void T92GCBranchTree::recursiveUpdate(const RevBayesCore::TopologyNode &from) {
size_t index = from.getIndex();
double gc = 0.5;
if (from.isRoot()) {
gc = rootgc->getValue();
}
else {
gc = gctree->getValue()[index];
}
RateMatrix_HKY& matrix = static_cast<RateMatrix_HKY&>( (*value)[index] );
std::vector<double> v(4);
v[0] = v[3] = 0.5 * (1 - gc);
v[1] = v[2] = 0.5 * gc;
matrix.setStationaryFrequenciesByCopy(v);
matrix.setKappa(kappa->getValue());
// simulate the val for each child (if any)
size_t numChildren = from.getNumberOfChildren();
for (size_t i = 0; i < numChildren; ++i) {
const TopologyNode& child = from.getChild(i);
recursiveUpdate(child);
}
}
void BranchLengthTree::reverseParentChild(RevBayesCore::TopologyNode &n)
{
if ( !n.isRoot() )
{
TopologyNode &p = n.getParent();
reverseParentChild( p );
p.removeChild( &n );
p.setParent( &n );
n.addChild( &p );
// swap branch lengths
double parent_branch_length = branchLengths[p.getIndex()];
double child_branch_length = branchLengths[n.getIndex()];
branchLengths[p.getIndex()] = child_branch_length;
branchLengths[n.getIndex()] = parent_branch_length;
}
}
void Func_simTree::setAges(RevBayesCore::TimeTree *t, RevBayesCore::TopologyNode &n)
{
if ( n.isTip() )
{
t->setAge(n.getIndex(), 0.0);
}
else
{
RevBayesCore::TopologyNode &left = n.getChild( 0 );
setAges(t, left);
RevBayesCore::TopologyNode &right = n.getChild( 1 );
setAges(t, right);
double a = t->getAge(left.getIndex());
double b = t->getAge(right.getIndex());
double max = (a > b ? a : b);
t->setAge(n.getIndex(), max + 1.0);
}
}