@Override
protected void setChart() {
SeriesManager<Double, Double> sf = new SeriesManager<Double, Double>(intermediateData);
List<DataSeries<Double, Double>> seriesList = sf.getSeries();
DataSeries<Double, Double> series = seriesList.get(0);
List<SeriesPair<Double, Double>> values = series.getSeriesValues(Double.class, Double.class);
XYSeries deltaMassSeries = new XYSeries(series.getIdentifier());
for (SeriesPair<Double, Double> value : values) {
deltaMassSeries.add(value.getX(), value.getY());
}
XYSeriesCollection dataset = new XYSeriesCollection();
dataset.addSeries(deltaMassSeries);
chart =
ChartFactory.createXYLineChart(
getChartTitle(), // chart title
"Experimental m/z - Theoretical m/z", // x axis label
"Relative Frequency", // y axis label
dataset, // chartData
PlotOrientation.VERTICAL,
false, // include legend
true, // tooltips
false // urls
);
chart.addSubtitle(new TextTitle(getChartSubTitle()));
XYPlot plot = chart.getXYPlot();
plot.setDomainZeroBaselineVisible(true);
plot.setBackgroundAlpha(0f);
plot.setDomainGridlinePaint(Color.red);
plot.setRangeGridlinePaint(Color.blue);
}
private DataSeries<Integer, Integer> getAllSpectraSeries(
List<DataSeries<Integer, Integer>> seriesList) {
List<Integer> keys = new ArrayList<Integer>();
Map<Integer, Integer> map = new HashMap<Integer, Integer>();
for (DataSeries<Integer, Integer> series : seriesList) {
for (SeriesPair<Integer, Integer> sp : series.getSeriesValues(Integer.class, Integer.class)) {
Integer key = sp.getX();
Integer value = map.containsKey(key) ? map.get(key) + sp.getY() : sp.getY();
if (!keys.contains(key)) keys.add(key);
map.put(key, value);
}
}
List<SeriesPair<Integer, Integer>> seriesPairs = new ArrayList<SeriesPair<Integer, Integer>>();
for (Integer key : keys) {
Integer value = map.get(key);
SeriesPair<Integer, Integer> seriesPair = new SeriesPair<Integer, Integer>(key, value);
seriesPairs.add(seriesPair);
}
return new DataSeries<Integer, Integer>(
DataSeriesType.ALL_SPECTRA, DataSeriesType.ALL_SPECTRA.getType(), seriesPairs);
}
@Override
protected void setChart() {
SeriesManager<Integer, Integer> sf = new SeriesManager<Integer, Integer>(intermediateData);
List<DataSeries<Integer, Integer>> seriesList = sf.getSeries();
// Adds the 'All Spectra' series at the end in the local variable 'seriesList'
// **NOTE** The intermediateData is NOT modified
seriesList.add(getAllSpectraSeries(seriesList));
List<Color> seriesColor = new ArrayList<Color>();
DefaultCategoryDataset dataset = new DefaultCategoryDataset();
for (DataSeries<Integer, Integer> series : seriesList) {
DataSeriesType seriesType = series.getType();
if (!visibleTypes.contains(seriesType)) continue;
String serieKey = series.getIdentifier();
List<SeriesPair<Integer, Integer>> values =
series.getSeriesValues(Integer.class, Integer.class);
Map<String, Integer> map = new HashMap<String, Integer>();
// The map is filled with the intermediate data values
int greaterThanTopValue = 0;
for (SeriesPair<Integer, Integer> value : values) {
int xValue = value.getX();
int yValue = value.getY();
if (xValue > TOP_VALUE) {
greaterThanTopValue += yValue;
} else {
map.put("" + xValue, yValue);
}
}
// Finally the JFreeChart data object is created and filled with the processed data
// DefaultKeyedValues data = new DefaultKeyedValues();
for (int i = 1; i <= TOP_VALUE; i++) {
String category = "" + i;
int value = map.containsKey(category) ? map.get(category) : 0;
dataset.addValue(value, serieKey, category);
}
dataset.addValue(greaterThanTopValue, serieKey, GT_TOP_VALUE_KEY);
seriesColor.add(seriesType.getColor());
}
chart =
ChartFactory.createBarChart(
getChartTitle(), // chart title
"Precursor Ion Charge", // x axis label
"Frequency", // y axis label
dataset, // chartData
PlotOrientation.VERTICAL,
true, // include legend
true, // tooltips
false // urls
);
chart.addSubtitle(new TextTitle());
CategoryPlot plot = (CategoryPlot) chart.getPlot();
BarRenderer renderer = (BarRenderer) plot.getRenderer();
renderer.setBaseItemLabelGenerator(new NumberLegendGenerator());
for (int i = 0; i < dataset.getRowCount(); i++) {
renderer.setSeriesItemLabelsVisible(i, Boolean.TRUE);
renderer.setSeriesPaint(i, seriesColor.get(i));
}
plot.getRangeAxis().setUpperMargin(CHART_UPPER_MARGIN);
plot.setBackgroundAlpha(0f);
plot.setDomainGridlinePaint(Color.red);
plot.setRangeGridlinePaint(Color.blue);
renderer.setShadowVisible(false);
renderer.setDrawBarOutline(false);
renderer.setItemMargin(0);
}