private void setNorm(
double medDepth,
List<String> bad,
Map<String, Double> factor2,
Map<String, Double> sampleMedian) {
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
if (!bad.contains(entry.getKey())) {
for (Map.Entry<String, Sample> entrySample : entry.getValue().entrySet()) {
Sample sample = entrySample.getValue();
double norm1 = sample.getNorm1();
double fact2 = factor2.get(entry.getKey());
double smplMed = sampleMedian.get(sample.getSample());
sample.setNorm1b(Precision.round(norm1 * fact2 + 0.1, 2));
sample.setNorm2(
Precision.round(
medDepth != 0 ? log.value((norm1 * fact2 + 0.1) / medDepth) / log.value(2) : 0,
2));
sample.setNorm3(
Precision.round(
smplMed != 0 ? log.value((norm1 * fact2 + 0.1) / smplMed) / log.value(2) : 0, 2));
}
}
}
}
private void setFactor2(double medDepth, List<String> bad, Map<String, Double> factor2) {
for (Map.Entry<String, Map<String, Sample>> entry : samples.entrySet()) {
if (!bad.contains(entry.getKey())) {
List<Double> list = new LinkedList<>();
for (Map.Entry<String, Sample> entrySample : entry.getValue().entrySet()) {
Sample sample = entrySample.getValue();
list.add(sample.getNorm1());
}
double median = new Median().evaluate(toDoubleArray(list));
if (median != 0) {
factor2.put(entry.getKey(), medDepth / median);
} else {
factor2.put(entry.getKey(), 0.0);
}
}
}
}