double processInternalChild(Symbol parentSymbol,int parentID,int child,
NthOrdSubstMatrix &noPt) {
AlignmentSeq &track=A.getIthTrack(parentID);
AlignmentSeq &childTrack=A.getIthTrack(child);
int contextBegin=column-order;
if(contextBegin<0) contextBegin=0;
int contextLen=column-contextBegin;
Sequence context;
track.getSeq().getSubsequence(contextBegin,contextLen,context);//ACO
//A.getIthTrack(root->getID()).getSeq().getSubsequence(contextBegin,contextLen,context);//TRCO
int pos=MultSeqAlignment::rightmostGapPos(context,gapSymbols);
if(pos>=0) {
throw "this should not happen (FitchFelsenstein)::processInternalChild";
Sequence temp;
context.getSubsequence(pos+1,contextLen-pos-1,temp);
context=temp;
}
SubstitutionMatrix &Pt=*noPt.lookup(context,0,-1);
Array2D<double>::RowIn2DArray<double> row=L[child];
Symbol childSym=childTrack.getSeq()[column];
double ll;
if(gapSymbols.isMember(childSym)){
V.setAllTo(NEGATIVE_INFINITY);
for(Symbol a=0 ; a<numAlpha ; ++a) {
if(!gapSymbols.isMember(a)) {
V[(int)a]=safeAdd(row[a],Pt(parentSymbol,a));
}
}
ll=sumLogProbs(V);
}
else {
ll=safeAdd(row[childSym],Pt(parentSymbol,childSym));
}
return ll;
}
virtual void processNode(RootNode &u) {
int id=u.getID();
Symbol a=A.getIthTrack(id)[column];
int childID=u.getChild()->getID();
NthOrdSubstMatrix &Pt=*u.getSubstMatrix();
if(gapSymbols.isMember(a))
likelihood=0; // shouldn't happen...
else
likelihood=processInternalChild(a,childID,Pt,rootContextCode,
rootContextLength);
}
virtual void processNode(LeafNode &u) // DO NOT CHANGE THIS FUNCTION
{
int id=u.getID();
Symbol a=A.getIthTrack(id)[column];
Array2D<double>::RowIn2DArray<double> row=L[id];
if(gapSymbols.isMember(a))
for(Symbol i=0 ; i<numAlpha; ++i)
row[i]=0; //=log(1); missing data -- same as Seipel & Haussler
else
for(Symbol i=0 ; i<numAlpha; ++i)
row[i]=(i==a ? 0 : NEGATIVE_INFINITY);
}
double processInternalChild(Symbol parentSymbol,int child,
NthOrdSubstMatrix &noPt,
int contextCode,int contextLength) {
SubstitutionMatrix &Pt=*noPt.lookup(contextCode,contextLength);
Array2D<double>::RowIn2DArray<double> row=L[child];
Vector<double> V;
for(Symbol b=0 ; b<numAlpha ; ++b)
if(!gapSymbols.isMember(b))
V.push_back(row[b]+Pt(parentSymbol,b)); // Pt already in log space
double ll=sumLogProbs(V);
return ll;
}
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;
}
}
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);
}
}
