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

private void createUI() {
    plot = new XYImagePlot();
    plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5));
    NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis();
    NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
    domainAxis.setAutoRangeIncludesZero(false);
    rangeAxis.setAutoRangeIncludesZero(false);
    domainAxis.setUpperMargin(0);
    domainAxis.setLowerMargin(0);
    rangeAxis.setUpperMargin(0);
    rangeAxis.setLowerMargin(0);
    plot.setNoDataMessage(NO_DATA_MESSAGE);
    plot.getRenderer().setBaseToolTipGenerator(new XYPlotToolTipGenerator());
    JFreeChart chart = new JFreeChart(CHART_TITLE, plot);
    ChartFactory.getChartTheme().apply(chart);

    chart.removeLegend();
    createUI(createChartPanel(chart), createOptionsPanel(), bindingContext);
    updateUIState();
}
 

protected void configureChart(final JFreeChart chart) {
	chart.setBackgroundPaint(Color.white);
	final XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.lightGray);
	plot.setDomainGridlinePaint(Color.white);
	plot.setRangeGridlinePaint(Color.white);
	plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));

	final DateAxis dateAxis = (DateAxis) plot.getDomainAxis();
	final NumberAxis valueAxis = (NumberAxis) plot.getRangeAxis();

	dateAxis.setDateFormatOverride(new SimpleDateFormat("dd-MMM"));
	valueAxis.setAutoRangeIncludesZero(true);
	valueAxis.setUpperMargin(0.15);
	valueAxis.setLowerMargin(0.15);
}
 

/**
 * Creates a stacked XY area plot.  The chart object returned by this
 * method uses an {@link XYPlot} instance as the plot, with a
 * {@link NumberAxis} for the domain axis, a {@link NumberAxis} as the
 * range axis, and a {@link StackedXYAreaRenderer2} as the renderer.
 *
 * @param title  the chart title (<code>null</code> permitted).
 * @param xAxisLabel  a label for the X-axis (<code>null</code> permitted).
 * @param yAxisLabel  a label for the Y-axis (<code>null</code> permitted).
 * @param dataset  the dataset for the chart (<code>null</code> permitted).
 * @param legend  a flag specifying whether or not a legend is required.

 *
 * @return A stacked XY area chart.
 */
public static JFreeChart createStackedXYAreaChart(String title,
        String xAxisLabel, String yAxisLabel, TableXYDataset dataset,
        boolean legend) {

    NumberAxis xAxis = new NumberAxis(xAxisLabel);
    xAxis.setAutoRangeIncludesZero(false);
    xAxis.setLowerMargin(0.0);
    xAxis.setUpperMargin(0.0);
    NumberAxis yAxis = new NumberAxis(yAxisLabel);
    StackedXYAreaRenderer2 renderer = new StackedXYAreaRenderer2();
    renderer.setBaseToolTipGenerator(new StandardXYToolTipGenerator());
    renderer.setOutline(true);
    XYPlot plot = new XYPlot(dataset, xAxis, yAxis, renderer);
    plot.setRangeAxis(yAxis);  // forces recalculation of the axis range
    JFreeChart chart = new JFreeChart(title, JFreeChart.DEFAULT_TITLE_FONT,
            plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

public void setAxisTypes(Object xAxisType) {

    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();

    // set the X axis (retention time) properties
    final NumberAxis xAxis = (NumberAxis) this.plot.getDomainAxis();
    if (xAxisType.equals(ProductIonFilterParameters.xAxisPrecursor)) {
      xAxis.setLabel("Precursor ion m/z");
      xAxis.setNumberFormatOverride(mzFormat);
    } else {
      xAxis.setLabel("Retention time");
      xAxis.setNumberFormatOverride(rtFormat);
    }
    xAxis.setUpperMargin(0);
    xAxis.setLowerMargin(0);
    xAxis.setAutoRangeIncludesZero(false);
    // set the Y axis (intensity) properties
    final NumberAxis yAxis = (NumberAxis) this.plot.getRangeAxis();
    yAxis.setLabel("Product ion m/z");
    yAxis.setAutoRangeIncludesZero(false);
    yAxis.setNumberFormatOverride(mzFormat);
    yAxis.setUpperMargin(0);
    yAxis.setLowerMargin(0);
  }
 

public void setAxisTypes(Object xAxisType) {

    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();

    // set the X axis (retention time) properties
    final NumberAxis xAxis = (NumberAxis) this.plot.getDomainAxis();
    if (xAxisType.equals(NeutralLossParameters.xAxisPrecursor)) {
      xAxis.setLabel("Precursor m/z");
      xAxis.setNumberFormatOverride(mzFormat);
    } else {
      xAxis.setLabel("Retention time");
      xAxis.setNumberFormatOverride(rtFormat);
    }
    xAxis.setUpperMargin(0);
    xAxis.setLowerMargin(0);
    xAxis.setAutoRangeIncludesZero(false);
    // set the Y axis (intensity) properties
    final NumberAxis yAxis = (NumberAxis) this.plot.getRangeAxis();
    yAxis.setLabel("Neutral loss (Da)");
    yAxis.setAutoRangeIncludesZero(false);
    yAxis.setNumberFormatOverride(mzFormat);
    yAxis.setUpperMargin(0);
    yAxis.setLowerMargin(0);
  }
 

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);
    });

  }
 

public void initializePlot( XYPlot xyplot ) {
    NumberAxis rangeAxis = (NumberAxis) xyplot.getRangeAxis();
    NumberAxis domainAxis = (NumberAxis) xyplot.getDomainAxis();

    rangeAxis.setRange(-9.99, 109.99);
    rangeAxis.setNumberFormatOverride(pctFormat);
    rangeAxis.setTickLabelPaint(Color.decode("#666666"));
    rangeAxis.setMinorTickCount(5);
    rangeAxis.setTickUnit(new NumberTickUnit(10));
    rangeAxis.setAxisLineVisible(true);
    rangeAxis.setMinorTickMarksVisible(true);
    rangeAxis.setTickMarksVisible(true);
    rangeAxis.setLowerMargin(10);
    rangeAxis.setUpperMargin(10);
    
    domainAxis.setRange(-5, 175);
    domainAxis.setNumberFormatOverride(pctFormat);
    domainAxis.setTickLabelPaint(Color.decode("#666666"));
    domainAxis.setMinorTickCount(5);
    domainAxis.setTickUnit(new NumberTickUnit(10));
    domainAxis.setAxisLineVisible(true);
    domainAxis.setTickMarksVisible(true);
    domainAxis.setMinorTickMarksVisible(true);
    domainAxis.setLowerMargin(10);
    domainAxis.setUpperMargin(10);
    
    xyplot.setRangeGridlineStroke(new BasicStroke());
    xyplot.setRangeGridlinePaint(Color.lightGray);
    xyplot.setRangeMinorGridlinePaint(Color.decode("#DDDDDD"));
    xyplot.setRangeMinorGridlinesVisible(true);
    xyplot.setOutlineVisible(true);
    xyplot.setDomainGridlineStroke(new BasicStroke());
    xyplot.setDomainGridlinePaint(Color.lightGray);
    xyplot.setDomainMinorGridlinePaint(Color.decode("#DDDDDD"));
    xyplot.setDomainMinorGridlinesVisible(true);
    xyplot.getRenderer().setSeriesPaint(0, Color.decode("#4572a7"));

    chart.setTextAntiAlias(true);
    chart.setAntiAlias(true);
    chart.removeLegend();
    chart.setPadding(new RectangleInsets(20, 20, 20, 20));
    
    Point2D legendLocation = new Point2D.Double( 101, -10 );
    makeRect(xyplot, legendLocation, 120, 74, Color.WHITE );
   
    Point2D triangleLocation = new Point2D.Double( 101, -10 );
    Color grey = new Color(0.1f,0.1f,0.1f,0.1f);
    makeTriangle(xyplot, triangleLocation, grey );
    
    makeGuessingLine( xyplot );
}
 

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;
}
 

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);
}
 

MsMsPlot(final ActionListener listener, RawDataFile rawDataFile, MsMsVisualizerWindow visualizer,
    MsMsDataSet dataset, Range<Double> rtRange, Range<Double> mzRange) {

  super(null, true);

  this.visualizer = visualizer;
  this.rawDataFile = rawDataFile;
  this.rtRange = rtRange;
  this.mzRange = mzRange;

  // initialize the chart by default time series chart from factory
  chart = ChartFactory.createXYLineChart("", // title
      "", // x-axis label
      "", // y-axis label
      null, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // create legend
      false, // generate tooltips
      false // generate URLs
  );

  chart.setBackgroundPaint(Color.white);
  setChart(chart);

  // disable maximum size (we don't want scaling)
  setMaximumDrawWidth(Integer.MAX_VALUE);
  setMaximumDrawHeight(Integer.MAX_VALUE);

  // set the plot properties
  plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
  plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
  plot.setDomainGridlinePaint(gridColor);
  plot.setRangeGridlinePaint(gridColor);

  // Set the domain log axis
  xAxis = new NumberAxis("Retention time (min)");
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setNumberFormatOverride(rtFormat);
  xAxis.setUpperMargin(0.01);
  xAxis.setLowerMargin(0.01);
  plot.setDomainAxis(xAxis);

  // Set the range log axis
  yAxis = new NumberAxis("Precursor m/z");
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setNumberFormatOverride(mzFormat);
  yAxis.setUpperMargin(0.1);
  yAxis.setLowerMargin(0.1);
  plot.setRangeAxis(yAxis);

  // Set crosshair properties
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);
  plot.setDomainCrosshairPaint(crossHairColor);
  plot.setRangeCrosshairPaint(crossHairColor);
  plot.setDomainCrosshairStroke(crossHairStroke);
  plot.setRangeCrosshairStroke(crossHairStroke);

  // Create renderers
  mainRenderer = new MsMsPlotRenderer();
  plot.setRenderer(0, mainRenderer);

  // title
  chartTitle = chart.getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  chartSubTitle = new TextTitle();
  chartSubTitle.setFont(subTitleFont);
  chartSubTitle.setMargin(5, 0, 0, 0);
  chart.addSubtitle(chartSubTitle);

  // Add data sets;
  plot.setDataset(0, dataset);

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

  peakDataRenderer = new PeakDataRenderer();

  // Add EMF and EPS options to the save as menu
  JPopupMenu popupMenu = getPopupMenu();
  JMenuItem saveAsMenu = (JMenuItem) popupMenu.getComponent(3);
  GUIUtils.addMenuItem(saveAsMenu, "EMF...", this, "SAVE_EMF");
  GUIUtils.addMenuItem(saveAsMenu, "EPS...", this, "SAVE_EPS");

  // Register for mouse-wheel events
  addMouseWheelListener(this);

  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

public SimpleScatterPlot(double[] xValues, double[] yValues, double[] colors, String xLabel,
    String yLabel) {
  super(null, true);

  setBackground(Color.white);
  setCursor(Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));

  xAxis = new NumberAxis(xLabel);
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setUpperMargin(0);
  xAxis.setLowerMargin(0);

  yAxis = new NumberAxis(yLabel);
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setUpperMargin(0);
  yAxis.setLowerMargin(0);

  xyDataset = new DefaultXYZDataset();
  int length = Math.min(xValues.length, yValues.length);
  double[][] data = new double[3][length];
  System.arraycopy(xValues, 0, data[0], 0, length);
  System.arraycopy(yValues, 0, data[1], 0, length);
  System.arraycopy(colors, 0, data[2], 0, length);
  xyDataset.addSeries(SERIES_ID, data);

  XYDotRenderer renderer = new XYDotRenderer() {
    @Override
    public Paint getItemPaint(int row, int col) {
      double c = xyDataset.getZ(row, col).doubleValue();
      return Color.getHSBColor((float) c, 1.0f, 1.0f);
    }
  };

  renderer.setDotHeight(3);
  renderer.setDotWidth(3);

  plot = new XYPlot(xyDataset, xAxis, yAxis, renderer);
  plot.setBackgroundPaint(Color.white);
  plot.setDomainGridlinesVisible(true);
  plot.setRangeGridlinesVisible(true);

  chart = new JFreeChart("", new Font("SansSerif", Font.BOLD, 12), plot, false);
  chart.setBackgroundPaint(Color.white);

  super.setChart(chart);

  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

public RTMZPlot(RTMZAnalyzerWindow masterFrame, AbstractXYZDataset dataset,
    InterpolatingLookupPaintScale paintScale) {
  super(null);

  this.paintScale = paintScale;

  chart = ChartFactory.createXYAreaChart("", "Retention time", "m/z", dataset,
      PlotOrientation.VERTICAL, false, false, false);
  chart.setBackgroundPaint(Color.white);
  setChart(chart);

  // title

  TextTitle chartTitle = chart.getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  chart.removeSubtitle(chartTitle);

  // disable maximum size (we don't want scaling)
  setMaximumDrawWidth(Integer.MAX_VALUE);
  setMaximumDrawHeight(Integer.MAX_VALUE);

  // set the plot properties
  plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));

  // set grid properties
  plot.setDomainGridlinePaint(gridColor);
  plot.setRangeGridlinePaint(gridColor);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);
  plot.setDomainCrosshairPaint(crossHairColor);
  plot.setRangeCrosshairPaint(crossHairColor);
  plot.setDomainCrosshairStroke(crossHairStroke);
  plot.setRangeCrosshairStroke(crossHairStroke);

  NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
  NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(rtFormat);
  xAxis.setUpperMargin(0.001);
  xAxis.setLowerMargin(0.001);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setNumberFormatOverride(mzFormat);

  plot.setDataset(dataset);
  spotRenderer = new RTMZRenderer(dataset, paintScale);
  plot.setRenderer(spotRenderer);
  spotRenderer.setDefaultToolTipGenerator(new RTMZToolTipGenerator());

  // Add a paintScaleLegend to chart

  paintScaleAxis = new NumberAxis("Logratio");
  paintScaleAxis.setRange(paintScale.getLowerBound(), paintScale.getUpperBound());

  paintScaleLegend = new PaintScaleLegend(paintScale, paintScaleAxis);
  paintScaleLegend.setPosition(plot.getDomainAxisEdge());
  paintScaleLegend.setMargin(5, 25, 5, 25);

  chart.addSubtitle(paintScaleLegend);


  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

@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 SimpleScatterPlot(double[] xValues, double[] yValues, double[] colors, String xLabel,
    String yLabel) {
  super(null);

  // setBackground(Color.white);
  setCursor(Cursor.CROSSHAIR);

  xAxis = new NumberAxis(xLabel);
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setUpperMargin(0);
  xAxis.setLowerMargin(0);

  yAxis = new NumberAxis(yLabel);
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setUpperMargin(0);
  yAxis.setLowerMargin(0);

  xyDataset = new DefaultXYZDataset();
  int length = Math.min(xValues.length, yValues.length);
  double[][] data = new double[3][length];
  System.arraycopy(xValues, 0, data[0], 0, length);
  System.arraycopy(yValues, 0, data[1], 0, length);
  System.arraycopy(colors, 0, data[2], 0, length);
  xyDataset.addSeries(SERIES_ID, data);

  XYDotRenderer renderer = new XYDotRenderer() {
    @Override
    public Paint getItemPaint(int row, int col) {
      double c = xyDataset.getZ(row, col).doubleValue();
      return Color.getHSBColor((float) c, 1.0f, 1.0f);
    }
  };

  renderer.setDotHeight(3);
  renderer.setDotWidth(3);

  plot = new XYPlot(xyDataset, xAxis, yAxis, renderer);
  plot.setBackgroundPaint(Color.white);
  plot.setDomainGridlinesVisible(true);
  plot.setRangeGridlinesVisible(true);

  chart = new JFreeChart("", new Font("SansSerif", Font.BOLD, 12), plot, false);
  chart.setBackgroundPaint(Color.white);

  super.setChart(chart);

  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

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 RTMZPlot(RTMZAnalyzerWindow masterFrame, AbstractXYZDataset dataset,
    InterpolatingLookupPaintScale paintScale) {
  super(null);

  this.paintScale = paintScale;

  chart = ChartFactory.createXYAreaChart("", "Retention time", "m/z", dataset,
      PlotOrientation.VERTICAL, false, false, false);
  chart.setBackgroundPaint(Color.white);
  setChart(chart);

  // title

  TextTitle chartTitle = chart.getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  chart.removeSubtitle(chartTitle);

  // disable maximum size (we don't want scaling)
  // setMaximumDrawWidth(Integer.MAX_VALUE);
  // setMaximumDrawHeight(Integer.MAX_VALUE);

  // set the plot properties
  plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));

  // set grid properties
  plot.setDomainGridlinePaint(gridColor);
  plot.setRangeGridlinePaint(gridColor);

  // set crosshair (selection) properties
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);
  plot.setDomainCrosshairPaint(crossHairColor);
  plot.setRangeCrosshairPaint(crossHairColor);
  plot.setDomainCrosshairStroke(crossHairStroke);
  plot.setRangeCrosshairStroke(crossHairStroke);

  NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
  NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();

  // set the X axis (retention time) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(rtFormat);
  xAxis.setUpperMargin(0.001);
  xAxis.setLowerMargin(0.001);

  // set the Y axis (intensity) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setNumberFormatOverride(mzFormat);

  plot.setDataset(dataset);
  spotRenderer = new RTMZRenderer(dataset, paintScale);
  plot.setRenderer(spotRenderer);
  spotRenderer.setDefaultToolTipGenerator(new RTMZToolTipGenerator());

  // Add a paintScaleLegend to chart

  paintScaleAxis = new NumberAxis("Logratio");
  paintScaleAxis.setRange(paintScale.getLowerBound(), paintScale.getUpperBound());

  paintScaleLegend = new PaintScaleLegend(paintScale, paintScaleAxis);
  paintScaleLegend.setPosition(plot.getDomainAxisEdge());
  paintScaleLegend.setMargin(5, 25, 5, 25);

  chart.addSubtitle(paintScaleLegend);

  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

TwoDPlot(RawDataFile rawDataFile, TwoDVisualizerWindow visualizer, TwoDDataSet dataset,
    Range<Double> rtRange, Range<Double> mzRange, String whichPlotTypeStr) {

  super(null);

  this.rawDataFile = rawDataFile;
  this.rtRange = rtRange;
  this.mzRange = mzRange;

  // setBackground(Color.white);
  setCursor(Cursor.CROSSHAIR);

  // set the X axis (retention time) properties
  xAxis = new NumberAxis("Retention time");
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setNumberFormatOverride(rtFormat);
  xAxis.setUpperMargin(0);
  xAxis.setLowerMargin(0);

  // set the Y axis (intensity) properties
  yAxis = new NumberAxis("m/z");
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setNumberFormatOverride(mzFormat);
  yAxis.setUpperMargin(0);
  yAxis.setLowerMargin(0);

  // set the plot properties
  if (whichPlotTypeStr == "default") {
    plot = new TwoDXYPlot(dataset, rtRange, mzRange, xAxis, yAxis);
  } else if (whichPlotTypeStr == "point2D") {
    plot = new PointTwoDXYPlot(dataset, rtRange, mzRange, xAxis, yAxis);
  }
  plot.setBackgroundPaint(Color.white);
  plot.setDomainGridlinesVisible(false);
  plot.setRangeGridlinesVisible(false);

  // chart properties
  chart = new JFreeChart("", titleFont, plot, false);
  chart.setBackgroundPaint(Color.white);

  setChart(chart);

  // title
  chartTitle = chart.getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);

  chartSubTitle = new TextTitle();
  chartSubTitle.setFont(subTitleFont);
  chartSubTitle.setMargin(5, 0, 0, 0);
  chart.addSubtitle(chartSubTitle);

  // disable maximum size (we don't want scaling)
  // setMaximumDrawWidth(Integer.MAX_VALUE);
  // setMaximumDrawHeight(Integer.MAX_VALUE);

  // set crosshair (selection) properties
  plot.setRangeCrosshairVisible(false);
  plot.setDomainCrosshairVisible(true);
  plot.setDomainCrosshairPaint(crossHairColor);
  plot.setDomainCrosshairStroke(crossHairStroke);

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

  peakDataRenderer = new PeakDataRenderer();

  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

MsMsPlot(RawDataFile rawDataFile, MsMsVisualizerWindow visualizer, MsMsDataSet dataset,
    Range<Double> rtRange, Range<Double> mzRange) {

  super(ChartFactory.createXYLineChart("", "", "", null, PlotOrientation.VERTICAL, true, true,
      false), true, true, false, false, true);

  this.visualizer = visualizer;
  this.rawDataFile = rawDataFile;
  this.rtRange = rtRange;
  this.mzRange = mzRange;

  // initialize the chart by default time series chart from factory
  chart = getChart();
  chart.setBackgroundPaint(Color.white);

  // disable maximum size (we don't want scaling)
  // setMaximumDrawWidth(Integer.MAX_VALUE);
  // setMaximumDrawHeight(Integer.MAX_VALUE);

  // set the plot properties
  plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
  plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
  plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
  plot.setDomainGridlinePaint(gridColor);
  plot.setRangeGridlinePaint(gridColor);

  // Set the domain log axis
  xAxis = new NumberAxis("Retention time (min)");
  xAxis.setAutoRangeIncludesZero(false);
  xAxis.setNumberFormatOverride(rtFormat);
  xAxis.setUpperMargin(0.01);
  xAxis.setLowerMargin(0.01);
  plot.setDomainAxis(xAxis);

  // Set the range log axis
  yAxis = new NumberAxis("Precursor m/z");
  yAxis.setAutoRangeIncludesZero(false);
  yAxis.setNumberFormatOverride(mzFormat);
  yAxis.setUpperMargin(0.1);
  yAxis.setLowerMargin(0.1);
  plot.setRangeAxis(yAxis);

  // Set crosshair properties
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);
  plot.setDomainCrosshairPaint(crossHairColor);
  plot.setRangeCrosshairPaint(crossHairColor);
  plot.setDomainCrosshairStroke(crossHairStroke);
  plot.setRangeCrosshairStroke(crossHairStroke);

  // Create renderers
  mainRenderer = new MsMsPlotRenderer();
  plot.setRenderer(0, mainRenderer);

  // title
  chartTitle = chart.getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  chartSubTitle = new TextTitle();
  chartSubTitle.setFont(subTitleFont);
  chartSubTitle.setMargin(5, 0, 0, 0);
  chart.addSubtitle(chartSubTitle);

  // Add data sets;
  plot.setDataset(0, dataset);

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

  peakDataRenderer = new PeakDataRenderer();


  // reset zoom history
  ZoomHistory history = getZoomHistory();
  if (history != null)
    history.clear();
}
 

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;
}