string write_with_bootstrap_fraction(const vector<string>& names, const_branchview b,
const vector<double>& bf, bool print_lengths)
{
string output;
// If this is a leaf node, then print the name
if (b.target().is_leaf_node())
output += names[b.target()];
// If this is an internal node, then print the subtrees
else {
vector<const_branchview> branches = sorted_branches_after(b);
output = "(";
for(int i=0;i<branches.size();i++) {
output += write_with_bootstrap_fraction(names,branches[i],bf,print_lengths);
if (i+1<branches.size())
output += ",";
}
output += ")";
}
// print the branch length if requested
double bfb = bf[b.undirected_name()];
if (bfb >= 0)
output += " " + convertToString<double>(bf[b.undirected_name()]);
if (print_lengths)
output += ":" + convertToString(b.length());
else if (bfb >= 0)
output += ":1.0";
return output;
}
string write_no_names(const_branchview b, bool print_lengths)
{
string output;
// If this is a leaf node, then print the name
if (b.target().is_leaf_node())
output += convertToString(b.target().name()+1);
// If this is an internal node, then print the subtrees
else {
vector<const_branchview> branches = sorted_branches_after(b);
output = "(";
for(int i=0;i<branches.size();i++) {
output += write_no_names(branches[i],print_lengths);
if (i+1<branches.size())
output += ",";
}
output += ")";
}
// print the branch length if requested
if (print_lengths)
output += ":" + convertToString(b.length());
return output;
}
vector<const_branchview> randomized_branches_after(const const_branchview& b)
{
vector<const_branchview> branches;
append(b.branches_after(), branches);
sort(branches.begin(), branches.end());
return randomize(branches);
}
vector<const_branchview> sorted_branches_after(const_branchview b) {
vector<const_branchview> branches;
append(b.branches_after(),branches);
std::sort(branches.begin(),branches.end(),branch_order);
return branches;
}
bool branch_order(const const_branchview& b1,const const_branchview& b2) {
return b1.target().name() < b2.target().name();
}
