/** Get node indexed by this string */
public AcgtTree get(String bases) {
if (bases.isEmpty()) return this;
char base = bases.charAt(0);
AcgtTree node = get(base);
if (node == null) return null;
return node.get(bases.substring(1));
}
protected void pAll(int thresholdCount, List<Double> ps) {
for (int i = 0; i < nodes.length; i++) {
AcgtTree node = nodes[i];
double p[] = p();
if (node != null) {
if (counts[i] >= thresholdCount) ps.add(p[i]);
node.pAll(thresholdCount, ps);
}
}
}
public void add(String sequence) {
if ((sequence == null) || sequence.isEmpty()) {
totalCount++;
return;
}
// Count for this node
char base = sequence.charAt(0);
inc(base);
AcgtTree node = getOrCreate(base);
// Recurse into tree
node.add(sequence.substring(1));
}
/** 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;
}
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();
}
void entropyAll(int thresholdCount, ArrayList<Double> entropies) {
if (totalCount >= thresholdCount) entropies.add(entropy());
for (AcgtTree node : nodes) if (node != null) node.entropyAll(thresholdCount, entropies);
}