/*
 * 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 static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import org.junit.Test;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.HashSet;
import java.util.Set;


/**
 * Created by IntelliJ IDEA.
 * User: jrobinso
 * Date: Sep 18, 2009
 * Time: 6:19:28 PM
 * To change this template use File | Settings | File Templates.
 */
public class SorterTest {

    @Test
    public void testBlankTest() {
        System.out.println("Test");
    }

    @Test
    public void testRun() {
        System.out.println("Test run");

        File ifile = new File("/Users/jrobinso/IGV/hela.txt.bowtie.aligned");
        File ofile = new File("/Users/jrobinso/IGV/hela.txt.bowtie.sorted.aligned");

        Sorter sorter = Sorter.getSorter(ifile, ofile);

        sorter.run();


        BufferedReader reader = null;

        try {
            reader = new BufferedReader(new FileReader(ofile));
            String nextLine = "";
            String lastChr = "";
            int lastStart = 0;
            Set<String> chromosomes = new HashSet();
            while ((nextLine = reader.readLine()) != null) {
                String[] tokens = nextLine.split("\t");
                String chr = tokens[0];
                System.out.println(chr);
                int start = Integer.parseInt(tokens[1]);
                if (chr.equals(lastChr)) {
                    assertTrue(start >= lastStart);
                } else {
                    assertFalse(chromosomes.contains(chr));
                    chromosomes.add(chr);
                    System.out.println(chr);
                }
                lastChr = chr;
                lastStart = start;
            }
        }
        catch (Exception e) {

        }

        finally {
            try {
                reader.close();
            }
            catch (Exception e) {

            }
        }

    }
}
