/// Load a tree from command line args "--tree filename"
RootedSequenceTree load_T(const variables_map& args) {
if (not args.count("tree"))
throw myexception()<<"Tree file not specified! (--tree <filename>)";
RootedSequenceTree RT;
RT.read(args["tree"].as<string>());
return RT;
}
/// Construct a multifurcating tree representing topology constraints from file \a filename.
///
/// \param filename The name of the file to load the tree from.
/// \param names The order of the leaf labels.
/// \return a multifurcating tree.
///
SequenceTree load_constraint_tree(const string& filename,const vector<string>& names)
{
RootedSequenceTree RT;
RT.read(filename);
SequenceTree constraint = RT;
remove_sub_branches(constraint);
try{
remap_T_indices(constraint,names);
}
catch(const bad_mapping<string>& b) {
bad_mapping<string> b2(b.missing,b.from);
if (b.from == 0)
b2<<"Constraint tree leaf sequence '"<<b2.missing<<"' not found in the alignment.";
else
b2<<"Alignment sequence '"<<b2.missing<<"' not found in the constraint tree.";
throw b2;
}
return constraint;
}