/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on June 9, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment;

import org.biojava.nbio.alignment.template.GapPenalty;
import org.junit.Test;

import static org.junit.Assert.assertEquals;

public class SimpleGapPenaltyTest {

	@Test
	public void testSimpleGapPenalty() {
		int gop = -12, gep = -3;
		GapPenalty defaults = new SimpleGapPenalty();
		SimpleGapPenalty.setDefaultOpenPenalty(gop);
		SimpleGapPenalty.setDefaultExtensionPenalty(gep);
		GapPenalty gaps = new SimpleGapPenalty();
		assertEquals(gaps.getOpenPenalty(), gop);
		assertEquals(gaps.getExtensionPenalty(), gep);
		assertEquals(gaps.getType(), GapPenalty.Type.AFFINE);
		SimpleGapPenalty.setDefaultOpenPenalty(defaults.getOpenPenalty());
		SimpleGapPenalty.setDefaultExtensionPenalty(defaults.getExtensionPenalty());
	}

	@Test
	public void testSimpleGapPenaltyShortShort() {
		short gop = -10, gep = -4;
		GapPenalty gaps = new SimpleGapPenalty(gop, gep);
		assertEquals(gaps.getOpenPenalty(), gop);
		assertEquals(gaps.getExtensionPenalty(), gep);
		assertEquals(gaps.getType(), GapPenalty.Type.AFFINE);
	}

	@Test
	public void testExtensionPenalty() {
		GapPenalty gaps = new SimpleGapPenalty();
		short gep = -14;
		gaps.setExtensionPenalty(gep);
		assertEquals(gaps.getExtensionPenalty(), gep);
	}

	@Test
	public void testOpenPenalty() {
		GapPenalty gaps = new SimpleGapPenalty();
		short gop = -27;
		gaps.setOpenPenalty(gop);
		assertEquals(gaps.getOpenPenalty(), gop);
	}

	@Test
	public void testType() {
		assertEquals(new SimpleGapPenalty((short) 7, (short) 0).getType(), GapPenalty.Type.CONSTANT);
		assertEquals(new SimpleGapPenalty((short) 0, (short) 5).getType(), GapPenalty.Type.LINEAR);
		assertEquals(new SimpleGapPenalty((short) 8, (short) 3).getType(), GapPenalty.Type.AFFINE);
	}

}