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

public void addSeries(String yaxisName, TimeSeries series) {
  NumberAxis axis2 = new NumberAxis(yaxisName);
  axis2.setAutoRangeIncludesZero(false);

  XYPlot plot = (XYPlot) chart.getPlot();
  plot.setRangeAxis(axisNum, axis2);
  plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

  TimeSeriesCollection dataset = new TimeSeriesCollection();
  dataset.addSeries(series);

  plot.setDataset(axisNum, dataset);
  plot.mapDatasetToRangeAxis(axisNum, axisNum);
  XYItemRenderer renderer2 = new StandardXYItemRenderer();
  plot.setRenderer(axisNum, renderer2);

  axisNum++;
}
 

/**
 * Creates a sample plot.
 * 
 * @return A sample plot.
 */
private CombinedRangeXYPlot createPlot() {
    // create subplot 1...
    XYDataset data1 = createDataset1();
    XYItemRenderer renderer1 = new StandardXYItemRenderer();
    NumberAxis rangeAxis1 = new NumberAxis("Range 1");
    XYPlot subplot1 = new XYPlot(data1, null, rangeAxis1, renderer1);
    subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
     
    XYTextAnnotation annotation 
        = new XYTextAnnotation("Hello!", 50.0, 10000.0);
    annotation.setFont(new Font("SansSerif", Font.PLAIN, 9));
    annotation.setRotationAngle(Math.PI / 4.0);
    subplot1.addAnnotation(annotation);
     
    // create subplot 2...
    XYDataset data2 = createDataset2();
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    NumberAxis rangeAxis2 = new NumberAxis("Range 2");
    rangeAxis2.setAutoRangeIncludesZero(false);
    XYPlot subplot2 = new XYPlot(data2, null, rangeAxis2, renderer2);
    subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT); 

    // parent plot...
    CombinedRangeXYPlot plot 
        = new CombinedRangeXYPlot(new NumberAxis("Range"));
    plot.setGap(10.0);
    
    // add the subplots...
    plot.add(subplot1, 1);
    plot.add(subplot2, 1);
    plot.setOrientation(PlotOrientation.VERTICAL);
    return plot;
}
 

/**
 * Creates a sample plot.
 * 
 * @return A sample plot.
 */
private CombinedDomainXYPlot createPlot() {
    // create subplot 1...
    XYDataset data1 = createDataset1();
    XYItemRenderer renderer1 = new StandardXYItemRenderer();
    NumberAxis rangeAxis1 = new NumberAxis("Range 1");
    XYPlot subplot1 = new XYPlot(data1, null, rangeAxis1, renderer1);
    subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
    
    XYTextAnnotation annotation 
        = new XYTextAnnotation("Hello!", 50.0, 10000.0);
    annotation.setFont(new Font("SansSerif", Font.PLAIN, 9));
    annotation.setRotationAngle(Math.PI / 4.0);
    subplot1.addAnnotation(annotation);
    
    // create subplot 2...
    XYDataset data2 = createDataset2();
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    NumberAxis rangeAxis2 = new NumberAxis("Range 2");
    rangeAxis2.setAutoRangeIncludesZero(false);
    XYPlot subplot2 = new XYPlot(data2, null, rangeAxis2, renderer2);
    subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);

    // parent plot...
    CombinedDomainXYPlot plot 
        = new CombinedDomainXYPlot(new NumberAxis("Domain"));
    plot.setGap(10.0);
    
    // add the subplots...
    plot.add(subplot1, 1);
    plot.add(subplot2, 1);
    plot.setOrientation(PlotOrientation.VERTICAL);
    return plot;
}
 

/**
 * Creates a sample plot.
 *
 * @return A sample plot.
 */
private CombinedRangeXYPlot createPlot() {
    // create subplot 1...
    XYDataset data1 = createDataset1();
    XYItemRenderer renderer1 = new StandardXYItemRenderer();
    NumberAxis xAxis1 = new NumberAxis("X1");
    XYPlot subplot1 = new XYPlot(data1, xAxis1, null, renderer1);
    subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);

    XYTextAnnotation annotation
            = new XYTextAnnotation("Hello!", 50.0, 10000.0);
    annotation.setFont(new Font("SansSerif", Font.PLAIN, 9));
    annotation.setRotationAngle(Math.PI / 4.0);
    subplot1.addAnnotation(annotation);

    // create subplot 2...
    XYDataset data2 = createDataset2();
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    NumberAxis xAxis2 = new NumberAxis("X2");
    xAxis2.setAutoRangeIncludesZero(false);
    XYPlot subplot2 = new XYPlot(data2, xAxis2, null, renderer2);
    subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);

    // parent plot...
    CombinedRangeXYPlot plot = new CombinedRangeXYPlot(new NumberAxis(
            "Range"));
    plot.setGap(10.0);

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

/**
 * Creates a combined chart.
 *
 * @return The combined chart.
 */
private JFreeChart createCombinedChart(DataSequence tsOne, DataSequence tsTwo, ArrayList<Anomaly> anomalyList) {

    // create subplot 1.
    final XYDataset data1 = createDataset(tsOne, "Original");
    final XYItemRenderer renderer1 = new StandardXYItemRenderer();
    final NumberAxis rangeAxis1 = new NumberAxis("Original Value");
    XYPlot subplot1 = new XYPlot(data1, null, rangeAxis1, renderer1);
    subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
    
    // plot anomalies on subplot 1.
    addAnomalies(subplot1, anomalyList);
    
    // create subplot 2.
    final XYDataset data2 = createDataset(tsTwo, "Forecast");
    final XYItemRenderer renderer2 = new StandardXYItemRenderer();
    final NumberAxis rangeAxis2 = new NumberAxis("Forecast Value");
    rangeAxis2.setAutoRangeIncludesZero(false);
    final XYPlot subplot2 = new XYPlot(data2, null, rangeAxis2, renderer2);
    subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);

    // parent plot.
    final CombinedDomainXYPlot plot = new CombinedDomainXYPlot(new NumberAxis("Time"));
    plot.setGap(10.0);
    
    // add the subplots.
    plot.add(subplot1, 1);
    plot.add(subplot2, 1);
    
    // Add anomaly score time-series.
    addAnomalyTS(plot, tsOne, tsTwo);
    
    plot.setOrientation(PlotOrientation.VERTICAL);

    // return a new chart containing the overlaid plot.
    return new JFreeChart("EGADS GUI",
                          JFreeChart.DEFAULT_TITLE_FONT,
                          plot,
                          true);
}
 

/**
 * Compute the time-series of anomalies.
 */
public void addAnomalyTS(CombinedDomainXYPlot plot, DataSequence observedSeries, DataSequence expectedSeries) {
    // Compute the time-series of errors.
    HashMap<String, ArrayList<Float>> allErrors = aes.initAnomalyErrors(observedSeries, expectedSeries);
    Float sDAutoSensitivity = (float) 0.0;
    Float amntAutoSensitivity = (float) 0.0;
    if (config.getProperty("AUTO_SENSITIVITY_ANOMALY_PCNT") != null) {
      amntAutoSensitivity = new Float(config.getProperty("AUTO_SENSITIVITY_ANOMALY_PCNT"));
    }
    
    if (config.getProperty("AUTO_SENSITIVITY_SD") != null) {
      sDAutoSensitivity = new Float(config.getProperty("AUTO_SENSITIVITY_SD"));
    }

    String errorDebug = "";
    for (int i = 0; i < (aes.getIndexToError().keySet()).size(); i++) {
        Float[] fArray = (allErrors.get(aes.getIndexToError().get(i))).toArray(new Float[(allErrors.get(aes.getIndexToError().get(i))).size()]);
        XYDataset data1 = createDataset(fArray, aes.getIndexToError().get(i));
        XYItemRenderer renderer1 = new StandardXYItemRenderer();
        NumberAxis rangeAxis1 = new NumberAxis(aes.getIndexToError().get(i));
        XYPlot subplot1 = new XYPlot(data1, null, rangeAxis1, renderer1);
        // Get threshold.
        Float d = AutoSensitivity.getLowDensitySensitivity(fArray, sDAutoSensitivity, amntAutoSensitivity);
        subplot1.addRangeMarker(new ValueMarker(d));
        subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
        plot.add(subplot1, 1);
        errorDebug += aes.getIndexToError().get(i) + ": " + d + " ";
    }
    
    System.out.println(errorDebug);
}
 

private void addDataset(String pId, XYDataset pDataset) {
    if (chart == null) {
        setupChart(pId, pDataset);
    } else {
        XYPlot plot = (XYPlot) chart.getPlot();
        plot.setDataset(plot.getDatasetCount(), pDataset);
        NumberAxis axis = new NumberAxis(pId);
        NumberFormat nf = NumberFormat.getInstance();
        nf.setMinimumFractionDigits(0);
        nf.setMaximumFractionDigits(0);
        axis.setNumberFormatOverride(nf);
        plot.setRangeAxis(plot.getDatasetCount() - 1, axis);
        plot.setRangeAxisLocation(plot.getDatasetCount() - 1, AxisLocation.TOP_OR_LEFT);
        plot.mapDatasetToRangeAxis(plot.getDatasetCount() - 1, plot.getDatasetCount() - 1);
        XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
        renderer.setSeriesLinesVisible(0, jShowLines.isSelected());
        renderer.setSeriesShapesVisible(0, jShowDataPoints.isSelected());
        plot.setRenderer(plot.getDatasetCount() - 1, renderer);
        renderer.setDefaultItemLabelsVisible(jShowItemValues.isSelected());
        renderer.setDefaultItemLabelGenerator(new org.jfree.chart.labels.StandardXYItemLabelGenerator());
        renderer.setDefaultToolTipGenerator(new StandardXYToolTipGenerator(StandardXYToolTipGenerator.DEFAULT_TOOL_TIP_FORMAT, new SimpleDateFormat("dd.MM.yyyy HH:mm:ss"), NumberFormat.getInstance()));
        axis.setAxisLinePaint(plot.getLegendItems().get(plot.getDatasetCount() - 1).getLinePaint());
        axis.setLabelPaint(plot.getLegendItems().get(plot.getDatasetCount() - 1).getLinePaint());
        axis.setTickLabelPaint(plot.getLegendItems().get(plot.getDatasetCount() - 1).getLinePaint());
        axis.setTickMarkPaint(plot.getLegendItems().get(plot.getDatasetCount() - 1).getLinePaint());
    }
}
 

/**
 * add a new series to the graph
 *
 * @param series The new series to be added
 */
public synchronized void addSeries(TimeSeries series)
{

	if (oneRangePerSeries)
	{
		// get paint for current axis/range/...
		Paint currPaint =
			DefaultDrawingSupplier.DEFAULT_PAINT_SEQUENCE[
				raIndex % DefaultDrawingSupplier.DEFAULT_PAINT_SEQUENCE.length];

		XYPlot plot = (XYPlot) chart.getPlot();
		// set dataset
		plot.setDataset(raIndex, new TimeSeriesCollection(series));
		// ** set axis
		NumberAxis axis = new NumberAxis();
		axis.setTickLabelFont(legendFont);
		axis.setAxisLinePaint(currPaint);
		axis.setTickLabelPaint(currPaint);
		axis.setTickMarkPaint(currPaint);
		// ** set axis in plot
		plot.setRangeAxis(raIndex, axis);
		plot.setRangeAxisLocation(raIndex, raIndex % 2 == 0 ? AxisLocation.TOP_OR_LEFT : AxisLocation.BOTTOM_OR_RIGHT);
		plot.mapDatasetToRangeAxis(raIndex, raIndex);
		// ** create renderer
		XYItemRenderer renderer = new XYLineAndShapeRenderer(true, false);
		renderer.setBaseToolTipGenerator(toolTipGen);
		renderer.setSeriesPaint(0, currPaint);
		// ** set renderer in plot
		plot.setRenderer(raIndex, renderer);

		raIndex++;
	}
	dataset.addSeries(series);
}
 

/**
 * Creates a sample plot.
 *
 * @return A sample plot.
 */
private CombinedDomainXYPlot createPlot() {
    // create subplot 1...
    XYDataset data1 = createDataset1();
    XYItemRenderer renderer1 = new StandardXYItemRenderer();
    NumberAxis rangeAxis1 = new NumberAxis("Range 1");
    XYPlot subplot1 = new XYPlot(data1, null, rangeAxis1, renderer1);
    subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);

    XYTextAnnotation annotation
        = new XYTextAnnotation("Hello!", 50.0, 10000.0);
    annotation.setFont(new Font("SansSerif", Font.PLAIN, 9));
    annotation.setRotationAngle(Math.PI / 4.0);
    subplot1.addAnnotation(annotation);

    // create subplot 2...
    XYDataset data2 = createDataset2();
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    NumberAxis rangeAxis2 = new NumberAxis("Range 2");
    rangeAxis2.setAutoRangeIncludesZero(false);
    XYPlot subplot2 = new XYPlot(data2, null, rangeAxis2, renderer2);
    subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);

    // parent plot...
    CombinedDomainXYPlot plot
        = new CombinedDomainXYPlot(new NumberAxis("Domain"));
    plot.setGap(10.0);

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

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);
}
 

/**
 * Creates the demo chart.
 *
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(),
            200);

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3",
        "Time of Day",
        "Primary Range Axis",
        dataset1,
        true,
        true,
        false
    );

    chart.setBackgroundPaint(Color.white);
    chart.setBorderVisible(true);
    chart.setBorderPaint(Color.BLACK);
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");
    chart.addSubtitle(subtitle);
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinePaint(Color.white);
    plot.setRangeGridlinePaint(Color.white);

    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);

    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(),
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);

    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible(true);
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(),
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);

    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);

    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);
    plot.setRenderer(3, renderer4);

    return chart;
}
 

/**
 * Creates the demo chart.
 * 
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(), 
            200);
    
    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3", 
        "Time of Day", 
        "Primary Range Axis",
        dataset1, 
        true, 
        true, 
        false
    );

    chart.setBackgroundPaint( Color.white );
    chart.setBorderVisible( true );
    chart.setBorderPaint( Color.BLACK );
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");  
    chart.addSubtitle( subtitle );
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    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.getRangeAxis().setFixedDimension(15.0);
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);
   
    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setFixedDimension(10.0);
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(), 
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);
    
    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible( true );
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(), 
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4        
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);
    
    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);
    
    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);        
    plot.setRenderer(3, renderer4);
            
    return chart;
}
 

/**
 * Creates the demo chart.
 *
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(),
            200);

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3",
        "Time of Day",
        "Primary Range Axis",
        dataset1,
        true,
        true,
        false
    );

    chart.setBackgroundPaint( Color.white );
    chart.setBorderVisible( true );
    chart.setBorderPaint( Color.BLACK );
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");
    chart.addSubtitle( subtitle );
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    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.getRangeAxis().setFixedDimension(15.0);
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);

    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setFixedDimension(10.0);
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(),
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);

    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible( true );
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(),
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);

    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);

    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);
    plot.setRenderer(3, renderer4);

    return chart;
}
 

/**
 * Creates the demo chart.
 *
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(),
            200);

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3",
        "Time of Day",
        "Primary Range Axis",
        dataset1,
        true,
        true,
        false
    );

    chart.setBackgroundPaint(Color.white);
    chart.setBorderVisible(true);
    chart.setBorderPaint(Color.BLACK);
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");
    chart.addSubtitle(subtitle);
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinePaint(Color.white);
    plot.setRangeGridlinePaint(Color.white);

    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);

    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(),
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);

    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible(true);
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(),
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);

    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);

    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);
    plot.setRenderer(3, renderer4);

    return chart;
}
 

/**
 * Creates the demo chart.
 *
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(),
            200);

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3",
        "Time of Day",
        "Primary Range Axis",
        dataset1,
        true,
        true,
        false
    );

    chart.setBackgroundPaint(Color.white);
    chart.setBorderVisible(true);
    chart.setBorderPaint(Color.BLACK);
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");
    chart.addSubtitle(subtitle);
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinePaint(Color.white);
    plot.setRangeGridlinePaint(Color.white);

    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);

    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(),
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);

    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible(true);
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(),
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);

    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);

    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);
    plot.setRenderer(3, renderer4);

    return chart;
}
 

/**
 * Creates the demo chart.
 *
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(),
            200);

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3",
        "Time of Day",
        "Primary Range Axis",
        dataset1,
        true,
        true,
        false
    );

    chart.setBackgroundPaint(Color.white);
    chart.setBorderVisible(true);
    chart.setBorderPaint(Color.BLACK);
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");
    chart.addSubtitle(subtitle);
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinePaint(Color.white);
    plot.setRangeGridlinePaint(Color.white);

    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);

    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(),
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);

    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible(true);
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(),
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);

    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);

    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);
    plot.setRenderer(3, renderer4);

    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;
}
 

/**
 * Creates the demo chart.
 *
 * @return The chart.
 */
private static JFreeChart createChart() {

    XYDataset dataset1 = createDataset("Series 1", 100.0, new Minute(),
            200);

    JFreeChart chart = ChartFactory.createTimeSeriesChart(
        "Multiple Axis Demo 3",
        "Time of Day",
        "Primary Range Axis",
        dataset1,
        true,
        true,
        false
    );

    chart.setBackgroundPaint(Color.white);
    chart.setBorderVisible(true);
    chart.setBorderPaint(Color.BLACK);
    TextTitle subtitle = new TextTitle("Four datasets and four range axes.");
    chart.addSubtitle(subtitle);
    XYPlot plot = (XYPlot) chart.getPlot();
    plot.setOrientation(PlotOrientation.VERTICAL);
    plot.setBackgroundPaint(Color.lightGray);
    plot.setDomainGridlinePaint(Color.white);
    plot.setRangeGridlinePaint(Color.white);

    plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
    XYItemRenderer renderer = plot.getRenderer();
    renderer.setSeriesPaint(0, Color.black);

    // AXIS 2
    NumberAxis axis2 = new NumberAxis("Range Axis 2");
    axis2.setAutoRangeIncludesZero(false);
    axis2.setLabelPaint(Color.red);
    axis2.setTickLabelPaint(Color.red);
    plot.setRangeAxis(1, axis2);
    plot.setRangeAxisLocation(1, AxisLocation.BOTTOM_OR_LEFT);

    XYDataset dataset2 = createDataset("Series 2", 1000.0, new Minute(),
            170);
    plot.setDataset(1, dataset2);
    plot.mapDatasetToRangeAxis(1, 1);
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    renderer2.setSeriesPaint(0, Color.red);
    plot.setRenderer(1, renderer2);

    // AXIS 3
    NumberAxis axis3 = new NumberAxis("Range Axis 3");
    axis3.setLabelPaint(Color.blue);
    axis3.setTickLabelPaint(Color.blue);
    //axis3.setPositiveArrowVisible(true);
    plot.setRangeAxis(2, axis3);

    XYDataset dataset3 = createDataset("Series 3", 10000.0, new Minute(),
            170);
    plot.setDataset(2, dataset3);
    plot.mapDatasetToRangeAxis(2, 2);
    XYItemRenderer renderer3 = new StandardXYItemRenderer();
    renderer3.setSeriesPaint(0, Color.blue);
    plot.setRenderer(2, renderer3);

    // AXIS 4
    NumberAxis axis4 = new NumberAxis("Range Axis 4");
    axis4.setLabelPaint(Color.green);
    axis4.setTickLabelPaint(Color.green);
    plot.setRangeAxis(3, axis4);

    XYDataset dataset4 = createDataset("Series 4", 25.0, new Minute(), 200);
    plot.setDataset(3, dataset4);
    plot.mapDatasetToRangeAxis(3, 3);

    XYItemRenderer renderer4 = new StandardXYItemRenderer();
    renderer4.setSeriesPaint(0, Color.green);
    plot.setRenderer(3, renderer4);

    return chart;
}