Java Code Examples for org.jfree.chart.title.TextTitle#setMargin()

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

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

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

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

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

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

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

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

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

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

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

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

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

  peakDataRenderer = new PeakDataRenderer();


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

public 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();
}
 

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

  this.paintScale = paintScale;

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

  // title

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

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

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

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

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

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

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

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

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

  // Add a paintScaleLegend to chart

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

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

  chart.addSubtitle(paintScaleLegend);

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

public ProjectionPlotPanel(ProjectionPlotWindow masterFrame, ProjectionPlotDataset dataset,
    ParameterSet parameters) {
  super(null);

  boolean createLegend = false;
  if ((dataset.getNumberOfGroups() > 1) && (dataset.getNumberOfGroups() < 20))
    createLegend = true;

  chart = ChartFactory.createXYAreaChart("", dataset.getXLabel(), dataset.getYLabel(), dataset,
      PlotOrientation.VERTICAL, createLegend, false, false);
  chart.setBackgroundPaint(Color.white);

  setChart(chart);

  // title

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

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

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

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

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

  plot.setForegroundAlpha(dataPointAlpha);

  NumberFormat numberFormat = NumberFormat.getNumberInstance();

  // set the X axis (component 1) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(numberFormat);

  // set the Y axis (component 2) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(numberFormat);

  plot.setDataset(dataset);

  spotRenderer = new ProjectionPlotRenderer(plot, dataset);
  itemLabelGenerator = new ProjectionPlotItemLabelGenerator(parameters);
  spotRenderer.setDefaultItemLabelGenerator(itemLabelGenerator);
  spotRenderer.setDefaultItemLabelsVisible(true);
  spotRenderer.setDefaultToolTipGenerator(new ProjectionPlotToolTipGenerator(parameters));
  plot.setRenderer(spotRenderer);

  // Setup legend
  if (createLegend) {
    LegendItemCollection legendItemsCollection = new LegendItemCollection();
    for (int groupNumber = 0; groupNumber < dataset.getNumberOfGroups(); groupNumber++) {
      Object paramValue = dataset.getGroupParameterValue(groupNumber);
      if (paramValue == null) {
        // No parameter value available: search for raw data files
        // within this group, and use their names as group's name
        String fileNames = new String();
        for (int itemNumber = 0; itemNumber < dataset.getItemCount(0); itemNumber++) {
          String rawDataFile = dataset.getRawDataFile(itemNumber);
          if (dataset.getGroupNumber(itemNumber) == groupNumber)
            fileNames = fileNames.concat(rawDataFile);
        }
        if (fileNames.length() == 0)
          fileNames = "Empty group";

        paramValue = fileNames;
      }
      Color nextColor = (Color) spotRenderer.getGroupPaint(groupNumber);
      Color groupColor = new Color(nextColor.getRed(), nextColor.getGreen(), nextColor.getBlue(),
          Math.round(255 * dataPointAlpha));
      legendItemsCollection.add(new LegendItem(paramValue.toString(), "-", null, null,
          spotRenderer.getDataPointsShape(), groupColor));
    }
    plot.setFixedLegendItems(legendItemsCollection);
  }

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

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

  this.paintScale = paintScale;

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

  // title

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

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

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

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

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

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

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

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

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

  // Add a paintScaleLegend to chart

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

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

  chart.addSubtitle(paintScaleLegend);


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

public ProjectionPlotPanel(ProjectionPlotWindow masterFrame, ProjectionPlotDataset dataset,
    ParameterSet parameters) {
  super(null);

  boolean createLegend = false;
  if ((dataset.getNumberOfGroups() > 1) && (dataset.getNumberOfGroups() < 20))
    createLegend = true;

  chart = ChartFactory.createXYAreaChart("", dataset.getXLabel(), dataset.getYLabel(), dataset,
      PlotOrientation.VERTICAL, createLegend, false, false);
  chart.setBackgroundPaint(Color.white);

  setChart(chart);

  // title

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

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

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

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

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

  plot.setForegroundAlpha(dataPointAlpha);

  NumberFormat numberFormat = NumberFormat.getNumberInstance();

  // set the X axis (component 1) properties
  NumberAxis xAxis = (NumberAxis) plot.getDomainAxis();
  xAxis.setNumberFormatOverride(numberFormat);

  // set the Y axis (component 2) properties
  NumberAxis yAxis = (NumberAxis) plot.getRangeAxis();
  yAxis.setNumberFormatOverride(numberFormat);

  plot.setDataset(dataset);

  spotRenderer = new ProjectionPlotRenderer(plot, dataset);
  itemLabelGenerator = new ProjectionPlotItemLabelGenerator(parameters);
  spotRenderer.setDefaultItemLabelGenerator(itemLabelGenerator);
  spotRenderer.setDefaultItemLabelsVisible(true);
  spotRenderer.setDefaultToolTipGenerator(new ProjectionPlotToolTipGenerator(parameters));
  plot.setRenderer(spotRenderer);

  // Setup legend
  if (createLegend) {
    LegendItemCollection legendItemsCollection = new LegendItemCollection();
    for (int groupNumber = 0; groupNumber < dataset.getNumberOfGroups(); groupNumber++) {
      Object paramValue = dataset.getGroupParameterValue(groupNumber);
      if (paramValue == null) {
        // No parameter value available: search for raw data files
        // within this group, and use their names as group's name
        String fileNames = new String();
        for (int itemNumber = 0; itemNumber < dataset.getItemCount(0); itemNumber++) {
          String rawDataFile = dataset.getRawDataFile(itemNumber);
          if (dataset.getGroupNumber(itemNumber) == groupNumber)
            fileNames = fileNames.concat(rawDataFile);
        }
        if (fileNames.length() == 0)
          fileNames = "Empty group";

        paramValue = fileNames;
      }
      Color nextColor = (Color) spotRenderer.getGroupPaint(groupNumber);
      Color groupColor = new Color(nextColor.getRed(), nextColor.getGreen(), nextColor.getBlue(),
          (int) Math.round(255 * dataPointAlpha));
      legendItemsCollection.add(new LegendItem(paramValue.toString(), "-", null, null,
          spotRenderer.getDataPointsShape(), groupColor));
    }
    plot.setFixedLegendItems(legendItemsCollection);
  }

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

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 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();
}
 

@Override
public void run() {
  setStatus(TaskStatus.PROCESSING);
  logger.info("Create Kendrick mass plot of " + peakList);
  // Task canceled?
  if (isCanceled())
    return;

  JFreeChart chart = null;
  // 2D, if no third dimension was selected
  if (zAxisLabel.equals("none")) {
    chart = create2DKendrickMassPlot();
  }
  // 3D, if a third dimension was selected
  else {
    chart = create3DKendrickMassPlot();
  }
  chart.setBackgroundPaint(Color.white);

  // create chart JPanel
  EChartPanel chartPanel = new EChartPanel(chart, true, true, true, true, false);

  // Create Kendrick mass plot Window
  KendrickMassPlotWindow frame = new KendrickMassPlotWindow(chart, parameters, chartPanel);
  frame.add(chartPanel, BorderLayout.CENTER);

  // set title properties
  TextTitle chartTitle = chart.getTitle();
  chartTitle.setMargin(5, 0, 0, 0);
  chartTitle.setFont(titleFont);
  LegendTitle legend = chart.getLegend();
  legend.setVisible(false);
  frame.setTitle(title);
  frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
  frame.setBackground(Color.white);
  frame.setVisible(true);
  frame.pack();

  setStatus(TaskStatus.FINISHED);
  logger.info("Finished creating Kendrick mass plot of " + peakList);
}
 

@Override
public void run() {
  try {
    setStatus(TaskStatus.PROCESSING);
    logger.info("Create Van Krevelen diagram of " + peakList);
    // Task canceled?
    if (isCanceled())
      return;
    JFreeChart chart = null;
    // 2D, if no third dimension was selected
    if (zAxisLabel.equals("none")) {
      chart = create2DVanKrevelenDiagram();
    }
    // 3D, if a third dimension was selected
    else {
      chart = create3DVanKrevelenDiagram();
    }

    chart.setBackgroundPaint(Color.white);

    // create chart JPanel
    EChartPanel chartPanel = new EChartPanel(chart, true, true, true, true, false);

    // Create Van Krevelen Diagram window
    VanKrevelenDiagramWindow frame =
        new VanKrevelenDiagramWindow(chart, chartPanel, filteredRows);

    // create chart JPanel
    frame.add(chartPanel, BorderLayout.CENTER);

    // set title properties
    TextTitle chartTitle = chart.getTitle();
    chartTitle.setMargin(5, 0, 0, 0);
    chartTitle.setFont(titleFont);
    LegendTitle legend = chart.getLegend();
    legend.setVisible(false);
    frame.setTitle(title);
    frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
    frame.setBackground(Color.white);
    frame.setVisible(true);
    frame.pack();
    logger.info("Finished creating van Krevelen diagram of " + peakList);
    JOptionPane.showMessageDialog(frame, "Results summary:\n" + displayedFeatures
        + " feature list rows are displayed in the Van Krevelen diagram.\n"
        + featuresWithFormulasWithoutCHO
        + " feature list rows are not displayed, because the annotated molecular formula does not contain the elements C, H, and O.\n"
        + featuresWithoutFormula
        + " feature list rows are not displayed, because no molecular formula was assigned.");
    setStatus(TaskStatus.FINISHED);
  } catch (Throwable t) {
    setErrorMessage(
        "Nothing to plot here or some peaks have other identities than molecular formulas.\n"
            + "Have you annotated your features with molecular formulas?\n"
            + "You can use the feature list method \"Formula prediction\" to handle the task.");
    setStatus(TaskStatus.ERROR);
  }
}
 

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();
}