Example usage for javafx.scene.input KeyCode UP

List of usage examples for javafx.scene.input KeyCode UP

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Introduction

In this page you can find the example usage for javafx.scene.input KeyCode UP.

Prototype

KeyCode UP

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Document

Constant for the non-numpad up arrow key.

Usage

From source file:com.playonlinux.javafx.mainwindow.console.ConsoleTab.java

public ConsoleTab(CommandLineInterpreterFactory commandLineInterpreterFactory) {
    final VBox content = new VBox();

    commandInterpreter = commandLineInterpreterFactory.createInstance();

    this.setText(translate("Console"));
    this.setContent(content);

    final TextField command = new TextField();
    command.getStyleClass().add("consoleCommandType");
    final TextFlow console = new TextFlow();
    final ScrollPane consolePane = new ScrollPane(console);
    content.getStyleClass().add("rightPane");

    consolePane.getStyleClass().add("console");
    consolePane.setVbarPolicy(ScrollPane.ScrollBarPolicy.NEVER);
    content.getChildren().addAll(consolePane, command);

    command.requestFocus();/*from  w  w  w .  jav  a 2  s .c  o m*/

    command.setOnKeyPressed(event -> {
        if (event.getCode() == KeyCode.ENTER) {
            final String commandToSend = command.getText();
            final int cursorPosition = command.getCaretPosition();
            command.setDisable(true);
            commandHistory.add(new CommandHistory.Item(commandToSend, cursorPosition));
            Text commandText = new Text(nextSymbol + commandToSend + "\n");
            commandText.getStyleClass().add("commandText");
            console.getChildren().add(commandText);
            command.setText("");

            if (commandInterpreter.sendLine(commandToSend, message -> {
                Platform.runLater(() -> {
                    if (!StringUtils.isBlank(message)) {
                        Text resultText = new Text(message);
                        resultText.getStyleClass().add("resultText");
                        console.getChildren().add(resultText);
                    }
                    command.setDisable(false);
                    command.requestFocus();
                    consolePane.setVvalue(consolePane.getVmax());
                });
            })) {
                nextSymbol = NOT_INSIDE_BLOCK;
            } else {
                nextSymbol = INSIDE_BLOCK;
            }
        }
    });

    command.setOnKeyReleased(event -> {
        if (event.getCode() == KeyCode.UP) {
            CommandHistory.Item historyItem = commandHistory.up();
            command.setText(historyItem.getCommand());
            command.positionCaret(historyItem.getCursorPosition());
        } else if (event.getCode() == KeyCode.DOWN) {
            CommandHistory.Item historyItem = commandHistory.down();
            command.setText(historyItem.getCommand());
            command.positionCaret(historyItem.getCursorPosition());
        }
    });

    this.setOnCloseRequest(event -> commandInterpreter.close());
}

From source file:ca.wumbo.doommanager.client.controller.ConsoleController.java

@FXML
private void initialize() {
    textField.setOnKeyPressed(event -> {
        // Submit any text on enter.
        if (event.getCode().equals(KeyCode.ENTER))
            submitLineToConsole();/*from   w  w w.ja  v  a 2 s  .com*/

        // If we press up/down, look for lines we stored.
        if (event.getCode().equals(KeyCode.UP) || event.getCode().equals(KeyCode.DOWN)) {
            if (commandBuffer.size() > 0) {
                commandBufferIndex += (event.getCode().equals(KeyCode.UP) ? -1 : 1);
                commandBufferIndex = Math.min(Math.max(0, commandBufferIndex), commandBuffer.size());
                textField.setText(commandBufferIndex == commandBuffer.size() ? ""
                        : commandBuffer.get(commandBufferIndex));
                textField.end();
                event.consume(); // Has to be consumed or else it will mess up the end() caret setting.
            } else {
                textField.setText("");
            }
        }
    });
}

From source file:com.bekwam.resignator.JarsignerConfigController.java

@FXML
public void initialize() {

    if (logger.isDebugEnabled()) {
        logger.debug("[INIT] instance={}, configurationDS={}", this.hashCode(), configurationDS.hashCode());
    }//from   w  ww .  ja v a  2  s  .  c om

    cbVerbose.getItems().addAll(Boolean.TRUE, Boolean.FALSE);

    pfStorepass.textProperty().bindBidirectional(activeProfile.jarsignerConfigStorepassProperty());
    tfKeystore.textProperty().bindBidirectional(activeProfile.jarsignerConfigKeystoreProperty());
    pfKeypass.textProperty().bindBidirectional(activeProfile.jarsignerConfigKeypassProperty());
    cbVerbose.valueProperty().bindBidirectional(activeProfile.jarsignerConfigVerboseProperty());

    lblConfKeypass.setVisible(false);
    lblConfStorepass.setVisible(false);
    lblKeystoreNotFound.setVisible(false);

    //
    // Enables ChoiceBox controls to use the arrow keys without losing focus
    //
    vbox.addEventFilter(KeyEvent.KEY_PRESSED, (evt) -> {
        if (evt.getCode() == KeyCode.UP || evt.getCode() == KeyCode.DOWN) {
            evt.consume();
        }
    });

    //
    // #7 fire action event when tfs lose focus
    //
    InvalidationListener pfConfStorepassListener = (evt) -> {
        if (!pfConfStorepass.isFocused()) {
            verifyStorepass();
        }
    };

    pfConfStorepass.focusedProperty().addListener(new WeakInvalidationListener(pfConfStorepassListener));

    InvalidationListener pfConfKeypassListener = (evt) -> {
        if (!pfConfKeypass.isFocused()) {
            verifyKeypass();
        }
    };

    pfConfKeypass.focusedProperty().addListener(new WeakInvalidationListener(pfConfKeypassListener));

    tfKeystore.textProperty().addListener(new WeakInvalidationListener(needsSaveListener));
    pfStorepass.textProperty().addListener(new WeakInvalidationListener(needsSaveListener));
    pfKeypass.textProperty().addListener(new WeakInvalidationListener(needsSaveListener));
    cbAlias.valueProperty().addListener(new WeakInvalidationListener(needsSaveListener));
}

From source file:by.zuyeu.deyestracker.reader.ui.readpane.ReadPaneController.java

private void addScrollTracker() throws DEyesTrackerException {
    LOG.info("addScrollTracker() - start;");
    if (!scrollExist) {
        application.getStage().addEventFilter(KeyEvent.KEY_PRESSED, (KeyEvent evt) -> {
            if (evt.getCode().equals(KeyCode.DOWN)) {
                Platform.runLater(() -> {
                    LOG.debug("down - vvalue = {}", spText.getVvalue());
                    spText.setVvalue(spText.getVvalue() + spText.getVmax() / 10);
                });//www . ja  v a  2 s .c o m
            }
            if (evt.getCode().equals(KeyCode.UP)) {
                Platform.runLater(() -> {
                    LOG.debug("up - vvalue = {}", spText.getVvalue());
                    spText.setVvalue(spText.getVvalue() - spText.getVmax() / 10);
                });
            }
        });
        final Thread t = new Thread() {
            @Override
            public void run() {
                runEyeTracker();
            }
        };
        t.setDaemon(true);
        t.start();

        scrollExist = true;
    }
    LOG.info("addScrollTracker() - end;");
}

From source file:com.hengyi.japp.print.client.controller.MdController.java

@FXML
private void autoCompleteSapMara(KeyEvent ev) {
    try {/*from  ww  w  . j a  v a 2s  .  co  m*/
        if (KeyCode.RIGHT.equals(ev.getCode())) {
            List<SapMara> sapMaras = md.getSapT001().autoCompleteSapMara(matnrField.getText());
            sapMaraListView.setItems(observableArrayList(sapMaras));
            sapMaraListView.setVisible(true);
            sapMaraListView.getSelectionModel().selectFirst();
        } else if (KeyCode.UP.equals(ev.getCode()) || KeyCode.DOWN.equals(ev.getCode())) {
            sapMaraListView.fireEvent(new KeyEvent(null, sapMaraListView, KeyEvent.KEY_PRESSED,
                    ev.getCharacter(), ev.getText(), ev.getCode(), false, false, false, false));
        } else if (KeyCode.ENTER.equals(ev.getCode())) {
            selectSapMara(sapMaraListView.getSelectionModel().getSelectedItem());
            sapMaraListView.setVisible(false);
        }
    } catch (Exception ex) {
        Util.alertDialog(ex);
    }
}

From source file:com.heliosdecompiler.helios.gui.controller.FileTreeController.java

@FXML
public void initialize() {
    this.rootItem = new TreeItem<>(new TreeNode("[root]"));
    this.root.setRoot(this.rootItem);
    this.root.setCellFactory(new TreeCellFactory<>(node -> {
        if (node.getParent() == null) {
            ContextMenu export = new ContextMenu();

            MenuItem exportItem = new MenuItem("Export");

            export.setOnAction(e -> {
                File file = messageHandler.chooseFile().withInitialDirectory(new File("."))
                        .withTitle(Message.GENERIC_CHOOSE_EXPORT_LOCATION_JAR.format())
                        .withExtensionFilter(new FileFilter(Message.FILETYPE_JAVA_ARCHIVE.format(), "*.jar"),
                                true)//from w  w w  .  j ava 2  s .  co m
                        .promptSave();

                OpenedFile openedFile = (OpenedFile) node.getMetadata().get(OpenedFile.OPENED_FILE);

                Map<String, byte[]> clone = new HashMap<>(openedFile.getContents());

                backgroundTaskHelper.submit(
                        new BackgroundTask(Message.TASK_SAVING_FILE.format(node.getDisplayName()), true, () -> {
                            try {
                                if (!file.exists()) {
                                    if (!file.createNewFile()) {
                                        throw new IOException("Could not create export file");
                                    }
                                }

                                try (ZipOutputStream zipOutputStream = new ZipOutputStream(
                                        new FileOutputStream(file))) {
                                    for (Map.Entry<String, byte[]> ent : clone.entrySet()) {
                                        ZipEntry zipEntry = new ZipEntry(ent.getKey());
                                        zipOutputStream.putNextEntry(zipEntry);
                                        zipOutputStream.write(ent.getValue());
                                        zipOutputStream.closeEntry();
                                    }
                                }

                                messageHandler.handleMessage(Message.GENERIC_EXPORTED.format());
                            } catch (IOException ex) {
                                messageHandler.handleException(Message.ERROR_IOEXCEPTION_OCCURRED.format(), ex);
                            }
                        }));
            });

            export.getItems().add(exportItem);
            return export;
        }
        return null;
    }));

    root.addEventHandler(KeyEvent.KEY_RELEASED, event -> {
        if (event.getCode() == KeyCode.ENTER) {
            TreeItem<TreeNode> selected = this.root.getSelectionModel().getSelectedItem();
            if (selected != null) {
                if (selected.getChildren().size() != 0) {
                    selected.setExpanded(!selected.isExpanded());
                } else {
                    getParentController().getAllFilesViewerController().handleClick(selected.getValue());
                }
            }
        }
    });

    Tooltip tooltip = new Tooltip();
    StringBuilder search = new StringBuilder();

    List<TreeItem<TreeNode>> searchContext = new ArrayList<>();
    AtomicInteger searchIndex = new AtomicInteger();

    root.focusedProperty().addListener((observable, oldValue, newValue) -> {
        if (!newValue) {
            tooltip.hide();
            search.setLength(0);
        }
    });

    root.boundsInLocalProperty().addListener((observable, oldValue, newValue) -> {
        Bounds bounds = root.localToScreen(newValue);
        tooltip.setAnchorX(bounds.getMinX());
        tooltip.setAnchorY(bounds.getMinY());
    });

    root.addEventHandler(KeyEvent.KEY_PRESSED, event -> {
        if (tooltip.isShowing() && event.getCode() == KeyCode.UP) {
            if (searchIndex.decrementAndGet() < 0) {
                searchIndex.set(searchContext.size() - 1);
            }
        } else if (tooltip.isShowing() && event.getCode() == KeyCode.DOWN) {
            if (searchIndex.incrementAndGet() >= searchContext.size()) {
                searchIndex.set(0);
            }
        } else {
            return;
        }
        event.consume();

        root.scrollTo(root.getRow(searchContext.get(searchIndex.get())));
        root.getSelectionModel().select(searchContext.get(searchIndex.get()));
    });

    root.addEventHandler(KeyEvent.KEY_TYPED, event -> {
        if (event.getCharacter().charAt(0) == '\b') {
            if (search.length() > 0) {
                search.setLength(search.length() - 1);
            }
        } else if (event.getCharacter().charAt(0) == '\u001B') { //esc
            tooltip.hide();
            search.setLength(0);
            return;
        } else if (search.length() > 0
                || (search.length() == 0 && StringUtils.isAlphanumeric(event.getCharacter()))) {
            search.append(event.getCharacter());
            if (!tooltip.isShowing()) {
                tooltip.show(root.getScene().getWindow());
            }
        }

        if (!tooltip.isShowing())
            return;

        String str = search.toString();
        tooltip.setText("Search for: " + str);

        searchContext.clear();

        ArrayDeque<TreeItem<TreeNode>> deque = new ArrayDeque<>();
        deque.addAll(rootItem.getChildren());

        while (!deque.isEmpty()) {
            TreeItem<TreeNode> item = deque.poll();
            if (item.getValue().getDisplayName().contains(str)) {
                searchContext.add(item);
            }
            if (item.isExpanded() && item.getChildren().size() > 0)
                deque.addAll(item.getChildren());
        }

        searchIndex.set(0);
        if (searchContext.size() > 0) {
            root.scrollTo(root.getRow(searchContext.get(0)));
            root.getSelectionModel().select(searchContext.get(0));
        }
    });

    openedFileController.loadedFiles().addListener((MapChangeListener<String, OpenedFile>) change -> {
        if (change.getValueAdded() != null) {
            updateTree(change.getValueAdded());
        }
        if (change.getValueRemoved() != null) {
            this.rootItem.getChildren()
                    .removeIf(ti -> ti.getValue().equals(change.getValueRemoved().getRoot()));
        }
    });
}

From source file:jobhunter.gui.FXMLController.java

@FXML
void subscriptionTableKey(KeyEvent e) {
    if (e.getCode() == KeyCode.UP || e.getCode() == KeyCode.DOWN)
        subscriptionTableClick(null);
}

From source file:jobhunter.gui.FXMLController.java

@FXML
void jobsListKey(KeyEvent e) {
    if (e.getCode() == KeyCode.UP || e.getCode() == KeyCode.DOWN)
        jobsListClick(null);
}

From source file:com.cdd.bao.editor.EditSchema.java

private void createMenuItems() {
    final KeyCombination.Modifier cmd = KeyCombination.SHORTCUT_DOWN, shift = KeyCombination.SHIFT_DOWN,
            alt = KeyCombination.ALT_DOWN;

    addMenu(menuFile, "_New", new KeyCharacterCombination("N", cmd)).setOnAction(event -> actionFileNew());
    addMenu(menuFile, "_Open", new KeyCharacterCombination("O", cmd)).setOnAction(event -> actionFileOpen());
    addMenu(menuFile, "_Save", new KeyCharacterCombination("S", cmd))
            .setOnAction(event -> actionFileSave(false));
    addMenu(menuFile, "Save _As", new KeyCharacterCombination("S", cmd, shift))
            .setOnAction(event -> actionFileSave(true));
    addMenu(menuFile, "_Export Dump", new KeyCharacterCombination("E", cmd))
            .setOnAction(event -> actionFileExportDump());
    addMenu(menuFile, "_Merge", null).setOnAction(event -> actionFileMerge());
    menuFile.getItems().add(new SeparatorMenuItem());
    addMenu(menuFile, "Confi_gure", new KeyCharacterCombination(",", cmd))
            .setOnAction(event -> actionFileConfigure());
    addMenu(menuFile, "_Browse Endpoint", new KeyCharacterCombination("B", cmd, shift))
            .setOnAction(event -> actionFileBrowse());
    if (false) {//from w  w  w  . j  a va2 s. c  om
        addMenu(menuFile, "_Upload Endpoint", new KeyCharacterCombination("U", cmd, shift))
                .setOnAction(event -> actionFileUpload());
    }
    Menu menuFileGraphics = new Menu("Graphics");
    addMenu(menuFileGraphics, "_Template", null).setOnAction(event -> actionFileGraphicsTemplate());
    addMenu(menuFileGraphics, "_Assay", null).setOnAction(event -> actionFileGraphicsAssay());
    addMenu(menuFileGraphics, "_Properties", null).setOnAction(event -> actionFileGraphicsProperties());
    addMenu(menuFileGraphics, "_Values", null).setOnAction(event -> actionFileGraphicsValues());
    menuFile.getItems().add(menuFileGraphics);
    addMenu(menuFile, "Assay Stats", null).setOnAction(event -> actionFileAssayStats());
    menuFile.getItems().add(new SeparatorMenuItem());
    addMenu(menuFile, "_Close", new KeyCharacterCombination("W", cmd)).setOnAction(event -> actionFileClose());
    addMenu(menuFile, "_Quit", new KeyCharacterCombination("Q", cmd)).setOnAction(event -> actionFileQuit());

    addMenu(menuEdit, "Add _Group", new KeyCharacterCombination("G", cmd, shift))
            .setOnAction(event -> actionGroupAdd());
    addMenu(menuEdit, "Add _Assignment", new KeyCharacterCombination("A", cmd, shift))
            .setOnAction(event -> actionAssignmentAdd());
    addMenu(menuEdit, "Add Assa_y", new KeyCharacterCombination("Y", cmd, shift))
            .setOnAction(event -> actionAssayAdd());
    menuEdit.getItems().add(new SeparatorMenuItem());
    addMenu(menuEdit, "Cu_t", new KeyCharacterCombination("X", cmd)).setOnAction(event -> actionEditCopy(true));
    addMenu(menuEdit, "_Copy", new KeyCharacterCombination("C", cmd))
            .setOnAction(event -> actionEditCopy(false));
    Menu menuCopyAs = new Menu("Copy As");
    menuEdit.getItems().add(menuCopyAs);
    addMenu(menuEdit, "_Paste", new KeyCharacterCombination("V", cmd)).setOnAction(event -> actionEditPaste());
    menuEdit.getItems().add(new SeparatorMenuItem());
    addMenu(menuEdit, "_Delete", new KeyCodeCombination(KeyCode.DELETE, cmd, shift))
            .setOnAction(event -> actionEditDelete());
    addMenu(menuEdit, "_Undo", new KeyCharacterCombination("Z", cmd, shift))
            .setOnAction(event -> actionEditUndo());
    addMenu(menuEdit, "_Redo", new KeyCharacterCombination("Z", cmd, shift, alt))
            .setOnAction(event -> actionEditRedo());
    menuEdit.getItems().add(new SeparatorMenuItem());
    addMenu(menuEdit, "Move _Up", new KeyCharacterCombination("[", cmd))
            .setOnAction(event -> actionEditMove(-1));
    addMenu(menuEdit, "Move _Down", new KeyCharacterCombination("]", cmd))
            .setOnAction(event -> actionEditMove(1));

    addMenu(menuCopyAs, "Layout Tab-Separated", null).setOnAction(event -> actionEditCopyLayoutTSV());

    addMenu(menuValue, "_Add Value", new KeyCharacterCombination("V", cmd, shift))
            .setOnAction(event -> detail.actionValueAdd());
    addMenu(menuValue, "Add _Multiple Values", new KeyCharacterCombination("M", cmd, shift))
            .setOnAction(event -> detail.actionValueMultiAdd());
    addMenu(menuValue, "_Delete Value", new KeyCodeCombination(KeyCode.DELETE, cmd))
            .setOnAction(event -> detail.actionValueDelete());
    addMenu(menuValue, "Move _Up", new KeyCodeCombination(KeyCode.UP, cmd))
            .setOnAction(event -> detail.actionValueMove(-1));
    addMenu(menuValue, "Move _Down", new KeyCodeCombination(KeyCode.DOWN, cmd))
            .setOnAction(event -> detail.actionValueMove(1));
    menuValue.getItems().add(new SeparatorMenuItem());
    addMenu(menuValue, "_Lookup URI", new KeyCharacterCombination("U", cmd))
            .setOnAction(event -> detail.actionLookupURI());
    addMenu(menuValue, "Lookup _Name", new KeyCharacterCombination("L", cmd))
            .setOnAction(event -> detail.actionLookupName());
    menuValue.getItems().add(new SeparatorMenuItem());
    addMenu(menuValue, "_Sort Values", null).setOnAction(event -> actionValueSort());
    addMenu(menuValue, "_Remove Duplicates", null).setOnAction(event -> actionValueDuplicates());
    addMenu(menuValue, "Cleanup Values", null).setOnAction(event -> actionValueCleanup());

    (menuViewSummary = addCheckMenu(menuView, "_Summary Values", new KeyCharacterCombination("-", cmd)))
            .setOnAction(event -> actionViewToggleSummary());
    addMenu(menuView, "_Template", new KeyCharacterCombination("1", cmd))
            .setOnAction(event -> actionViewTemplate());
    addMenu(menuView, "_Assays", new KeyCharacterCombination("2", cmd))
            .setOnAction(event -> actionViewAssays());
    addMenu(menuView, "_Derived Tree", new KeyCharacterCombination("3", cmd))
            .setOnAction(event -> detail.actionShowTree());
}

From source file:snpviewer.SnpViewer.java

@Override
public void initialize(URL url, ResourceBundle rb) {
    labelSplitPane.setDividerPositions();
    chromSplitPane.setDividerPositions();
    Pane lpane = (Pane) horizontalSplit.getItems().get(0);
    SplitPane.setResizableWithParent(lpane, false);
    //mnemonics/shortcuts for menus        
    mainMenu.useSystemMenuBarProperty().set(true);
    fileMenu.setMnemonicParsing(true);/*from www .ja  v a 2  s  .  co m*/
    sampleMenu.setMnemonicParsing(true);
    goMenu.setMnemonicParsing(true);
    helpMenu.setMnemonicParsing(true);
    newProjectMenu.setAccelerator(new KeyCodeCombination(KeyCode.N, KeyCombination.SHORTCUT_DOWN));
    loadProjectMenu.setAccelerator(new KeyCodeCombination(KeyCode.L, KeyCombination.SHORTCUT_DOWN));
    addAffSampleMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.A, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    addUnSampleMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.U, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    nextChromMenu.setAccelerator(new KeyCodeCombination(KeyCode.EQUALS, KeyCombination.SHORTCUT_DOWN));
    prevChromMenu.setAccelerator(new KeyCodeCombination(KeyCode.MINUS, KeyCombination.SHORTCUT_DOWN));
    firstChromMenu.setAccelerator(new KeyCodeCombination(KeyCode.DIGIT1, KeyCombination.SHORTCUT_DOWN));
    lastChromMenu.setAccelerator(new KeyCodeCombination(KeyCode.DIGIT0, KeyCombination.SHORTCUT_DOWN));
    redrawMenu.setAccelerator(new KeyCodeCombination(KeyCode.R, KeyCombination.SHORTCUT_DOWN));
    cacheChromsMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.C, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    saveToPngMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.S, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    autoFindRegions.setAccelerator(new KeyCodeCombination(KeyCode.F, KeyCombination.SHORTCUT_DOWN));
    //need to disable hideSavedRegionsMenu accelerator for linux - doesn't work for check menus
    hideSavedRegionsMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.H, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    clearSavedRegionsMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.X, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    displaySavedsRegionsMenu.setAccelerator(new KeyCodeCombination(KeyCode.T, KeyCombination.SHORTCUT_DOWN));
    outputSavedRegionsMenu.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCombination.SHORTCUT_DOWN));
    removeSampleMenu.setAccelerator(
            new KeyCodeCombination(KeyCode.R, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN));
    //set radio menu item toggle group
    ArrayList<RadioMenuItem> callQualityRadios = new ArrayList<>(
            Arrays.asList(noFilteringRadio, filter99, filter95, filter90, filter85));
    ToggleGroup callQualityToggle = new ToggleGroup();
    for (RadioMenuItem r : callQualityRadios) {
        r.setToggleGroup(callQualityToggle);
    }
    noFilteringRadio.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            setQualityFilter(null);
        }
    });

    filter99.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            setQualityFilter(0.01);
        }
    });

    filter95.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            setQualityFilter(0.05);
        }
    });

    filter90.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            setQualityFilter(0.10);
        }
    });

    filter85.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            setQualityFilter(0.15);
        }
    });

    nextChromMenu.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            selectNextChromosome(true);
        }
    });

    prevChromMenu.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            selectNextChromosome(false);
        }
    });

    firstChromMenu.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            if (!cancelButton.isDisabled()) {
                cancelButton.fire();
            }
            if (!chromosomeSelector.isDisabled()) {

                chromosomeSelector.getSelectionModel().selectFirst();
            }
        }
    });

    lastChromMenu.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            if (!cancelButton.isDisabled()) {
                cancelButton.fire();
            }
            if (!chromosomeSelector.isDisabled()) {
                chromosomeSelector.getSelectionModel().selectLast();
            }
        }
    });

    hideSavedRegionsMenu.setOnAction(new EventHandler() {
        @Override
        public void handle(Event ev) {
            showHideSavedRegions();
        }
    });

    colorComp.addAll(Arrays.asList(colorComponants));

    //selection context menu
    final ContextMenu scm = new ContextMenu();
    final MenuItem scmItem1 = new MenuItem("Display Flanking SNP IDs");
    scmItem1.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            /* get coordinates of selection and report back
             * flanking snp ids and coordinates
             */
            displayFlankingSnpIDs(dragSelectRectangle);

        }
    });
    final MenuItem scmItem2 = new MenuItem("Write Selected Region to File");
    scmItem2.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            Platform.runLater(new Runnable() {
                @Override
                public void run() {
                    /* get coordinates of selection and report back
                     * write SNPs in region to file
                     */
                    writeRegionToFile(dragSelectRectangle);
                }
            });
        }
    });
    final MenuItem scmItem3 = new MenuItem("Add To Saved Regions");
    scmItem3.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            /* get coordinates of selection and report back
             * write SNPs in region to file
             */
            saveSelection();
        }
    });
    final MenuItem scmItem4 = new MenuItem("Show/Hide Saved Regions");
    scmItem4.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            /* get coordinates of selection and report back
             * write SNPs in region to file
             */
            hideSavedRegionsMenu.selectedProperty().setValue(!hideSavedRegionsMenu.isSelected());
            hideSavedRegionsMenu.fire();
        }
    });
    final MenuItem scmItem5 = new MenuItem("Zoom Region");
    scmItem5.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            Platform.runLater(new Runnable() {
                @Override
                public void run() {
                    /* get coordinates of selection and report back
                     * write SNPs in region to file
                     */
                    zoomRegion(dragSelectRectangle);
                }
            });
        }
    });
    final MenuItem scmItem6 = new MenuItem("Write Saved Regions to File");
    scmItem6.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            Platform.runLater(new Runnable() {
                @Override
                public void run() {
                    /* get coordinates of selection and report back
                     * write SNPs in region to file
                     */
                    writeSavedRegionsToFile();
                }
            });
        }
    });

    scm.getItems().add(scmItem1);
    scm.getItems().add(scmItem2);
    scm.getItems().add(scmItem3);
    scm.getItems().add(scmItem4);
    scm.getItems().add(scmItem5);
    scm.getItems().add(scmItem6);
    //overlayPane context menu
    ocm = new ContextMenu();
    final MenuItem ocmItem1 = new MenuItem("Save Image to File");
    ocmItem1.setOnAction(new EventHandler<ActionEvent>() {
        @Override
        public void handle(ActionEvent e) {
            Platform.runLater(new Runnable() {
                @Override
                public void run() {
                    drawPaneToPng();
                }
            });
        }
    });

    ocm.getItems().add(ocmItem1);
    ocm.getItems().add(scmItem4);
    ocm.getItems().add(scmItem6);

    //color selections
    colorComponantSelector.getItems().clear();
    colorComponantSelector.getItems().add("AA");
    colorComponantSelector.getItems().add("BB");
    colorComponantSelector.getItems().add("AB");
    colorComponantSelector.getItems().add("Selection Outline");
    colorComponantSelector.getItems().add("Selection Fill");
    colorComponantSelector.getItems().add("Saved Region Outline");
    colorComponantSelector.getItems().add("Saved Region Fill");
    colorComponantSelector.getSelectionModel().selectFirst();
    colorPicker.setValue(colorComponants[0]);
    colorComponantSelector.getSelectionModel().selectedIndexProperty()
            .addListener(new ChangeListener<Number>() {
                @Override
                public void changed(ObservableValue ov, Number value, Number new_value) {
                    colorPicker.setValue(colorComp.get(new_value.intValue()));
                    colorPicker.fireEvent(new ActionEvent());
                }
            });
    colorPicker.setOnAction(new EventHandler() {
        @Override
        public void handle(Event t) {
            if (!colorComp.get(colorComponantSelector.getSelectionModel().getSelectedIndex())
                    .equals(colorPicker.getValue())) {
                colorComp.set(colorComponantSelector.getSelectionModel().getSelectedIndex(),
                        colorPicker.getValue());
                saveProject();
                //colorComponants[colorComponantSelector.getSelectionModel().getSelectedIndex()] = colorPicker.getValue();
                if (colorComponantSelector.getSelectionModel().getSelectedIndex() == Colors.fill.value) {
                    dragSelectRectangle.setFill(colorPicker.getValue());
                } else if (colorComponantSelector.getSelectionModel().getSelectedIndex() == Colors.line.value) {
                    dragSelectRectangle.setStroke(colorPicker.getValue());
                } else if (colorComponantSelector.getSelectionModel()
                        .getSelectedIndex() == Colors.saveLine.value) {
                    for (Rectangle r : savedRegionsDisplay) {
                        r.setStroke(colorPicker.getValue());
                    }
                } else if (colorComponantSelector.getSelectionModel()
                        .getSelectedIndex() == Colors.saveFill.value) {
                    for (Rectangle r : savedRegionsDisplay) {
                        r.setFill(colorPicker.getValue());
                    }
                } else {
                    removeSavedChromosomeImages();
                    if (redrawCheckBox.isSelected()) {
                        refreshView(null, true);
                    }
                }
            }
        }
    });

    /*perform appropriate action when user selects a chromosome
     * from the chromosome choice box
     */
    chromosomeSelector.getSelectionModel().selectedIndexProperty().addListener(new ChangeListener<Number>() {
        @Override
        public void changed(ObservableValue ov, Number value, Number new_value) {
            chromosomeBoxList = chromosomeSelector.getItems().toArray();

            if (new_value.intValue() > -1) {
                chromosomeSelected((String) chromosomeBoxList[new_value.intValue()]);
            }
        }
    });

    chromosomeSelector.addEventFilter(KeyEvent.ANY, new EventHandler<KeyEvent>() {
        @Override
        public void handle(KeyEvent ke) {
            if (ke.getCode() == KeyCode.UP) {
                ke.consume();
                chromosomeSelector.show();
            }
        }
    });

    selectionOverlayPane.heightProperty().addListener(new ChangeListener<Number>() {
        @Override
        public void changed(ObservableValue<? extends Number> observableValue, Number oldSceneWidth,
                Number newSceneWidth) {
            windowResized(new ActionEvent());

        }
    });

    selectionOverlayPane.widthProperty().addListener(new ChangeListener<Number>() {
        @Override
        public void changed(ObservableValue<? extends Number> observableValue, Number oldSceneWidth,
                Number newSceneWidth) {
            windowResized(new ActionEvent());
        }
    });

    /*upon addition of a new affected file adjust components accordingly
     * i.e. ensure appropriate chromosomes are in the choice box
     * adjust the split panes to fit all files and redisplay
     */

    affObserve.addListener(new ListChangeListener() {
        @Override
        public void onChanged(ListChangeListener.Change change) {
            change.next();/*from the javadoc 
                          * 'Go to the next change. In initial state is invalid a require 
                          * a call to next() before calling other methods. The first 
                          * next() call will make this object represent the first change.
                          */
            if (change.getRemovedSize() > 0) {
                List<SnpFile> both = new ArrayList<>(unFiles);
                both.addAll(affFiles);
                recheckChromosomeSelector(both);//need to check all files again, not just affFiles
            } else if (change.getAddedSize() > 0) {
                addToChromosomeSelector(affFiles);
            }
        }
    });

    /*as above 
     * but for unaffected files
     */
    unObserve.addListener(new ListChangeListener() {
        @Override
        public void onChanged(ListChangeListener.Change change) {
            change.next();
            if (change.getRemovedSize() > 0) {
                List<SnpFile> both = new ArrayList<>(unFiles);
                both.addAll(affFiles);
                recheckChromosomeSelector(both);//need to check all files again, not just unFiles
            } else if (change.getAddedSize() > 0) {
                addToChromosomeSelector(unFiles);
            }

        }
    });

    selectionOverlayPane.addEventHandler(MouseEvent.MOUSE_MOVED, new EventHandler<MouseEvent>() {
        @Override
        public void handle(MouseEvent e) {
            if (!genomeVersion.equals("") && chromosomeSelector.getSelectionModel().getSelectedIndex() > -1) {
                try {
                    ChromosomeLength chromLength = new ChromosomeLength(genomeVersion);
                    String currentChrom = (String) chromosomeBoxList[chromosomeSelector.getSelectionModel()
                            .getSelectedIndex()];
                    double coordinate = chromLength.getLength(currentChrom) / chromSplitPane.getWidth()
                            * e.getX();
                    positionIndicator.setText(nf.format(coordinate));

                } catch (Exception ex) {
                    positionIndicator.setText("Build Error!");
                }

            }
        }
    });
    /*handle mouse dragging and effect on dragSelectRectangle
     * 
     */
    dragSelectRectangle.widthProperty().bind(dragSelectRectX.subtract(dragSelectRectInitX));
    dragSelectRectangle.heightProperty().bind(selectionOverlayPane.heightProperty());
    //dragSelectRectangle.strokeProperty().set(colorComponants[Colors.line.value]);
    dragSelectRectangle.setStrokeWidth(4.0);

    //dragSelectRectangle.setBlendMode(BlendMode.SCREEN);
    dragSelectRectangle.setOpacity(0.45);
    dragSelectRectangle.setVisible(false);
    selectionOverlayPane.getChildren().add(dragSelectRectangle);

    selectionOverlayPane.addEventHandler(MouseEvent.MOUSE_PRESSED, new EventHandler<MouseEvent>() {
        @Override
        public void handle(MouseEvent e) {
            if (scm.isShowing()) {
                scm.hide();
            }
            if (!e.isPrimaryButtonDown()) {
                if (e.isSecondaryButtonDown()) {
                    //check we're not overlapping selection
                    if (e.getX() >= dragSelectRectangle.getX()
                            && e.getX() <= (dragSelectRectangle.getX() + dragSelectRectangle.getWidth())) {
                        return;
                    }
                    //check we're not overlapping saved regions
                    for (Rectangle r : savedRegionsDisplay) {
                        if (r.isVisible() && e.getX() >= r.getX() && e.getX() <= r.getX() + r.getWidth()) {
                            return;
                        }
                    }
                    if (chromosomeSelector.getSelectionModel().isEmpty()) {
                        ocmItem1.setDisable(true);
                    } else {
                        ocmItem1.setDisable(false);
                    }
                    ocm.show(selectionOverlayPane, e.getScreenX(), e.getScreenY());

                    return;
                }
            }
            if (ocm.isShowing()) {
                ocm.hide();
            }

            dragSelectRectangle.strokeProperty().set(colorComp.get(Colors.line.value));
            dragSelectRectangle.fillProperty().set(colorComp.get(Colors.fill.value));
            dragSelectRectX.set(0);
            dragSelectRectangle.setVisible(true);
            dragSelectRectangle.setX(e.getX());
            dragSelectRectangle.setY(0);
            dragSelectRectInitX.set(e.getX());
            anchorInitX.set(e.getX());

        }
    });
    selectionOverlayPane.addEventHandler(MouseEvent.MOUSE_DRAGGED, new EventHandler<MouseEvent>() {
        @Override
        public void handle(MouseEvent e) {
            if (!e.isPrimaryButtonDown()) {
                return;
            }
            dragSelectRectangle.setVisible(true);
            if (e.getX() > anchorInitX.doubleValue()) {//dragging to the right
                if (e.getX() <= selectionOverlayPane.getLayoutX() + selectionOverlayPane.getWidth()) {
                    //mouse is before the edge of the pane
                    dragSelectRectInitX.set(anchorInitX.doubleValue());
                    dragSelectRectX.set(e.getX());
                } else {
                    //mouse is over the edge
                    dragSelectRectX.set(selectionOverlayPane.getWidth());
                }
            } else {
                if (e.getX() > selectionOverlayPane.getLayoutX()) {
                    dragSelectRectInitX.set(e.getX());
                    dragSelectRectangle.setX(e.getX());
                    dragSelectRectX.set(anchorInitX.doubleValue());
                } else {
                    dragSelectRectInitX.set(0);
                    dragSelectRectangle.setX(0);
                    /* the two lines below are just to trigger 
                    * dragSelectRectangle.widthProperty listener 
                    * so that start coordinate changes to 1
                    */
                    dragSelectRectX.set(anchorInitX.doubleValue() + 1);
                    dragSelectRectX.set(anchorInitX.doubleValue() + 1);

                }
            }
        }
    });

    selectionOverlayPane.addEventHandler(MouseEvent.MOUSE_RELEASED, new EventHandler<MouseEvent>() {
        @Override
        public void handle(MouseEvent e) {
            //dragSelectRectX.set(e.getX());
            if (!e.isPrimaryButtonDown()) {
                return;
            }
            dragSelectRectangle.setVisible(true);
            if (dragSelectRectangle.getWidth() == 0) {
                clearDragSelectRectangle();
            }
        }
    });

    dragSelectRectangle.widthProperty().addListener(new ChangeListener() {
        @Override
        public void changed(ObservableValue observableValue, Object oldValue, Object newRectWidth) {
            if (!genomeVersion.equals("") && chromosomeSelector.getSelectionModel().getSelectedIndex() > -1
                    && dragSelectRectangle.getWidth() > 0) {
                try {
                    ChromosomeLength chromLength = new ChromosomeLength(genomeVersion);
                    String currentChrom = (String) chromosomeBoxList[chromosomeSelector.getSelectionModel()
                            .getSelectedIndex()];
                    double startCoordinate = chromLength.getLength(currentChrom)
                            / selectionOverlayPane.getWidth() * dragSelectRectangle.getX();
                    double selectionWidth = chromLength.getLength(currentChrom)
                            / selectionOverlayPane.getWidth() * dragSelectRectangle.getWidth();
                    if (dragSelectRectangle.getX() == 0) {
                        startCoordinate = 1;
                    }
                    selectionIndicator.setText("chr" + currentChrom + ":" + nf.format(startCoordinate) + "-"
                            + nf.format(startCoordinate + selectionWidth));
                } catch (Exception ex) {
                    selectionIndicator.setText("Build Error!");
                }
            } else {
                selectionIndicator.setText("");
            }

        }
    });

    dragSelectRectangle.addEventHandler(MouseEvent.MOUSE_CLICKED, new EventHandler<MouseEvent>() {
        @Override
        public void handle(MouseEvent e) {
            if (e.getButton() == MouseButton.SECONDARY) {
                if (chromosomeSelector.getSelectionModel().isEmpty()) {
                    scmItem1.setDisable(true);
                    scmItem2.setDisable(true);
                } else {
                    scmItem1.setDisable(false);
                    scmItem2.setDisable(false);
                }
                if (ocm.isShowing()) {
                    ocm.hide();
                }

                scm.show(selectionOverlayPane, e.getScreenX(), e.getScreenY());
            }
        }
    });

}