/**
* 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;
}
/**
* This works just like getValueRange, in that it computes the sum of the values in the
* frequencies array over a the given range. But instead of returning sum / number counted, this
* returns the two values separately in the array (sum first, then number counted).
*
* @param begin
* @param length
* @param partitionIndex
* @return
*/
public Double[] getSumAndCount(int begin, int length, double partitionIndex) {
if (freqs == null || freqs.length == 0) {
// ErrorWindow.showErrorWindow(new NullPointerException("BaseCounter " + getName() + " was not
// properly initialized"), null);
System.out.println("Value is NaN, freqs is : " + freqs);
return new Double[] {0.0, Double.NaN};
}
double sum = 0;
double counted = 0;
for (int i = begin; i < (begin + length); i++) {
if (partitionIndex < 0 || sg.getPartitionNumForSite(i) == partitionIndex) {
if (!Double.isNaN(freqs[i])) {
sum += freqs[i];
counted++;
}
}
}
return new Double[] {sum, counted};
}
