Java Code Examples for javafx.scene.layout.BorderPane#setRight()

@Override
protected void updateItem(AnnotationItem item, boolean empty)
{
	super.updateItem(item, empty);
	if (item == null)
		return;
	String text = item.annotation.getTrace().getLabel() + ": " + item.annotation.getText().replaceAll("\n", "\\\\n");
	if (text.length() > MAX_LENGTH)
		text = text.substring(0, MAX_LENGTH) + "...";
	final CheckBox selector = new CheckBox(text);
	selector.setTextFill(item.annotation.getTrace().getColor());
	selector.setSelected(true);
	final Button edit = new Button(Messages.AnnotationEditBtn);
	final BorderPane line = new BorderPane();
	line.setLeft(selector);
	line.setRight(edit);
	setGraphic(line); // 'Graphic' == any Node that represents the cell

	selector.setOnAction(event -> item.selected = selector.isSelected());
	edit.setOnAction(event -> editAnnotation(item.annotation));
}
 

protected Node createStatusBar()
{
	BorderPane p = new BorderPane();
	p.setLeft(statusField);
	p.setRight(FX.label(DockDemoApp.COPYRIGHT, new Insets(1, 20, 1, 10)));
	return p;
}
 

public static Node createIconContent() {
    StackPane sp = new StackPane();
    BorderPane borderPane = new BorderPane();

    Rectangle rectangle = new Rectangle(62, 62, Color.LIGHTGREY);
    rectangle.setStroke(Color.BLACK);
    borderPane.setPrefSize(rectangle.getWidth(), rectangle.getHeight());
 
    Rectangle recTop = new Rectangle(62, 5, Color.web("#349b00"));
    recTop.setStroke(Color.BLACK);
    Rectangle recBottom = new Rectangle(62, 14, Color.web("#349b00"));
    recBottom.setStroke(Color.BLACK);
    Rectangle recLeft = new Rectangle(20, 41, Color.TRANSPARENT);
    recLeft.setStroke(Color.BLACK);
    Rectangle recRight = new Rectangle(20, 41, Color.TRANSPARENT);
    recRight.setStroke(Color.BLACK);
    Rectangle centerRight = new Rectangle(20, 41, Color.TRANSPARENT);
    centerRight.setStroke(Color.BLACK);
    borderPane.setRight(recRight);
    borderPane.setTop(recTop);
    borderPane.setLeft(recLeft);
    borderPane.setBottom(recBottom);
    borderPane.setCenter(centerRight);
 
    sp.getChildren().addAll(rectangle, borderPane);
    return new Group(sp);
}
 

public static Node createIconContent() {
    StackPane sp = new StackPane();
    BorderPane borderPane = new BorderPane();

    Rectangle rectangle = new Rectangle(62, 62, Color.LIGHTGREY);
    rectangle.setStroke(Color.BLACK);
    borderPane.setPrefSize(rectangle.getWidth(), rectangle.getHeight());
 
    Rectangle recTop = new Rectangle(62, 5, Color.web("#349b00"));
    recTop.setStroke(Color.BLACK);
    Rectangle recBottom = new Rectangle(62, 14, Color.web("#349b00"));
    recBottom.setStroke(Color.BLACK);
    Rectangle recLeft = new Rectangle(20, 41, Color.TRANSPARENT);
    recLeft.setStroke(Color.BLACK);
    Rectangle recRight = new Rectangle(20, 41, Color.TRANSPARENT);
    recRight.setStroke(Color.BLACK);
    Rectangle centerRight = new Rectangle(20, 41, Color.TRANSPARENT);
    centerRight.setStroke(Color.BLACK);
    borderPane.setRight(recRight);
    borderPane.setTop(recTop);
    borderPane.setLeft(recLeft);
    borderPane.setBottom(recBottom);
    borderPane.setCenter(centerRight);
 
    sp.getChildren().addAll(rectangle, borderPane);
    return new Group(sp);
}
 

@Override
protected PopOver initInfo() {
	PopOver info = super.initInfo();
	GridPane content = new GridPane();
	content.getStyleClass().add("grid");

	int rowCount = 0;

	if (maps.size() > 1) {
		content.add(new Label("Map count:"), 0, rowCount);
		content.add(new Label(Integer.toString(maps.size())), 1, rowCount++);
	}

	for (de.piegames.blockmap.world.LevelMetadata.MapPin map : maps) {
		BorderPane mapPane = new BorderPane();
		mapPane.setLeft(new Label("Scale:"));
		mapPane.setRight(new Label("1:" + (1 << map.getScale())));

		if (map.getColors().isPresent()) {
			byte[] data = map.getColors().get();
			WritableImage image = new WritableImage(128, 128);
			for (int x = 0; x < 128; x++)
				for (int y = 0; y < 128; y++)
					image.getPixelWriter().setColor(x, y, COLOR_IDS[0xFF & data[y << 7 | x]]);
			mapPane.setBottom(new ImageView(image));
		}
		content.add(mapPane, 0, rowCount++, 1, 2);
	}
	info.setContentNode(content);
	return info;
}
 

private BorderPane getStatusBar ()
{
  Separator[] div = new Separator[6];
  for (int i = 0; i < div.length; i++)
  {
    div[i] = new Separator ();
    div[i].setOrientation (Orientation.VERTICAL);
  }

  HBox leftBox = getHBox (new Insets (2, GAP, 2, 3), Pos.CENTER_LEFT);
  leftBox.getChildren ().addAll (div[0], fieldLocation, div[1], insertMode, div[2]);

  HBox centerBox = getHBox (new Insets (2, GAP, 2, GAP), Pos.CENTER);
  centerBox.getChildren ().add (status);

  HBox rightBox = getHBox (new Insets (2, 0, 2, GAP), Pos.CENTER_RIGHT);
  rightBox.getChildren ().addAll (div[3], fieldType, div[4], cursorLocation, div[5]);

  setStatusFont ();

  BorderPane statusPane = new BorderPane ();
  statusPane.setLeft (leftBox);
  statusPane.setCenter (centerBox);
  statusPane.setRight (rightBox);

  return statusPane;
}
 

public AttributeBox(final String label, final AttributeList attributeList) {
    final BorderPane borderPane = new BorderPane();
    borderPane.setTop(attributeList);

    setMaxHeight(USE_PREF_SIZE);
    setMaxWidth(Double.MAX_VALUE);
    setCenter(borderPane);

    final Label heading = new Label(label);
    heading.setStyle("-fx-font-weight: bold;");

    BorderPane labelPane = new BorderPane();
    labelPane.setPadding(new Insets(1));
    labelPane.setMinWidth(0);
    labelPane.setLeft(heading);

    final Button button = new Button("", new ImageView(ADD_IMAGE));
    button.setOnAction((ActionEvent event) -> {
        Attribute attribute = importController.showNewAttributeDialog(attributeList.getAttributeType().getElementType());
        if (attribute != null) {
            importController.createManualAttribute(attribute);
        }
    });
    button.setTooltip(new Tooltip("Add a new " + attributeList.getAttributeType().getElementType() + " attribute"));
    labelPane.setRight(button);

    setTop(labelPane);
}
 

public ScatterPlotWindow(PeakList peakList) {

    setTitle("Scatter plot of " + peakList);

    mainPane = new BorderPane();
    mainScene = new Scene(mainPane);

    // Use main CSS
    mainScene.getStylesheets()
        .addAll(MZmineCore.getDesktop().getMainWindow().getScene().getStylesheets());
    setScene(mainScene);

    // setDefaultCloseOperation(DISPOSE_ON_CLOSE);

    topPanel = new ScatterPlotTopPanel();
    mainPane.setTop(topPanel);

    chart = new ScatterPlotChart(this, topPanel, peakList);
    // Border border = BorderFactory.createEtchedBorder(EtchedBorder.RAISED);
    // chart.setBorder(border);
    // chart.setBackground(Color.white);
    mainPane.setCenter(chart);

    toolbar = new ToolBar();
    toolbar.setOrientation(Orientation.VERTICAL);

    axesButton = new Button(null, new ImageView(axesIcon));
    axesButton.setTooltip(new Tooltip("Setup ranges for axes"));
    axesButton.setOnAction(e -> {
      AxesSetupDialog dialog = new AxesSetupDialog(this, chart.getPlot());
      dialog.show();
    });
    toolbar.getItems().add(axesButton);

    mainPane.setRight(toolbar);

    // JComponent leftMargin = (JComponent) Box.createRigidArea(new Dimension(10, 10));
    // leftMargin.setOpaque(false);
    // add(leftMargin, BorderLayout.WEST);

    bottomPanel = new ScatterPlotBottomPanel(this, chart, peakList);
    mainPane.setBottom(bottomPanel);

    // Add the Windows menu
    WindowsMenu.addWindowsMenu(mainScene);


    // get the window settings parameter
    ParameterSet paramSet =
        MZmineCore.getConfiguration().getModuleParameters(ScatterPlotVisualizerModule.class);
    WindowSettingsParameter settings = paramSet.getParameter(ScatterPlotParameters.windowSettings);

    // update the window and listen for changes
    // settings.applySettingsToWindow(this);
    // this.addComponentListener(settings);

    setMinWidth(500.0);
    setMinHeight(400.0);

  }
 

public TransfersTab (Screen screen, TSOCommand tsoCommand)
{
  super ("Transfers", screen, tsoCommand);

  btnTracks.setSelected (true);
  btnFiles.setSelected (true);
  btnFB.setSelected (true);

  grpFileName.getToggles ().addAll (btnDatasets, btnFiles, btnJobs, btnSpecify);
  grpSpaceUnits.getToggles ().addAll (btnTracks, btnCylinders, btnBlocks);

  grpFileName.selectedToggleProperty ()
      .addListener ( (ov, oldToggle, newToggle) -> toggleSelected (newToggle));

  grpSpaceUnits.selectedToggleProperty ()
      .addListener ( (ov, oldToggle, newToggle) -> toggleSelected (newToggle));

  VBox datasetBlock = new VBox (10);
  datasetBlock.setPadding (new Insets (10, 10, 10, 10));

  HBox line1 = getLine (btnDatasets, txtDatasets);
  HBox line2 = getLine (btnJobs, txtJobs);
  HBox line3 = getLine (btnFiles, txtFiles);
  HBox line4 = getLine (btnSpecify, txtSpecify);

  txtDatasets.setPromptText ("no dataset selected");
  txtJobs.setPromptText ("no batch job selected");
  txtFiles.setPromptText ("no file selected");

  txtSpecify.setEditable (true);
  txtBlksize.setText ("0");
  txtLrecl.setText ("80");

  datasetBlock.getChildren ().addAll (line1, line2, line3, line4);

  VBox spaceBlock = new VBox (10);
  spaceBlock.setPadding (new Insets (10, 10, 10, 10));

  HBox line5 = getLine (lblLrecl, txtLrecl);
  HBox line6 = getLine (lblBlksize, txtBlksize);
  HBox line7 = getLine (btnTracks, btnCylinders, btnBlocks);
  HBox line8 = getLine (lblSpace, txtSpace, line7);
  HBox line9 = getLine (btnFB, btnPS);
  HBox line10 = getLine (lblDisposition, line9);

  spaceBlock.getChildren ().addAll (line10, line5, line6, line8);

  datasetBlock.setStyle ("-fx-border-color: grey; -fx-border-width: 1;"
      + " -fx-border-insets: 10");
  spaceBlock.setStyle ("-fx-border-color: grey; -fx-border-width: 1;"
      + " -fx-border-insets: 10");

  txtDescription.setText ("Not finished yet");

  VBox columnLeft = new VBox ();
  columnLeft.setPadding (new Insets (10, 10, 10, 10));
  columnLeft.getChildren ().addAll (datasetBlock, spaceBlock);

  VBox columnRight = new VBox ();
  columnRight.setPadding (new Insets (10, 10, 10, 10));
  columnRight.getChildren ().addAll (txtDescription);

  BorderPane borderPane = new BorderPane ();
  borderPane.setLeft (columnLeft);
  borderPane.setRight (columnRight);

  setContent (borderPane);
}
 

public ProjectionPlotWindow(PeakList peakList, ProjectionPlotDataset dataset,
    ParameterSet parameters) {

  mainPane = new BorderPane();
  mainScene = new Scene(mainPane);

  // Use main CSS
  mainScene.getStylesheets()
      .addAll(MZmineCore.getDesktop().getMainWindow().getScene().getStylesheets());
  setScene(mainScene);

  toolbar = new ToolBar();
  toolbar.setOrientation(Orientation.VERTICAL);
  Button axesButton = new Button(null, new ImageView(axesIcon));
  axesButton.setTooltip(new Tooltip("Setup ranges for axes"));
  Button labelsButton = new Button(null, new ImageView(labelsIcon));
  labelsButton.setTooltip(new Tooltip("Toggle sample names"));
  toolbar.getItems().addAll(axesButton, labelsButton);
  mainPane.setRight(toolbar);

  plot = new ProjectionPlotPanel(this, dataset, parameters);
  mainPane.setCenter(plot);

  axesButton.setOnAction(e -> {
    AxesSetupDialog dialog = new AxesSetupDialog(this, plot.getChart().getXYPlot());
    dialog.showAndWait();
  });

  labelsButton.setOnAction(e -> plot.cycleItemLabelMode());

  String title = peakList.getName();
  title = title.concat(" : ");
  title = title.concat(dataset.toString());
  if (parameters.getParameter(ProjectionPlotParameters.peakMeasurementType)
      .getValue() == PeakMeasurementType.HEIGHT)
    title = title.concat(" (using peak heights)");
  else
    title = title.concat(" (using peak areas)");

  this.setTitle(title);

  // Add the Windows menu
  WindowsMenu.addWindowsMenu(mainScene);

  ParameterSet paramSet =
      MZmineCore.getConfiguration().getModuleParameters(ScatterPlotVisualizerModule.class);
  WindowSettingsParameter settings = paramSet.getParameter(ScatterPlotParameters.windowSettings);

}
 

private void initComponent() {
	Label titleLabel = new Label("", logoImageView);
	titleLabel.setStyle("-fx-text-fill: white;");

	titleHBox.setPadding(new Insets(5, 0, 0, 10));
	titleHBox.setPrefHeight(30);
	titleHBox.getChildren().add(titleLabel);

	topVBox.getChildren().add(titleHBox);
	topVBox.getChildren().add(userDataPane);

	listBaseStackPane.getChildren().add(tabPane);
	listBaseStackPane.getChildren().add(findListPane);

	centerBorderPane.setTop(searchBox);
	centerBorderPane.setCenter(listBaseStackPane);

	findTextField.setPromptText("搜索：联系人、多人聊天、群");
	findTextField.getStyleClass().remove("text-field");
	findTextField.setBackground(Background.EMPTY);
	findTextField.setMinHeight(30);
	findTextField.setStyle("-fx-prompt-text-fill:#ffffff;");

	Image image = ImageBox.getImageClassPath("/classics/images/main/search/search_icon.png");
	ImageView searchImageView = new ImageView();
	searchImageView.setImage(image);

	searchBox.getChildren().add(findTextField);
	searchBox.getChildren().add(searchImageView);
	HBox.setHgrow(findTextField, Priority.ALWAYS);

	searchBox.setAlignment(Pos.CENTER_RIGHT);
	searchBox.setStyle("-fx-background-color:rgba(0, 0, 0, 0.3)");

	tabPane.setStyle("-fx-background-color:rgba(230, 230, 230, 0.8)");

	functionBox.setBackground(Background.EMPTY);
	functionBox.setPadding(new Insets(0, 5, 5, 0));

	VBox separator = new VBox();
	separator.setPrefHeight(1);
	separator.setMinHeight(1);
	separator.setBackground(Background.EMPTY);
	// separator.setStyle("-fx-background-color:rgba(230, 230, 230, 1)");

	BorderPane bottomBorderPane = new BorderPane();
	bottomBorderPane.setCenter(functionBox);
	bottomBorderPane.setRight(rightFunctionBox);

	bottomBox.setPadding(new Insets(5, 2, 1, 2));
	bottomBox.setStyle("-fx-background-color:rgba(230, 230, 230, 0.7)");

	bottomBox.getChildren().add(separator);
	bottomBox.getChildren().add(bottomBorderPane);

	borderPane.setTop(topVBox);
	borderPane.setCenter(centerBorderPane);
	borderPane.setBottom(bottomBox);

	this.setCenter(borderPane);
	tabPane.setVisible(true);
	findListPane.setVisible(false);

	functionBox.setOnMouseEntered(m -> {
		functionBox.setCursor(Cursor.DEFAULT);
	});
}
 

private BorderPane buildStatusBar() {
    BorderPane statusBar = new BorderPane();
    statusBar.setLeft(statusLabel);
    statusBar.setRight(bytesBar);
    return statusBar;
}
 

/**
     * Creates organises the TimelinePanel's layers.
     */
    private void doLayout() {
        // Layer that contains the timelinechart component:
        final BorderPane timelinePane = new BorderPane();

        timelinePane.setCenter(timeline);
        // The layer that contains the time extent labels:
        final BorderPane labelsPane = new BorderPane();
        BorderPane.setAlignment(lowerTime, Pos.CENTER);
        BorderPane.setAlignment(upperTime, Pos.CENTER);
        BorderPane.setMargin(lowerTime, new Insets(-32.0, -40.0, 0.0, -60.0));
        BorderPane.setMargin(upperTime, new Insets(-32.0, -60.0, 0.0, -40.0));
        labelsPane.setLeft(lowerTime);
        labelsPane.setRight(upperTime);
        labelsPane.setMouseTransparent(true);

        // Layer that combines the newly constructed time-extents with the timeline layer:
        final StackPane stackPane = new StackPane();
        StackPane.setAlignment(labelsPane, Pos.CENTER);
//        extentLabelPane.maxHeightProperty().bind(stackPane.heightProperty());
        StackPane.setAlignment(timelinePane, Pos.CENTER);
//        timelinePane.prefHeightProperty().bind(stackPane.heightProperty());
        stackPane.setPadding(Insets.EMPTY);
        stackPane.getChildren().addAll(timelinePane, labelsPane);

        // Layout the menu bar and the timeline object:
        final VBox vbox = new VBox();
//        stackPane.prefHeightProperty().bind(vbox.heightProperty());
        VBox.setVgrow(toolbar, Priority.NEVER);
        VBox.setVgrow(stackPane, Priority.ALWAYS);
        vbox.getChildren().addAll(toolbar, stackPane);
        vbox.setAlignment(Pos.TOP_CENTER);
        vbox.setFillWidth(true);

        // Organise the inner pane:
        AnchorPane.setTopAnchor(vbox, 0d);
        AnchorPane.setBottomAnchor(vbox, 0d);
        AnchorPane.setLeftAnchor(vbox, 0d);
        AnchorPane.setRightAnchor(vbox, 0d);
        innerPane.getChildren().add(vbox);
        innerPane.prefHeightProperty().bind(super.heightProperty());
        innerPane.prefWidthProperty().bind(super.widthProperty());

        // Attach the inner pane to the root:
        this.getChildren().add(innerPane);
    }
 

public MainframeStage (TelnetState telnetState, int mainframePort)     // usually 5555
{
  this.telnetState = telnetState;

  mainframeServer = new MainframeServer (mainframePort);
  mainframeServer.setStage (this);

  GuiFactory gui = new GuiFactory ();
  final VBox vbox1 = gui.getVBox ();

  for (int i = 0; i < 10; i++)
    buttons.add (gui.getButton ("Empty", vbox1, BUTTON_WIDTH));

  Separator separator = new Separator ();
  separator.setOrientation (Orientation.HORIZONTAL);

  final VBox vbox2 = gui.getVBox ();
  btnReadBuffer = gui.getButton ("Read Buffer", vbox2, BUTTON_WIDTH);
  btnReadModified = gui.getButton ("Read Modified", vbox2, BUTTON_WIDTH);
  btnReadModifiedAll = gui.getButton ("Read Mod All", vbox2, BUTTON_WIDTH);
  btnEraseAllUnprotected = gui.getButton ("Erase All Unpr", vbox2, BUTTON_WIDTH);
  btnProgramTab1 = gui.getButton ("PT 1", vbox2, BUTTON_WIDTH);
  btnProgramTab2 = gui.getButton ("PT 2", vbox2, BUTTON_WIDTH);
  btnProgramTab3 = gui.getButton ("PT 3", vbox2, BUTTON_WIDTH);

  final ToggleGroup modeGroup = new ToggleGroup ();

  btnFieldMode = gui.getRadioButton ("Field Mode", vbox2, modeGroup);
  btnExtendedFieldMode = gui.getRadioButton ("Extended Field Mode", vbox2, modeGroup);
  btnCharacterMode = gui.getRadioButton ("Character Mode", vbox2, modeGroup);
  btnFieldMode.setSelected (true);                    // match the default setting

  modeGroup.selectedToggleProperty ().addListener (new OnToggleHandler ());

  BorderPane borderPane = new BorderPane ();
  borderPane.setLeft (vbox1);
  borderPane.setRight (vbox2);

  Scene scene = new Scene (borderPane);
  setTitle ("Mainframe: " + mainframePort);
  setScene (scene);

  setX (1000);
  setY (100);

  prepareButtons ();

  setOnCloseRequest (e -> Platform.exit ());
}
 

@Override
public void start(Stage primaryStage) throws Exception {
	Group root = new Group();
	Scene scene = new Scene(root);
	
	BorderPane borderPane = new BorderPane();
	root.getChildren().add(borderPane);
	
	Node toolbar = createToolbar();
	borderPane.setTop(toolbar);

	Node editor = createEditor();
	borderPane.setRight(editor);

	graphCanvas = createGraphCanvas();
	borderPane.setCenter(graphCanvas);
	
	graphCanvas.requestFocus();

	primaryStage.setScene(scene);
	primaryStage.show();
			
	function1Property.addListener((observable, oldValue, newValue) -> {
		updateFunctions();
	});
	function2Property.addListener((observable, oldValue, newValue) -> {
		updateFunctions();
	});
	function3Property.addListener((observable, oldValue, newValue) -> {
		updateFunctions();
	});
	
	ChangeListener<? super Number> graphDrawingListener = (observable, oldValue, newValue) -> drawGraph(graphCanvas);
	xStartProperty.addListener(graphDrawingListener);
	xEndProperty.addListener(graphDrawingListener);
	yStartProperty.addListener(graphDrawingListener);
	yEndProperty.addListener(graphDrawingListener);
	precisionProperty.addListener(graphDrawingListener);
	
	updateFunctions();
}
 

private void initComponent() {

		headImageView.setClip(headImageClip);

		StackPane headStackPane = new StackPane();
		headStackPane.setPadding(new Insets(12, 8, 12, 18));
		headStackPane.getChildren().add(headImageView);

		redLabel.setStyle("-fx-text-fill:rgba(255, 255, 255, 1);");

		StackPane redStackPane = new StackPane();
		redStackPane.getChildren().add(redImageView);
		redStackPane.getChildren().add(redLabel);

		HBox redHBox = new HBox();
		redHBox.setAlignment(Pos.TOP_RIGHT);
		redHBox.getChildren().add(redStackPane);

		VBox redVBox = new VBox();
		redVBox.setAlignment(Pos.TOP_RIGHT);
		redVBox.getChildren().add(redHBox);

		StackPane leftStackPane = new StackPane();

		leftStackPane.getChildren().add(headStackPane);
		leftStackPane.getChildren().add(redVBox);

		nameLabel.setStyle("-fx-text-fill:rgba(255, 255, 255, 1);-fx-font-size: 14px;");

		HBox nameHBox = new HBox();
		nameHBox.getChildren().add(nameLabel);

		timeLabel.setStyle("-fx-text-fill:#666a77;");

		BorderPane nameBorderPane = new BorderPane();

		nameBorderPane.setCenter(nameHBox);
		nameBorderPane.setRight(timeLabel);

		textLabel.setStyle("-fx-text-fill:rgba(152, 152, 152, 1);");

		HBox textHBox = new HBox();
		textHBox.setAlignment(Pos.CENTER_LEFT);
		textHBox.getChildren().add(textLabel);

		VBox centerVBox = new VBox();
		centerVBox.setSpacing(5);
		centerVBox.setPadding(new Insets(10, 0, 0, 0));
		centerVBox.getChildren().add(nameBorderPane);
		centerVBox.getChildren().add(textHBox);

		HBox lineHBox = new HBox();
		lineHBox.setPrefHeight(0.5);
		lineHBox.setStyle("-fx-background-color:#292c33;");

		borderPane.setLeft(leftStackPane);
		borderPane.setCenter(centerVBox);
		borderPane.setBottom(lineHBox);
		// borderPane.getStyleClass().add("selected-button");
		// this.getStyleClass().add("chat-item-pane");
		this.getChildren().add(borderPane);
	}
 

public ProductIonFilterVisualizerWindow(RawDataFile dataFile, ParameterSet parameters) {
  borderPane = new BorderPane();
  scene = new Scene(borderPane);
  setScene(scene);

  this.dataFile = dataFile;

  // Retrieve parameter's values
  Range<Double> rtRange =
      parameters.getParameter(ProductIonFilterParameters.retentionTimeRange).getValue();
  Range<Double> mzRange = parameters.getParameter(ProductIonFilterParameters.mzRange).getValue();
  Object xAxisType = parameters.getParameter(ProductIonFilterParameters.xAxisType).getValue();

  mzDifference = parameters.getParameter(ProductIonFilterParameters.mzDifference).getValue();

  targetedMZ_List =
      parameters.getParameter(ProductIonFilterParameters.targetedMZ_List).getValue();
  targetedNF_List =
      parameters.getParameter(ProductIonFilterParameters.targetedNF_List).getValue();

  fileName = parameters.getParameter(ProductIonFilterParameters.fileName).getValue();

  basePeakPercent =
      parameters.getParameter(ProductIonFilterParameters.basePeakPercent).getValue();

  // Set window components
  dataset = new ProductIonFilterDataSet(dataFile, xAxisType, rtRange, mzRange, this, mzDifference,
      targetedMZ_List, targetedNF_List, basePeakPercent, fileName);

  productIonFilterPlot = new ProductIonFilterPlot(this);
  productIonFilterPlot.setAxisTypes(xAxisType);
  productIonFilterPlot.addProductionFilterDataSet(dataset);
  productIonFilterPlot.setMenuItems();
  borderPane.setCenter(productIonFilterPlot);

  toolBar = new ToolBar();
  toolBar.setOrientation(Orientation.VERTICAL);
  Button highlightPrecursorBtn = new Button(null, new ImageView(PRECURSOR_MASS_ICON));
  highlightPrecursorBtn.setTooltip(new Tooltip("Highlight selected precursor mass range"));
  highlightPrecursorBtn.setOnAction(e -> {
    ProductIonFilterSetHighlightDialog dialog =
        new ProductIonFilterSetHighlightDialog(this, productIonFilterPlot, "HIGHLIGHT_PRECURSOR");
    dialog.show();
  });
  toolBar.getItems().add(highlightPrecursorBtn);
  borderPane.setRight(toolBar);

  MZmineCore.getTaskController().addTask(dataset, TaskPriority.HIGH);

  updateTitle();

  // Add the Windows menu
  WindowsMenu.addWindowsMenu(getScene());

  // get the window settings parameter
  ParameterSet paramSet =
      MZmineCore.getConfiguration().getModuleParameters(ProductIonFilterVisualizerModule.class);
  WindowSettingsParameter settings =
      paramSet.getParameter(ProductIonFilterParameters.windowSettings);

  // update the window and listen for changes
  settings.applySettingsToWindow(this);

}
 

public HighlightOptions( SimpleObjectProperty<LogLineColors> standardLogColors,
                         ObservableList<HighlightExpression> observableExpressions,
                         BooleanProperty isFilterEnabled ) {
    this.standardLogColors = standardLogColors;
    this.observableExpressions = observableExpressions;
    this.isFilterEnabled = isFilterEnabled;
    this.expressionsBox = new VBox( 2 );

    expressionsBox.getChildren().addAll( observableExpressions.stream()
            .map( ex -> new HighlightExpressionRow( ex, observableExpressions, expressionsBox ) )
            .toArray( HighlightExpressionRow[]::new ) );

    setSpacing( 5 );
    setPadding( new Insets( 5 ) );
    Label headerLabel = new Label( "Enter highlight expressions:" );
    headerLabel.setFont( Font.font( "Lucida", FontWeight.BOLD, 14 ) );

    CheckBox enableFilter = new CheckBox( "Filter?" );
    enableFilter.selectedProperty().bindBidirectional( isFilterEnabled );
    enableFilter.setTooltip( new Tooltip( "Filter log lines that match selected rules" ) );

    Node helpIcon = createHelpIcon();

    HBox headerRow = new HBox( 10 );
    headerRow.getChildren().addAll( headerLabel, helpIcon );

    BorderPane headerPane = new BorderPane();
    headerPane.setLeft( headerRow );
    headerPane.setRight( enableFilter );

    BorderPane buttonsPane = new BorderPane();

    Button newRow = new Button( "Add rule" );
    newRow.setOnAction( this::addRow );

    Button selectAllFilters = new Button( "All" );
    selectAllFilters.setOnAction( ( event ) -> enableFilters( true ) );
    Button disableAllFilters = new Button( "None" );
    disableAllFilters.setOnAction( ( event ) -> enableFilters( false ) );

    HBox filterButtons = new HBox( 5, new Label( "Select Filters:" ),
            selectAllFilters, disableAllFilters );

    buttonsPane.setLeft( newRow );
    buttonsPane.setRight( filterButtons );

    getChildren().addAll(
            headerPane,
            expressionsBox,
            new StandardLogColorsRow( standardLogColors ),
            buttonsPane );
}
 

public ColorPicker(javafx.stage.Window stage, Color color) {
	super(stage);
	cancel.setOnAction(e -> {
		result = null;
		close();
	});
	ok.setOnAction(e -> close());

	red.setValue(color.getRed() * 255);
	green.setValue(color.getGreen() * 255);
	blue.setValue(color.getBlue() * 255);
	opacity.setValue(color.getOpacity() * 255);

	red.valueProperty().addListener((l, o, n) -> onValueChange());
	green.valueProperty().addListener((l, o, n) -> onValueChange());
	blue.valueProperty().addListener((l, o, n) -> onValueChange());
	opacity.valueProperty().addListener((l, o, n) -> onValueChange());

	preview.getStyleClass().add("color-picker-preview");

	GridPane grid = new GridPane();
	grid.getStyleClass().add("color-picker-sliders");
	grid.add(label("R", "color-picker-slider-label"), 0, 0, 1, 1);
	grid.add(label("G", "color-picker-slider-label"), 0, 1, 1, 1);
	grid.add(label("B", "color-picker-slider-label"), 0, 2, 1, 1);
	grid.add(label("A", "color-picker-slider-label"), 0, 3, 1, 1);
	grid.add(red, 1, 0, 1, 1);
	grid.add(green, 1, 1, 1, 1);
	grid.add(blue, 1, 2, 1, 1);
	grid.add(opacity, 1, 3, 1, 1);
	grid.add(UIFactory.attachTextFieldToSlider(red), 2, 0, 1, 1);
	grid.add(UIFactory.attachTextFieldToSlider(green), 2, 1, 1, 1);
	grid.add(UIFactory.attachTextFieldToSlider(blue), 2, 2, 1, 1);
	grid.add(UIFactory.attachTextFieldToSlider(opacity), 2, 3, 1, 1);

	HBox buttonBox = new HBox();
	buttonBox.getChildren().addAll(ok, cancel);
	buttonBox.getStyleClass().add("color-picker-button-box");

	BorderPane borderPane = new BorderPane();
	borderPane.getStyleClass().add("color-picker");
	borderPane.setTop(grid);
	borderPane.setCenter(preview);
	borderPane.setBottom(buttonBox);
	borderPane.setLeft(borderElement("border-element-vertical"));
	borderPane.setRight(borderElement("border-element-vertical"));

	setContent(borderPane);
}
 

public TransfersTab (Screen screen, TSOCommand tsoCommand)
{
  super ("Transfers", screen, tsoCommand);

  btnTracks.setSelected (true);
  btnFiles.setSelected (true);
  btnFB.setSelected (true);

  grpFileName.getToggles ().addAll (btnDatasets, btnFiles, btnJobs, btnSpecify);
  grpSpaceUnits.getToggles ().addAll (btnTracks, btnCylinders, btnBlocks);

  grpFileName.selectedToggleProperty ()
      .addListener ( (ov, oldToggle, newToggle) -> toggleSelected (newToggle));

  grpSpaceUnits.selectedToggleProperty ()
      .addListener ( (ov, oldToggle, newToggle) -> toggleSelected (newToggle));

  VBox datasetBlock = new VBox (10);
  datasetBlock.setPadding (new Insets (10, 10, 10, 10));

  HBox line1 = getLine (btnDatasets, txtDatasets);
  HBox line2 = getLine (btnJobs, txtJobs);
  HBox line3 = getLine (btnFiles, txtFiles);
  HBox line4 = getLine (btnSpecify, txtSpecify);

  txtDatasets.setPromptText ("no dataset selected");
  txtJobs.setPromptText ("no batch job selected");
  txtFiles.setPromptText ("no file selected");

  txtSpecify.setEditable (true);
  txtBlksize.setText ("0");
  txtLrecl.setText ("80");

  datasetBlock.getChildren ().addAll (line1, line2, line3, line4);

  VBox spaceBlock = new VBox (10);
  spaceBlock.setPadding (new Insets (10, 10, 10, 10));

  HBox line5 = getLine (lblLrecl, txtLrecl);
  HBox line6 = getLine (lblBlksize, txtBlksize);
  HBox line7 = getLine (btnTracks, btnCylinders, btnBlocks);
  HBox line8 = getLine (lblSpace, txtSpace, line7);
  HBox line9 = getLine (btnFB, btnPS);
  HBox line10 = getLine (lblDisposition, line9);

  spaceBlock.getChildren ().addAll (line10, line5, line6, line8);

  datasetBlock.setStyle ("-fx-border-color: grey; -fx-border-width: 1;"
      + " -fx-border-insets: 10");
  spaceBlock.setStyle ("-fx-border-color: grey; -fx-border-width: 1;"
      + " -fx-border-insets: 10");

  txtDescription.setText ("Not finished yet");

  VBox columnLeft = new VBox ();
  columnLeft.setPadding (new Insets (10, 10, 10, 10));
  columnLeft.getChildren ().addAll (datasetBlock, spaceBlock);

  VBox columnRight = new VBox ();
  columnRight.setPadding (new Insets (10, 10, 10, 10));
  columnRight.getChildren ().addAll (txtDescription);

  BorderPane borderPane = new BorderPane ();
  borderPane.setLeft (columnLeft);
  borderPane.setRight (columnRight);

  setContent (borderPane);
}