private void zeroSubtreeCoalCountsIntensities(PopsIONode node) {
if (node.lft >= 0) {
zeroSubtreeCoalCountsIntensities(pionodes[node.lft]);
zeroSubtreeCoalCountsIntensities(pionodes[node.rgt]);
}
node.coalcount = 0;
node.coalintensity = 0.0;
}
private void recordSubtreeLineageCounts(PopsIONode node) {
if (node.lft < 0) {
int spIndex = piosb.speciesId2index(node.getTaxon().getId());
node.nlineages = piosb.nLineages(spIndex);
} else {
node.nlineages = 0;
recordSubtreeLineageCounts(pionodes[node.lft]);
node.nlineages += pionodes[node.lft].nlineages - pionodes[node.lft].coalheights.size();
recordSubtreeLineageCounts(pionodes[node.rgt]);
node.nlineages += pionodes[node.rgt].nlineages - pionodes[node.rgt].coalheights.size();
}
}
private void accumSubtreeCoalCountsIntensities(PopsIONode node) {
if (node.lft >= 0) {
accumSubtreeCoalCountsIntensities(pionodes[node.lft]);
accumSubtreeCoalCountsIntensities(pionodes[node.rgt]);
}
int k = node.coalheights.size();
node.coalcount += k;
double[] t = new double[k + 2];
t[0] = node.height;
for (int i = 0; i < k; i++) {
t[i + 1] = node.coalheights.get(i);
}
t[k + 1] = (node.anc < 0) ? piosb.maxGeneTreeHeight() : pionodes[node.anc].height;
int n = node.nlineages;
for (int i = 0; i <= k; i++) {
node.coalintensity += (t[i + 1] - t[i]) * 0.5 * (n - i) * (n - i - 1);
}
}
private String subtreeAsText(PopsIONode node, String s, Stack<Integer> x, int depth, String b) {
Integer[] y = x.toArray(new Integer[x.size()]);
StringBuffer indent = new StringBuffer();
for (int i = 0; i < depth; i++) {
indent.append(" ");
}
for (int i = 0; i < y.length; i++) {
indent.replace(2 * y[i], 2 * y[i] + 1, "|");
}
if (b.length() > 0) {
indent.replace(indent.length() - b.length(), indent.length(), b);
}
s += indent;
s += node.asText(indent.length());
s += System.getProperty("line.separator");
String subs = "";
if (node.lft >= 0) {
x.push(depth);
subs += subtreeAsText(pionodes[node.lft], "", x, depth + 1, "-");
x.pop();
subs += subtreeAsText(pionodes[node.rgt], "", x, depth + 1, "`-");
}
return s + subs;
}