Java Code Examples for org.jfree.chart.axis.NumberAxis#setTickLabelInsets()

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend, boolean tooltips, boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend, boolean tooltips, boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as 
 * angles in degrees).  The chart object returned by this method uses a 
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for 
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title,
                                          XYDataset dataset,
                                          boolean legend,
                                          boolean tooltips,
                                          boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend, boolean tooltips, boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend, boolean tooltips, boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as 
 * angles in degrees).  The chart object returned by this method uses a 
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for 
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title,
                                          XYDataset dataset,
                                          boolean legend,
                                          boolean tooltips,
                                          boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend, boolean tooltips, boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates a polar plot for the specified dataset (x-values interpreted as
 * angles in degrees).  The chart object returned by this method uses a
 * {@link PolarPlot} instance as the plot, with a {@link NumberAxis} for
 * the radial axis.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param dataset  the dataset (<code>null</code> permitted).
 * @param legend  legend required?
 * @param tooltips  tooltips required?
 * @param urls  URLs required?
 *
 * @return A chart.
 */
public static JFreeChart createPolarChart(String title, XYDataset dataset,
        boolean legend, boolean tooltips, boolean urls) {

    PolarPlot plot = new PolarPlot();
    plot.setDataset(dataset);
    NumberAxis rangeAxis = new NumberAxis();
    rangeAxis.setAxisLineVisible(false);
    rangeAxis.setTickMarksVisible(false);
    rangeAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setAxis(rangeAxis);
    plot.setRenderer(new DefaultPolarItemRenderer());
    JFreeChart chart = new JFreeChart(
            title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

public static EChartPanel createMirrorChartPanel(String labelA, double precursorMZA, double rtA,
    DataPoint[] dpsA, String labelB, double precursorMZB, double rtB, DataPoint[] dpsB,
    boolean showTitle, boolean showLegend) {
  PseudoSpectrumDataSet data =
      dpsA == null ? null : createMSMSDataSet(precursorMZA, rtA, dpsA, labelA);
  PseudoSpectrumDataSet dataMirror =
      dpsB == null ? null : createMSMSDataSet(precursorMZB, rtB, dpsB, labelB);

  NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat intensityFormat = new DecimalFormat("0.#");

  // set the X axis (retention time) properties
  NumberAxis xAxis = new NumberAxis("m/z");
  xAxis.setNumberFormatOverride(mzForm);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setMinorTickCount(5);

  PseudoSpectraRenderer renderer1 = new PseudoSpectraRenderer(Color.BLACK, false);
  PseudoSpectraRenderer renderer2 = new PseudoSpectraRenderer(Color.BLACK, false);

  // create subplot 1...
  final NumberAxis rangeAxis1 = new NumberAxis("rel. intensity [%]");
  final XYPlot subplot1 = new XYPlot(data, null, rangeAxis1, renderer1);
  subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
  rangeAxis1.setNumberFormatOverride(intensityFormat);
  rangeAxis1.setAutoRangeIncludesZero(true);
  rangeAxis1.setAutoRangeStickyZero(true);

  // create subplot 2...
  final NumberAxis rangeAxis2 = new NumberAxis("rel. intensity [%]");
  rangeAxis2.setNumberFormatOverride(intensityFormat);
  rangeAxis2.setAutoRangeIncludesZero(true);
  rangeAxis2.setAutoRangeStickyZero(true);
  rangeAxis2.setInverted(true);
  final XYPlot subplot2 = new XYPlot(dataMirror, null, rangeAxis2, renderer2);
  subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);

  // parent plot...
  final CombinedDomainXYPlot plot = new CombinedDomainXYPlot(new NumberAxis("Domain"));
  plot.setGap(0);

  // add the subplots...
  plot.add(subplot1, 1);
  plot.add(subplot2, 1);
  plot.setOrientation(PlotOrientation.VERTICAL);


  // set the plot properties
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  // return a new chart containing the overlaid plot...
  JFreeChart chart = new JFreeChart("", JFreeChart.DEFAULT_TITLE_FONT, plot, true);
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);

  // chart.getXYPlot().setRangeZeroBaselineVisible(true);
  chart.getTitle().setVisible(showTitle);
  chart.getLegend().setVisible(showLegend);

  return new EChartPanel(chart);
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, RawDataFile raw, boolean sum,
    String title) {
  //
  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzFormat);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  return chart;
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, boolean showTitle,
    boolean showLegend, double rt, double precursorMZ) {
  //
  if (dataset == null)
    return null;
  //
  NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat rtForm = MZmineCore.getConfiguration().getRTFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  String title = "";
  if (precursorMZ == 0)
    title = "RT=" + mzForm.format(precursorMZ);
  else
    title = MessageFormat.format("MSMS for m/z={0} RT={1}", mzForm.format(precursorMZ),
        rtForm.format(rt));

  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzForm);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  chart.getTitle().setVisible(showTitle);
  chart.getLegend().setVisible(showLegend);
  //
  if (precursorMZ != 0)
    addPrecursorMarker(chart, precursorMZ);
  return chart;
}
 

@FXML
public void initialize() {

  final JFreeChart chart = chartNode.getChart();
  final XYPlot plot = chart.getXYPlot();

  // Do not set colors and strokes dynamically. They are instead provided
  // by the dataset and configured in configureRenderer()
  plot.setDrawingSupplier(null);
  plot.setDomainGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
  plot.setRangeGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
  plot.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));
  plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
  plot.setDomainCrosshairPaint(JavaFXUtil.convertColorToAWT(crossHairColor));
  plot.setRangeCrosshairPaint(JavaFXUtil.convertColorToAWT(crossHairColor));
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);

  // chart properties
  chart.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));

  // legend properties
  LegendTitle legend = chart.getLegend();
  // legend.setItemFont(legendFont);
  legend.setFrame(BlockBorder.NONE);

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setLabel("Retention time (min)");
  xAxis.setUpperMargin(0.03);
  xAxis.setLowerMargin(0.03);
  xAxis.setRangeType(RangeType.POSITIVE);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setLabel("Intensity");
  yAxis.setRangeType(RangeType.POSITIVE);
  yAxis.setAutoRangeIncludesZero(true);

  // set the fixed number formats, because otherwise JFreeChart sometimes
  // shows exponent, sometimes it doesn't
  DecimalFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
  xAxis.setNumberFormatOverride(mzFormat);
  DecimalFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
  yAxis.setNumberFormatOverride(intensityFormat);

  chartTitle = chartNode.getChart().getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  chartTitle.setText("Chromatogram");

  chartNode.setCursor(Cursor.CROSSHAIR);

  // Remove the dataset if it is removed from the list
  datasets.addListener((Change<? extends ChromatogramPlotDataSet> c) -> {
    while (c.next()) {
      if (c.wasRemoved()) {
        for (ChromatogramPlotDataSet ds : c.getRemoved()) {
          int index = plot.indexOf(ds);
          plot.setDataset(index, null);
        }
      }
    }
  });

  itemLabelsVisible.addListener((prop, oldVal, newVal) -> {
    for (ChromatogramPlotDataSet dataset : datasets) {
      int datasetIndex = plot.indexOf(dataset);
      XYItemRenderer renderer = plot.getRenderer(datasetIndex);
      renderer.setBaseItemLabelsVisible(newVal);
    }
  });

  legendVisible.addListener((prop, oldVal, newVal) -> {
    legend.setVisible(newVal);
  });
}
 

public void initialize() {

    final JFreeChart chart = chartNode.getChart();
    final XYPlot plot = chart.getXYPlot();

    // Do not set colors and strokes dynamically. They are instead provided
    // by the dataset and configured in configureRenderer()
    plot.setDrawingSupplier(null);
    plot.setDomainGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
    plot.setRangeGridlinePaint(JavaFXUtil.convertColorToAWT(gridColor));
    plot.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));
    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
    plot.setDomainCrosshairVisible(false);
    plot.setRangeCrosshairVisible(false);

    // chart properties
    chart.setBackgroundPaint(JavaFXUtil.convertColorToAWT(backgroundColor));

    // legend properties
    LegendTitle legend = chart.getLegend();
    // legend.setItemFont(legendFont);
    legend.setFrame(BlockBorder.NONE);

    // set the X axis (m/z) properties
    NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
    xAxis.setLabel("m/z");
    xAxis.setUpperMargin(0.03);
    xAxis.setLowerMargin(0.03);
    xAxis.setRangeType(RangeType.POSITIVE);
    xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));

    // set the Y axis (intensity) properties
    NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
    yAxis.setLabel("Intensity");
    yAxis.setRangeType(RangeType.POSITIVE);
    yAxis.setAutoRangeIncludesZero(true);

    // set the fixed number formats, because otherwise JFreeChart sometimes
    // shows exponent, sometimes it doesn't
    DecimalFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    xAxis.setNumberFormatOverride(mzFormat);
    DecimalFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();
    yAxis.setNumberFormatOverride(intensityFormat);

    chartTitle = chartNode.getChart().getTitle();
    chartTitle.setMargin(5, 0, 0, 0);
    chartTitle.setFont(titleFont);

    chartNode.setCursor(Cursor.CROSSHAIR);

    // Remove the dataset if it is removed from the list
    datasets.addListener((Change<? extends MsSpectrumDataSet> c) -> {
      while (c.next()) {
        if (c.wasRemoved()) {
          for (MsSpectrumDataSet ds : c.getRemoved()) {
            int index = plot.indexOf(ds);
            plot.setDataset(index, null);
          }
        }
      }
    });

    itemLabelsVisible.addListener((prop, oldVal, newVal) -> {
      for (MsSpectrumDataSet dataset : datasets) {
        int datasetIndex = plot.indexOf(dataset);
        XYItemRenderer renderer = plot.getRenderer(datasetIndex);
        renderer.setBaseItemLabelsVisible(newVal);
      }
    });

    legendVisible.addListener((prop, oldVal, newVal) -> {
      legend.setVisible(newVal);
    });

  }
 

private static JFreeChart createMirrorChart(String labelA, double precursorMZA, double rtA,
    DataPoint[] dpsA, String labelB, double precursorMZB, double rtB, DataPoint[] dpsB,
    boolean showTitle, boolean showLegend) {
  PseudoSpectrumDataSet data =
      dpsA == null ? null : createMSMSDataSet(precursorMZA, rtA, dpsA, labelA);
  PseudoSpectrumDataSet dataMirror =
      dpsB == null ? null : createMSMSDataSet(precursorMZB, rtB, dpsB, labelB);

  NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat intensityFormat = new DecimalFormat("0.#");

  // set the X axis (retention time) properties
  NumberAxis xAxis = new NumberAxis("m/z");
  xAxis.setNumberFormatOverride(mzForm);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setMinorTickCount(5);

  PseudoSpectraRenderer renderer1 = new PseudoSpectraRenderer(Color.BLACK, false);
  PseudoSpectraRenderer renderer2 = new PseudoSpectraRenderer(Color.BLACK, false);

  // create subplot 1...
  final NumberAxis rangeAxis1 = new NumberAxis("rel. intensity [%]");
  final XYPlot subplot1 = new XYPlot(data, null, rangeAxis1, renderer1);
  subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
  rangeAxis1.setNumberFormatOverride(intensityFormat);
  rangeAxis1.setAutoRangeIncludesZero(true);
  rangeAxis1.setAutoRangeStickyZero(true);

  // create subplot 2...
  final NumberAxis rangeAxis2 = new NumberAxis("rel. intensity [%]");
  rangeAxis2.setNumberFormatOverride(intensityFormat);
  rangeAxis2.setAutoRangeIncludesZero(true);
  rangeAxis2.setAutoRangeStickyZero(true);
  rangeAxis2.setInverted(true);
  final XYPlot subplot2 = new XYPlot(dataMirror, null, rangeAxis2, renderer2);
  subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);

  // parent plot...
  final CombinedDomainXYPlot plot = new CombinedDomainXYPlot(xAxis);
  plot.setGap(0);

  // add the subplots...
  plot.add(subplot1, 1);
  plot.add(subplot2, 1);
  plot.setOrientation(PlotOrientation.VERTICAL);

  // set the plot properties
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  // return a new chart containing the overlaid plot...
  JFreeChart chart = new JFreeChart("", JFreeChart.DEFAULT_TITLE_FONT, plot, true);
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);

  chart.getXYPlot().setRangeZeroBaselineVisible(true);
  chart.getTitle().setVisible(showTitle);
  chart.getLegend().setVisible(showLegend);

  return chart;
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, RawDataFile raw, boolean sum,
    String title) {
  //
  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzFormat);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  return chart;
}
 

public static JFreeChart createChart(PseudoSpectrumDataSet dataset, boolean showTitle,
    boolean showLegend, double rt, double precursorMZ) {
  //
  if (dataset == null)
    return null;
  //
  NumberFormat mzForm = MZmineCore.getConfiguration().getMZFormat();
  NumberFormat rtForm = MZmineCore.getConfiguration().getRTFormat();
  NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

  String title = "";
  if (precursorMZ == 0)
    title = "RT=" + mzForm.format(precursorMZ);
  else
    title = MessageFormat.format("MSMS for m/z={0} RT={1}", mzForm.format(precursorMZ),
        rtForm.format(rt));

  JFreeChart chart = ChartFactory.createXYLineChart(title, // title
      "m/z", // x-axis label
      "Intensity", // y-axis label
      dataset, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // isotopeFlag, // create legend?
      true, // generate tooltips?
      false // generate URLs?
  );
  chart.setBackgroundPaint(Color.white);
  chart.getTitle().setVisible(false);
  // set the plot properties
  XYPlot plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(RectangleInsets.ZERO_INSETS);

  // set rendering order
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(false);
  plot.setRangeCrosshairVisible(false);

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(mzForm);
  xAxis.setUpperMargin(0.08);
  xAxis.setLowerMargin(0.00);
  xAxis.setTickLabelInsets(new RectangleInsets(0, 0, 20, 20));
  xAxis.setAutoRangeIncludesZero(true);
  xAxis.setMinorTickCount(5);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(intensityFormat);
  yAxis.setUpperMargin(0.20);

  PseudoSpectraRenderer renderer = new PseudoSpectraRenderer(Color.BLACK, false);
  plot.setRenderer(0, renderer);
  plot.setRenderer(1, renderer);
  plot.setRenderer(2, renderer);
  renderer.setSeriesVisibleInLegend(1, false);
  renderer.setSeriesPaint(2, Color.ORANGE);
  //
  chart.getTitle().setVisible(showTitle);
  chart.getLegend().setVisible(showLegend);
  //
  if (precursorMZ != 0)
    addPrecursorMarker(chart, precursorMZ);
  return chart;
}