/**
* Selects the columns in the associated sequence group that correspond to the selected range in
* the current chart.
*/
protected void selectSitesFromAxesRange() {
if (chart.isRangeSelected()) {
double[] range = chart.getRangeSelection();
int rangeStart = (int) Math.round(range[0]);
int rangeEnd = (int) Math.round(range[1]);
try {
SGContentPanelDisplay sgDisplay = (SGContentPanelDisplay) source;
sgDisplay.selectColumns(rangeStart, rangeEnd);
} catch (ClassCastException ex) {
// apparently source wasn't an sgDisplay, not sure what should happen here
}
}
}
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();
}
/**
* Retrieve a new window series, but only using those sites in the specified partition. This is
* trickier than it should be. We only add a new value if TWO conditions are met: 1. The central
* site is in the specified partition. 2. At least windowSize / 10 sites in the range are in the
* partition
*
* @param windowSize The breadth of the window (in sites) over which to calculate a single value
* @param stepSize The amount the window is moved each step
* @param partitionIndex The partition to calculate the value for
* @return
*/
public ArrayList<Point2D> getWindowPointSeries(int windowSize, int stepSize, int partitionIndex) {
ArrayList<Point2D> points = new ArrayList<Point2D>();
for (int i = 0; i + windowSize < sg.getMaxSeqLength(); i += stepSize) {
double xValue = i;
double yValue = Double.NaN;
int startSite = Math.max(0, i - windowSize / 2);
if (sg.getPartitionNumForSite(i) == partitionIndex
|| sg.getPartitionNumForSite(i + 1) == partitionIndex
|| sg.getPartitionNumForSite(i + 2) == partitionIndex) {
Double[] sumCount = getSumAndCount(startSite, windowSize, partitionIndex);
if (sumCount[1] > ((double) windowSize / 10.0)) yValue = sumCount[0] / sumCount[1];
else yValue = Double.NaN;
}
points.add(new Point2D.Double(xValue, yValue));
}
return points;
}