/**
* 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();
}
/**
* Remove all series associated with the class specified
*
* @param toRemove
*/
public void removeSeriesByClass(Class toRemove) {
List<AbstractSeries> activeSeries = chart.getAllSeries();
for (AbstractSeries series : activeSeries) {
if (series instanceof BaseCounterSeries) {
BaseCounter bc = ((BaseCounterSeries) series).getCalculator();
if (bc.getClass() == toRemove) {
chart.removeSeries(series);
}
}
}
}
private JScrollPane createStatisticListPanel() {
Map<String, BaseCounter> statMap = sgReg.getBaseCounters();
int count = 0;
JPanel panel = new JPanel();
panel.setBackground(Color.white);
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
Color stripeColor = new Color(235, 235, 235);
for (final BaseCounter calc : statMap.values()) {
JPanel calcPanel = new JPanel();
calcPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
final String name = calc.getName();
JCheckBox box = new JCheckBox();
if (name.equals(
SGStatisticsRegistry.NUC_DIVERSITY)) // bit of a hack here to make sure this box starts
box.setSelected(true); // out selected
box.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
toggleCalculator(name);
}
});
calcPanel.add(box);
JLabel lab = new JLabel(name);
lab.setFont(new Font("Sans", Font.PLAIN, 11));
calcPanel.add(lab);
calcPanel.setBackground(Color.white);
calcPanel.setMaximumSize(new Dimension(500, 24));
calcPanel.setToolTipText(calc.getDescription());
if (count % 2 == 0) {
calcPanel.setBackground(stripeColor);
} else {
calcPanel.setBackground(Color.white);
}
panel.add(calcPanel);
count++;
}
JScrollPane pane = new JScrollPane(panel);
pane.getVerticalScrollBar().setAlignmentX(JComponent.LEFT_ALIGNMENT);
return pane;
}
/**
* 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();
}
}
}