void add_internal_labels(SequenceTree& T)
{
for(int i=0;i<T.n_nodes();i++)
if (T.node(i).is_internal_node())
{
if (T.get_label(i) == "")
T.set_label(i, string("A") + convertToString(i));
}
}
/// \brief Remap the leaf indices of tree \a T to match the alignment \a A: check the result
///
/// \param A The alignment.
/// \param T The tree.
/// \param internal_sequences Should the resulting alignment have sequences for internal nodes on the tree?
///
void link(alignment& A,SequenceTree& T,bool internal_sequences)
{
check_names_unique(A);
// Later, might we WANT sub-branches???
if (has_sub_branches(T))
remove_sub_branches(T);
if (internal_sequences and not is_Cayley(T) and T.n_leaves() > 1) {
assert(has_polytomy(T));
throw myexception()<<"Cannot link a multifurcating tree to an alignment with internal sequences.";
}
//------ IF sequences < leaf nodes THEN complain ---------//
if (A.n_sequences() < T.n_leaves())
throw myexception()<<"Tree has "<<T.n_leaves()<<" leaves but Alignment only has "
<<A.n_sequences()<<" sequences.";
//----- IF sequences = leaf nodes THEN maybe add internal sequences.
else if (A.n_sequences() == T.n_leaves())
{
A = remap_A_indices(A,T);
if (internal_sequences)
{
add_internal_labels(T);
A = add_internal(A,T);
connect_leaf_characters(A,T);
}
}
//----- IF sequences > leaf nodes THEN maybe complain -------//
else if (A.n_sequences() > T.n_nodes())
throw myexception()<<"More alignment sequences ("<<A.n_sequences()<<") than tree nodes ("<<T.n_nodes()<<")!";
else if (A.n_sequences() < T.n_nodes())
throw myexception()<<"Fewer alignment sequences ("<<A.n_sequences()<<") than tree nodes ("<<T.n_nodes()<<")!";
else
{
A = remap_A_indices(A,T);
if (not internal_sequences)
A = chop_internal(A);
}
//---------- double-check that we have the right number of sequences ---------//
if (internal_sequences)
assert(A.n_sequences() == T.n_nodes());
else
assert(A.n_sequences() == T.n_leaves());
//----- Check that each alignment sequence maps to a corresponding name in the tree -----//
for(int i=0;i<A.n_sequences();i++)
assert(T.get_label(i) == A.seq(i).name);
//---- Check to see that internal nodes satisfy constraints ----//
check_alignment(A,T,internal_sequences);
}