@Override
public void update() {
if (burninMessage != null && logger.getBurninExceeded()) {
seriesFig.removeElement(burninMessage);
burninMessage = null;
}
if (logger.getBurninExceeded()) {
seriesFig.inferBoundsFromCurrentSeries();
meanSeries.setYVals(rhLogger.getMeans());
if (upper95Series == null && rhLogger.getHistoTriggerReached()) {
upper95Series =
new ConstSizeSeries("Upper 95%", rhLogger.getUpper95s(), rhLogger.getBinPositions());
XYSeriesElement upperEl =
new XYSeriesElement(upper95Series, seriesFig.getAxes(), seriesFig);
upperEl.setLineColor(Color.blue);
upperEl.setLineWidth(0.75f);
upperEl.setCanConfigure(true);
seriesFig.addSeriesElement(upperEl);
}
if (lower95Series == null && rhLogger.getHistoTriggerReached()) {
lower95Series =
new ConstSizeSeries("Lower 95%", rhLogger.getLower95s(), rhLogger.getBinPositions());
XYSeriesElement lowerEl =
new XYSeriesElement(lower95Series, seriesFig.getAxes(), seriesFig);
lowerEl.setLineColor(Color.blue);
lowerEl.setLineWidth(0.75f);
lowerEl.setCanConfigure(true);
seriesFig.addSeriesElement(lowerEl);
}
if (upper95Series != null) upper95Series.setYVals(rhLogger.getUpper95s());
if (lower95Series != null) {
lower95Series.setYVals(rhLogger.getLower95s());
}
}
seriesFig.repaint();
}
@Override
public void initialize() {
this.rhLogger = (RootHeightDensity) logger;
meanSeries =
new ConstSizeSeries("Mean height", rhLogger.getMeans(), rhLogger.getBinPositions());
XYSeriesElement meanEl = new XYSeriesElement(meanSeries, seriesFig.getAxes(), seriesFig);
meanEl.setLineColor(Color.blue);
meanEl.setLineWidth((float) 1.5);
meanEl.setCanConfigure(true);
seriesFig.addSeriesElement(meanEl);
seriesFig.setXLabel("Sequence Position");
seriesFig.setYLabel("Time to most recent common ancestor");
burninMessage =
new TextElement("Burnin period (" + logger.getBurnin() + ") not exceeded", seriesFig);
burninMessage.setPosition(0.45, 0.5);
seriesFig.addElement(burninMessage);
}