virtual void processNode(InternalNode &V)
{
V.setLeftSubstMatrix(Q.instantiate(V.getLeftDistance()));
V.setRightSubstMatrix(Q.instantiate(V.getRightDistance()));
int id=V.getID();
if(id>largestID) largestID=id;
++numNodes;
}
virtual void processNode(InternalNode &u) {
int id=u.getID();
PhylogenyNode *left=u.getLeft(), *right=u.getRight();
NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
Array2D<double>::RowIn2DArray<double> row=L[id];
for(Symbol a=0 ; a<numAlpha ; ++a) {
row[a]=
processInternalChild(a,left,leftPt,&u)+
processInternalChild(a,right,rightPt,&u);
}
}
virtual void processNode(InternalNode &u)
{
int id=u.getID();
Array2D<double>::RowIn2DArray<double> row=L[id];
Taxon *taxon=static_cast<Taxon*>(u.getDecoration());
SubstitutionMatrix &leftPt=getMatrix(*taxon,LEFT);
SubstitutionMatrix &rightPt=getMatrix(*taxon,RIGHT);
int left=u.getLeft()->getID(), right=u.getRight()->getID();
for(Symbol a=0 ; a<numAlpha ; ++a)
if(a!=gap) row[a]=
processInternalChild(a,left,leftPt)+
processInternalChild(a,right,rightPt);
}
virtual void processNode(InternalNode &u) {
int id=u.getID();
int left=u.getLeft()->getID(), right=u.getRight()->getID();
NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
Array2D<double>::RowIn2DArray<double> row=L[id];
for(Symbol a=0 ; a<numAlpha ; ++a) {
if(gapSymbols.isMember(a)) continue;
row[a]=
processInternalChild(a,left,leftPt,0,0)+
processInternalChild(a,right,rightPt,0,0);
}
}
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);
}
}
virtual void processNode(InternalNode &u) {
int id=u.getID();
NthOrdSubstMatrix &leftPt=*u.getLeftSubstMatrix();
NthOrdSubstMatrix &rightPt=*u.getRightSubstMatrix();
int left=u.getLeft()->getID(), right=u.getRight()->getID();
Array2D<double>::RowIn2DArray<double> row=L[id];
Symbol a=A.getIthTrack(id)[column];
if(gapSymbols.isMember(a))
for(a=0 ; a<numAlpha ; ++a) {
if(gapSymbols.isMember(a)) continue;
row[a]=
processInternalChild(a,id,left,leftPt)+
processInternalChild(a,id,right,rightPt);
}
else {
for(Symbol b=0 ; b<numAlpha ; ++b) row[b]=NEGATIVE_INFINITY;
double l=processInternalChild(a,id,left,leftPt);
double r=processInternalChild(a,id,right,rightPt);
row[a]=l+r;
}
}