org.jfree.chart.plot.DatasetRenderingOrder Java Examples

/**
 * Returns a CategoryPlot.
 */
private CategoryPlot getCategoryPlot( CategoryDataset dataSet, CategoryItemRenderer renderer,
    PlotOrientation orientation, CategoryLabelPositions labelPositions )
{
    CategoryPlot plot = new CategoryPlot( dataSet, new CategoryAxis(), new NumberAxis(), renderer );

    plot.setDatasetRenderingOrder( DatasetRenderingOrder.FORWARD );
    plot.setOrientation( orientation );

    CategoryAxis xAxis = plot.getDomainAxis();
    xAxis.setCategoryLabelPositions( labelPositions );

    return plot;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYLineChart("",
			// x axis label
			bundle.getString("JPanelAnalysisTimeDist.labelX"), // "Distance"
			// y axis label
			bundle.getString("JPanelAnalysisTimeDist.labelY1"), // "Elevation"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	// -- Background color
	chart.setBackgroundPaint(Color.white);
	chart.setAntiAlias(true);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis(bundle.getString("JPanelAnalysisTimeTemperature.labelY2")); // "Time"
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);
	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

public static void main(String[] args) {
    /**
     * Getting time series
     */
    TimeSeries series = CsvTradesLoader.loadBitstampSeries();
    
    /**
     * Creating the OHLC dataset
     */
    OHLCDataset ohlcDataset = createOHLCDataset(series);
    
    /**
     * Creating the additional dataset
     */
    TimeSeriesCollection xyDataset = createAdditionalDataset(series);
    
    /**
     * Creating the chart
     */
    JFreeChart chart = ChartFactory.createCandlestickChart(
            "Bitstamp BTC price",
            "Time",
            "USD",
            ohlcDataset,
            true);
    // Candlestick rendering
    CandlestickRenderer renderer = new CandlestickRenderer();
    renderer.setAutoWidthMethod(CandlestickRenderer.WIDTHMETHOD_SMALLEST);
    XYPlot plot = chart.getXYPlot();
    plot.setRenderer(renderer);
    // Additional dataset
    int index = 1;
    plot.setDataset(index, xyDataset);
    plot.mapDatasetToRangeAxis(index, 0);
    XYLineAndShapeRenderer renderer2 = new XYLineAndShapeRenderer(true, false);
    renderer2.setSeriesPaint(index, Color.blue);
    plot.setRenderer(index, renderer2);
    // Misc
    plot.setRangeGridlinePaint(Color.lightGray);
    plot.setBackgroundPaint(Color.white);
    NumberAxis numberAxis = (NumberAxis) plot.getRangeAxis();
    numberAxis.setAutoRangeIncludesZero(false);
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
    
    /**
     * Displaying the chart
     */
    displayChart(chart);
}
 

ScatterPlotPanel(TopComponent parentDialog, String helpId) {
    super(parentDialog, helpId, CHART_TITLE, false);
    userSettingsMap = new HashMap<>();
    productRemovedListener = new ProductManager.Listener() {
        @Override
        public void productAdded(ProductManager.Event event) {
        }

        @Override
        public void productRemoved(ProductManager.Event event) {
            final UserSettings userSettings = userSettingsMap.remove(event.getProduct());
            if (userSettings != null) {
                userSettings.dispose();
            }
        }
    };

    xAxisRangeControl = new AxisRangeControl("X-Axis");
    yAxisRangeControl = new AxisRangeControl("Y-Axis");
    scatterPlotModel = new ScatterPlotModel();
    bindingContext = new BindingContext(PropertyContainer.createObjectBacked(scatterPlotModel));
    scatterpointsDataset = new XYIntervalSeriesCollection();
    acceptableDeviationDataset = new XYIntervalSeriesCollection();
    regressionDataset = new XYIntervalSeriesCollection();
    r2Annotation = new XYTitleAnnotation(0, 0, new TextTitle(""));
    chart = ChartFactory.createScatterPlot(CHART_TITLE, "", "", scatterpointsDataset, PlotOrientation.VERTICAL,
                                           true, true, false);
    chart.getXYPlot().setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
    createDomainAxisChangeListener();
    final PropertyChangeListener userSettingsUpdateListener = evt -> {
        if (getRaster() != null) {
            final VectorDataNode pointDataSourceValue = scatterPlotModel.pointDataSource;
            final AttributeDescriptor dataFieldValue = scatterPlotModel.dataField;
            final UserSettings userSettings = getUserSettings(getRaster().getProduct());
            userSettings.set(getRaster().getName(), pointDataSourceValue, dataFieldValue);
        }
    };

    bindingContext.addPropertyChangeListener(PROPERTY_NAME_DATA_FIELD, userSettingsUpdateListener);
    bindingContext.addPropertyChangeListener(PROPERTY_NAME_POINT_DATA_SOURCE, userSettingsUpdateListener);
}
 

public void plot (Point upperLeft)
        {
            // All values, quorum line & spread line
            plotValues();
            plotQuorumLine();
            plotSpreadLine("", peak);

            // Second peak spread line?
            if (secondPeak != null) {
                plotSpreadLine("Second", secondPeak);
            }

            // Chart
//            JFreeChart chartLines = ChartFactory.createXYLineChart(
//                    sheet.getId() + " (" + name + " runs)", // Title
//                    "Lengths " + ((scale != null) ? scale : "*no scale*"), // X-Axis label
//                    "Counts", // Y-Axis label
//                    dataset, // Dataset
//                    PlotOrientation.VERTICAL, // orientation,
//                    true, // Show legend
//                    false, // Show tool tips
//                    false // urls
//                    );
            // use a histogram so we can see the actual buckets values
            // rather than being left to interpolate for any given length
	    JFreeChart chart = ChartFactory.createHistogram(
                    sheet.getId() + " (" + name + " runs)", // Title
                    "", // X-Axis label - already labeled in chartLines
                    "", // Y-Axis label - already labeled in chartLines
                    dataset, // Dataset
                    PlotOrientation.VERTICAL, // orientation,
                    true, // Show legend
                    false, // Show tool tips
                    false // urls
                    );
            // have the quorum and spread be lines rather than bars
            XYPlot xyPlot = (XYPlot) chart.getPlot();
            xyPlot.setDataset(1, datasetLines);
            XYLineAndShapeRenderer renderer1 = new XYLineAndShapeRenderer();
            renderer1.setSeriesPaint(0, Color.GREEN); 
            xyPlot.setRenderer(1, renderer1);
            // "FORWARD" causes the added dataset of 
            // lines to be overlayed on histogram bars
            xyPlot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
            
            // Hosting frame
            ChartFrame frame = new ChartFrame(
                    sheet.getId() + " - " + name + " runs",
                    chart,
                    true);
            frame.pack();
            frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
            frame.setLocation(upperLeft);
            frame.setVisible(true);
        }
 

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

  super(null, true);

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

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

  // 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();

  JMenuItem plotTypeMenuItem = new JMenuItem("Toggle centroid/continuous mode");
  plotTypeMenuItem.addActionListener(visualizer);
  plotTypeMenuItem.setActionCommand("SWITCH_PLOTMODE");
  add(plotTypeMenuItem);

  JPopupMenu popupMenu = getPopupMenu();
  popupMenu.addSeparator();
  popupMenu.add(plotTypeMenuItem);

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


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

public ScatterPlotChart(ScatterPlotWindow window, ScatterPlotTopPanel topPanel,
    PeakList peakList) {

  super(null, true);

  this.window = window;
  this.peakList = peakList;
  this.topPanel = topPanel;

  // 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
      false, // 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
  LogAxis logAxisDomain = new LogAxis();
  logAxisDomain.setMinorTickCount(1);
  logAxisDomain.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat());
  logAxisDomain.setAutoRange(true);
  plot.setDomainAxis(logAxisDomain);

  // Set the range log axis
  LogAxis logAxisRange = new LogAxis();
  logAxisRange.setMinorTickCount(1);
  logAxisRange.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat());
  logAxisRange.setAutoRange(true);
  plot.setRangeAxis(logAxisRange);

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

  // Create data sets;
  mainDataSet = new ScatterPlotDataSet(peakList);
  plot.setDataset(0, mainDataSet);
  diagonalLineDataset = new DiagonalLineDataset();
  plot.setDataset(1, diagonalLineDataset);

  // Create renderers
  mainRenderer = new ScatterPlotRenderer();
  plot.setRenderer(0, mainRenderer);
  diagonalLineRenderer = new DiagonalLineRenderer();
  plot.setRenderer(1, diagonalLineRenderer);

  // Set tooltip properties
  ttm = new ComponentToolTipManager();
  ttm.registerComponent(this);
  setDismissDelay(Integer.MAX_VALUE);
  setInitialDelay(0);

  // add items to popup menu TODO: add other Show... items
  JPopupMenu popupMenu = getPopupMenu();
  popupMenu.addSeparator();
  GUIUtils.addMenuItem(popupMenu, "Show Chromatogram", this, "TIC");

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

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

public HistogramChart() {
  super(null, true);

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

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

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

  // legend constructed by ChartFactory
  LegendTitle legend = chart.getLegend();
  legend.setItemFont(legendFont);
  legend.setFrame(BlockBorder.NONE);

  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.REVERSE);
  plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);

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

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

  // set the logarithmic axis
  NumberAxis axisDomain = new HistogramDomainAxis();
  axisDomain.setMinorTickCount(1);
  axisDomain.setAutoRange(true);

  NumberAxis axisRange = new NumberAxis();
  axisRange.setMinorTickCount(1);
  axisRange.setAutoRange(true);

  plot.setDomainAxis(axisDomain);
  plot.setRangeAxis(axisRange);

  ClusteredXYBarRenderer renderer = new ClusteredXYBarRenderer();
  renderer.setMargin(marginSize);
  renderer.setShadowVisible(false);
  plot.setRenderer(renderer);

  this.setMinimumSize(new Dimension(400, 400));
  this.setDismissDelay(Integer.MAX_VALUE);
  this.setInitialDelay(0);


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

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 AlignmentRansacPlot() {
  super(null, true);

  dataset = new XYSeriesCollection();
  chart = ChartFactory.createXYLineChart("", null, null, dataset, PlotOrientation.VERTICAL, true,
      true, false);

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

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

  // legend constructed by ChartFactory
  legend = chart.getLegend();
  legend.setItemFont(legendFont);
  legend.setFrame(BlockBorder.NONE);

  // 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);

  // 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);

  // set default renderer properties
  XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
  renderer.setDefaultLinesVisible(false);
  renderer.setDefaultShapesVisible(true);
  renderer.setSeriesShape(0, dataPointsShape);
  renderer.setSeriesShape(1, dataPointsShape);
  renderer.setSeriesLinesVisible(2, true);
  renderer.setSeriesShapesVisible(2, false);
  renderer.setSeriesPaint(0, Color.RED);
  renderer.setSeriesPaint(1, Color.GRAY);
  renderer.setSeriesPaint(2, Color.BLUE);
  renderer.setDefaultItemLabelPaint(labelsColor);
  renderer.setDrawSeriesLineAsPath(true);

  plot.setRenderer(renderer);


  // 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 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 JFreeChart createChart() {
	if (data.getItemCount() > 0) {
		// get cumulative percentages
		KeyedValues cumulative = DataUtilities.getCumulativePercentages(data);

		CategoryDataset categoryDataset = DatasetUtilities.createCategoryDataset(
				"Count for " + this.dataTable.getColumnName(this.countColumn) + " = " + countValue, data);

		// create the chart...
		final JFreeChart chart = ChartFactory.createBarChart(null, // chart title
				this.dataTable.getColumnName(this.groupByColumn), // domain axis label
				"Count", // range axis label
				categoryDataset, // data
				PlotOrientation.VERTICAL, true, // include legend
				true, false);

		// set the background color for the chart...
		chart.setBackgroundPaint(Color.WHITE);

		// get a reference to the plot for further customization...
		CategoryPlot plot = chart.getCategoryPlot();

		CategoryAxis domainAxis = plot.getDomainAxis();
		domainAxis.setLowerMargin(0.02);
		domainAxis.setUpperMargin(0.02);
		domainAxis.setLabelFont(LABEL_FONT_BOLD);
		domainAxis.setTickLabelFont(LABEL_FONT);

		// set the range axis to display integers only...
		NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
		rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits(Locale.US));
		rangeAxis.setLabelFont(LABEL_FONT_BOLD);
		rangeAxis.setTickLabelFont(LABEL_FONT);

		// second data set (cumulative percentages)
		CategoryDataset dataset2 = DatasetUtilities.createCategoryDataset("Cumulative (Percent)", cumulative);

		LineAndShapeRenderer renderer2 = new LineAndShapeRenderer();
		renderer2.setSeriesPaint(0, SwingTools.VERY_DARK_BLUE.darker());

		NumberAxis axis2 = new NumberAxis("Percent of " + countValue);
		axis2.setNumberFormatOverride(NumberFormat.getPercentInstance());
		axis2.setLabelFont(LABEL_FONT_BOLD);
		axis2.setTickLabelFont(LABEL_FONT);

		plot.setRangeAxis(1, axis2);
		plot.setDataset(1, dataset2);
		plot.setRenderer(1, renderer2);
		plot.mapDatasetToRangeAxis(1, 1);

		axis2.setTickUnit(new NumberTickUnit(0.1));

		// show grid lines
		plot.setRangeGridlinesVisible(true);

		// bring cumulative line to front
		plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

		if (isLabelRotating()) {
			domainAxis.setTickLabelsVisible(true);
			domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 2.0d));
		}

		return chart;
	} else {
		return null;
	}
}
 

public AlignmentRansacPlot() {
  super(ChartFactory.createXYLineChart("", null, null, new XYSeriesCollection(),
      PlotOrientation.VERTICAL, true, true, false));

  chart = this.getChart();
  chart.setBackgroundPaint(Color.white);

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

  // legend constructed by ChartFactory
  legend = chart.getLegend();
  legend.setItemFont(legendFont);
  legend.setFrame(BlockBorder.NONE);

  // 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);
  dataset = (XYSeriesCollection) plot.getDataset();

  // 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);

  // set default renderer properties
  XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
  renderer.setDefaultLinesVisible(false);
  renderer.setDefaultShapesVisible(true);
  renderer.setSeriesShape(0, dataPointsShape);
  renderer.setSeriesShape(1, dataPointsShape);
  renderer.setSeriesLinesVisible(2, true);
  renderer.setSeriesShapesVisible(2, false);
  renderer.setSeriesPaint(0, Color.RED);
  renderer.setSeriesPaint(1, Color.GRAY);
  renderer.setSeriesPaint(2, Color.BLUE);
  renderer.setDefaultItemLabelPaint(labelsColor);
  renderer.setDrawSeriesLineAsPath(true);

  plot.setRenderer(renderer);

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

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYAreaChart("",
			// x axis label
			bundle.getString("JPanelAnalysisTimeDist.labelX"), // "Distance"
			// y axis label
			bundle.getString("JPanelAnalysisTimeDist.labelY1"), // "Elevation"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	// -- Background color
	chart.setBackgroundPaint(Color.white);
	chart.setAntiAlias(true);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis(bundle.getString("JPanelAnalysisTimeDist.labelY2")); // "Time"
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);
	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createScatterPlot("",
			// x axis label
			bundle.getString("JPanelAnalysisSpeedSlope.labelX"), // "Slope",
			// y axis label
			bundle.getString("JPanelAnalysisSpeedSlope.labelY"), // "Speed",
			// data
			dataset1, PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	chart.setBackgroundPaint(Color.white); // Panel background color
	chart.setAntiAlias(true);

	XYPlot plot = chart.getXYPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);
	plot.setRangeCrosshairLockedOnData(false);

	XYDotRenderer renderer = new XYDotRenderer();
	renderer.setSeriesPaint(0, new Color(0x6B, 0xB2, 0x00));
	renderer.setDotWidth(2);
	renderer.setDotHeight(2);
	plot.setRenderer(renderer);

	NumberAxis rangeAxis2 = new NumberAxis();
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);

	XYAreaRenderer renderer2 = new XYAreaRenderer();
	renderer2.setSeriesPaint(0, new Color(0x99, 0xff, 0x00, 0x80));
	renderer2.setOutline(true);
	renderer2.setSeriesOutlinePaint(0, new Color(0x80, 0x80, 0x80, 0x80));
	renderer2.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(1, renderer2);

	/*
	 * StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	 * renderer2.setSeriesPaint(0, Color.red); plot.setRenderer(1, renderer2);
	 */

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.REVERSE);

	return chart;
}
 

private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYAreaChart("",
			// x axis label
			bundle.getString("JPanelAnalysisSpeed.labelX"), // "Distance",
			// y axis label
			bundle.getString("JPanelAnalysisSpeed.labelY"), // "Speed"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	chart.setBackgroundPaint(Color.white); // Panel background color
	chart.setAntiAlias(true);

	XYPlot plot = chart.getXYPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis();
	plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	plot.mapDatasetToRangeAxis(1, 1);

	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

/**
 * Update the chart
 * 
 * @param dataset1
 * @param dataset2
 * @return
 */
private JFreeChart CreateChart(XYDataset dataset1, XYDataset dataset2) {
	JFreeChart chart = ChartFactory.createXYAreaChart("",
			// x axis label
			bundle.getString("frmElevationFilter.labelX"), // "Distance"
			// y axis label
			bundle.getString("frmElevationFilter.labelY1"), // "Elevation"
			dataset1, // data
			PlotOrientation.VERTICAL, false, // include legend
			true, // tooltips
			false // urls
	);

	// -- Background color
	chart.setBackgroundPaint(Color.white);
	chart.setAntiAlias(true);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.white);
	plot.setDomainGridlinePaint(Color.gray);
	plot.setRangeGridlinePaint(Color.gray);
	plot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT);

	XYAreaRenderer renderer = new XYAreaRenderer();
	renderer.setSeriesPaint(0, new Color(0x99, 0xff, 0x00));
	renderer.setOutline(true);
	renderer.setSeriesOutlineStroke(0, new BasicStroke(2.0f));
	plot.setRenderer(0, renderer);

	NumberAxis rangeAxis2 = new NumberAxis("");// bundle.getString("JPanelAnalysisTimeDist.labelY2")); // "Time"
	// plot.setRangeAxis(1, rangeAxis2);
	plot.setDataset(1, dataset2);
	plot.setRangeAxis(1, rangeAxis2);
	// plot.mapDatasetToRangeAxis(1, 1);
	StandardXYItemRenderer renderer2 = new StandardXYItemRenderer();
	renderer2.setSeriesPaint(0, Color.red);
	renderer2.setSeriesStroke(0, new BasicStroke(1.0f));
	plot.setRenderer(1, renderer2);

	// -- Select the display order
	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

	return chart;
}
 

public JFreeChart createChart(DatasetMap datasetMap) {
	CategoryDataset datasetValue=(CategoryDataset)datasetMap.getDatasets().get("1");
	CategoryDataset datasetCumulative=(CategoryDataset)datasetMap.getDatasets().get("2");


	JFreeChart chart = ChartFactory.createBarChart(
			name,  // chart title
			xLabel,                     // domain axis label
			yLabel,                     // range axis label
			datasetValue,                        // data
			PlotOrientation.VERTICAL,
			true,                           // include legend
			true,
			false
	);

	chart.setBackgroundPaint(Color.white);

	// get a reference to the plot for further customisation...
	CategoryPlot plot = (CategoryPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.lightGray);
	plot.setRangeGridlinePaint(Color.white);
	CategoryAxis domainAxis = plot.getDomainAxis();
	domainAxis.setLowerMargin(0.02);
	domainAxis.setUpperMargin(0.02);
	domainAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90);
	// set the range axis to display integers only...
	NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
	rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());

	LineAndShapeRenderer renderer2 = new LineAndShapeRenderer();

	NumberAxis axis2 = new NumberAxis("Percent");
	axis2.setNumberFormatOverride(NumberFormat.getPercentInstance());
	plot.setRangeAxis(1, axis2);
	plot.setDataset(1, datasetCumulative);
	plot.setRenderer(1, renderer2);
	plot.mapDatasetToRangeAxis(1, 1);

	plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
	return chart;   
}
 

private static JFreeChart createChart(XYZDataset dataset, double[] mins, double[] maxs, int nPoints, XYDataset xyData) {
    NumberAxis xAxis = new NumberAxis("X");
    xAxis.setRange(mins[0],maxs[0]);


    NumberAxis yAxis = new NumberAxis("Y");
    yAxis.setRange(mins[1], maxs[1]);

    XYBlockRenderer renderer = new XYBlockRenderer();
    renderer.setBlockWidth((maxs[0]-mins[0])/(nPoints-1));
    renderer.setBlockHeight((maxs[1] - mins[1]) / (nPoints - 1));
    PaintScale scale = new GrayPaintScale(0, 1.0);
    renderer.setPaintScale(scale);
    XYPlot plot = new XYPlot(dataset, xAxis, yAxis, renderer);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinesVisible(false);
    plot.setRangeGridlinesVisible(false);
    plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5));
    JFreeChart chart = new JFreeChart("", plot);
    chart.getXYPlot().getRenderer().setSeriesVisibleInLegend(0, false);


    NumberAxis scaleAxis = new NumberAxis("Probability (class 0)");
    scaleAxis.setAxisLinePaint(Color.white);
    scaleAxis.setTickMarkPaint(Color.white);
    scaleAxis.setTickLabelFont(new Font("Dialog", Font.PLAIN, 7));
    PaintScaleLegend legend = new PaintScaleLegend(new GrayPaintScale(),
            scaleAxis);
    legend.setStripOutlineVisible(false);
    legend.setSubdivisionCount(20);
    legend.setAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
    legend.setAxisOffset(5.0);
    legend.setMargin(new RectangleInsets(5, 5, 5, 5));
    legend.setFrame(new BlockBorder(Color.red));
    legend.setPadding(new RectangleInsets(10, 10, 10, 10));
    legend.setStripWidth(10);
    legend.setPosition(RectangleEdge.LEFT);
    chart.addSubtitle(legend);

    ChartUtilities.applyCurrentTheme(chart);

    plot.setDataset(1, xyData);
    XYLineAndShapeRenderer renderer2 = new XYLineAndShapeRenderer();
    renderer2.setBaseLinesVisible(false);
    plot.setRenderer(1, renderer2);

    plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);

    return chart;
}
 

/**
 * All params can be null.
 *
 * @param min - the minimum number on the left range axis (must be set if max is set)
 * @param max - the maximum number on the left range axis (must be set if min is set)
 * @param method2 - the method to run out of Record, and populates a bar series (right range axis)
 * @param highLightIndex - the index to highlight
 * @return
 * @throws Exception
 */
public JFreeChart makeTimeChart(Double min, Double max, String method2, Integer highLightIndex)
    throws Exception {
  startTms = System.currentTimeMillis();
  endTms = 0;
  XYBarRenderer.setDefaultShadowsVisible(false);
  TimeSeriesCollection data = new TimeSeriesCollection();
  Map<String, TimeSeries> timeSeriesMap = makeTimeSeriesMap(method, recordMap, keyNames);
  for (TimeSeries timeSeries : timeSeriesMap.values()) {
    data.addSeries(timeSeries);
  }
  String yAxisLabel = method;
  String denominator = Record.getDenominator(report.getRecordClass(), method.toLowerCase());
  if (denominator != null) {
    yAxisLabel += " (" + denominator + ")";
  }
  chart = ChartFactory.createTimeSeriesChart(title, "Time", yAxisLabel, data, true, true, true);
  XYPlot plot = (XYPlot) chart.getPlot();
  if (method2 != null) {
    Map<Key, R> recordMap2 = recordMap;
    TimeSeriesCollection data2 = new TimeSeriesCollection();
    if (keyNames.length > 0) {
      recordMap2 = report.getMapAggregatedOn();
    }
    Map<String, TimeSeries> timeSeriesMap2 = makeTimeSeriesMap(method2, recordMap2);
    if (timeSeriesMap2.get("Total (" + method2 + ")") != null) {
      data2.addSeries(timeSeriesMap2.get("Total (" + method2 + ")"));
    }
    String y2AxisLabel = method2;
    String demoninator2 = Record.getDenominator(report.getRecordClass(), method2.toLowerCase());
    if (demoninator2 != null) {
      y2AxisLabel += " (" + demoninator2 + ")";
    }
    NumberAxis axis2 = new NumberAxis(y2AxisLabel);
    XYBarRenderer renderer2 = new XYBarRenderer(0.20);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_RIGHT);
    plot.setDataset(1, data2);
    plot.setRenderer(1, renderer2);
    plot.mapDatasetToRangeAxis(1, 1);
    renderer2.setBarPainter(new StandardXYBarPainter());
    plot.setDatasetRenderingOrder(DatasetRenderingOrder.REVERSE);
  }
  if (min != null && max != null) {
    plot.getRangeAxis(0).setRange(min, max);
  }

  if (highLightIndex != null) {
    chart.getXYPlot().getRenderer().setSeriesStroke(highLightIndex, new BasicStroke(5f));
  }

  XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer();
  renderer.setDefaultShapesVisible(true);
  renderer.setUseFillPaint(true);
  renderer.setDefaultFillPaint(Color.white);

  long diff = endTms - startTms;
  String format;
  if (diff > NINTY_DAYS) {
    format = "MMM-yyyy";
  } else if (diff > TWO_DAYS) {
    format = "dd-MMM";
  } else if (diff > TWO_MINUTES) {
    format = "HH:mm";
  } else {
    format = "HH:mm:ss";
  }
  DateAxis axis = (DateAxis) plot.getDomainAxis();
  axis.setDateFormatOverride(new SimpleDateFormat(format));

  LegendTitle lt = chart.getLegend(0);
  lt.setPosition(RectangleEdge.RIGHT);

  if (displayFrame) {
    ChartFrame frame = new ChartFrame(title, chart);
    frame.pack();
    frame.setVisible(true);
  }

  return chart;
}
 

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;
}
 

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();
}
 

public ScatterPlotChart(ScatterPlotWindow window, ScatterPlotTopPanel topPanel,
    PeakList peakList) {

  super(null);

  this.window = window;
  this.peakList = peakList;
  this.topPanel = topPanel;

  // 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
      false, // 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
  LogAxis logAxisDomain = new LogAxis();
  logAxisDomain.setMinorTickCount(1);
  logAxisDomain.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat());
  logAxisDomain.setAutoRange(true);
  plot.setDomainAxis(logAxisDomain);

  // Set the range log axis
  LogAxis logAxisRange = new LogAxis();
  logAxisRange.setMinorTickCount(1);
  logAxisRange.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat());
  logAxisRange.setAutoRange(true);
  plot.setRangeAxis(logAxisRange);

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

  // Create data sets;
  mainDataSet = new ScatterPlotDataSet(peakList);
  plot.setDataset(0, mainDataSet);
  diagonalLineDataset = new DiagonalLineDataset();
  plot.setDataset(1, diagonalLineDataset);

  // Create renderers
  mainRenderer = new ScatterPlotRenderer();
  plot.setRenderer(0, mainRenderer);
  diagonalLineRenderer = new DiagonalLineRenderer();
  plot.setRenderer(1, diagonalLineRenderer);

  // Set tooltip properties
  // ttm = new ComponentToolTipManager();
  // ttm.registerComponent(this);
  // setDismissDelay(Integer.MAX_VALUE);
  // setInitialDelay(0);

  // add items to popup menu TODO: add other Show... items
  ContextMenu popupMenu = getContextMenu();
  // popupMenu.addSeparator();
  // GUIUtils.addMenuItem(popupMenu, "Show Chromatogram", this, "TIC");

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

public HistogramChart() {
  super(ChartFactory.createHistogram("", // title
      "", // x-axis label
      "", // y-axis label
      null, // data set
      PlotOrientation.VERTICAL, // orientation
      true, // create legend
      false, // generate tooltips
      false // generate URLs
  ));

  // initialize the chart by default time series chart from factory
  chart = getChart();

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

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

  // legend constructed by ChartFactory
  LegendTitle legend = chart.getLegend();
  legend.setItemFont(legendFont);
  legend.setFrame(BlockBorder.NONE);

  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.REVERSE);
  plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);

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

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

  // set the logarithmic axis
  NumberAxis axisDomain = new HistogramDomainAxis();
  axisDomain.setMinorTickCount(1);
  axisDomain.setAutoRange(true);

  NumberAxis axisRange = new NumberAxis();
  axisRange.setMinorTickCount(1);
  axisRange.setAutoRange(true);

  plot.setDomainAxis(axisDomain);
  plot.setRangeAxis(axisRange);

  ClusteredXYBarRenderer renderer = new ClusteredXYBarRenderer();
  renderer.setMargin(marginSize);
  renderer.setShadowVisible(false);
  plot.setRenderer(renderer);

  // this.setMinimumSize(new Dimension(400, 400));
  // this.setDismissDelay(Integer.MAX_VALUE);
  // this.setInitialDelay(0);

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

public void setPlot(RawDataFile dataFile, CombinedModuleVisualizerWindowController visualizer,
    Range<Double> rtRange, Range<Double> mzRange, AxisType xAxisType, AxisType yAxisType,
    String massList, Double noiseLevel, ColorScale colorScale) {

  this.visualizer = visualizer;
  this.dataFile = dataFile;
  this.rtRange = rtRange;
  this.mzRange = mzRange;
  this.noiseLevel = noiseLevel;
  this.colorScale = colorScale;
  this.massList = massList;

  chart = getChart();
  chart.setBackgroundPaint(Color.white);

  plot = chart.getXYPlot();
  plot.setBackgroundPaint(Color.white);
  plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
  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);
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);
  plot.setDomainCrosshairPaint(crossHairColor);
  plot.setRangeCrosshairPaint(crossHairColor);
  plot.setDomainCrosshairStroke(crossHairStroke);
  plot.setRangeCrosshairStroke(crossHairStroke);

  defaultRenderer = new CombinedModuleDataPointRenderer(false, true);
  defaultRenderer.setTransparency(0.4f);
  LookupPaintScale scale = new LookupPaintScale(rtRange.lowerEndpoint(), rtRange.upperEndpoint(),
      new Color(0, 0, 0));
  defaultRenderer.setPaintScale(scale);

  NumberAxis xAxis = (NumberAxis) this.plot.getDomainAxis();
  if (xAxisType == AxisType.RETENTIONTIME) {
    setAxes(xAxis, xAxisType, rtFormat);
  } else {
    setAxes(xAxis, xAxisType, mzFormat);
  }
  NumberAxis yAxis = (NumberAxis) this.plot.getRangeAxis();
  setAxes(yAxis, yAxisType, mzFormat);
}
 

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();
}