Merge pull request #96 from ProgrammingLife3/refactor/inspection

Refactor/inspection

Author: kwendel

checkstyle.xml

@@ -13,6 +13,7 @@ Checkstyle configuration that checks the Google coding conventions (https://goog
   <property name="severity" value="warning"/>
   <property name="charset" value="UTF-8"/>
   <module name="TreeWalker">
+    <property name="tabWidth" value="4"/>
     <module name="OuterTypeFilename"/>
     <module name="LineLength">
       <property name="ignorePattern" value="^package.*|^import.*|a href|href|http://|https://|ftp://"/>
@@ -99,10 +100,10 @@ Checkstyle configuration that checks the Google coding conventions (https://goog
       <message key="ws.illegalFollow" value="GenericWhitespace ''{0}'' should followed by whitespace."/>
     </module>
     <module name="Indentation">
-      <property name="basicOffset" value="8"/>
-      <property name="caseIndent" value="8"/>
+      <property name="basicOffset" value="4"/>
+      <property name="caseIndent" value="4"/>
       <property name="throwsIndent" value="1"/>
-      <property name="arrayInitIndent" value="16"/>
+      <property name="arrayInitIndent" value="8"/>
       <property name="lineWrappingIndentation" value="1"/>
     </module>
     <module name="AbbreviationAsWordInName">

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

@@ -6,12 +6,12 @@
 import tudelft.ti2806.pl3.controls.ScrollListener;
 import tudelft.ti2806.pl3.controls.WindowController;
 import tudelft.ti2806.pl3.data.graph.GraphDataRepository;
-import tudelft.ti2806.pl3.metafilter.MetaFilterController;
 import tudelft.ti2806.pl3.exception.FileSelectorException;
 import tudelft.ti2806.pl3.findgenes.FindGenesController;
 import tudelft.ti2806.pl3.loading.LoadingMouse;
 import tudelft.ti2806.pl3.menubar.LastOpenedController;
 import tudelft.ti2806.pl3.menubar.MenuBarController;
+import tudelft.ti2806.pl3.metafilter.MetaFilterController;
 import tudelft.ti2806.pl3.sidebar.SideBarController;
 import tudelft.ti2806.pl3.sidebar.phylotree.PhyloController;
 import tudelft.ti2806.pl3.ui.util.DialogUtil;
@@ -44,7 +44,7 @@ public class Application extends JFrame implements ControllerContainer {
 	/**
 	 * The value of the layers used in the view.
 	 */
-	private static final Integer MIDDEL_LAYER = 50;
+	private static final Integer MIDDLE_LAYER = 50;
 	private static final Integer HIGHEST_LAYER = 100;
 
 	private final GraphDataRepository graphDataRepository;
@@ -74,7 +74,7 @@ public Application() {
 			LastOpenedStack<File> files = ParserLastOpened.readLastOpened();
 			FileSelector.setLastOpened(files);
 		} catch (IOException e) {
-			// the file is missing so there are no lastopened
+			// the file is missing so there are no last opened.
 			FileSelector.setLastOpened(new LastOpenedStack<>(ParserLastOpened.limit));
 		}
 
@@ -138,16 +138,16 @@ private void setUpUi() {
 	 */
 	public void makeGraphFromFolder() {
 		try {
-			File folder = FileSelector.selectFolder("Select data folder", this);
-
-			File[] files = FileSelector.getFilesFromFolder(folder, ".node.graph", ".edge.graph", ".nwk", ".txt");
+			File folder = FileSelector.selectFolder(Constants.DIALOG_SELECT_DATA_FOLDER, this);
+			File[] files = FileSelector.getFilesFromFolder(folder, Constants.EXTENSION_NODE,
+					Constants.EXTENSION_EDGE, Constants.EXTENSION_PHYLOTREE, Constants.EXTENSION_TEXT);
 			makeGraph(files[0], files[1], files[2], files[3]);
 		} catch (ArrayIndexOutOfBoundsException exception) {
-			if (DialogUtil.confirm("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("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();
 			}
 		}
@@ -158,19 +158,19 @@ public void makeGraphFromFolder() {
 	 */
 	public void makeGraphFromFiles() {
 		try {
-			File nodeFile = FileSelector.selectFile("Select node file", this, ".node.graph");
-
-			File edgeFile = FileSelector.getOtherExtension(nodeFile, ".node.graph", ".edge.graph");
+			File nodeFile = FileSelector.selectFile(Constants.DIALOG_SELECT_NODE_FILE, this, Constants.EXTENSION_NODE);
+			File edgeFile = FileSelector.getOtherExtension(nodeFile,
+					Constants.EXTENSION_EDGE, Constants.EXTENSION_NODE);
 			makeGraph(nodeFile, edgeFile, null, null);
 		} catch (FileSelectorException exception) {
-			if (DialogUtil.confirm("Error!", "Your file was not found. Want to try again?")) {
+			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR, Constants.DIALOG_FILE_NOT_FOUND)) {
 				makeGraphFromFiles();
 			}
 		}
 	}
 
 	/**
-	 * Parses the graph files and makes a graphview.
+	 * Parses the graph files and makes a GraphView.
 	 */
 	public void makeGraph(File nodeFile, File edgeFile, File treeFile, File metaFile) {
 		try {
@@ -180,7 +180,7 @@ public void makeGraph(File nodeFile, File edgeFile, File treeFile, File metaFile
 				makePhyloTree(treeFile);
 			}
 		} catch (FileNotFoundException exception) {
-			if (DialogUtil.confirm("Error!", "Your file was not found. Want to try again?")) {
+			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR, Constants.DIALOG_FILE_NOT_FOUND)) {
 				makeGraph(nodeFile, edgeFile, treeFile, metaFile);
 			}
 		}
@@ -200,19 +200,20 @@ public void makePhyloTree(File input) {
 		try {
 			File treeFile;
 			if (input == null) {
-				treeFile = FileSelector.selectFile("Select phylogenetic tree file", this, ".nwk");
+				treeFile = FileSelector.selectFile(Constants.DIALOG_SELECT_PHYLOTREE_FILE, this,
+						Constants.EXTENSION_PHYLOTREE);
 			} else {
 				treeFile = input;
 			}
 
 			getSideBarController().getPhyloController().parseTree(treeFile);
 
 		} catch (FileSelectorException exception) {
-			if (DialogUtil.confirm("Error!", "Your file was not found. Want to try again?")) {
+			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR, Constants.DIALOG_FILE_NOT_FOUND)) {
 				makePhyloTree();
 			}
 		} catch (ParseException exception) {
-			if (DialogUtil.confirm("Error!", "Your file was not formatted correctly. Want to try again?")) {
+			if (DialogUtil.confirm(Constants.DIALOG_TITLE_ERROR, Constants.DIALOG_FILE_FORMATTED_INCORRECTLY)) {
 				makePhyloTree();
 			}
 		}
@@ -238,11 +239,11 @@ public void loadMetaData() {
 	@SuppressFBWarnings({"DM_EXIT"})
 	public void stop() {
 		// save data or do something else here
-		if (DialogUtil.confirm("Exit", "Are you sure you want to exit the application? ")) {
+		if (DialogUtil.confirm(Constants.DIALOG_TITLE_EXIT, Constants.DIALOG_EXIT)) {
 			try {
 				ParserLastOpened.saveLastOpened(FileSelector.getLastopened());
 			} catch (IOException | InterruptedException e) {
-				System.out.println("Unable to save the files");
+				DialogUtil.displayError(Constants.DIALOG_TITLE_ERROR, Constants.DIALOG_FAIL_SAVE_FILES);
 				e.printStackTrace();
 			}
 			this.dispose();
@@ -281,7 +282,7 @@ private void setGraphView() {
 		Component view = getGraphController().getPanel();
 		view.setBounds(0, 0, size.getWidth(),
 				size.getHeight() - size.getZoomBarHeight());
-		main.add(view, MIDDEL_LAYER);
+		main.add(view, MIDDLE_LAYER);
 		view.setVisible(true);
 		view.addKeyListener(keys);
 		view.addMouseWheelListener(new ScrollListener(this));
@@ -294,7 +295,7 @@ private void setZoomBarView() {
 		Component view = getZoomBarController().getPanel();
 		view.setBounds(0, size.getHeight() - size.getZoomBarHeight(),
 				size.getWidth(), size.getZoomBarHeight());
-		main.add(view, MIDDEL_LAYER);
+		main.add(view, MIDDLE_LAYER);
 		view.setVisible(true);
 	}
 

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

@@ -6,11 +6,11 @@
  */
 public class Constants {
 	// Special chars
-	public static final char POWER = '\u00B2';
+	public static final char POWER = '\u00B2'; // Power of 2 character (^2).
 	public static final char PLUS = '+';
 	public static final char MINUS = '-';
-	public static final char ARROW_RIGHT = '\u2192';
-	public static final char ARROW_LEFT = '\u2190';
+	public static final char ARROW_RIGHT = '\u2192'; // Arrow to the right character.
+	public static final char ARROW_LEFT = '\u2190'; // Arrow to the left character.
 	public static final String SPACE = "Space";
 
 	// Name of the application.
@@ -73,13 +73,33 @@ public class Constants {
 	public static final String MENU_HELP_CONTROLS = "Controls";
 	public static final String MENU_HELP_ABOUT = "About " + APP_NAME;
 
-	public static final String DIALOG_ERROR = "Error!";
+	public static final String DIALOG_TITLE_ERROR = "Error!";
+	public static final String DIALOG_TITLE_EXIT = "Exit";
+	public static final String DIALOG_FILE_NOT_FOUND = "Your file was not found. Want to try again?";
+	public static final String DIALOG_FILE_FORMATTED_INCORRECTLY = "Your file was not formatted correctly. "
+			+ "Want to try again?";
+	public static final String DIALOG_EXIT = "Are you sure you want to exit the application? ";
+	public static final String DIALOG_SELECT_PHYLOTREE_FILE = "Select phylogenetic tree file";
+	public static final String DIALOG_SELECT_NODE_FILE = "Select node file";
+	public static final String DIALOG_SELECT_DATA_FOLDER = "Select data folder";
+	public static final String DIALOG_FAIL_SAVE_FILES = "Unable to save the last opened files";
+
 	public static final String DETAILVIEW_GENOMES = "Genomes:";
 	public static final String DETAILVIEW_LABELS = "Labels:";
 
+	public static final String EXTENSION_GRAPH = ".graph";
+	public static final String EXTENSION_NODE = ".node" + EXTENSION_GRAPH;
+	public static final String EXTENSION_EDGE = ".edge" + EXTENSION_GRAPH;
+	public static final String EXTENSION_PHYLOTREE = ".nwk";
+	public static final String EXTENSION_TEXT = ".txt";
+
 	// Phylogenetic view constants.
 	public static final String PHYLO_WINDOW_TITLE = "Select Genomes";
 	public static final String PHYLO_BUTTON_LABEL_UPDATE = "Update";
 	public static final String PHYLO_LABEL_PHYLOGENETIC_TREE = "Phylogenetic tree";
 	public static final String PHYLO_LABEL_COMMON_ANCESTOR = "Common ancestor";
+
+	// MetaFilter view constants
+	public static final String META_VIEW_TITLE = "Select options to filter on";
+
 }

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

@@ -90,7 +90,7 @@ public void calculate() {
 	 *            size of the dimension
 	 * @return percentage*size rounded to nearest integer
 	 */
-	public int calculate(double percentage, int integer) {
+	private int calculate(double percentage, int integer) {
 		return (int) (percentage * integer);
 	}
 }

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

@@ -11,7 +11,7 @@
  */
 public class KeyController implements KeyListener {
 
-	private Application app;
+	private final Application app;
 
 	/**
 	 * Constructor removes the old keylisteners and makes our own.

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

@@ -66,7 +66,7 @@ public void mouseMoved(MouseEvent e) {
 	 * @param y
 	 * 		y location of the mouse cursor.
 	 */
-	public void mouseMoved(int x, int y) {
+	private void mouseMoved(int x, int y) {
 		node = getNodeAtPosition(x, y);
 		if (node == null) {
 			removeDetailView();

src/main/java/tudelft/ti2806/pl3/data/gene/GeneData.java

@@ -21,24 +21,24 @@
  * Class containing all gene data.
  */
 public class GeneData {
-	public static final String PREFIX_GENE_START = "_start_";
-	public static final String PREFIX_GENE_END = "_end_";
+	private static final String PREFIX_GENE_START = "_start_";
+	private static final String PREFIX_GENE_END = "_end_";
 
 	/**
 	 * List of all genes.
 	 */
-	private ArrayList<Gene> genes;
-	private Map<String, Label> labelMap;
+	private final ArrayList<Gene> genes;
+	private final Map<String, Label> labelMap;
 
 	/**
 	 * Mapping from start index to the actual gene.
 	 */
-	private Map<Integer, Gene> geneStart;
+	private final Map<Integer, Gene> geneStart;
 
 	/**
 	 * Mapping from end index to the actual gene.
 	 */
-	private Map<Integer, Gene> geneEnd;
+	private final Map<Integer, Gene> geneEnd;
 
 	private static final char COMMENT_IDENTIFIER = '#';
 	private static final String TAB = "\t";
@@ -75,10 +75,6 @@ public ArrayList<Gene> getGenes() {
 		return genes;
 	}
 
-	public Map<String, Label> getLabelMap() {
-		return labelMap;
-	}
-
 	public Label getLabel(String key) {
 		return labelMap.get(key);
 	}

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

@@ -10,7 +10,7 @@
  * GraphData parses the data as nodes,edges and genomes.
  */
 public class GraphData extends AbstractGraphData {
-	private AbstractGraphData origin;
+	private final AbstractGraphData origin;
 
 	/**
 	 * Constructs an instance of {@code GraphData}.

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

@@ -24,8 +24,8 @@
 
 public class GraphDataRepository extends AbstractGraphData implements LoadingObservable {
 
-	private ArrayList<LoadingObserver> observers = new ArrayList<>();
-	private List<GraphParsedObserver> graphParsedObserver = new ArrayList<>();
+	private final ArrayList<LoadingObserver> observers = new ArrayList<>();
+	private final List<GraphParsedObserver> graphParsedObserver = new ArrayList<>();
 
 	/**
 	 * Construct a empty {@code GraphDataRepository}.
@@ -308,27 +308,6 @@ public DataNode getNodeByNodeId(int id) {
 		return null;
 	}
 
-	/**
-	 * Search for the edge in the graph with the given from and to id.
-	 *
-	 * @param fromId
-	 * 		the id of the from node on the edge
-	 * @param toId
-	 * 		the id of the to node on the edge
-	 * @return the found edge<br>
-	 * {@code null} if there is no node with this id in the graph
-	 */
-	// TODO This is never used, can it be deleted?
-	public Edge getEdge(int fromId, int toId) {
-		for (Edge edge : edges) {
-			if (edge.getFrom().getId() == fromId
-					&& edge.getTo().getId() == toId) {
-				return edge;
-			}
-		}
-		return null;
-	}
-
 	@Override
 	public AbstractGraphData getOrigin() {
 		return this;
@@ -341,9 +320,7 @@ public void addLoadingObserver(LoadingObserver loadingObserver) {
 
 	@Override
 	public void addLoadingObserversList(ArrayList<LoadingObserver> loadingObservers) {
-		for (LoadingObserver loadingObserver : loadingObservers) {
-			addLoadingObserver(loadingObserver);
-		}
+		loadingObservers.forEach(this::addLoadingObserver);
 	}
 
 	@Override

src/main/java/tudelft/ti2806/pl3/data/label/Label.java

@@ -6,14 +6,14 @@
  */
 public abstract class Label {
 
-	private String text;
+	private final String text;
 
 	/**
 	 * Constructs an instance of the label.
 	 * @param s
 	 * 			the String label to set
 	 */
-	public Label(String s) {
+	Label(String s) {
 		if (s != null) {
 			text = s;
 		} else {
@@ -31,14 +31,12 @@ public boolean equals(Object o) {
 		}
 
 		Label label = (Label) o;
-
-		return !(text != null ? !text.equals(label.text) : label.text != null);
-
+		return text.equals(label.text);
 	}
 
 	@Override
 	public int hashCode() {
-		return text != null ? text.hashCode() : 0;
+		return text.hashCode();
 	}
 
 	public String getText() {