN = 0;
    private static int START_COLUMN = 1;
    private static int END_COLUMN = 2;
    private static int STRAND_COLUMN = 3;
    private static int NAME_COLUMN = -1;
    private String[] fields = new String[20];
    boolean bedFormat = false;

    public DotAlignedParser() {
        bedFormat = false;
    }

    public DotAlignedParser(boolean bedFormat) {
        this.bedFormat = bedFormat;
        if (bedFormat) {
            STRAND_COLUMN = 5;
            NAME_COLUMN = 3;
        }
    }

    public DotAlignedAlignment readNextRecord(AsciiLineReader reader) {
        String nextLine;
        while ((nextLine = reader.readLine()) != null) {
            DotAlignedAlignment alignment = createAlignment(nextLine);
            if (alignment != null) {
                return alignment;
            }
        }
        return null;
    }

    private DotAlignedAlignment createAlignment(String nextLine) {


        try {
            int nTokens = ParsingUtils.split(nextLine, fields, '\t');
            if(nTokens <= END_COLUMN)  {
                System.out.println("Skipping line: " + nextLine);
                return null;
            }

            String chr = fields[0];
            int start = Integer.parseInt(fields[START_COLUMN]);
            int end = Integer.parseInt(fields[END_COLUMN]);


            if (bedFormat) {
                boolean isNegative = false;
                String name = "";
                if (nTokens > STRAND_COLUMN) {
                    isNegative = fields[STRAND_COLUMN].equals("-");
                }
                if (nTokens > NAME_COLUMN) {
                    name = fields[NAME_COLUMN];
                }
                return new DotAlignedAlignment(chr, start, end, isNegative, name);
            } else {

                boolean isNegative = fields[STRAND_COLUMN].equals("-");
                return new DotAlignedAlignment(chr, start, end, isNegative);
            }
        } catch (NumberFormatException e) {
            System.out.println("Skipping line: " + nextLine);
            return null;
        }
    }
}
