content: package aliview;
  
  import static org.junit.Assert.assertEquals;
  
  import java.io.File;
  import java.net.URL;
  import java.util.ArrayList;
  import java.util.HashSet;
  
  import org.apache.log4j.Level;
  import org.apache.log4j.Logger;
  import org.junit.After;
  import org.junit.Before;
  import org.junit.BeforeClass;
  import org.junit.Test;
  
  import aliview.alignment.Alignment;
  import aliview.gui.AliViewJMenuBarFactory;
  
  public class AlignmentTest {
  
  	private static final Logger logger = Logger.getLogger(AlignmentTest.class);
  	private static Alignment alignment;
  
  	@BeforeClass
  	public static void initAlignment() {
  		Logger.getRootLogger().setLevel(Level.DEBUG);
  		URL fileUrl = new AlignmentTest().getClass().getResource("/woodsia_chloropl_excl_hybrid.fasta");
  		File fastaNucleotideFile = new File(fileUrl.getFile());
  		AliView.openAlignmentFile(fastaNucleotideFile);
  		AliViewWindow aliWin = AliView.getActiveWindow();
  		alignment = aliWin.getAlignment();
  	}
  
  	@Before
  	public void beforeEachTest() {
  		System.out.println("This is executed before each Test");
  	}
  
  	@After
  	public void afterEachTest() {
  		System.out.println("This is exceuted after each Test");
  	}
  
  	@Test
  	public void testCountStopCodons() {
  		int result = alignment.countStopCodons();
  		assertEquals("This alignment should contain 485 stop codons", 485, result);
  	}
  	
  	@Test
  	public void testFindAndSelectDuplicates() {
  		HashSet<String> result = alignment.findDuplicateNames();
  		assertEquals(0, result.size());
  	}
  	
  
  }
  