uint64 rank(Perm p) {
Perm p2;
copyPerm(p2, p);
Perm r;
invertPerm(p2, r);
return rankRecur(PERM_LEN, p2, r);
}
bool SpidirParams::order(SpeciesTree *stree)
{
if (stree->nnodes != nsnodes) {
printError("wrong number of parameters: %d %d\n", stree->nnodes, nsnodes);
return false;
}
ExtendArray<Node*> nodeorder(0, stree->nnodes);
getTreePreOrder(stree, &nodeorder);
// make interior node names
ExtendArray<int> inodes(stree->nnodes);
int inodename = 1;
for (int i=0; i<stree->nnodes; i++) {
Node *node = nodeorder[i];
if (node->isLeaf()) {
inodes[node->name] = -1;
} else {
inodes[node->name] = inodename++;
}
}
// loop through preordered nodes to construct permutation
ExtendArray<int> invperm(0, stree->nnodes);
for (int j=0; j<nsnodes; j++) {
if (invperm.size() != j) {
printError("unable to match '%s' to the species tree",
names[j].c_str());
return false;
}
// try to parse node id as an int
int id;
bool isint = (sscanf(names[j].c_str(), "%d", &id) == 1);
for (int i=0; i<stree->nnodes; i++) {
if (stree->nodes[i]->isLeaf()) {
// if leaf, check if names match
if (names[j] == stree->nodes[i]->longname) {
invperm.append(i);
break;
}
} else {
if (isint && id == inodes[i]) {
invperm.append(i);
break;
}
}
}
}
// apply permutation
ExtendArray<int> perm(stree->nnodes);
invertPerm(invperm, perm, nsnodes);
permute(names, perm, nsnodes);
permute(sp_alpha, perm, nsnodes);
permute(sp_beta, perm, nsnodes);
return true;
}