/*
 * NibFileTest.java
 * JUnit based test
 *
 * Created on January 18, 2007, 5:02 PM
 */

package lab.seq;

import junit.framework.*;
import java.io.*;

import org.biojava.bio.symbol.*;

/**
 * Distributed under the GNU Library General Public License, v.2 or greater.
 *
 * @author jburdick
 */
public class NibFileTest extends TestCase {
    
    public NibFile nf;
    
    public NibFileTest(String testName) {
        super(testName);
    }

    protected void setUp() throws Exception {
        RandomAccessFile f =
            new RandomAccessFile("/home/jburdick/Desktop/chr18_chunk.nib", "r");
        nf = new NibFile(f);
    }

    protected void tearDown() throws Exception {
    }

    /**
     * Test of getLength method, of class lab.seq.NibFile.
     */
    public void testGetLength() {
        System.out.println("length is " + nf.getLength());
    }

    private void printOneChunk(int start, int end, boolean plusStrand)
            throws IOException, IllegalSymbolException {
        System.out.println("chr21:" + start + "-" + end + ", " +
            (plusStrand ? "+" : "-") + " strand:" +
            nf.getSymbolListByLocation(start, end, plusStrand).seqString());
    }
    
    /**
     * Test of getSequenceByLocation method, of class lab.seq.NibFile.
     */
    public void testGetSequenceByLocation() throws Exception {
        System.out.println("getting chunks of sequence from hg18 chr. 19");
        printOneChunk(1, 30, true);
        printOneChunk(1, 30, false); 
        printOneChunk(1, 31, true);
        printOneChunk(1, 31, false);
        printOneChunk(2, 30, true);        
        printOneChunk(2, 31, true);
        printOneChunk(5000, 5075, true);
    }
    
}