Get the tests working in intellij with junit

src/characterization/ChromosomeBand.java

@@ -1,23 +1,23 @@
 package characterization;
 
 public class ChromosomeBand {
-	public static enum Type {
+	public enum BandType {
 		BLACK, WHITE, GREY, CENTROMERE
-	};
+	}
 
-	private final Type type;
+	private final BandType type;
 	private final int length;
 
-	public ChromosomeBand(Type type, int length) {
-		if (type == this.type.CENTROMERE && length == 0) {
+	public ChromosomeBand(BandType type, int length) {
+		if (type == BandType.CENTROMERE && length == 0) {
 			throw new IllegalArgumentException("Length of a centromere band cannot be non-zero.");
 		}
 
 		this.type = type;
 		this.length = length;
 	}
 
-	public Type type() {
+	public BandType type() {
 		return type;
 	}
 

src/idiogram/IdiogramMap.java

@@ -8,7 +8,7 @@
 import java.util.regex.Pattern;
 
 import characterization.ChromosomeBand;
-import characterization.ChromosomeBand.Type;
+import characterization.ChromosomeBand.BandType;
 
 /**
  * Wrapper for a Java HashMap that maps an idiogram to a chromosome number.
@@ -60,7 +60,7 @@ private void idiogramSheetParser(File file) {
 
 		String token = null;
 		int chromosomeNumber = 0;
-		ChromosomeBand.Type bandType;
+		ChromosomeBand.BandType bandType;
 		int bandLength = 0;
 		ChromosomeBand band = null;
 		int resolution = 0;
@@ -85,22 +85,22 @@ private void idiogramSheetParser(File file) {
 				// End debug
 
 				if (token.toLowerCase().equals("white")) {
-					bandType = Type.WHITE;
+					bandType = BandType.WHITE;
 					bandLength = lineReader.nextInt();
 					band = new ChromosomeBand(bandType, bandLength);
 					newIdiogram.add(band);
 				} else if (token.toLowerCase().equals("black")) {
-					bandType = Type.BLACK;
+					bandType = BandType.BLACK;
 					bandLength = lineReader.nextInt();
 					band = new ChromosomeBand(bandType, bandLength);
 					newIdiogram.add(band);
 				} else if (token.toLowerCase().equals("grey")) {
-					bandType = Type.GREY;
+					bandType = BandType.GREY;
 					bandLength = lineReader.nextInt();
 					band = new ChromosomeBand(bandType, bandLength);
 					newIdiogram.add(band);
 				} else if (token.toLowerCase().equals("centromere")) {
-					bandType = Type.CENTROMERE;
+					bandType = BandType.CENTROMERE;
 					bandLength = lineReader.nextInt();
 					band = new ChromosomeBand(bandType, bandLength);
 					newIdiogram.add(band);
@@ -123,7 +123,7 @@ private void idiogramSheetParser(File file) {
 	 * Gets the chromosome number that the requested idiogram maps to. If the idiogram requested is
 	 * not in the list of keys then null is returned.
 	 * 
-	 * @param i
+	 * @param index
 	 *            Requested idiogram
 	 * @return Chromosome number mapped to or null if the requested idiogram doesn't exist.
 	 */

src/testing/TestShape.java

@@ -1,68 +1,68 @@
-package testing;
-
-import runner.ImageQueue;
-import chromosome.ChromosomeCluster;
-import chromosome.GeneticSlideImage;
-import extraction.Extractor;
-
-public class TestShape {
-	private static GeneticSlideImage image = null;
-	private static ChromosomeCluster cluster = null;
-
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) {
-		String filename;
-		ImageQueue images = new ImageQueue();
-		// put new images in the queue and return the next image from the folder
-		// args
-		filename = images.getNextFile(args[0]);
-		// create a slideImage from the filename
-		GeneticSlideImage image = new GeneticSlideImage(filename);
-		Extractor extractor = new Extractor();
-		if (filename != null) {
-			// extract the background from the image
-			int shapeNum = extractor.removeBackground(image);
-			// extract the clusters from the image
-			shapeNum = extractor.findClusters(image);
-			// pass on the list of clusters
-			ChromosomeCluster testCluster = extractor.getClusterList().get(0);
-			// print out the first cluster in the list
-			extractor.getClusterList().get(0).clusterOut();
-		}
-	}
-
-	/**
-	 * Returns the chromosome cluster object from an image.
-	 * 
-	 * @param filename
-	 *            File containing cluster
-	 * @return The chromosome cluster object
-	 */
-	public static ChromosomeCluster getCluster(String filename) {
-		image = new GeneticSlideImage(filename);
-		Extractor extractor = new Extractor();
-		ChromosomeCluster testCluster = null;
-		if (filename != null) {
-			// extract the background from the image
-			int shapeNum = extractor.removeBackground(image);
-			// extract the clusters from the image
-			shapeNum = extractor.findClusters(image);
-			// pass on the list of clusters
-			testCluster = extractor.getClusterList().get(0);
-			// print out the first cluster in the list
-			extractor.getClusterList().get(0).clusterOut();
-		}
-		return testCluster;
-	}
-
-	public static GeneticSlideImage getGeneticSlideImage() {
-		return image;
-	}
-
-	public static ChromosomeCluster getCluster() {
-		return cluster;
-	}
-
-}
+package testing;
+
+import runner.ImageQueue;
+import chromosome.ChromosomeCluster;
+import chromosome.GeneticSlideImage;
+import extraction.Extractor;
+
+public class TestShape {
+	private static GeneticSlideImage image = null;
+	private static ChromosomeCluster cluster = null;
+
+	/**
+	 * @param args
+	 */
+	public static void main(String[] args) {
+		String filename;
+		ImageQueue images = new ImageQueue();
+		// put new images in the queue and return the next image from the folder
+		// args
+		filename = images.getNextFile(args[0]);
+		// create a slideImage from the filename
+		GeneticSlideImage image = new GeneticSlideImage(filename);
+		Extractor extractor = new Extractor();
+		if (filename != null) {
+			// extract the background from the image
+			int shapeNum = extractor.removeBackground(image);
+			// extract the clusters from the image
+			shapeNum = extractor.findClusters(image);
+			// pass on the list of clusters
+			ChromosomeCluster testCluster = extractor.getClusterList().get(0);
+			// print out the first cluster in the list
+			extractor.getClusterList().get(0).clusterOut();
+		}
+	}
+
+	/**
+	 * Returns the chromosome cluster object from an image.
+	 * 
+	 * @param filename
+	 *            File containing cluster
+	 * @return The chromosome cluster object
+	 */
+	public static ChromosomeCluster getCluster(String filename) {
+		image = new GeneticSlideImage(filename);
+		Extractor extractor = new Extractor();
+		ChromosomeCluster testCluster = null;
+		if (filename != null) {
+			// extract the background from the image
+			int shapeNum = extractor.removeBackground(image);
+			// extract the clusters from the image
+			shapeNum = extractor.findClusters(image);
+			// pass on the list of clusters
+			testCluster = extractor.getClusterList().get(0);
+			// print out the first cluster in the list
+			extractor.getClusterList().get(0).clusterOut();
+		}
+		return testCluster;
+	}
+
+	public static GeneticSlideImage getGeneticSlideImage() {
+		return image;
+	}
+
+	public static ChromosomeCluster getCluster() {
+		return cluster;
+	}
+
+}

test/basic_objects/AroundPixelTest.java

@@ -1,16 +1,15 @@
 package basic_objects;
 
 import java.util.LinkedList;
+import org.junit.Test;
 
-import basic_objects.AroundPixel;
-import junit.framework.TestCase;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 
-public class AroundPixelTest extends TestCase {
-	protected void setUp() throws Exception {
-		super.setUp();
-
-	}
+public class AroundPixelTest {
 
+	@Test
 	public void testGetPositionsBetweenNeg() {
 		LinkedList<Integer> posList = AroundPixel.getPositionsBetweenNeg(0, 4);
 		assertEquals(posList.size(), 3);
@@ -24,7 +23,7 @@ public void testGetPositionsBetweenNeg() {
 		assertFalse(posList.contains(0));
 
 	}
-
+	@Test
 	public void testGetPositionsBetweenPlus() {
 		LinkedList<Integer> posList = AroundPixel.getPositionsBetweenPlus(0, 4);
 		assertEquals(posList.size(), 3);
@@ -38,7 +37,7 @@ public void testGetPositionsBetweenPlus() {
 		assertFalse(posList.contains(0));
 
 	}
-
+	@Test
 	public void testGetOppisitPos() {
 		assertEquals(4, AroundPixel.getOppisitePos(0));
 		assertEquals(5, AroundPixel.getOppisitePos(1));
@@ -50,7 +49,7 @@ public void testGetOppisitPos() {
 		assertEquals(3, AroundPixel.getOppisitePos(7));
 
 	}
-
+	@Test
 	public void testHandleLoop() {
 		assertEquals(7, AroundPixel.handleLoop(-1));
 		assertEquals(6, AroundPixel.handleLoop(-2));

test/basic_objects/IdiogramMapTest.java

@@ -4,44 +4,33 @@
 package basic_objects;
 
 import java.io.File;
-
-import characterization.ChromosomeBand;
 import idiogram.IdiogramMap;
-import junit.framework.TestCase;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.fail;
 
 /**
  * @author Robert
  *
  */
-public class IdiogramMapTest extends TestCase {
+public class IdiogramMapTest {
 
 	private IdiogramMap map;
-
-	/**
-	 * @param name
-	 */
-	public IdiogramMapTest(String name) {
-		super(name);
-		map = new IdiogramMap(new File(".\\ChromosomeIdiogramSheet.csv"));
-	}
 
 	/* (non-Javadoc)
 	 * @see junit.framework.TestCase#setUp()
 	 */
-	protected void setUp() throws Exception {
-		super.setUp();
-	}
+	@Before
+	public void setUp() throws Exception {
+		map = new IdiogramMap(new File(".\\ChromosomeIdiogramSheet.csv"));
 
-	/* (non-Javadoc)
-	 * @see junit.framework.TestCase#tearDown()
-	 */
-	protected void tearDown() throws Exception {
-		super.tearDown();
 	}
 
 	/**
 	 * Test method for {@link idiogram.IdiogramMap#get(Idiogram)}.
 	 */
+	@Test
 	public void testGet() {
 //		Chromosome chromosome = new Chromosome(10);
 //		chromosome.add(new ChromosomeBand(ChromosomeBand.Type.WHITE, 21));

test/basic_objects/PointListTest.java

@@ -1,17 +1,14 @@
 package basic_objects;
 
 import java.awt.Point;
+import org.junit.Test;
 
-import basic_objects.PointList;
-
-import junit.framework.TestCase;
-
-public class PointListTest extends TestCase {
-
-	protected void setUp() throws Exception {
-		super.setUp();
-	}
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 
+public class PointListTest{
+	@Test
 	public void testSetList() {
 		PointList tempList = new PointList(new Point(10, 2), 2);
 		tempList.addPoint(new Point(3, 2), 2);
@@ -27,7 +24,7 @@ public void testSetList() {
 		assertFalse(pointList.getList().contains(new Point(6, 10)));
 
 	}
-
+	@Test
 	public void testAddPoint() {
 		PointList tempList = new PointList(new Point(10, 2), 2);
 		assertTrue(tempList.addPoint(new Point(3, 2), 2));