/**
* Returns a sequence plot as a ChartPanel.
*
* @param aProteinSequencePanelParent the protein sequence panel parent
* @param sparklineDataset the dataset
* @param proteinAnnotations the protein annotations
* @param addReferenceLine if true, a reference line is added
* @param allowZooming if true, the user can zoom in the created plot/chart
* @return a sequence plot
*/
public ChartPanel getSequencePlot(
ProteinSequencePanelParent aProteinSequencePanelParent,
JSparklinesDataset sparklineDataset,
HashMap<Integer, ArrayList<ResidueAnnotation>> proteinAnnotations,
boolean addReferenceLine,
boolean allowZooming) {
this.proteinSequencePanelParent = aProteinSequencePanelParent;
DefaultCategoryDataset barChartDataset = new DefaultCategoryDataset();
StackedBarRenderer renderer = new StackedBarRenderer();
renderer.setShadowVisible(false);
CategoryToolTipGenerator myTooltips = new ProteinAnnotations(proteinAnnotations);
// add the data
for (int i = 0; i < sparklineDataset.getData().size(); i++) {
JSparklinesDataSeries sparklineDataSeries = sparklineDataset.getData().get(i);
for (int j = 0; j < sparklineDataSeries.getData().size(); j++) {
barChartDataset.addValue(sparklineDataSeries.getData().get(j), "" + i, "" + j);
renderer.setSeriesPaint(i, sparklineDataSeries.getSeriesColor());
renderer.setSeriesToolTipGenerator(i, myTooltips);
}
}
// create the chart
JFreeChart chart =
ChartFactory.createStackedBarChart(
null, null, null, barChartDataset, PlotOrientation.HORIZONTAL, false, false, false);
// fine tune the chart properites
CategoryPlot plot = chart.getCategoryPlot();
// remove space before/after the domain axis
plot.getDomainAxis().setUpperMargin(0);
plot.getDomainAxis().setLowerMargin(0);
// remove space before/after the range axis
plot.getRangeAxis().setUpperMargin(0);
plot.getRangeAxis().setLowerMargin(0);
renderer.setRenderAsPercentages(true);
renderer.setBaseToolTipGenerator(new IntervalCategoryToolTipGenerator());
// add the dataset to the plot
plot.setDataset(barChartDataset);
// hide unwanted chart details
plot.getRangeAxis().setVisible(false);
plot.getDomainAxis().setVisible(false);
plot.setRangeGridlinesVisible(false);
plot.setDomainGridlinesVisible(false);
// add a reference line in the middle of the dataset
if (addReferenceLine) {
DefaultCategoryDataset referenceLineDataset = new DefaultCategoryDataset();
referenceLineDataset.addValue(1.0, "A", "B");
plot.setDataset(1, referenceLineDataset);
LayeredBarRenderer referenceLineRenderer = new LayeredBarRenderer();
referenceLineRenderer.setSeriesBarWidth(0, referenceLineWidth);
referenceLineRenderer.setSeriesFillPaint(0, referenceLineColor);
referenceLineRenderer.setSeriesPaint(0, referenceLineColor);
plot.setRenderer(1, referenceLineRenderer);
}
// set up the chart renderer
plot.setRenderer(0, renderer);
// hide the outline
chart.getPlot().setOutlineVisible(false);
// make sure the background is the same as the panel
chart.getPlot().setBackgroundPaint(backgroundColor);
chart.setBackgroundPaint(backgroundColor);
final HashMap<Integer, ArrayList<ResidueAnnotation>> blockTooltips = proteinAnnotations;
// create the chart panel
ChartPanel chartPanel = new ChartPanel(chart);
chartPanel.addChartMouseListener(
new ChartMouseListener() {
@Override
public void chartMouseClicked(ChartMouseEvent cme) {
if (cme.getEntity() != null && cme.getTrigger().getButton() == MouseEvent.BUTTON1) {
((CategoryItemEntity) cme.getEntity()).getDataset();
Integer blockNumber =
new Integer((String) ((CategoryItemEntity) cme.getEntity()).getRowKey());
ArrayList<ResidueAnnotation> annotation = blockTooltips.get(blockNumber);
if (annotation != null) {
proteinSequencePanelParent.annotationClicked(annotation, cme);
}
}
}
@Override
public void chartMouseMoved(ChartMouseEvent cme) {
cme.getTrigger()
.getComponent()
.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
if (cme.getEntity() != null && cme.getEntity() instanceof CategoryItemEntity) {
((CategoryItemEntity) cme.getEntity()).getDataset();
Integer blockNumber =
new Integer((String) ((CategoryItemEntity) cme.getEntity()).getRowKey());
ArrayList<ResidueAnnotation> annotation = blockTooltips.get(blockNumber);
if (annotation != null && !annotation.isEmpty()) {
if (blockTooltips.get(blockNumber).get(0).isClickable()) {
cme.getTrigger()
.getComponent()
.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}
}
}
}
});
if (!allowZooming) {
chartPanel.setPopupMenu(null);
chartPanel.setRangeZoomable(false);
}
chartPanel.setBackground(Color.WHITE);
return chartPanel;
}
public static String getBarSeries(Map dataSource, String objectName, HttpSession session)
throws Exception {
DefaultKeyedValues barValues = new DefaultKeyedValues();
DefaultKeyedValues seriesValues = new DefaultKeyedValues();
Element chartObject =
XMLHandler.getElementByAttribute(getChartObjectList(), "name", objectName);
Element barField = chartObject.getChild("BarFields").getChild("Field");
Element seriesField = chartObject.getChild("SeriesFields").getChild("Field");
for (int i = 0; i < dataSource.size(); i++) {
Map rec = (Map) dataSource.get("ROW" + i);
barValues.addValue(
DataFilter.show(rec, chartObject.getChildText("ColumnLabel")),
Double.parseDouble(rec.get(barField.getAttributeValue("name")).toString()));
seriesValues.addValue(
DataFilter.show(rec, chartObject.getChildText("ColumnLabel")),
Double.parseDouble(rec.get(seriesField.getAttributeValue("name")).toString()));
}
CategoryDataset dataset =
DatasetUtilities.createCategoryDataset(barField.getAttributeValue("label"), barValues);
PlotOrientation plotOrientation =
chartObject.getAttributeValue("plotOrientation").equalsIgnoreCase("VERTICAL")
? PlotOrientation.VERTICAL
: PlotOrientation.HORIZONTAL;
JFreeChart chart =
ChartFactory.createBarChart3D(
chartObject.getAttributeValue("title"),
chartObject.getAttributeValue("categoryAxisLabel"),
chartObject.getAttributeValue("valueAxisLabel"),
dataset,
plotOrientation,
chartObject.getAttribute("showLegend").getBooleanValue(),
chartObject.getAttribute("showToolTips").getBooleanValue(),
chartObject.getAttribute("urls").getBooleanValue());
CategoryPlot categoryplot = chart.getCategoryPlot();
LineRenderer3D lineRenderer = new LineRenderer3D();
CategoryDataset datasetSeries =
DatasetUtilities.createCategoryDataset(
seriesField.getAttributeValue("label"), seriesValues);
categoryplot.setDataset(1, datasetSeries);
categoryplot.setRangeAxis(1, new NumberAxis3D(seriesField.getAttributeValue("label")));
categoryplot.setRenderer(1, lineRenderer);
categoryplot.mapDatasetToRangeAxis(1, 1);
BarRenderer3D barrenderer = (BarRenderer3D) categoryplot.getRenderer();
barrenderer.setLabelGenerator(new StandardCategoryLabelGenerator());
barrenderer.setItemLabelsVisible(true);
barrenderer.setPositiveItemLabelPosition(
new ItemLabelPosition(ItemLabelAnchor.OUTSIDE1, TextAnchor.BASELINE_CENTER));
// lineRenderer.setLabelGenerator(new StandardCategoryLabelGenerator());
// lineRenderer.setItemLabelsVisible(true);
// lineRenderer.setPositiveItemLabelPosition(
// new ItemLabelPosition(ItemLabelAnchor.OUTSIDE10, TextAnchor.CENTER));
float alpha = 0.7F;
if (chartObject.getAttribute("alpha") != null) {
alpha = chartObject.getAttribute("alpha").getFloatValue();
}
categoryplot.setForegroundAlpha(alpha);
int width, height;
if (chartObject.getAttributeValue("width").equalsIgnoreCase("auto")) {
width = (50 * dataSource.size()) + 100;
} else {
width = Integer.parseInt(chartObject.getAttributeValue("width"));
}
if (chartObject.getAttributeValue("height").equalsIgnoreCase("auto")) {
height = (50 * dataSource.size()) + 100;
} else {
height = Integer.parseInt(chartObject.getAttributeValue("height"));
}
return ServletUtilities.saveChartAsPNG(chart, width, height, session);
}
