public String toString(
String tabs, double thresholdEntropy, double thresholdP, int thresholdCount) {
if (getTotalCount() == 0) return "";
StringBuilder sb = new StringBuilder();
double p[] = p();
for (int idx = 0; idx < 4; idx++) {
char base = BASES[idx];
AcgtTree n = nodes[idx];
if (n != null) {
sb.append(
String.format(
"%s%s%s: %d\te:%4.3f\tp:%4.2f\n",
tabs, name, base, counts[idx], n.entropy(), p[idx]));
if (((n.entropy() <= thresholdEntropy) || (p[idx] >= thresholdP)) //
&& (counts[idx] >= thresholdCount) //
) {
Gpr.debug(
"Name:"
+ n.name
+ "\tIdx:"
+ +idx
+ "\tEntropy: "
+ n.entropy()
+ "\tP:"
+ p[idx]
+ "\tCount:"
+ counts[idx]);
sb.append(n.toString(tabs + "\t", thresholdEntropy, thresholdP, thresholdCount));
}
}
}
return sb.toString();
}
/** Find node names that are within the thresholds */
public List<String> findNodeNames(
double thresholdEntropy, double thresholdP, int thresholdCount) {
ArrayList<String> names = new ArrayList<String>();
if (getTotalCount() == 0) return names;
double p[] = p();
for (int idx = 0; idx < 4; idx++) {
AcgtTree n = nodes[idx];
if (n != null) {
if (((parent == null)
|| (parent.entropy() <= thresholdEntropy)) // Parent's entropy is low enough?
&& (p[idx] >= thresholdP) // Probability is high enough?
&& (counts[idx] >= thresholdCount) // Do we have enough counts?
) {
names.add(n.name);
}
names.addAll(n.findNodeNames(thresholdEntropy, thresholdP, thresholdCount));
}
}
return names;
}
