Merge pull request #84 from ProgrammingLife3/tests/moretests

Tests/moretests

Author: kwendel

.gitignore

@@ -58,7 +58,8 @@ hs_err_pid*
 /local/*
 !/data/testdata/
 !/data/testdata/*.graph
-
+!/data/testdata/*/*.nwk
 !resources/pictures/*
 
+.save-helix2.txt
 lastOpenedSave.txt

.save-helix2.txt

@@ -0,0 +1,5 @@
+/Users/tombrouws/Downloads/100_strains_graph
+/Users/tombrouws/context/ProgrammingLife3/data/10_strains_graph
+/Users/tombrouws/Downloads/38_strains_graph
+/Users/tombrouws/context/ProgrammingLife3/data/10_strains_graph/metadata.txt
+/Users/tombrouws/Downloads/38_strains_graph/simple_graph.node.graph

.travis.yml

@@ -8,6 +8,8 @@ notifications:
   - http://octopull.rmhartog.me/api/travis/webhook
 before_install:
   - "[ \"$BUILD_PR_BRANCH\" = \"true\" ] && git checkout $TRAVIS_BRANCH && echo \"OCTOPULL_SHA=$(git rev-parse HEAD)\"; true"
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
 env:
   - BUILD_PR_BRANCH=true
   - BUILD_PR_BRANCH=false

data/testdata/LastOpenedTest/test.edge.graph

@@ -9,14 +9,32 @@
   <url>http://maven.apache.org</url>
   <properties>
     <checkstyle.config.location>checkstyle.xml</checkstyle.config.location>
+    <powermock.version>1.6.1</powermock.version>
   </properties>
   <dependencies>
+    <dependency>
+      <groupId>org.powermock</groupId>
+      <artifactId>powermock-module-junit4</artifactId>
+      <version>${powermock.version}</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.powermock</groupId>
+      <artifactId>powermock-api-mockito</artifactId>
+      <version>${powermock.version}</version>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
       <version>4.12</version>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>com.github.stefanbirkner</groupId>
+      <artifactId>system-rules</artifactId>
+      <version>1.3.0</version>
+    </dependency>
     <dependency>
       <groupId>org.graphstream</groupId>
       <artifactId>gs-core</artifactId>
@@ -37,11 +55,11 @@
       <artifactId>findbugs</artifactId>
       <version>3.0.1</version>
     </dependency>
-    <dependency>
-      <groupId>org.mockito</groupId>
-      <artifactId>mockito-all</artifactId>
-      <version>1.9.5</version>
-    </dependency>
+    <!--<dependency>-->
+      <!--<groupId>org.mockito</groupId>-->
+      <!--<artifactId>mockito-all</artifactId>-->
+      <!--<version>1.9.5</version>-->
+    <!--</dependency>-->
     <dependency>
       <groupId>org.swinglabs</groupId>
       <artifactId>swingx</artifactId>

data/testdata/LastOpenedTest/test.node.graph

@@ -162,15 +162,10 @@ public void makeGraphFromFiles() {
 	 */
 	public void makeGraph(File nodeFile, File edgeFile, File treeFile) {
 		try {
-			final long startTime = System.currentTimeMillis();
-
 			graphController.parseGraph(nodeFile, edgeFile);
 			if (treeFile != null) {
 				makePhyloTree(treeFile);
 			}
-
-			long loadTime = System.currentTimeMillis() - startTime;
-			System.out.println("Loadtime: " + loadTime);
 		} catch (FileNotFoundException exception) {
 			if (DialogUtil.confirm("Error!", "Your file was not found. Want to try again?")) {
 				makeGraph(nodeFile, edgeFile, treeFile);
@@ -305,7 +300,7 @@ public Rectangle getBounds() {
 		return new Rectangle(main.getWidth(), main.getHeight());
 	}
 
-	public void repaint(){
+	public void repaint() {
 		main.repaint();
 	}
 

data/testdata/LastOpenedTest/test.nwk

@@ -9,10 +9,10 @@
  */
 public class ScreenSize {
 
-	private static int minimumWidth = 800;
-	private static int minimumHeight = 600;
+	public static int minimumWidth = 800;
+	public static int minimumHeight = 600;
 	private static ScreenSize size;
-	private static int menubarHeight = 25;
+	public static int menubarHeight = 25;
 	private int width;
 	private int height;
 	private int zoombarHeight;
@@ -93,12 +93,4 @@ public void calculate() {
 	public int calculate(double percentage, int integer) {
 		return (int) (percentage * integer);
 	}
-
-	public int calculateHeight(double percentage) {
-		return calculate(percentage, height);
-	}
-
-	public int calculateWidth(double percentage) {
-		return calculate(percentage, width);
-	}
 }

data/testdata/savetest

@@ -9,7 +9,7 @@
 
 /**
  * Creates an adapter that updates screen sizes for the components in the view.
- *
+ * <p>
  * Created by Kasper on 16-6-2015.
  */
 public class ResizeAdapter extends ComponentAdapter {
@@ -22,7 +22,6 @@ public ResizeAdapter(Application application) {
 	}
 
 
-
 	@Override
 	public void componentResized(ComponentEvent e) {
 		Rectangle bounds = application.getBounds();
@@ -44,7 +43,7 @@ public void componentResized(ComponentEvent e) {
 		application.repaint();
 	}
 
-	public ComponentAdapter getResizer(){
+	public ComponentAdapter getResizer() {
 		return this;
 	}
 }

pom.xml

@@ -9,8 +9,6 @@
 import tudelft.ti2806.pl3.ui.util.DialogUtil;
 import tudelft.ti2806.pl3.visualization.GraphController;
 
-import javax.swing.JOptionPane;
-
 /**
  * This controller controls the view that lets you select a gene from a list, and will navigate you to it in the graph.
  * Created by Boris Mattijssen on 30-05-15.
@@ -52,9 +50,7 @@ public void openDialog() {
 				Gene selected = (Gene) findgenesView.getSelectedItem();
 				DataNode node = graphData.getGeneToStartNodeMap().get(selected);
 				if (node == null) {
-					JOptionPane.showMessageDialog(null,
-							"Couldn't find the selected gene. Try again");
-					tryAgain = true;
+					tryAgain = DialogUtil.confirm("Error!", "Couldn't find the selected gene. Please try again");
 				} else {
 					cc.getGraphController().centerOnNode(node);
 				}

src/main/java/tudelft/ti2806/pl3/Application.java

@@ -46,7 +46,6 @@ public void actionPerformed(ActionEvent e) {
 
 		if (chosenfile.endsWith(".nwk")) {
 			// tree file
-			System.out.println("phylo tree");
 			FileSelector.lastopened.add(file);
 			application.makePhyloTree(file);
 		} else if (chosenfile.endsWith(".node.graph")) {

src/main/java/tudelft/ti2806/pl3/ScreenSize.java

@@ -42,12 +42,12 @@ public class MenuBarController implements ActionListener, Controller {
 	/**
 	 * Text that is displayed in the About Me option in the Help menu.
 	 */
-	final String about = "Helix² is an interactive DNA sequence viewer. "
+	static final String about = "Helix\u00B2 is an interactive DNA sequence viewer. "
 			+ "It uses semantic zooming to only display relative information. \n"
 			+ "This application was created as part of an assignment"
 			+ "for the Context Project at TU Delft.\n"
 			+ "\n"
-			+ "Helix� was created by: \n"
+			+ "Helix\u00B2 was created by: \n"
 			+ "- Tom Brouws\n"
 			+ "- Boris Mattijssen\n"
 			+ "- Mathieu Post\n"
@@ -59,7 +59,7 @@ public class MenuBarController implements ActionListener, Controller {
 	/**
 	 * Text that is displayed in the Controls option in the Help menu.
 	 */
-	final String controls = "Helix² uses key shortcuts to make life easier. "
+	static final String controls = "Helix\u00B2 uses key shortcuts to make life easier. "
 			+ "All the controls that can be used are listed below. \n"
 			+ "\n"
 			+ "Zooming in     \t+ \n"
@@ -132,10 +132,19 @@ private void showFindGenes() {
 	public void setLastOpenedMenu(Component lastOpenedMenu) {
 		menuBarView.setLastOpenedMenu(lastOpenedMenu);
 	}
+
+	/**
+	 * Displays the controls text in a {@link DialogUtil}.
+	 */
+	private void displayControls() {
+		DialogUtil.displayMessageWithView(new JScrollPane(makeControls()), "Controls");
+	}
+
 	/**
-	 * Displays the controls text in a {@link JTextPane}.
+	 * Make a {@link JTextPane} with controls text.
+	 * @return JTextpane with control text.
 	 */
-	public void displayControls() {
+	public JTextPane makeControls() {
 		JTextPane textPane = new JTextPane();
 		TabStop[] tabs = new TabStop[1];
 		tabs[0] = new TabStop(300, TabStop.ALIGN_LEFT, TabStop.LEAD_NONE);
@@ -150,13 +159,21 @@ public void displayControls() {
 		textPane.setBackground(new Color(240, 240, 240));
 		textPane.setPreferredSize(new Dimension(500, 200));
 
-		DialogUtil.displayMessageWithView(new JScrollPane(textPane), "Controls");
+		return textPane;
 	}
 
 	/**
-	 * Displays the about me text in a {@link JTextPane}.
+	 * Displays the about me text in {@link DialogUtil}.
 	 */
 	private void displayAbout() {
+		DialogUtil.displayMessageWithView(new JScrollPane(makeAbout()), "About me");
+	}
+
+	/**
+	 * Make a {@link JTextPane} with about me text.
+	 * @return JTextpane with about me text.
+	 */
+	public JTextPane makeAbout() {
 		StyleContext styleContext = new StyleContext();
 		DefaultStyledDocument doc = new DefaultStyledDocument(styleContext);
 		JTextPane textPane = new JTextPane(doc);
@@ -174,7 +191,7 @@ private void displayAbout() {
 		textPane.setBackground(new Color(240, 240, 240));
 		textPane.setPreferredSize(new Dimension(500, 200));
 
-		DialogUtil.displayMessageWithView(new JScrollPane(textPane), "About me");
+		return textPane;
 	}
 
 	/**
@@ -184,7 +201,7 @@ private void displayAbout() {
 	 *
 	 * @return clickable JLabel with URL
 	 */
-	private JLabel website() {
+	public JLabel website() {
 		JLabel website = new JLabel("https://github.com/ProgrammingLife3/ProgrammingLife3");
 		website.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
 		website.addMouseListener(new MouseAdapter() {
@@ -195,8 +212,8 @@ public void mouseClicked(MouseEvent e) {
 					Desktop.getDesktop().browse(github);
 				} catch (IOException | URISyntaxException exception) {
 					String message = "An error has occurred!"
-					 	+ " We are unable to display the GitHub link in your browser.";
-					DialogUtil.displayError(message,"Error!");
+							+ " We are unable to display the GitHub link in your browser.";
+					DialogUtil.displayError(message, "Error!");
 				}
 			}
 		});

src/main/java/tudelft/ti2806/pl3/controls/ResizeAdapter.java

@@ -0,0 +1,13 @@
+package tudelft.ti2806.pl3.ui.util;
+
+/**
+ * Interface for the ConfirmOptionPane
+ * Created by Kasper on 17-6-2015.
+ */
+public interface ConfirmOptionPane {
+
+	/**
+	 *  @see {@link javax.swing.JOptionPane}
+	 */
+	boolean showConfirmDialog(Object message, String title);
+}

src/main/java/tudelft/ti2806/pl3/findgenes/FindgenesController.java

@@ -0,0 +1,18 @@
+package tudelft.ti2806.pl3.ui.util;
+
+import javax.swing.JOptionPane;
+
+/**
+ * Default implementation of the {@link ConfirmOptionPane}.
+ * Created by Kasper on 17-6-2015.
+ */
+public class DefaultConfirmOptionPane implements ConfirmOptionPane {
+	@Override
+	public boolean showConfirmDialog(Object message, String title) {
+		int answer = JOptionPane
+				.showConfirmDialog(null, message, title,
+						JOptionPane.YES_NO_OPTION,
+						JOptionPane.QUESTION_MESSAGE);
+		return answer == JOptionPane.YES_OPTION;
+	}
+}

src/main/java/tudelft/ti2806/pl3/menubar/LastOpenedController.java

@@ -8,6 +8,7 @@
  * Created by Boris Mattijssen on 14-06-15.
  */
 public class DialogUtil {
+	static ConfirmOptionPane confirmOptionPane = new DefaultConfirmOptionPane();
 
 	private DialogUtil() {
 	}
@@ -22,11 +23,7 @@ private DialogUtil() {
 	 * @return the dialog
 	 */
 	public static boolean confirm(String title, String message) {
-		int answer = JOptionPane
-				.showConfirmDialog(null, message, title,
-						JOptionPane.YES_NO_OPTION,
-						JOptionPane.QUESTION_MESSAGE);
-		return answer == JOptionPane.YES_OPTION;
+		return confirmOptionPane.showConfirmDialog(message, title);
 	}
 
 	/**
@@ -75,4 +72,8 @@ public static void displayError(String message, String title) {
 		JOptionPane.showMessageDialog(null, message, title, JOptionPane.ERROR_MESSAGE);
 	}
 
+	public static void setConfirmOptionPane(ConfirmOptionPane pane) {
+		confirmOptionPane = pane;
+	}
+
 }

src/main/java/tudelft/ti2806/pl3/menubar/MenuBarController.java

@@ -28,6 +28,7 @@ public class GraphController implements Controller {
 	private GraphDataRepository graphDataRepository;
 	private Map<String, Filter<DataNode>> filters = new HashMap<>();
 	private static final int DEFAULT_VIEW = 1;
+	private GeneData geneData;
 
 	/**
 	 * Percentage of the screen that is moved.
@@ -76,7 +77,7 @@ public void addLoadingObservers(ArrayList<LoadingObserver> loadingObservers) {
 	 */
 	public void parseGraph(File nodeFile, File edgeFile) throws FileNotFoundException {
 		try {
-			GeneData geneData = GeneData.parseGenes("geneAnnotationsRef");
+			geneData = GeneData.parseGenes("geneAnnotationsRef");
 			graphDataRepository.parseGraph(nodeFile, edgeFile, geneData);
 			graphView.getPanel().setVisible(false);
 			graphView.getPanel().setVisible(true);
@@ -245,4 +246,8 @@ public float getOffsetToCenter() {
 	public void removeDetailView() {
 		graphView.removeDetailView();
 	}
+
+	public GeneData getGeneData() {
+		return geneData;
+	}
 }