Merge pull request #301 from ProgrammingLife2017/rip-annotations

R.I.P. annotations

Author: YDutchy

src/main/java/programminglife/gui/controller/GuiController.java

@@ -29,12 +29,10 @@
 import programminglife.gui.Alerts;
 import programminglife.gui.NumbersOnlyListener;
 import programminglife.gui.ResizableCanvas;
-import programminglife.model.Feature;
 import programminglife.model.GenomeGraph;
 import programminglife.model.drawing.DrawableEdge;
 import programminglife.model.drawing.DrawableNode;
 import programminglife.model.drawing.DrawableSegment;
-import programminglife.parser.AnnotationParser;
 import programminglife.parser.GraphParser;
 import programminglife.parser.ProgressCounter;
 import programminglife.utility.Console;
@@ -45,7 +43,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.Charset;
-import java.util.Map;
 import java.util.Observable;
 import java.util.Observer;
 import java.util.Random;
@@ -61,13 +58,11 @@ public class GuiController implements Observer {
 
     //FXML imports.
     @FXML private MenuItem btnOpenGFA;
-    @FXML private MenuItem btnOpenGFF;
     @FXML private MenuItem btnQuit;
     @FXML private MenuItem btnBookmarks;
     @FXML private MenuItem btnAbout;
     @FXML private MenuItem btnInstructions;
     @FXML private Menu menuRecentGFA;
-    @FXML private Menu menuRecentGFF;
 
     @FXML private RadioMenuItem btnSNP;
     @FXML private RadioMenuItem btnConsole;
@@ -97,12 +92,9 @@ public class GuiController implements Observer {
     private double scale;
     private GraphController graphController;
     private RecentFileController recentFileControllerGFA;
-    private RecentFileController recentFileControllerGFF;
     private MiniMapController miniMapController;
     private File file;
-    private final File recentFileGFA = new File("RecentGFA.txt");
-    private final File recentFileGFF = new File("RecentGFF.txt");
-    private Map<String, Feature> features;
+    private File recentFileGFA = new File("RecentGFA.txt");
     private Thread parseThread;
 
     private final ExtensionFilter extFilterGFF = new ExtensionFilter("GFF files (*.gff)", "*.GFF");
@@ -124,8 +116,6 @@ private void initialize() {
 
         this.recentFileControllerGFA = new RecentFileController(this.recentFileGFA, this.menuRecentGFA);
         this.recentFileControllerGFA.setGuiController(this);
-        this.recentFileControllerGFF = new RecentFileController(this.recentFileGFF, this.menuRecentGFF);
-        this.recentFileControllerGFF.setGuiController(this);
         initMenuBar();
         initBookmarkMenu();
         initLeftControlpanelScreenModifiers();
@@ -168,29 +158,6 @@ public GraphParser openFile(File file) {
         return null;
     }
 
-    /**
-     * Open and parse a GFF file.
-     *
-     * @param file The {@link File} to open.
-     * @return AnnotationParser to be notified when finished.
-     */
-    private AnnotationParser openAnnotationFile(File file) {
-        AnnotationParser annotationParser = null;
-        if (file != null) {
-            Console.println("Opening annotation " + file);
-            annotationParser = new AnnotationParser(file);
-            annotationParser.addObserver(this);
-            annotationParser.getProgressCounter().addObserver(this);
-
-            if (this.parseThread != null) {
-                this.parseThread.interrupt();
-            }
-            this.parseThread = new Thread(annotationParser);
-            this.parseThread.start();
-        }
-        return annotationParser;
-    }
-
     @Override
     public void update(Observable o, Object arg) {
         if (o instanceof GraphParser) {
@@ -208,11 +175,6 @@ public void update(Observable o, Object arg) {
                 String msg = (String) arg;
                 Platform.runLater(() -> ProgrammingLife.getStage().setTitle(msg));
             }
-        } else if (o instanceof AnnotationParser) {
-            if (arg instanceof Map) {
-                Console.println("[%s] Annotations parsed.", Thread.currentThread().getName());
-                this.setFeatures(((AnnotationParser) o).getFeatures());
-            }
         } else if (o instanceof ProgressCounter) {
             progressBar.setVisible(true);
             ProgressCounter progress = (ProgressCounter) o;
@@ -268,12 +230,6 @@ private void fileChooser(ExtensionFilter filter, boolean isGFA) {
                     File recentFileGFA = recentFileControllerGFA.getRecentFile();
                     recentFileControllerGFA.updateRecent(recentFileGFA, file);
                 });
-            } else {
-                this.openAnnotationFile(file);
-                Platform.runLater(() -> {
-                    File recentFileGFF = recentFileControllerGFA.getRecentFile();
-                    recentFileControllerGFF.updateRecent(recentFileGFF, file);
-                });
             }
         }
     }
@@ -286,8 +242,6 @@ private void fileChooser(ExtensionFilter filter, boolean isGFA) {
     private void initMenuBar() {
         btnOpenGFA.setOnAction((ActionEvent event) -> fileChooser(extFilterGFA, true));
         btnOpenGFA.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCodeCombination.CONTROL_DOWN));
-        btnOpenGFF.setOnAction((ActionEvent event) -> fileChooser(extFilterGFF, false));
-        btnOpenGFF.setAccelerator(new KeyCodeCombination(KeyCode.P, KeyCodeCombination.CONTROL_DOWN));
 
         btnQuit.setOnAction(event -> Alerts.quitAlert());
         btnQuit.setAccelerator(new KeyCodeCombination(KeyCode.Q, KeyCodeCombination.CONTROL_DOWN));
@@ -584,7 +538,6 @@ private void initRightSearchTab() {
             searchTab.setDisable(true);
             searchTab.setOnSelectionChanged(event -> {
                 highlightController.initGenome();
-                highlightController.initAnnotations();
                 highlightController.initMinMax();
             });
         } catch (IOException e) {
@@ -790,14 +743,6 @@ public void setFile(File file) {
         this.file = file;
     }
 
-    private void setFeatures(Map<String, Feature> features) {
-        this.features = features;
-    }
-
-    Map<String, Feature> getFeatures() {
-        return this.features;
-    }
-
     GraphController getGraphController() {
         return this.graphController;
     }

src/main/java/programminglife/gui/controller/HighlightController.java

@@ -7,12 +7,6 @@
 import javafx.scene.paint.Color;
 import programminglife.gui.AutoCompleteTextField;
 import programminglife.gui.NumbersOnlyListener;
-import programminglife.model.Annotation;
-import programminglife.model.Feature;
-
-import java.util.LinkedHashSet;
-import java.util.Set;
-import java.util.stream.Collectors;
 
 /**
  * Controller class for the highlights.
@@ -25,7 +19,6 @@ public class HighlightController {
 
     @FXML private Button btnHighlight;
     @FXML private AutoCompleteTextField txtGenome;
-    @FXML private AutoCompleteTextField txtAnnotations;
     @FXML private TextField txtMin;
     @FXML private TextField txtMax;
     @FXML private CheckBox checkMin;
@@ -67,31 +60,6 @@ public void initGenome() {
         txtGenome.getEntries().addAll(graphController.getGraph().getGenomeNames());
     }
 
-    /**
-     * Initializes the annotations.
-     */
-    public void initAnnotations() {
-        txtAnnotations.getEntries().clear();
-        if (guiController.getFeatures() != null) {
-            txtAnnotations.getEntries().addAll(guiController.getFeatures().keySet());
-
-            Set<Set<Annotation>> c = guiController.getFeatures()
-                    .values()
-                    .stream()
-                    .map(Feature::getAnnotations)
-                    .collect(Collectors.toSet());
-
-            Set<String> search = new LinkedHashSet<>();
-
-            c.forEach(setOfAnno -> setOfAnno.forEach(anno -> anno.getTextFields().forEach((key, value) -> {
-                search.add(key);
-                search.addAll(value);
-            })));
-
-            txtAnnotations.getEntries().addAll(search);
-        }
-    }
-
     /**
      * Initializes the Min and Max field + checkbox.
      */
@@ -144,7 +112,7 @@ void setGraphController(GraphController graphController) {
         this.graphController = graphController;
     }
 
-    public void setGUIController(GuiController guiController) {
+    void setGUIController(GuiController guiController) {
         this.guiController = guiController;
     }
 }