/********************************************************************************************
Posterior of observing a certain state substitution along a branch:
P(Node=x,Father=y|D) = P(D,Node=x,Father=y)/P(D)
usage: posteriorPerNodePer2States[mynode->id()][fatherState][sonState]
*********************************************************************************************/
void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble &posteriorPerNodePer2States, int pos){
int numNodes = _tr.getNodesNum();
int alphabetSize = _sp->alphabetSize();
posteriorPerNodePer2States.resize(numNodes);
for (int n=0;n<posteriorPerNodePer2States.size();++n)
resizeMatrix(posteriorPerNodePer2States[n],alphabetSize,alphabetSize);
suffStatGlobalHomPos sscUp;
suffStatGlobalGamPos sscDownNonRev; // The "Gam" is used for the letter at father - sscGivenRoot
sscUp.allocatePlace(numNodes,alphabetSize);
computePijHom pi;
pi.fillPij(_tr,*_sp);
computeUpAlg comp_Up;
computeDownAlg comp_Down;
comp_Up.fillComputeUp(_tr,_sc,pos,pi,sscUp);
comp_Down.fillComputeDownNonReversible(_tr,_sc,pos,pi,sscDownNonRev,sscUp);
treeIterTopDownConst tIt(_tr);
MDOUBLE ll = convert(likelihoodComputation::getLofPos(pos,_tr,_sc,pi,*_sp));
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for (int sonState = 0; sonState<alphabetSize; ++sonState){
for (int fatherState = 0; fatherState<alphabetSize; ++fatherState){
posteriorPerNodePer2States[mynode->id()][fatherState][sonState]= computePosterioGivenTerminalsPerBranch(mynode->id(),sonState,fatherState,sscUp,sscDownNonRev, pi,ll,mynode->name());
}
}
}
}
void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(
VVVdouble & likelihoodArray)
{
unsigned int nbSites = likelihoodArray.size();
unsigned int nbClasses = likelihoodArray[0].size();
unsigned int nbStates = likelihoodArray[0][0].size();
for(unsigned int i = 0; i < nbSites; i++)
{
for(unsigned int c = 0; c < nbClasses; c++)
{
for(unsigned int s = 0; s < nbStates; s++)
{
likelihoodArray[i][c][s] = 1.;
}
}
}
}
void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(
const VVVdouble & likelihoodArray)
{
unsigned int nbSites = likelihoodArray.size();
unsigned int nbClasses = likelihoodArray[0].size();
unsigned int nbStates = likelihoodArray[0][0].size();
for(unsigned int i = 0; i < nbSites; i++)
{
cout << "Site " << i << ":" << endl;
for(unsigned int c = 0; c < nbClasses; c++)
{
cout << "Rate class " << c;
for(unsigned int s = 0; s < nbStates; s++)
{
cout << "\t" << likelihoodArray[i][c][s];
}
cout << endl;
}
cout << endl;
}
}
void DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(int nodeId, VVVdouble& likelihoodArray) const
{
const Node * node = _tree->getNode(nodeId);
likelihoodArray.resize(_nbDistinctSites);
map<int, VVVdouble> * likelihoods_node = & _likelihoodData->getLikelihoodArrays(nodeId);
//Initialize likelihood array:
if(node->isLeaf())
{
VVdouble * leavesLikelihoods_node = & _likelihoodData->getLeafLikelihoods(nodeId);
for(unsigned int i = 0; i < _nbDistinctSites; i++)
{
VVdouble * likelihoodArray_i = & likelihoodArray[i];
Vdouble * leavesLikelihoods_node_i = & (* leavesLikelihoods_node)[i];
likelihoodArray_i->resize(_nbClasses);
for(unsigned int c = 0; c < _nbClasses; c++)
{
Vdouble * likelihoodArray_i_c = & (* likelihoodArray_i)[c];
likelihoodArray_i_c->resize(_nbStates);
for(unsigned int x = 0; x < _nbStates; x++)
{
(* likelihoodArray_i_c)[x] = (* leavesLikelihoods_node_i)[x];
}
}
}
}
else
{
// Otherwise:
// Set all likelihoods to 1 for a start:
for(unsigned int i = 0; i < _nbDistinctSites; i++)
{
VVdouble * likelihoodArray_i = & likelihoodArray[i];
likelihoodArray_i->resize(_nbClasses);
for(unsigned int c = 0; c < _nbClasses; c++)
{
Vdouble * likelihoodArray_i_c = & (* likelihoodArray_i)[c];
likelihoodArray_i_c->resize(_nbStates);
for(unsigned int x = 0; x < _nbStates; x++)
{
(* likelihoodArray_i_c)[x] = 1.;
}
}
}
}
unsigned int nbNodes = node->getNumberOfSons();
vector<const VVVdouble *> iLik(nbNodes);
vector<const VVVdouble *> tProb(nbNodes);
for(unsigned int n = 0; n < nbNodes; n++)
{
const Node * son = node->getSon(n);
tProb[n] = & _pxy[son->getId()];
iLik[n] = & (* likelihoods_node)[son->getId()];
}
if(node->hasFather())
{
const Node * father = node->getFather();
computeLikelihoodFromArrays(iLik, tProb, & (* likelihoods_node)[father->getId()], & _pxy[nodeId], likelihoodArray, nbNodes, _nbDistinctSites, _nbClasses, _nbStates, false);
}
else
{
computeLikelihoodFromArrays(iLik, tProb, likelihoodArray, nbNodes, _nbDistinctSites, _nbClasses, _nbStates, false);
//We have to account for the root frequencies:
for(unsigned int i = 0; i < _nbDistinctSites; i++)
{
VVdouble * likelihoodArray_i = & likelihoodArray[i];
for(unsigned int c = 0; c < _nbClasses; c++)
{
Vdouble * likelihoodArray_i_c = & (* likelihoodArray_i)[c];
for(unsigned int x = 0; x < _nbStates; x++)
{
(* likelihoodArray_i_c)[x] *= _rootFreqs[x];
}
}
}
}
}