Java Code Examples for javafx.scene.control.ToolBar#setOrientation()

The following examples show how to use javafx.scene.control.ToolBar#setOrientation() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.

Example 1

Source File: ProductIonFilterVisualizerWindow.java From mzmine3 with GNU General Public License v2.0

4 votes

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);

}

Example 2

Source File: NeutralLossVisualizerWindow.java From mzmine3 with GNU General Public License v2.0

4 votes

/**
 * Constructor.
 *
 * @param dataFile   file containing the data of one sample
 * @param parameters plot parameters set by the user
 */
public NeutralLossVisualizerWindow(RawDataFile dataFile, ParameterSet parameters) {

  this.dataFile = dataFile;

  // Retrieve parameter's values
  Range<Double> rtRange =
      parameters.getParameter(NeutralLossParameters.retentionTimeRange).getValue();
  Range<Double> mzRange = parameters.getParameter(NeutralLossParameters.mzRange).getValue();
  int numOfFragments = parameters.getParameter(NeutralLossParameters.numOfFragments).getValue();

  Object xAxisType = parameters.getParameter(NeutralLossParameters.xAxisType).getValue();

  // Set window components
  dataset = new NeutralLossDataSet(dataFile, xAxisType, rtRange, mzRange, numOfFragments, this);

  borderPane = new BorderPane();
  scene = new Scene(borderPane);

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

  setMinWidth(400.0);
  setMinHeight(300.0);

  neutralLossPlot = new NeutralLossPlot();
  neutralLossPlot.setAxisTypes(xAxisType);
  neutralLossPlot.addNeutralLossDataSet(dataset);
  neutralLossPlot.setVisualizer(this);
  neutralLossPlot.setMenuItems();
  borderPane.setCenter(neutralLossPlot);

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

  Button highlightPrecursorBtn = new Button(null, new ImageView(PRECURSOR_MASS_ICON));
  highlightPrecursorBtn.setTooltip(new Tooltip("Highlight precursor m/z range..."));
  highlightPrecursorBtn.setOnAction(e -> {
    NeutralLossSetHighlightDialog dialog =
        new NeutralLossSetHighlightDialog(this, neutralLossPlot, "HIGHLIGHT_PRECURSOR");
    dialog.show();
  });

  toolBar.getItems().add(highlightPrecursorBtn);
  borderPane.setRight(toolBar);

  WindowsMenu.addWindowsMenu(scene);

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

  updateTitle();

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

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

}

Example 3

Source File: ScatterPlotWindow.java From mzmine3 with GNU General Public License v2.0

4 votes

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);

  }

Example 4

Source File: RTMZAnalyzerWindow.java From mzmine3 with GNU General Public License v2.0

4 votes

public RTMZAnalyzerWindow(AbstractXYZDataset dataset, PeakList peakList,
    InterpolatingLookupPaintScale paintScale) {

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

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

  setMinWidth(600.0);
  setMinHeight(500.0);

  toolbar = new ToolBar();
  toolbar.setOrientation(Orientation.VERTICAL);
  Button axesButton = new Button(null, new ImageView(axesIcon));
  axesButton.setTooltip(new Tooltip("Setup ranges for axes"));
  Button colorButton = new Button(null, new ImageView(colorbarIcon));
  colorButton.setTooltip(new Tooltip("Setup color palette"));
  toolbar.getItems().addAll(axesButton, colorButton);
  mainPane.setRight(toolbar);

  plot = new RTMZPlot(this, dataset, paintScale);
  mainPane.setCenter(plot);

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

  colorButton.setOnAction(e -> {
      Platform.runLater(new Runnable() {
        @Override
        public void run() {
          InterpolatingLookupPaintScaleSetupDialogFX colorDialog =
                  new InterpolatingLookupPaintScaleSetupDialogFX(plot.getPaintScale());
          colorDialog.showAndWait();

          if (colorDialog.getExitCode() == ExitCode.OK)
            plot.setPaintScale(colorDialog.getPaintScale());
        }
      });

    });

  String title = peakList.getName();
  title = title.concat(" : ");
  title = title.concat(dataset.toString());
  this.setTitle(title);

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

}

Example 5

Source File: ProjectionPlotWindow.java From mzmine3 with GNU General Public License v2.0

4 votes

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);

}