int choose_SPR_target(SequenceTree& T1, int b1_)
{
    const_branchview b1 = T1.directed_branch(b1_);

    //----- Select the branch to move to ------//
    dynamic_bitset<> subtree_nodes = T1.partition(b1.reverse());
    subtree_nodes[b1.target()] = true;

    vector<int> branches;
    vector<double> lengths;

    for(int i=0; i<T1.n_branches(); i++)
    {
        const_branchview bi = T1.branch(i);

        // skip branch if its contained in the subtree
        if (subtree_nodes[bi.target()] and
                subtree_nodes[bi.source()])
            continue;

        double L = 1.0;

        // down-weight branch if it is one of the subtree's 2 neighbors
        if (subtree_nodes[bi.target()] or
                subtree_nodes[bi.source()])
            L = 0.5;

        branches.push_back(i);
        lengths.push_back(L);
    }

    int b2 = branches[ choose(lengths) ];

    return b2;
}
Beispiel #2
0
Partition partition_from_branch(const SequenceTree& T,int b) 
{
  dynamic_bitset<> group(T.n_leaves());
  const dynamic_bitset<>& with_internal = T.partition(b);

  for(int i=0;i<group.size();i++)
    group[i] = with_internal[i];

  return Partition(T.get_leaf_labels(), group);
}