Merge pull request #102 from ProgrammingLife3/feature/moreDetails

Feature/more details

Author: Tom Brouws

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

@@ -143,11 +143,13 @@ public void makeGraphFromFolder() {
 					Constants.EXTENSION_EDGE, Constants.EXTENSION_PHYLOTREE, Constants.EXTENSION_TEXT);
 			makeGraph(files[0], files[1], files[2], files[3]);
 		} catch (ArrayIndexOutOfBoundsException exception) {
-			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR, "Some necessary files were not found. Want to select a new folder?")) {
+			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR,
+					"Some necessary files were not found. Want to select a new folder?")) {
 				makeGraphFromFolder();
 			}
 		} catch (FileSelectorException exception) {
-			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR, "You have not selected a folder, want to try again?")) {
+			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR,
+					"You have not selected a folder, want to try again?")) {
 				makeGraphFromFolder();
 			}
 		}

src/main/java/tudelft/ti2806/pl3/data/graph/GraphDataRepository.java

@@ -114,7 +114,8 @@ public void parseGraph(File nodesFile, File edgesFile, GeneData geneData) throws
 	 * @throws FileNotFoundException
 	 * 		if the file is not found
 	 */
-	public void parseGraph(File nodesFile, File edgesFile, File metaFile, GeneData geneData) throws FileNotFoundException {
+	public void parseGraph(File nodesFile, File edgesFile, File metaFile, GeneData geneData)
+			throws FileNotFoundException {
 		notifyLoadingObservers(true);
 		geneToStartNodeMap = new HashMap<>(geneData.getGenes().size());
 		genes = new ArrayList<>();

src/main/java/tudelft/ti2806/pl3/data/wrapper/CombineWrapper.java

@@ -96,4 +96,13 @@ public boolean contains(Wrapper object) {
 		}
 		return false;
 	}
+
+	@Override
+	public String getBasePairString() {
+		String result = "";
+		for (Wrapper wrapper : nodeList) {
+			result += wrapper.getBasePairString();
+		}
+		return result;
+	}
 }

src/main/java/tudelft/ti2806/pl3/data/wrapper/DataNodeWrapper.java

@@ -110,7 +110,12 @@ public void calculateX() {
 	public int getWidth() {
 		return 1;
 	}
-	
+
+	@Override
+	public String getBasePairString() {
+		return node.getContent();
+	}
+
 	@Override
     public boolean contains(Wrapper object) {
         return false;

src/main/java/tudelft/ti2806/pl3/data/wrapper/FixWrapper.java

@@ -68,6 +68,11 @@ public int getWidth() {
 		return 0;
 	}
 
+	@Override
+	public String getBasePairString() {
+		return null;
+	}
+
 	@Override
 	public boolean contains(Wrapper object) {
 		return false;

src/main/java/tudelft/ti2806/pl3/data/wrapper/SingleWrapper.java

@@ -84,7 +84,12 @@ public void calculateX() {
 	public int getWidth() {
 		return this.getNode().getWidth();
 	}
-	
+
+	@Override
+	public String getBasePairString() {
+		return target.getBasePairString();
+	}
+
 	@Override
 	public boolean contains(Wrapper object) {
 		return object == this.target || this.target.contains(object);

src/main/java/tudelft/ti2806/pl3/data/wrapper/Wrapper.java

@@ -42,6 +42,8 @@ public abstract class Wrapper implements Comparable<Wrapper> {
 	 * @return the distance between the start x and end x of this node.
 	 */
 	public abstract int getWidth();
+
+	public abstract String getBasePairString();
 
 	public int getPreviousNodesCount() {
 		return previousNodesCount;

src/main/java/tudelft/ti2806/pl3/data/wrapper/WrapperClone.java

@@ -90,7 +90,12 @@ public void calculateX() {
 	public int getWidth() {
 		return originalNode.getWidth();
 	}
-	
+
+	@Override
+	public String getBasePairString() {
+		return originalNode.getBasePairString();
+	}
+
 	@Override
     public boolean contains(Wrapper object) {
         return this.originalNode.contains(object);

src/main/java/tudelft/ti2806/pl3/data/wrapper/WrapperPlaceholder.java

@@ -60,7 +60,12 @@ public void calculateX() {
 	public int getWidth() {
 		return 0;
 	}
-	
+
+	@Override
+	public String getBasePairString() {
+		return null;
+	}
+
 	@Override
 	public boolean contains(Wrapper object) {
 		return false;

src/main/java/tudelft/ti2806/pl3/detailview/DetailView.java

@@ -27,6 +27,7 @@ public class DetailView extends JPanel {
 	private static final int BORDER = 10;
 	private static final int POSITION_OFFSET = 30;
 	private static final String REF_GENOME = "REF";
+	private static final int MAX_BASEPAIR_LENGTH = 10;
 
 	/**
 	 * Custom string comparator to prioritize the reference genome.
@@ -44,9 +45,9 @@ public class DetailView extends JPanel {
 	 * Constructs a DetailView and set a border and the preferred layout.
 	 */
 	public DetailView() {
-		BoxLayout layout = new BoxLayout(this, BoxLayout.X_AXIS);
+		BoxLayout layout = new BoxLayout(this, BoxLayout.Y_AXIS);
 		setLayout(layout);
-		setBorder(BorderFactory.createEmptyBorder(BORDER, BORDER, BORDER, BORDER));
+		setBorder(BorderFactory.createEmptyBorder(0, BORDER, BORDER, BORDER));
 	}
 
 	/**
@@ -61,13 +62,35 @@ public DetailView() {
 	public void setNode(WrapperClone node, int x, int y) {
 		removeAll();
 
+		addLabels(node);
 		addList(node.getGenome(), Constants.DETAILVIEW_GENOMES);
 		addList(node.getLabels(), Constants.DETAILVIEW_LABELS);
 
 		Dimension size = getPreferredSize();
 		setBounds(x, y, size.width, size.height);
 	}
 
+	/**
+	 * Adds labels for the node id and the base pair string if the node can not be unwrapped.
+	 * @param node
+	 * 		The node for which the id and base pair string should be added.
+	 */
+	public void addLabels(WrapperClone node) {
+		if (!node.canUnwrap()) {
+			JLabel label = new JLabel("Node id: " + node.getIdString());
+			label.setBorder(BorderFactory.createEmptyBorder(BORDER, 0, BORDER, 0));
+			add(label);
+			String basePairString = node.getBasePairString();
+			int length = basePairString.length();
+			if (length > MAX_BASEPAIR_LENGTH) {
+				basePairString = basePairString.substring(0, MAX_BASEPAIR_LENGTH / 2) + "..."
+						+ basePairString.substring(length - MAX_BASEPAIR_LENGTH / 2);
+			}
+			add(new JLabel("Base pairs:"));
+			add(new JLabel(basePairString));
+		}
+	}
+
 	/**
 	 * Adds a collection as a scrollable list to itself.
 	 * @param collection
@@ -93,6 +116,7 @@ private void addList(Collection collection, String title) {
 		if (title != null) {
 			listScroller.setColumnHeaderView(new JLabel(title));
 		}
+		listScroller.setBorder(BorderFactory.createEmptyBorder(BORDER, 0, 0, 0));
 		add(listScroller);
 	}
 

src/test/java/tudelft/ti2806/pl3/data/wrapper/TestWrapper.java

@@ -42,7 +42,12 @@ public long getBasePairCount() {
 	public int getWidth() {
 		return 1;
 	}
-	
+
+	@Override
+	public String getBasePairString() {
+		return null;
+	}
+
 	@Override
 	public void calculateX() {
 	}

src/test/java/tudelft/ti2806/pl3/util/OrderedListUtilTest.java

@@ -179,7 +179,12 @@ public void calculateX() {
 		public int getWidth() {
 			return 0;
 		}
-		
+
+		@Override
+		public String getBasePairString() {
+			return null;
+		}
+
 		@Override
 		public boolean contains(Wrapper originalNode) {
 			return false;