/**
* Overloaded assignment operator.
* We need a deep copy of the operator.
*/
MetropolisHastingsMove& MetropolisHastingsMove::operator=(const RevBayesCore::MetropolisHastingsMove &m)
{
if ( this != &m )
{
// free memory
delete proposal;
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->removeMove( this );
// decrease the DAG node reference count because we also have a pointer to it
if ( theNode->decrementReferenceCount() == 0 )
{
delete theNode;
}
}
affectedNodes = m.affectedNodes;
nodes = m.nodes;
numAccepted = m.numAccepted;
proposal = m.proposal->clone();
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
return *this;
}
/**
* Overloaded assignment operator.
* We need a deep copy of the operator.
*/
AbstractMove& AbstractMove::operator=(const RevBayesCore::AbstractMove &m)
{
if ( this != &m )
{
// delegate
Move::operator=(m);
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->removeMove( this );
// decrease the DAG node reference count because we also have a pointer to it
if ( theNode->decrementReferenceCount() == 0 )
{
delete theNode;
}
}
affectedNodes = m.affectedNodes;
nodes = m.nodes;
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
return *this;
}
/**
* Constructor
*
* Here we simply allocate and initialize the move object.
*
* \param[in] w The weight how often the proposal will be used (per iteration).
* \param[in] t If auto tuning should be used.
*/
AbstractMove::AbstractMove( const std::vector<DagNode*> &n, double w, bool t ) :
nodes( n ),
affectedNodes( ),
weight( w ),
autoTuning( t )
{
for (std::vector<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
// remove all "core" nodes from affectedNodes so their probabilities are not double-counted
for (size_t i = 0; i < affectedNodes.size(); ++i)
{
RbOrderedSet<DagNode*>::iterator it = affectedNodes.begin();
std::advance(it, i);
for (size_t j = 0; j < nodes.size(); ++j)
{
if ( nodes[j] == *it )
{
affectedNodes.erase(*it);
--i;
break;
}
}
}
}
/**
* Copy constructor.
* We need to create a deep copy of the proposal here.
*
* \param[in] m The object to copy.
*
*/
MetropolisHastingsMove::MetropolisHastingsMove(const MetropolisHastingsMove &m) : AbstractMove(m),
affectedNodes( m.affectedNodes ),
nodes( m.nodes ),
numAccepted( m.numAccepted ),
proposal( m.proposal->clone() )
{
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
AbstractMove::AbstractMove( const AbstractMove &m ) : Move( m ),
nodes( m.nodes ),
affectedNodes( m.affectedNodes ),
weight( m.weight ),
autoTuning( m.autoTuning )
{
for (size_t i = 0; i < nodes.size(); ++i)
{
// get the pointer to the current node
DagNode* theNode = nodes[i];
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
}
}
/**
* Constructor
*
* Here we simply allocate and initialize the move object.
*
* \param[in] w The weight how often the proposal will be used (per iteration).
* \param[in] t If auto tuning should be used.
*/
MetropolisHastingsMove::MetropolisHastingsMove( Proposal *p, double w, bool t ) : AbstractMove(w,t),
affectedNodes(),
nodes(),
numAccepted( 0 ),
proposal( p )
{
nodes = proposal->getNodes();
for (std::set<DagNode*>::iterator it = nodes.begin(); it != nodes.end(); ++it)
{
// get the pointer to the current node
DagNode* theNode = *it;
// add myself to the set of moves
theNode->addMove( this );
// increase the DAG node reference count because we also have a pointer to it
theNode->incrementReferenceCount();
// get the affected nodes if we would update this node
// then we don't need to get the affected nodes every time again
theNode->getAffectedNodes( affectedNodes );
}
// remove all "core" nodes from affectedNodes so their probabilities are not double-counted
for (size_t i = 0; i < affectedNodes.size(); ++i)
{
std::set<DagNode*>::iterator it = affectedNodes.begin();
std::advance(it, i);
if ( nodes.find(*it) != nodes.end() )
{
affectedNodes.erase(*it);
--i;
}
}
}
