///
/// Initializes a new instance of the class.
///
explicit basic_neighbor_joining(
const matrix_type & distances) ///< The distance matrix.
: _children ()
, _lengths ()
, _names ()
, _root (invalid_id)
{
//
// Allow empty matrices even though no tree will be produced from
// the write method.
//
if (distances.is_empty())
return;
//
// Allow just one node even though the tree produced from the write
// method will consist on only the node name ("0").
//
assert(distances.is_square());
auto n = distances.get_height();
id_type next_id = 0;
if (n == 1)
{
_root = _add_leaf(next_id);
return;
}
//
// Prepare a list of ids for the initial set of nodes.
//
typedef std::vector<id_type> vector_type;
vector_type x;
for (size_t i = 0; i < n; i++)
x.push_back(_add_leaf(next_id));
//
// Prepare the distance matrix that will be reduced by the
// algorithm.
//
matrix_type d (distances);
//
// Loop until there are only two nodes remaining in the distance
// matrix.
//
while (n > 2)
{
//
// Find the minimum Q value in the matrix, and use it to find
// the two nodes that will be joined. Join them by creating a
// new parent node.
//
const q_data q (d);
const id_type id (next_id++);
_add_parent(id, x[q.i], q.d_ik);
_add_parent(id, x[q.j], q.d_jk);
//
// Prepare the new, reduced distance matrix as well as the
// corresponding id vector.
//
matrix_type dd (n - 1, n - 1);
vector_type xx { id };
for (size_t r = 0, rr = 1; r < n; r++)
{
if (r == q.i || r == q.j)
continue;
xx.push_back(x[r]);
dd(rr, 0) = value_type(0.5) *
(d(r, q.i) + d(r, q.j) - q.d_ij);
for (size_t c = 0, cc = 1; c < r; c++)
if (c != q.i && c != q.j)
dd(rr, cc++) = d(r, c);
rr++;
}
//
// Copy the lower triangle to the upper triangle so the data
// in the next Q matrix matches the expected values.
//
dd.copy_lower_to_upper();
d.swap(dd);
x.swap(xx);
n--;
}
//
// Connect the last two nodes; note the loop above places new nodes
// at index zero, so here it is known that the leaf node must be at
// index 1, and so the root note must be at index 0.
//
_root = x[0];
_add_parent(_root, x[1], d(1, 0));
}
