double GeneralPathSuffStatMultipleMatrixMixtureProfileProcess::ProfileSuffStatLogProb(int cat, int l) {
double total = 0;
SubMatrix* mat = matrixarray[cat][l];
if (! mat) {
cerr << "error : null matrix\n";
cerr << cat << '\t' << Ncomponent << '\n';
cerr << occupancy[cat] << '\n';
exit(1);
}
const double* stat = mat->GetStationary();
for (map<int,int>::iterator i = profilerootcount[cat][l].begin(); i!= profilerootcount[cat][l].end(); i++) {
total += i->second * log(stat[i->first]);
}
for (map<int,double>::iterator i = profilewaitingtime[cat][l].begin(); i!= profilewaitingtime[cat][l].end(); i++) {
total += i->second * (*mat)(i->first,i->first);
}
for (map<pair<int,int>, int>::iterator i = profilepaircount[cat][l].begin(); i!= profilepaircount[cat][l].end(); i++) {
total += i->second * log((*mat)(i->first.first, i->first.second));
}
if (isnan(total)) {
cerr << "error: in GPSSMultipleMat ProfileSuffStatLogProb: nan\n";
exit(1);
}
return total;
}
double GeneralPathSuffStatMultipleMatrixMixtureProfileProcess::LogStatProb(int site, int cat) {
double total = 0;
int l = GetSubAlloc(site);
SubMatrix* mat = matrixarray[cat][l];
const double* stat = mat->GetStationary();
int rootstate = GetSiteRootState(site);
if (rootstate != -1) {
total += log(stat[GetSiteRootState(site)]);
map<int,double>& waitingtime = GetSiteWaitingTime(site);
for (map<int,double>::iterator i = waitingtime.begin(); i!= waitingtime.end(); i++) {
total += i->second * (*mat)(i->first,i->first);
}
map<pair<int,int>, int>& paircount = GetSitePairCount(site);
for (map<pair<int,int>, int>::iterator i = paircount.begin(); i!= paircount.end(); i++) {
total += i->second * log((*mat)(i->first.first, i->first.second));
}
}
return total;
}