RootedSequenceTree::RootedSequenceTree(const RootedSequenceTree& T1, const RootedSequenceTree& T2)
:RootedTree(T1,T2)
{
// We will create new names which will be the same as
// T1.order + T2.order
for(int i=0;i<T1.get_sequences().size();i++)
sequences.push_back(T1.seq(i));
for(int i=0;i<T2.get_sequences().size();i++)
sequences.push_back(T2.seq(i));
}
int main(int argc,char* argv[])
{
try {
//---------- Parse command line -------//
variables_map args = parse_cmd_line(argc,argv);
RootedSequenceTree T = load_T(args);
int root=-1;
if (args.count("outgroup"))
{
string outgroup = args["outgroup"].as<string>();
int leaf = find_leaf(T,outgroup);
root = split_branch(T,leaf);
}
else if (args.count("taxa"))
{
string taxa = args["taxa"].as<string>();
vector<string> taxon = split(taxa,',');
if (taxon.size() != 3)
throw myexception()<<"You must supply exactly 3 taxa, but you supplied "<<taxon.size();
int n1 = find_leaf(T,taxon[0]);
int n2 = find_leaf(T,taxon[1]);
int n3 = find_leaf(T,taxon[2]);
T.reroot(n1);
root = T.common_ancestor(n2,n3);
}
else if (args.count("leaf"))
{
string leaf_name = args["leaf"].as<string>();
root = find_leaf(T,leaf_name);
}
else if (args.count("parent-of"))
{
string leaf_name = args["parent-of"].as<string>();
int leaf = find_leaf(T,leaf_name);
root = T.branch(leaf).target();
}
else if (args.count("branch"))
{
string p = args["branch"].as<string>();
vector<string> taxa = split(p,' ');
dynamic_bitset<> mask(T.n_leaves());
dynamic_bitset<> group1(T.n_leaves());
int separator = find_index(taxa,string("|"));
if (separator == -1)
throw myexception()<<"Partition is missing a separator";
for(int i=0;i<separator;i++)
{
int ii = find_leaf(T,taxa[i]);
mask[ii] = true;
group1[ii] = true;
}
for(int i=separator+1;i<taxa.size();i++)
{
int ii = find_leaf(T,taxa[i]);
mask[ii] = true;
}
Partition P(T.get_sequences(),group1,mask);
cerr<<P<<endl;
int b = which_partition(T,P);
cerr<<partition_from_branch(T,b)<<endl;
root = split_branch(T,b);
}
else
throw myexception("neither --outgroup nor --taxa nor --leaf specified!");
T.reroot(root);
std::cout<<T<<endl;
}
catch (std::exception& e) {
std::cerr<<"tree-reroot: Error! "<<e.what()<<endl;
exit(1);
}
return 0;
}
bool reader_t::next_tree(RootedSequenceTree& T)
{
T.get_sequences() = leaf_names;
return next_tree(static_cast<RootedTree&>(T));
}