/**
* Uses the calculator with name calcName to construct & display a series for the sg. This should
* be the only way new series' are added to the chart, since we need to keep track of all the
* current series in the sgSeriesMap
*
* @param calcName
* @param sg
*/
protected void addSeriesForSG(String calcName, SequenceGroup sg) {
BaseCounter calc = null;
try {
calc = sgReg.getBaseCounterInstance(calcName, sg);
} catch (IllegalArgumentException ex) {
System.err.println("Could not find base counter of type : " + calcName);
return;
}
List<AbstractSeries> seriesList = sgSeriesMap.get(sg);
if (seriesList == null) {
System.out.println(
"Uh-oh, this sequence group doesn't have an associated list in the sgSeriesMap...");
}
// Make a new series from the calculator
int windowsize = ((Integer) windowSizeSpinner.getValue()).intValue();
int windowStep = ((Integer) windowStepSpinner.getValue()).intValue();
if (usePartitionsBox.isSelected()) {
for (int i = 0; i < sg.getPartitionCount(); i++) {
BaseCounterSeries ser = calc.getWindowSeries(windowsize, windowStep, i);
ser.setPartitionIndex(i);
seriesList.add(ser);
ser.setName(calc.getName() + " - " + sg.getPartitionKeyForIndex(i));
if (ser != null && ser.size() > 0) {
chart.addDataSeries(ser);
chart.repaint();
}
}
} else {
BaseCounterSeries ser = calc.getWindowSeries(windowsize, windowStep);
seriesList.add(ser);
if (sgSeriesMap.size() > 1) {
String name = sg.getName();
if (name == null) {
ser.setName(calc.getName());
} else {
ser.setName(calc.getName() + " - " + sg.getName());
}
}
if (ser != null && ser.size() > 0) {
chart.addDataSeries(ser);
chart.repaint();
}
}
}
/**
* Called when one of the sliding window size or step values has changed. This attempts to be
* 'smart' and instead of recalculating everything from scratch,
*/
private void newWindowSizeAction() {
if (sgSeriesMap == null) return;
XYSeries data;
int windowSize = (Integer) windowSizeSpinner.getValue();
int windowStep = (Integer) windowStepSpinner.getValue();
int tot = 0;
for (AbstractSeries series : chart.getAllSeries()) {
if (series instanceof BaseCounterSeries) {
BaseCounterSeries bcSer = (BaseCounterSeries) series;
BaseCounter bc = bcSer.getCalculator();
int partitionIndex = bcSer.getPartitionIndex();
// System.out.println("Replacing series for calc with name : " + bcSer.getName() + " and
// partition : " + bcSer.getPartitionIndex());
if (partitionIndex > -1) {
bcSer.replaceSeries(bc.getWindowPointSeries(windowSize, windowStep, partitionIndex));
} else bcSer.replaceSeries(bc.getWindowPointSeries(windowSize, windowStep));
} else {
// System.err.println("Hmm, one of the series (" + series.getName() + ") is not a
// basecounter, cannot recalculate it for the new window size.");/
}
}
chart.repaint();
}
public void analyze(String name, Object data) {
if (data.getClass() != SequenceGroup.class) {
ErrorWindow.showErrorWindow(
new IllegalArgumentException(
"Got a incompatible data type for SequenceLineChart: " + data.getClass()));
return;
}
SequenceGroup currentSG = (SequenceGroup) data;
originalSG = currentSG;
originalSG.addPartitionListener(this);
originalSG.addSGChangeListener(this);
sgSeriesMap.put((SequenceGroup) data, new ArrayList<AbstractSeries>());
currentName = name;
if (topLabel != null) topLabel.setText(currentName);
else topLabel = new JLabel(currentName);
topLabel.setFont(defaultFont);
int maxLength = currentSG.getMaxSeqLength();
// Guess some decent initial values for size of window and step
int windowSize = Math.min(100, maxLength);
int windowStep = maxLength > 50 ? 10 : 1;
if (maxLength > 9999) {
windowSize = 1000;
windowStep = 100;
}
SpinnerModel sizeModel = new SpinnerNumberModel(windowSize, 1, maxLength, 1);
SpinnerModel stepModel = new SpinnerNumberModel(windowStep, 1, maxLength / 2, 1);
windowSizeSpinner.setModel(sizeModel);
windowStepSpinner.setModel(stepModel);
if (currentSG.getPartitionCount() < 2) {
usePartitionsBox.setSelected(false);
usePartitionsBox.setEnabled(false);
} else {
usePartitionsBox.setEnabled(true);
usePartitionsBox.setSelected(true);
}
toggleCalculator(SGStatisticsRegistry.NUC_DIVERSITY);
chart.repaint();
}