Java Code Examples for org.jfree.chart.plot.XYPlot#setRangeCrosshairVisible()

/**
 * Creates a stepped XY plot with default settings.
 *
 * @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 chart.
 */
public static JFreeChart createXYStepChart(String title, String xAxisLabel,
        String yAxisLabel, XYDataset dataset, boolean legend) {

    DateAxis xAxis = new DateAxis(xAxisLabel);
    NumberAxis yAxis = new NumberAxis(yAxisLabel);
    yAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    XYItemRenderer renderer = new XYStepRenderer();
    renderer.setBaseToolTipGenerator(new StandardXYToolTipGenerator());
    XYPlot plot = new XYPlot(dataset, xAxis, yAxis, null);
    plot.setRenderer(renderer);
    plot.setDomainCrosshairVisible(false);
    plot.setRangeCrosshairVisible(false);
    JFreeChart chart = new JFreeChart(title, JFreeChart.DEFAULT_TITLE_FONT,
            plot, legend);
    currentTheme.apply(chart);
    return chart;

}
 

/**
 * Creates and returns a new plot with the specified dataset, axes and
 * renderer.
 * 
 * @param dataset
 *            the dataset (<code>null</code> permitted).
 * @param xAxis
 *            the x axis (<code>null</code> permitted).
 * @param yAxis
 *            the y axis (<code>null</code> permitted).
 * @param renderer
 *            the renderer (<code>null</code> permitted).
 * @return a new plot.
 */
private static XYPlot createXYPlot(XYDataset dataset, NumberAxis xAxis, NumberAxis yAxis, XYItemRenderer renderer) {
	final XYPlot plot = new XYPlot(dataset, xAxis, yAxis, renderer);
	plot.setOrientation(PlotOrientation.VERTICAL);
	plot.setDomainGridlinesVisible(false);
	plot.setDomainMinorGridlinesVisible(false);
	plot.setRangeGridlinesVisible(false);
	plot.setRangeMinorGridlinesVisible(false);
	plot.setRangeCrosshairVisible(false);
	plot.setDomainCrosshairVisible(false);
	plot.setBackgroundPaint(Color.white);
	// plot.getRangeAxis().setLabelFont(axisLabelFont);
	// plot.getDomainAxis().setLabelFont(axisLabelFont);
	plot.setDomainZeroBaselineVisible(true);
	plot.setRangeZeroBaselineVisible(true);
	return plot;
}
 

/**
 * Creates a chart.
 *
 * @param dataset a dataset.
 * @return A chart.
 */
private JFreeChart createChart(XYDataset dataset)
{

	chart = ChartFactory.createTimeSeriesChart(
		"OBD Data Graph", // title
		"Time", // x-axis label
		"Value", // y-axis label
		dataset, // data
		true, // create legend?
		true, // generate tooltips?
		false // generate URLs?
	);

	chart.setBackgroundPaint(Color.white);

	XYPlot plot = (XYPlot) chart.getPlot();
	plot.setBackgroundPaint(Color.lightGray);
	plot.setDomainGridlinePaint(Color.white);
	plot.setRangeGridlinePaint(Color.white);
	plot.setDomainCrosshairVisible(true);
	plot.setRangeCrosshairVisible(true);
	plot.getDomainAxis().setTickLabelFont(legendFont);

	DateAxis axis = (DateAxis) plot.getDomainAxis();
	axis.setDateFormatOverride(new SimpleDateFormat("HH:mm:ss"));
	chart.getLegend().setItemFont(legendFont);

	return chart;
}
 

public void applyToCrosshair(@Nonnull JFreeChart chart) {
  XYPlot p = chart.getXYPlot();
  p.setDomainCrosshairPaint(DEFAULT_CROSS_HAIR_COLOR);
  p.setRangeCrosshairPaint(DEFAULT_CROSS_HAIR_COLOR);
  p.setDomainCrosshairStroke(DEFAULT_CROSS_HAIR_STROKE);
  p.setRangeCrosshairStroke(DEFAULT_CROSS_HAIR_STROKE);
  p.setDomainCrosshairVisible(DEFAULT_CROSS_HAIR_VISIBLE);
  p.setRangeCrosshairVisible(DEFAULT_CROSS_HAIR_VISIBLE);
}
 

/**
 * Creates a chart.
 *
 * @param dataset  a dataset.
 *
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Legal & General Unit Trust Prices",  // title
        "Date",             // x-axis label
        "Price Per Unit",   // y-axis label
        dataset,            // data
        true,               // create legend?
        true,               // generate tooltips?
        false               // generate URLs?
    );

    chart.setBackgroundPaint(Color.white);

    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));
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);

    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setBaseShapesVisible(true);
        renderer.setBaseShapesFilled(true);
        renderer.setDrawSeriesLineAsPath(true);
    }

    DateAxis axis = (DateAxis) plot.getDomainAxis();
    axis.setDateFormatOverride(new SimpleDateFormat("MMM-yyyy"));

    return chart;

}
 

/**
 * Creates a chart.
 * 
 * @param dataset  a dataset.
 * 
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Legal & General Unit Trust Prices",  // title
        "Date",             // x-axis label
        "Price Per Unit",   // y-axis label
        dataset,            // data
        true,               // create legend?
        true,               // generate tooltips?
        false               // generate URLs?
    );

    chart.setBackgroundPaint(Color.white);

    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));
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);
    
    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setBaseShapesVisible(true);
        renderer.setBaseShapesFilled(true);
    }
    
    DateAxis axis = (DateAxis) plot.getDomainAxis();
    axis.setDateFormatOverride(new SimpleDateFormat("MMM-yyyy"));
    
    return chart;

}
 

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

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

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

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

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

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

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

@Override
public void initChart(final IScope scope, final String chartname) {
	super.initChart(scope, chartname);

	final XYPlot pp = (XYPlot) chart.getPlot();
	pp.setDomainGridlinePaint(axesColor);
	pp.setRangeGridlinePaint(axesColor);
	pp.setDomainCrosshairPaint(axesColor);
	pp.setRangeCrosshairPaint(axesColor);
	pp.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
	pp.setDomainCrosshairVisible(false);
	pp.setRangeCrosshairVisible(false);

	pp.getDomainAxis().setAxisLinePaint(axesColor);
	pp.getDomainAxis().setTickLabelFont(getTickFont());
	pp.getDomainAxis().setLabelFont(getLabelFont());
	if (textColor != null) {
		pp.getDomainAxis().setLabelPaint(textColor);
		pp.getDomainAxis().setTickLabelPaint(textColor);
	}

	NumberAxis axis = (NumberAxis) pp.getRangeAxis();
	axis = formatYAxis(scope, axis);
	pp.setRangeAxis(axis);
	if (ytickunit > 0) {
		((NumberAxis) pp.getRangeAxis()).setTickUnit(new NumberTickUnit(ytickunit));
		pp.setRangeGridlinesVisible(true);
	} else {
		pp.setRangeGridlinesVisible(GamaPreferences.Displays.CHART_GRIDLINES.getValue());
	}

	// resetAutorange(scope);

	if (getType() == ChartOutput.SERIES_CHART) {
		if (xlabel == null) {
			xlabel = "time";
		}
	}
	if (getType() == ChartOutput.XY_CHART) {}
	if (getType() == ChartOutput.SCATTER_CHART) {}
	if (!this.getXTickValueVisible(scope)) {
		pp.getDomainAxis().setTickMarksVisible(false);
		pp.getDomainAxis().setTickLabelsVisible(false);

	}

}
 

@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);
    });

  }
 

/**
 * Creates a chart.
 *
 * @param dataset  a dataset.
 *
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "International Coffee Organisation : Coffee Prices",    // title
        null,             // x-axis label
        "US cents/lb",      // y-axis label
        dataset);

    String fontName = "Palatino";
    chart.getTitle().setFont(new Font(fontName, Font.BOLD, 18));
    chart.addSubtitle(new TextTitle("Source: http://www.ico.org/historical/2010-19/PDF/HIST-PRICES.pdf", 
            new Font(fontName, Font.PLAIN, 14)));

    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setDomainPannable(true);
    plot.setRangePannable(true);
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);
    plot.getDomainAxis().setLowerMargin(0.0);
    plot.getDomainAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getDomainAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    plot.getRangeAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getRangeAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    chart.getLegend().setItemFont(new Font(fontName, Font.PLAIN, 14));
    chart.getLegend().setFrame(BlockBorder.NONE);
    chart.getLegend().setHorizontalAlignment(HorizontalAlignment.CENTER);
    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setBaseShapesVisible(false);
        renderer.setDrawSeriesLineAsPath(true);
        // set the default stroke for all series
        renderer.setAutoPopulateSeriesStroke(false);
        renderer.setBaseStroke(new BasicStroke(3.0f, BasicStroke.CAP_ROUND, 
                BasicStroke.JOIN_BEVEL), false);
        renderer.setSeriesPaint(0, Color.RED);
        renderer.setSeriesPaint(1, new Color(24, 123, 58));
        renderer.setSeriesPaint(2, new Color(149, 201, 136));
        renderer.setSeriesPaint(3, new Color(1, 62, 29));
        renderer.setSeriesPaint(4, new Color(81, 176, 86));
        renderer.setSeriesPaint(5, new Color(0, 55, 122));
        renderer.setSeriesPaint(6, new Color(0, 92, 165));
    }

    return chart;

}
 

/**
 * create 2D Van Krevelen Diagram chart
 */
private JFreeChart create2DVanKrevelenDiagram() {
  logger.info("Creating new 2D chart instance");
  appliedSteps++;

  // load dataset
  VanKrevelenDiagramXYDataset dataset2D = new VanKrevelenDiagramXYDataset(filteredRows);

  // create chart
  chart = ChartFactory.createScatterPlot(title, "O/C", "H/C", dataset2D, PlotOrientation.VERTICAL,
      true, true, false);

  XYPlot plot = (XYPlot) chart.getPlot();
  plot.setBackgroundPaint(Color.WHITE);
  plot.setDomainCrosshairPaint(Color.GRAY);
  plot.setRangeCrosshairPaint(Color.GRAY);
  plot.setDomainCrosshairVisible(true);
  plot.setRangeCrosshairVisible(true);
  appliedSteps++;

  // set renderer
  XYBlockPixelSizeRenderer renderer = new XYBlockPixelSizeRenderer();

  // calc block sizes
  double maxX = plot.getDomainAxis().getRange().getUpperBound();
  double maxY = plot.getRangeAxis().getRange().getUpperBound();

  renderer.setBlockWidth(0.001);
  renderer.setBlockHeight(renderer.getBlockWidth() / (maxX / maxY));

  // set tooltip generator
  ScatterPlotToolTipGenerator tooltipGenerator =
      new ScatterPlotToolTipGenerator("O/C", "H/C", zAxisLabel, filteredRows);
  renderer.setSeriesToolTipGenerator(0, tooltipGenerator);
  plot.setRenderer(renderer);

  // set item label generator
  NameItemLabelGenerator generator = new NameItemLabelGenerator(filteredRows);
  renderer.setDefaultItemLabelGenerator(generator);
  renderer.setDefaultItemLabelsVisible(false);
  renderer.setDefaultItemLabelFont(legendFont);
  renderer.setDefaultPositiveItemLabelPosition(new ItemLabelPosition(ItemLabelAnchor.CENTER,
      TextAnchor.TOP_RIGHT, TextAnchor.TOP_RIGHT, -45), true);

  return chart;
}
 

/**
 * Creates a chart.
 *
 * @param dataset  a dataset.
 *
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "International Coffee Organisation : Coffee Prices",    // title
        null,             // x-axis label
        "US cents/lb",      // y-axis label
        dataset);

    String fontName = "Palatino";
    chart.getTitle().setFont(new Font(fontName, Font.BOLD, 18));
    chart.addSubtitle(new TextTitle("Source: http://www.ico.org/historical/2010-19/PDF/HIST-PRICES.pdf", 
            new Font(fontName, Font.PLAIN, 14)));

    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setDomainPannable(true);
    plot.setRangePannable(true);
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);
    plot.getDomainAxis().setLowerMargin(0.0);
    plot.getDomainAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getDomainAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    plot.getRangeAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getRangeAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    chart.getLegend().setItemFont(new Font(fontName, Font.PLAIN, 14));
    chart.getLegend().setFrame(BlockBorder.NONE);
    chart.getLegend().setHorizontalAlignment(HorizontalAlignment.CENTER);
    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setBaseShapesVisible(false);
        renderer.setDrawSeriesLineAsPath(true);
        // set the default stroke for all series
        renderer.setAutoPopulateSeriesStroke(false);
        renderer.setBaseStroke(new BasicStroke(3.0f, BasicStroke.CAP_ROUND, 
                BasicStroke.JOIN_BEVEL), false);
        renderer.setSeriesPaint(0, Color.RED);
        renderer.setSeriesPaint(1, new Color(24, 123, 58));
        renderer.setSeriesPaint(2, new Color(149, 201, 136));
        renderer.setSeriesPaint(3, new Color(1, 62, 29));
        renderer.setSeriesPaint(4, new Color(81, 176, 86));
        renderer.setSeriesPaint(5, new Color(0, 55, 122));
        renderer.setSeriesPaint(6, new Color(0, 92, 165));
    }

    return chart;

}
 

/**
 * Creates a chart.
 * 
 * @param dataset  a dataset.
 * 
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Legal & General Unit Trust Prices",  // title
        "Date",             // x-axis label
        "Price Per Unit",   // y-axis label
        dataset,            // data
        true,               // create legend?
        true,               // generate tooltips?
        false               // generate URLs?
    );

    chart.setBackgroundPaint(Color.white);

    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));
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);
    
    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setBaseShapesVisible(true);
        renderer.setBaseShapesFilled(true);
    }
    
    DateAxis axis = (DateAxis) plot.getDomainAxis();
    axis.setDateFormatOverride(new SimpleDateFormat("MMM-yyyy"));
    
    return chart;

}
 

/**
 * Creates a chart.
 *
 * @param dataset  a dataset.
 *
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "International Coffee Organisation : Coffee Prices",    // title
        null,             // x-axis label
        "US cents/lb",      // y-axis label
        dataset);

    String fontName = "Palatino";
    chart.getTitle().setFont(new Font(fontName, Font.BOLD, 18));
    chart.addSubtitle(new TextTitle("Source: http://www.ico.org/historical/2010-19/PDF/HIST-PRICES.pdf", new Font(fontName, Font.PLAIN, 14)));

    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setDomainPannable(true);
    plot.setRangePannable(false);
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);
    plot.getDomainAxis().setLowerMargin(0.0);
    plot.getDomainAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getDomainAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    plot.getRangeAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getRangeAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    chart.getLegend().setItemFont(new Font(fontName, Font.PLAIN, 14));
    chart.getLegend().setFrame(BlockBorder.NONE);
    chart.getLegend().setHorizontalAlignment(HorizontalAlignment.CENTER);
    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setDefaultShapesVisible(false);
        renderer.setDrawSeriesLineAsPath(true);
        // set the default stroke for all series
        renderer.setAutoPopulateSeriesStroke(false);
        renderer.setDefaultStroke(new BasicStroke(3.0f, 
                BasicStroke.CAP_ROUND, BasicStroke.JOIN_BEVEL), false);
        renderer.setSeriesPaint(0, Color.RED);
        renderer.setSeriesPaint(1, new Color(24, 123, 58));
        renderer.setSeriesPaint(2, new Color(149, 201, 136));
        renderer.setSeriesPaint(3, new Color(1, 62, 29));
        renderer.setSeriesPaint(4, new Color(81, 176, 86));
        renderer.setSeriesPaint(5, new Color(0, 55, 122));
        renderer.setSeriesPaint(6, new Color(0, 92, 165));
        renderer.setDefaultLegendTextFont(new Font(fontName, Font.PLAIN, 14));
    }

    return chart;

}
 

@Override
public void initChart(final IScope scope, final String chartname) {
	super.initChart(scope, chartname);

	final XYPlot pp = (XYPlot) chart.getPlot();
	pp.setDomainGridlinePaint(axesColor);
	pp.setRangeGridlinePaint(axesColor);
	pp.setDomainCrosshairPaint(axesColor);
	pp.setRangeCrosshairPaint(axesColor);
	pp.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
	pp.setDomainCrosshairVisible(false);
	pp.setRangeCrosshairVisible(false);
	pp.setRangeGridlinesVisible(false);
	pp.setDomainGridlinesVisible(false);

	pp.getDomainAxis().setAxisLinePaint(axesColor);

	pp.getDomainAxis().setTickLabelFont(getTickFont());
	pp.getDomainAxis().setLabelFont(getLabelFont());
	if (textColor != null) {
		pp.getDomainAxis().setLabelPaint(textColor);
		pp.getDomainAxis().setTickLabelPaint(textColor);
	}
	if (xtickunit > 0) {
		((NumberAxis) pp.getDomainAxis()).setTickUnit(new NumberTickUnit(xtickunit));
	}

	pp.getRangeAxis().setAxisLinePaint(axesColor);
	pp.getRangeAxis().setLabelFont(getLabelFont());
	pp.getRangeAxis().setTickLabelFont(getTickFont());
	if (textColor != null) {
		pp.getRangeAxis().setLabelPaint(textColor);
		pp.getRangeAxis().setTickLabelPaint(textColor);
	}
	if (ytickunit > 0) {
		((NumberAxis) pp.getRangeAxis()).setTickUnit(new NumberTickUnit(ytickunit));
	}

	// resetAutorange(scope);

	if (xlabel != null && !xlabel.isEmpty()) {
		pp.getDomainAxis().setLabel(xlabel);
	}
	if (ylabel != null && !ylabel.isEmpty()) {
		pp.getRangeAxis().setLabel(ylabel);
	}

}
 

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 void updateCrosshairs(int screenX, int screenY) {
   XYPlot xyPlot = getChart().getXYPlot();
   if (showCrosshairs == true) {
      RectangleEdge xAxisLocation = xyPlot.getDomainAxisEdge();
      RectangleEdge yAxisLocation = xyPlot.getRangeAxisEdge();
      Rectangle2D dataArea = getScreenDataArea();
      double crosshairX = xyPlot.getDomainAxis().java2DToValue((double)screenX, dataArea, xAxisLocation);
      double crosshairY = xyPlot.getRangeAxis().java2DToValue((double)screenY, dataArea, yAxisLocation);
      if (crosshairX < xyPlot.getDomainAxis().getLowerBound() ||
          crosshairX > xyPlot.getDomainAxis().getUpperBound() ||
          crosshairY < xyPlot.getRangeAxis().getLowerBound() ||
          crosshairY > xyPlot.getRangeAxis().getUpperBound()) {
         xyPlot.setDomainCrosshairVisible(false);
         xyPlot.setRangeCrosshairVisible(false);
         crosshairAnnotation.setText("");
      } else {
         xyPlot.setDomainCrosshairVisible(true);
         xyPlot.setRangeCrosshairVisible(true);
         /** The xyPlot's crosshairs are updated with the screen coordinates of the XY location.
          * The annotation's text and location is updated with the data coordinates.
          * The format used for displaying the XY data coordinates is taken from the
          * format used for the X and Y axis tick labels. This format is not normally
          * accessible here, but a method was added to NumberTickUnit to provide it.
          * If this turns out to be problematic, the format could always be changed
          * to use a fixed number of significant digits.
          */
         NumberAxis dna = (NumberAxis)xyPlot.getDomainAxis();
         NumberFormat dnf = (NumberFormat)dna.getTickUnit().getFormatter().clone();
         dnf.setMaximumFractionDigits(dnf.getMaximumFractionDigits()+3);
         String xString = dnf.format(crosshairX);
         NumberAxis rna = (NumberAxis)xyPlot.getRangeAxis();
         NumberFormat rnf = (NumberFormat)rna.getTickUnit().getFormatter().clone();
         rnf.setMaximumFractionDigits(rnf.getMaximumFractionDigits()+3);
         String yString = rnf.format(crosshairY);
         crosshairAnnotation.setText("(" + xString + ", " + yString + ")");
         crosshairAnnotation.setX(crosshairX);
         crosshairAnnotation.setY(crosshairY);
         xyPlot.setDomainCrosshairValue(crosshairX);
         xyPlot.setRangeCrosshairValue(crosshairY);
         // JPL 11/19/09: the chart's plotInfo does not appear to be updated when the
         // FunctionPanel is resized. So the following call to handleClick will pass in
         // the wrong plot area for calculating crosshair coordinates. So instead, set
         // the crosshair directly with the two lines above this comment.
         //xyPlot.handleClick(screenX, screenY, this.getChartRenderingInfo().getPlotInfo());
      }
   }
}
 

/**
 * Creates a chart.
 *
 * @param dataset  a dataset.
 *
 * @return A chart.
 */
private static JFreeChart createChart(XYDataset dataset) {

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "International Coffee Organisation : Coffee Prices",    // title
        null,             // x-axis label
        "US cents/lb",      // y-axis label
        dataset);

    String fontName = "Palatino";
    chart.getTitle().setFont(new Font(fontName, Font.BOLD, 18));
    chart.addSubtitle(new TextTitle("Source: http://www.ico.org/historical/2010-19/PDF/HIST-PRICES.pdf", 
            new Font(fontName, Font.PLAIN, 14)));

    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setDomainPannable(true);
    plot.setRangePannable(true);
    plot.setDomainCrosshairVisible(true);
    plot.setRangeCrosshairVisible(true);
    plot.getDomainAxis().setLowerMargin(0.0);
    plot.getDomainAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getDomainAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    plot.getRangeAxis().setLabelFont(new Font(fontName, Font.BOLD, 14));
    plot.getRangeAxis().setTickLabelFont(new Font(fontName, Font.PLAIN, 12));
    chart.getLegend().setItemFont(new Font(fontName, Font.PLAIN, 14));
    chart.getLegend().setFrame(BlockBorder.NONE);
    chart.getLegend().setHorizontalAlignment(HorizontalAlignment.CENTER);
    XYItemRenderer r = plot.getRenderer();
    if (r instanceof XYLineAndShapeRenderer) {
        XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r;
        renderer.setBaseShapesVisible(false);
        renderer.setDrawSeriesLineAsPath(true);
        // set the default stroke for all series
        renderer.setAutoPopulateSeriesStroke(false);
        renderer.setBaseStroke(new BasicStroke(3.0f, BasicStroke.CAP_ROUND, 
                BasicStroke.JOIN_BEVEL), false);
        renderer.setSeriesPaint(0, Color.RED);
        renderer.setSeriesPaint(1, new Color(24, 123, 58));
        renderer.setSeriesPaint(2, new Color(149, 201, 136));
        renderer.setSeriesPaint(3, new Color(1, 62, 29));
        renderer.setSeriesPaint(4, new Color(81, 176, 86));
        renderer.setSeriesPaint(5, new Color(0, 55, 122));
        renderer.setSeriesPaint(6, new Color(0, 92, 165));
    }

    return chart;

}