double processInternalChild(Sequence &parentNmer,int childID,
NthOrdSubstMatrix &Pt) {
Array2D<double>::RowIn2DArray<double> row=L[childID];
Array1D<double> V(numNmers);
Sequence childNmer;
for(int i=0 ; i<numNmers ; ++i) {
childNmer.fromInt(i,numCols,alphabetMap);
double joint=jointProb(parentNmer,childNmer,Pt);
V[i]=safeAdd(joint,row[i]);
}
double ll=sumLogProbs(V);
return ll;
}
virtual void processNode(InternalNode &u) {
int id=u.getID();
Array2D<double>::RowIn2DArray<double> row=L[id];
int left=u.getLeft()->getID(), right=u.getRight()->getID();
NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
Sequence nmer;
for(int i=0 ; i<numNmers ; ++i) {
nmer.fromInt(i,numCols,alphabetMap);
row[i]=
processInternalChild(nmer,left,leftPt)+
processInternalChild(nmer,right,rightPt);
}
}
void NmerRateMatrix::eqFreqsFromMarginals(Array1D<double> singleNucEqFreqs)
{
eqSingle=singleNucEqFreqs;
const int n=order+1;
Sequence nmer;
for(int i=0 ; i<numNmers ; ++i) {
nmer.fromInt(i,n,alphabetMap);
double P=1.0;
for(int pos=0 ; pos<n ; ++pos) {
P*=singleNucEqFreqs[nmer[pos]]; // ### should be in log space??
//cout<<singleNucEqFreqs[nmer[pos]]<<" * ";
}
//cout<<" = "<<P<<endl;
eq[i]=P;
}
if(lowerOrderModel)
static_cast<NmerRateMatrix*>(lowerOrderModel)->
eqFreqsFromMarginals(singleNucEqFreqs);
}
