void testSingleRateModel(Params ¶ms, NGSAlignment &aln, NGSTree &tree, string model,
double *freq, DoubleVector &rate_info, StrVector &rate_name,
bool write_info, const char *report_file)
{
char model_name[20];
NGSAlignment sum_aln(aln.num_states, 1, freq);
ModelsBlock *models_block = new ModelsBlock;
NGSTree sum_tree(params, &sum_aln);
sum_aln.tree = &sum_tree;
if (model == "")
sprintf(model_name, "GTR+F1");
else
sprintf(model_name, "%s+F1", model.c_str());
try {
params.model_name = model_name;
sum_tree.setModelFactory(new ModelFactory(params, &sum_tree, models_block));
sum_tree.setModel(sum_tree.getModelFactory()->model);
sum_tree.setRate(sum_tree.getModelFactory()->site_rate);
double bestTreeScore = sum_tree.getModelFactory()->optimizeParameters(false, write_info);
cout << "LogL: " << bestTreeScore;
cout << " / Rate: " << sum_tree.getRate()->getRate(0) << endl;
} catch (...) {
cout << "Skipped due to sparse matrix" << endl;
//rate_info.push_back(MIN_SITE_RATE);
rate_info.insert(rate_info.end(), rate_name.size(), MIN_SITE_RATE);
return;
}
//return sum_tree.getRate()->getRate(0);
rate_info.push_back(sum_tree.getRate()->getRate(0));
double *rate_mat = new double[aln.num_states*aln.num_states];
memset(rate_mat, 0, aln.num_states*aln.num_states*sizeof(double));
sum_tree.getModel()->getRateMatrix(rate_mat);
rate_info.insert(rate_info.end(), rate_mat, rate_mat+sum_tree.getModel()->getNumRateEntries());
if (tree.getModel()->isReversible()) {
sum_tree.getModel()->getStateFrequency(rate_mat);
rate_info.insert(rate_info.end(), rate_mat, rate_mat+aln.num_states);
}
delete [] rate_mat;
delete models_block;
if (report_file) {
DoubleMatrix tmp(1);
tmp[0] = rate_info;
reportNGSAnalysis(report_file, params, sum_aln, sum_tree, tmp, rate_name);
}
}
void runttgamma(TString sample="all", TString ExtraOpts= "", int workers=8)
{
//TProof *proof = getProof("lite://",nwrks);
TString proofOpt(Form("workers=%i",workers));
//TProof *proof = TProof::Open(proofOpt);
//if (!proof) {
// Printf("runProof: could not start/attach a PROOF session");
// return;
//}
//proof->SetLogLevel(2); // verbose
TChain *chain = new TChain("ggNtuplizer/EventTree");
StrVecMap::iterator ite;//
bool foundSample = false;
for ( ite = vsamples.begin(); ite != vsamples.end(); ++ite) {//
std::string name(sample.Data());
std::string tmpname = (*ite).first;
if ( name != "all" && name != tmpname ) continue;
foundSample = true;
if ( name == "all" ) name = tmpname;
StrVector location = vsamples[name];
cout<< "Input sample: "<< name << endl;
//StrVecMap::iterator ite;
//for (ite = location.begin(); ite != location.end(); ++ite) {
for ( size_t i=0; i < location.size(); ++i ) {
//chain->Add(location.c_str());
chain->Add( location[i].c_str() );
}
cout << "List of files:" << endl;
chain->ls();
cout << endl;
//chain->SetProof(); // to run in PROOF mode
TString opts(Form("sample=%s",name.c_str()));
if (ExtraOpts != "" ) opts = ExtraOpts + " " + opts;
ttgamma3 *myselector = new ttgamma3();
//chain->Process("ttgamma3.C",opts.Data() );
chain->Process(myselector, opts.Data() );
cout << "Process: ttgamma.C done" << endl;
}
// logs
//TList *logList = proof->GetManager()->GetSessionLogs()->GetListOfLogs();
//for (int i=1; i< logList->GetSize(); ++i)
// {
// TProffLogElem *logElem = ( TProofLogElem* ) logList->At( i );
// macro = logElem->GetMacro();
// macro->SaveSource("data_muons_"+TString(Form("%i",i))+".stdout");
// }
//chain->SetProof(0);
//chain->Delete();
//delete chain;
//proof->ClearInput();
//proof->ClearData();
//proof->ClearInputData();
//delete proof;
if ( foundSample )
cout << "runttgamma done"<<endl;
else
cout << "Error: No sample found with name: " << sample.Data() << endl;
}
