void AACodonMutSelSBDPPhyloProcess::ReadPredictedOmega(string name, int burnin, int every, int until) {
if (GetNprocs() > 1) {
cerr << "error in read predicted omega: works only under non mpi\n";
exit(1);
}
double* meanomega = new double[GetNsite()];
for (int i=0; i<GetNsite(); i++) {
meanomega[i] = 0;
}
ifstream is((name + ".chain").c_str());
if (!is) {
cerr << "error: no .chain file found\n";
exit(1);
}
cerr << "burnin : " << burnin << "\n";
cerr << "until : " << until << '\n';
int i=0;
while ((i < until) && (i < burnin)) {
FromStream(is);
i++;
}
int samplesize = 0;
while (i < until) {
cerr << ".";
cerr.flush();
samplesize++;
FromStream(is);
i++;
UpdateMatrices();
for (int i=0; i<GetNsite(); i++) {
meanomega[i] += GetPredictedOmega(i);
}
int nrep = 1;
while ((i<until) && (nrep < every)) {
FromStream(is);
i++;
nrep++;
}
}
cerr << '\n';
double mean = 0;
ofstream os((name + ".predsiteomega").c_str());
os << "site\tomega\n";
for (int i=0; i<GetNsite(); i++) {
meanomega[i] /= samplesize;
mean += meanomega[i];
os << i+1 << '\t' << meanomega[i] << '\n';
}
cerr << "mean site-specific predicted dN/dS in" << name << ".predsiteomega\n";
mean /= GetNsite();
cerr << "global mean predicted omega: " << mean << '\n';
cerr << '\n';
}
bool iDibReader::FromFile(iPaletteDib& dib, const iStringT& fname) const
{
if (!iFile::Exists(fname)) return false;
IMG_TYPE it;
if (fname.Right(4).CompareIgnoreCase(_T(".bmp")) == 0) it = IT_BMP;
else if (fname.Right(4).CompareIgnoreCase(_T(".gif")) == 0) it = IT_GIF;
else return false;
iFilePtr pFile = NULL;
pFile = OpenWin32File(fname);
if (!pFile) return false;
bool bRes = FromStream(dib,pFile.get(),it);
return bRes;
}
void CodonMutSelSBDPPhyloProcess::Read(string name, int burnin, int every, int until) {
ifstream is((name + ".chain").c_str());
if (! is) {
cerr << "error: did not find " << name << ".chain\n";
exit(1);
}
//cerr << "In CodonMutSelDPPhyloProcess. GetDim() is : " << GetDim() << "\n";
int Nstate = CodonMutSelSBDPSubstitutionProcess::GetNstate();
//cerr << "Nstate is: " << Nstate << "\n";
//cerr.flush();
double TOOSMALL = 1e-20;
int Ncat = 241;
double min = -30;
double max = 30;
double step = 0.25;
double meanlength = 0;
double varlength = 0;
double** PosteriorMeanSiteCodonP = new double*[ProfileProcess::GetNsite()];
double** sshistoMut = new double*[ProfileProcess::GetNsite()];
double** sshistoSub = new double*[ProfileProcess::GetNsite()];
double** sshistoNonsynMut = new double*[ProfileProcess::GetNsite()];
double** sshistoNonsynSub = new double*[ProfileProcess::GetNsite()];
double** sshistoSynMut = new double*[ProfileProcess::GetNsite()];
double** sshistoSynSub = new double*[ProfileProcess::GetNsite()];
for (int site = 0; site < ProfileProcess::GetNsite(); site++) {
PosteriorMeanSiteCodonP[site] = new double[GetDim()];
sshistoMut[site] = new double[Ncat];
sshistoSub[site] = new double[Ncat];
sshistoNonsynMut[site] = new double[Ncat];
sshistoNonsynSub[site] = new double[Ncat];
sshistoSynMut[site] = new double[Ncat];
sshistoSynSub[site] = new double[Ncat];
for (int a = 0; a < GetDim(); a++) {
PosteriorMeanSiteCodonP[site][a] = 0;
}
for (int a = 0; a < Ncat; a++) {
sshistoMut[site][a] = 0;
sshistoSub[site][a] = 0;
sshistoNonsynMut[site][a] = 0;
sshistoNonsynSub[site][a] = 0;
sshistoSynMut[site][a] = 0;
sshistoSynSub[site][a] = 0;
}
}
double* meanNucStat = new double[Nnuc];
for (int i=0; i<Nnuc; i++) {
meanNucStat[i]=0.0;
}
double* meanNucRR = new double[Nnucrr];
for (int i=0; i<Nnucrr; i++) {
meanNucRR[i] = 0.0;
}
double* ghistoMut = new double[Ncat];
double* ghistoSub = new double[Ncat];
double* ghistoNonsynMut = new double[Ncat];
double* ghistoNonsynSub = new double[Ncat];
double* ghistoSynMut = new double[Ncat];
double* ghistoSynSub = new double[Ncat];
double* shistoMut = new double[Ncat];
double* shistoSub = new double[Ncat];
double* shistoNonsynMut = new double[Ncat];
double* shistoNonsynSub = new double[Ncat];
double* shistoSynMut = new double[Ncat];
double* shistoSynSub = new double[Ncat];
double* tsshistoMut = new double[Ncat];
double* tsshistoSub = new double[Ncat];
double* tsshistoNonsynMut = new double[Ncat];
double* tsshistoNonsynSub = new double[Ncat];
double* tsshistoSynMut = new double[Ncat];
double* tsshistoSynSub = new double[Ncat];
for (int c = 0; c < Ncat; c++) {
ghistoMut[c] = 0;
ghistoSub[c] = 0;
ghistoNonsynMut[c] = 0;
ghistoNonsynSub[c] = 0;
ghistoSynMut[c] = 0;
ghistoSynSub[c] = 0;
}
//const double* stat;
double* stat = new double[Nstate];
int pos, nucFrom, nucTo, nucRRIndex, c;
double statMutRate, S, statSubRate, totalMut, totalSub, totalNonsynMut, totalNonsynSub, totalSynMut, totalSynSub, siteTotalMut, siteTotalSub, siteTotalNonsynMut, siteTotalNonsynSub, siteTotalSynMut, siteTotalSynSub, Z;
cerr << "Ncat is " << Ncat << "\n";
cerr << "burnin : " << burnin << "\n";
cerr << "until : " << until << '\n';
int i=0;
while ((i < until) && (i < burnin)) {
cerr << ".";
cerr.flush();
FromStream(is);
i++;
}
int samplesize = 0;
while (i < until) {
// cerr << ".";
cerr.flush();
samplesize++;
FromStream(is);
i++;
QuickUpdate();
//UpdateMatrices();
//Trace(cerr);
double length = GetTotalLength();
// int nocc = process->GetNOccupiedComponent();
meanlength += length;
varlength += length * length;
for (int a=0; a<Nnuc; a++) {
meanNucStat[a] += GetNucStat(a);
}
for (int a=0; a<Nnucrr; a++) {
meanNucRR[a] += GetNucRR(a);
}
totalMut = 0;
totalSub = 0;
totalNonsynMut = 0;
totalNonsynSub = 0;
totalSynMut = 0;
totalSynSub = 0;
for (c = 0; c < Ncat; c++) {
shistoMut[c] = 0;
shistoSub[c] = 0;
shistoNonsynMut[c] = 0;
shistoNonsynSub[c] = 0;
shistoSynMut[c] = 0;
shistoSynSub[c] = 0;
}
for (int site=0; site<ProfileProcess::GetNsite(); site++) {
siteTotalMut = 0;
siteTotalSub = 0;
siteTotalNonsynMut = 0;
siteTotalNonsynSub = 0;
siteTotalSynMut = 0;
siteTotalSynSub = 0;
for (c = 0; c < Ncat; c++) {
tsshistoMut[c] = 0;
tsshistoSub[c] = 0;
tsshistoNonsynMut[c] = 0;
tsshistoNonsynSub[c] = 0;
tsshistoSynMut[c] = 0;
tsshistoSynSub[c] = 0;
}
for (int a=0; a<GetDim(); a++) {
PosteriorMeanSiteCodonP[site][a] += profile[alloc[site]][a];
}
Z = 0;
for (int s=0; s<Nstate; s++) {
stat[s] = GetNucStat(GetCodonStateSpace()->GetCodonPosition(0, s)) *
GetNucStat(GetCodonStateSpace()->GetCodonPosition(1, s)) *
GetNucStat(GetCodonStateSpace()->GetCodonPosition(2, s)) *
profile[alloc[site]][s];
Z += stat[s];
}
for (int s=0; s<Nstate; s++) {
stat[s] /= Z;
}
//stat = GetStationary(site);
//stat = matrixarray[alloc[site]]->GetStationary();
for (int codonFrom = 0; codonFrom<Nstate; codonFrom++) {
for (int codonTo = 0; codonTo<Nstate; codonTo++) {
pos = GetCodonStateSpace()->GetDifferingPosition(codonFrom, codonTo);
if ((pos != -1) && (pos != 3)) {
nucFrom = GetCodonStateSpace()->GetCodonPosition(pos, codonFrom);
nucTo = GetCodonStateSpace()->GetCodonPosition(pos, codonTo);
if (nucFrom<nucTo) {
nucRRIndex = (2 * Nnuc - nucFrom - 1) * nucFrom / 2 + nucTo - nucFrom - 1;
}
else {
nucRRIndex = (2 * Nnuc - nucTo - 1) * nucTo / 2 + nucFrom - nucTo - 1;
}
statMutRate = GetNucRR(nucRRIndex) * GetNucStat(nucTo) * stat[codonFrom];
S = log(profile[alloc[site]][codonTo]/profile[alloc[site]][codonFrom]);
if (fabs(S) < TOOSMALL) {
statSubRate = statMutRate * 1.0/( 1.0 - (S / 2) );
}
else {
statSubRate = statMutRate * (S/(1-(profile[alloc[site]][codonFrom]/profile[alloc[site]][codonTo])));
}
if (S < min) {
c = 0;
}
else if (S > max) {
c = Ncat-1;
}
else {
c = 0;
double tmp = min + ((double)c * step) - step/2 + step;
do {
c++;
tmp = min + ((double)(c) * step) - step/2 + step;
} while (tmp < S );
}
if (c == Ncat) {
cout << "error, c==Ncat.\n";
cout.flush();
}
shistoMut[c] += statMutRate;
shistoSub[c] += statSubRate;
tsshistoMut[c] += statMutRate;
tsshistoSub[c] += statSubRate;
if (!GetCodonStateSpace()->Synonymous(codonFrom, codonTo)) {
shistoNonsynMut[c] += statMutRate;
shistoNonsynSub[c] += statSubRate;
totalNonsynMut += statMutRate;
totalNonsynSub += statSubRate;
tsshistoNonsynMut[c] += statMutRate;
tsshistoNonsynSub[c] += statSubRate;
siteTotalNonsynMut += statMutRate;
siteTotalNonsynSub += statSubRate;
}
else {
shistoSynMut[c] += statMutRate;
shistoSynSub[c] += statSubRate;
totalSynMut += statMutRate;
totalSynSub += statSubRate;
tsshistoSynMut[c] += statMutRate;
tsshistoSynSub[c] += statSubRate;
siteTotalSynMut += statMutRate;
siteTotalSynSub += statSubRate;
}
totalMut += statMutRate;
totalSub += statSubRate;
siteTotalMut += statMutRate;
siteTotalSub += statSubRate;
}
}
}
for (c=0; c<Ncat; c++) {
sshistoMut[site][c] += tsshistoMut[c]/siteTotalMut;
sshistoSub[site][c] += tsshistoSub[c]/siteTotalSub;
sshistoNonsynMut[site][c] += tsshistoNonsynMut[c]/siteTotalNonsynMut;
sshistoNonsynSub[site][c] += tsshistoNonsynSub[c]/siteTotalNonsynSub;
sshistoSynMut[site][c] += tsshistoSynMut[c]/siteTotalSynMut;
sshistoSynSub[site][c] += tsshistoSynSub[c]/siteTotalSynSub;
}
}
for (c=0; c<Ncat; c++) {
ghistoMut[c] += shistoMut[c]/totalMut;
ghistoSub[c] += shistoSub[c]/totalSub;
ghistoNonsynMut[c] += shistoNonsynMut[c]/totalNonsynMut;
ghistoNonsynSub[c] += shistoNonsynSub[c]/totalNonsynSub;
ghistoSynMut[c] += shistoSynMut[c]/totalSynMut;
ghistoSynSub[c] += shistoSynSub[c]/totalSynSub;
}
int nrep = 1;
while ((i<until) && (nrep < every)) {
FromStream(is);
i++;
nrep++;
}
}
cerr << '\n';
meanlength /= samplesize;
varlength /= samplesize;
varlength -= meanlength * meanlength;
cerr << "mean length : " << meanlength << " +/- " << sqrt(varlength) << '\n';
double* ppvhistoMut = new double[Ncat];
double* ppvhistoSub = new double[Ncat];
double* ppvhistoNonsynMut = new double[Ncat];
double* ppvhistoNonsynSub = new double[Ncat];
for (c=0; c<Ncat; c++) {
ppvhistoMut[c] = 0;
ppvhistoSub[c] = 0;
ppvhistoNonsynMut[c] = 0;
ppvhistoNonsynSub[c] = 0;
}
totalMut = 0;
totalSub = 0;
totalNonsynMut = 0;
totalNonsynSub = 0;
ofstream codonp_os( (name + ".codonp").c_str(), std::ios::out);
for (int site=0; site<ProfileProcess::GetNsite(); site++) {
for (int a=0; a<GetDim(); a++) {
codonp_os << PosteriorMeanSiteCodonP[site][a] / samplesize << "\t";
}
codonp_os << "\n";
Z = 0;
for (int s=0; s<Nstate; s++) {
stat[s] = (meanNucStat[GetCodonStateSpace()->GetCodonPosition(0, s)] *
meanNucStat[GetCodonStateSpace()->GetCodonPosition(1, s)] *
meanNucStat[GetCodonStateSpace()->GetCodonPosition(2, s)] *
PosteriorMeanSiteCodonP[site][s]) / samplesize;
Z += stat[s];
}
for (int s=0; s<Nstate; s++) {
stat[s] /= Z;
}
for (int codonFrom = 0; codonFrom<Nstate; codonFrom++) {
for (int codonTo = 0; codonTo<Nstate; codonTo++) {
pos = GetCodonStateSpace()->GetDifferingPosition(codonFrom, codonTo);
if ((pos != -1) && (pos != 3)) {
nucFrom = GetCodonStateSpace()->GetCodonPosition(pos, codonFrom);
nucTo = GetCodonStateSpace()->GetCodonPosition(pos, codonTo);
if (nucFrom<nucTo) {
nucRRIndex = (2 * Nnuc - nucFrom - 1) * nucFrom / 2 + nucTo - nucFrom - 1;
}
else {
nucRRIndex = (2 * Nnuc - nucTo - 1) * nucTo / 2 + nucFrom - nucTo - 1;
}
statMutRate = meanNucRR[nucRRIndex] * meanNucStat[nucTo] * stat[codonFrom];
double expS = (PosteriorMeanSiteCodonP[site][codonTo]/samplesize)/(PosteriorMeanSiteCodonP[site][codonFrom]/samplesize);
S = log(expS);
statSubRate = statMutRate * (S/(1-((PosteriorMeanSiteCodonP[site][codonFrom]/samplesize)/(PosteriorMeanSiteCodonP[site][codonTo]/samplesize))));
if (S < min) {
c = 0;
}
else if (S > max) {
c = Ncat-1;
}
else {
c = 0;
double tmp = min + ((double)c * step) - step/2 + step;
do {
c++;
tmp = min + ((double)(c) * step) - step/2 + step;
} while (tmp < S );
}
if (c == Ncat) {
cout << "error, c==Ncat.\n";
cout.flush();
}
ppvhistoMut[c] += statMutRate;
ppvhistoSub[c] += statSubRate;
if (!GetCodonStateSpace()->Synonymous(codonFrom, codonTo)) {
ppvhistoNonsynMut[c] += statMutRate;
ppvhistoNonsynSub[c] += statSubRate;
totalNonsynMut += statMutRate;
totalNonsynSub += statSubRate;
}
totalMut += statMutRate;
totalSub += statSubRate;
}
}
}
}
ofstream mutmutsel_os( (name + ".mutsel").c_str(), std::ios::out);
ofstream mutsubsel_os( (name + ".subsel").c_str(), std::ios::out);
ofstream nonsynmutmutsel_os( (name + ".nonsynmutsel").c_str(), std::ios::out);
ofstream nonsynmutsubsel_os( (name + ".nonsynsubsel").c_str(), std::ios::out);
ofstream synmutmutsel_os( (name + ".synmutsel").c_str(), std::ios::out);
ofstream synmutsubsel_os( (name + ".synsubsel").c_str(), std::ios::out);
ofstream sitemutmutsel_os( (name + ".sitemutsel").c_str(), std::ios::out);
ofstream sitemutsubsel_os( (name + ".sitesubsel").c_str(), std::ios::out);
ofstream sitenonsynmutmutsel_os( (name + ".sitenonsynmutsel").c_str(), std::ios::out);
ofstream sitenonsynmutsubsel_os( (name + ".sitenonsynsubsel").c_str(), std::ios::out);
ofstream sitesynmutmutsel_os( (name + ".sitesynmutsel").c_str(), std::ios::out);
ofstream sitesynmutsubsel_os( (name + ".sitesynsubsel").c_str(), std::ios::out);
ofstream ppvmutmutsel_os( (name + ".ppvmutsel").c_str(), std::ios::out);
ofstream ppvmutsubsel_os( (name + ".ppvsubsel").c_str(), std::ios::out);
ofstream ppvnonsynmutmutsel_os( (name + ".ppvnonsynmutsel").c_str(), std::ios::out);
ofstream ppvnonsynmutsubsel_os( (name + ".ppvnonsynsubsel").c_str(), std::ios::out);
for (c = 0; c < Ncat; c++) {
mutmutsel_os << (min + (c * step)) << "\t" << (ghistoMut[c]/samplesize) << '\n';
mutsubsel_os << (min + (c * step)) << "\t" << (ghistoSub[c]/samplesize) << '\n';
nonsynmutmutsel_os << (min + (c * step)) << "\t" << (ghistoNonsynMut[c]/samplesize) << '\n';
nonsynmutsubsel_os << (min + (c * step)) << "\t" << (ghistoNonsynSub[c]/samplesize) << '\n';
synmutmutsel_os << (min + (c * step)) << "\t" << (ghistoSynMut[c]/samplesize) << '\n';
synmutsubsel_os << (min + (c * step)) << "\t" << (ghistoSynSub[c]/samplesize) << '\n';
ppvmutmutsel_os << (min + (c * step)) << "\t" << (ppvhistoMut[c]/totalMut) << '\n';
ppvmutsubsel_os << (min + (c * step)) << "\t" << (ppvhistoSub[c]/totalSub) << '\n';
ppvnonsynmutmutsel_os << (min + (c * step)) << "\t" << (ppvhistoNonsynMut[c]/totalNonsynMut) << '\n';
ppvnonsynmutsubsel_os << (min + (c * step)) << "\t" << (ppvhistoNonsynSub[c]/totalNonsynSub) << '\n';
for (int site = 0; site < ProfileProcess::GetNsite(); site++) {
if (site == 0) {
sitemutmutsel_os << (min + (c * step)) << '\t' << (sshistoMut[site][c]/samplesize) << '\t';
sitemutsubsel_os << (min + (c * step)) << '\t' << (sshistoSub[site][c]/samplesize) << '\t';
sitenonsynmutmutsel_os << (min + (c * step)) << '\t' << (sshistoNonsynMut[site][c]/samplesize) << '\t';
sitenonsynmutsubsel_os << (min + (c * step)) << '\t' << (sshistoNonsynSub[site][c]/samplesize) << '\t';
sitesynmutmutsel_os << (min + (c * step)) << '\t' << (sshistoSynMut[site][c]/samplesize) << '\t';
sitesynmutsubsel_os << (min + (c * step)) << '\t' << (sshistoSynSub[site][c]/samplesize) << '\t';
}
else if (site == ProfileProcess::GetNsite() - 1) {
sitemutmutsel_os << (sshistoMut[site][c]/samplesize) << '\n';
sitemutsubsel_os << (sshistoSub[site][c]/samplesize) << '\n';
sitenonsynmutmutsel_os << (sshistoNonsynMut[site][c]/samplesize) << '\n';
sitenonsynmutsubsel_os << (sshistoNonsynSub[site][c]/samplesize) << '\n';
sitesynmutmutsel_os << (sshistoSynMut[site][c]/samplesize) << '\n';
sitesynmutsubsel_os << (sshistoSynSub[site][c]/samplesize) << '\n';
}
else {
sitemutmutsel_os << (sshistoMut[site][c]/samplesize) << '\t';
sitemutsubsel_os << (sshistoSub[site][c]/samplesize) << '\t';
sitenonsynmutmutsel_os << (sshistoNonsynMut[site][c]/samplesize) << '\t';
sitenonsynmutsubsel_os << (sshistoNonsynSub[site][c]/samplesize) << '\t';
sitesynmutmutsel_os << (sshistoSynMut[site][c]/samplesize) << '\t';
sitesynmutsubsel_os << (sshistoSynSub[site][c]/samplesize) << '\t';
}
}
}
cerr << samplesize << '\n';
for (int site = 0; site < GetNmodeMax(); site++) {
delete[] PosteriorMeanSiteCodonP[site];
delete[] sshistoMut[site];
delete[] sshistoSub[site];
delete[] sshistoNonsynMut[site];
delete[] sshistoNonsynSub[site];
delete[] sshistoSynMut[site];
delete[] sshistoSynSub[site];
}
delete[] PosteriorMeanSiteCodonP;
delete[] sshistoMut;
delete[] sshistoSub;
delete[] sshistoNonsynMut;
delete[] sshistoNonsynSub;
delete[] sshistoSynMut;
delete[] sshistoSynSub;
delete[] tsshistoMut;
delete[] tsshistoSub;
delete[] tsshistoNonsynMut;
delete[] tsshistoNonsynSub;
delete[] tsshistoSynMut;
delete[] tsshistoSynSub;
delete[] ghistoMut;
delete[] ghistoSub;
delete[] ghistoNonsynMut;
delete[] ghistoNonsynSub;
delete[] ghistoSynMut;
delete[] ghistoSynSub;
delete[] shistoMut;
delete[] shistoSub;
delete[] shistoNonsynMut;
delete[] shistoNonsynSub;
delete[] shistoSynMut;
delete[] shistoSynSub;
delete[] ppvhistoMut;
delete[] ppvhistoSub;
delete[] ppvhistoNonsynMut;
delete[] ppvhistoNonsynSub;
delete[] stat;
delete[] meanNucStat;
delete[] meanNucRR;
}
void AACodonMutSelSBDPPhyloProcess::ReadMapStats(string name, int burnin, int every, int until){
ifstream is((name + ".chain").c_str());
if (!is) {
cerr << "error: no .chain file found\n";
exit(1);
}
cerr << "burnin : " << burnin << "\n";
cerr << "until : " << until << '\n';
int i=0;
while ((i < until) && (i < burnin)) {
FromStream(is);
i++;
}
ofstream ospost((name + ".nonsynpost").c_str());
ofstream ospred((name + ".nonsynpred").c_str());
ofstream ospvalue((name + ".nonsynpvalue").c_str());
int samplesize = 0;
int pvalue=0;
int obs, pred;
while (i < until) {
cerr << ".";
cerr.flush();
samplesize++;
FromStream(is);
i++;
MPI_Status stat;
MESSAGE signal = BCAST_TREE;
MPI_Bcast(&signal,1,MPI_INT,0,MPI_COMM_WORLD);
GlobalBroadcastTree();
GlobalUpdateConditionalLikelihoods();
GlobalCollapse();
GlobalUpdateSiteProfileSuffStat();
// write posterior
obs = GlobalNonSynMapping();
ospost << (double) (obs) / AACodonMutSelProfileProcess::GetNsite() << "\n";
cerr << (double) (obs) / AACodonMutSelProfileProcess::GetNsite() << "\t";
GlobalUnfold();
//Posterior Prededictive Mappings
GlobalUnclamp();
GlobalCollapse();
GlobalUpdateSiteProfileSuffStat();
GlobalSetDataFromLeaves();
// write posterior predictive
pred = GlobalNonSynMapping();
ospred << (double) (pred) / AACodonMutSelProfileProcess::GetNsite() << "\n";
cerr << (double) (pred) / AACodonMutSelProfileProcess::GetNsite() << "\n";
if (pred > obs) pvalue++;
GlobalRestoreData();
GlobalUnfold();
int nrep = 1;
while ((i<until) && (nrep < every)) {
FromStream(is);
i++;
nrep++;
}
}
ospvalue << (double) (pvalue) / samplesize << "\n";
cerr << '\n';
}
void AACodonMutSelSBDPPhyloProcess::ReadSiteProfiles(string name, int burnin, int every, int until) {
double** sitestat = new double*[GetNsite()];
for (int i=0; i<GetNsite(); i++) {
sitestat[i] = new double[GetDim()];
for (int k=0; k<GetDim(); k++) {
sitestat[i][k] = 0;
}
}
ifstream is((name + ".chain").c_str());
if (!is) {
cerr << "error: no .chain file found\n";
exit(1);
}
cerr << "burnin : " << burnin << "\n";
cerr << "until : " << until << '\n';
int i=0;
while ((i < until) && (i < burnin)) {
FromStream(is);
i++;
}
int samplesize = 0;
while (i < until) {
cerr << ".";
cerr.flush();
samplesize++;
FromStream(is);
i++;
for (int i=0; i<GetNsite(); i++) {
double* p = GetProfile(i);
for (int k=0; k<GetDim(); k++) {
sitestat[i][k] += p[k];
}
}
int nrep = 1;
while ((i<until) && (nrep < every)) {
FromStream(is);
i++;
nrep++;
}
}
cerr << '\n';
ofstream os((name + ".siteprofiles").c_str());
/*
if (GetDim() != Naa) {
cerr << "error in read site profiles: should be 20 states\n";
exit(1);
}
for (int k=0; k<GetDim(); k++) {
os << AminoAcids[k] << ' ';
}
os << '\n';
os << '\n';
*/
os << GetNsite() << '\n';
for (int i=0; i<GetNsite(); i++) {
os << i+1;
for (int k=0; k<GetDim(); k++) {
sitestat[i][k] /= samplesize;
os << '\t' << sitestat[i][k];
}
os << '\n';
}
cerr << "mean site-specific profiles in " << name << ".siteprofiles\n";
cerr << '\n';
}
