void FidoInterface::computeProbabilities(const std::string& fname) {
ifstream fin;
if (fname.size() > 0) {
fin.open(fname.c_str());
proteinGraph_->read(fin);
} else {
proteinGraph_->read(peptideScores_);
}
if (trivialGrouping_) updateTargetDecoySizes();
time_t startTime;
clock_t startClock;
time(&startTime);
startClock = clock();
if (mayufdr) {
computeFDR();
}
if (doGridSearch_) {
if (VERB > 1) {
std::cerr << "The parameters for the model will be estimated by grid search.\n" << std::endl;
}
if (kOptimizeParams)
gridSearchOptimize();
else
gridSearch();
time_t procStart;
clock_t procStartClock = clock();
time(&procStart);
double diff = difftime(procStart, startTime);
if (VERB > 1) cerr << "Estimating the parameters took : "
<< ((double)(procStartClock - startClock)) / (double)CLOCKS_PER_SEC
<< " cpu seconds or " << diff << " seconds wall time" << endl;
}
if (VERB > 1) {
cerr << "The following parameters have been chosen:\n";
std::cerr.precision(10);
cerr << "alpha = " << alpha_ << endl;
cerr << "beta = " << beta_ << endl;
cerr << "gamma = " << gamma_ << endl;
std::cerr.unsetf(std::ios::floatfield);
cerr << "\nProtein level probabilities will now be estimated\n";
}
if (gridSearchThreshold_ > 0.0 && doGridSearch_) {
//NOTE reset the tree after grid searching
proteinGraph_->setProteinThreshold(proteinThreshold_);
proteinGraph_->setPsmThreshold(kPsmThreshold);
proteinGraph_->setPeptideThreshold(kPeptideThreshold);
proteinGraph_->setNoClustering(noClustering_);
proteinGraph_->setNoPartitioning(noPartitioning_);
proteinGraph_->setNoPruning(noPruning_);
proteinGraph_->setTrivialGrouping(trivialGrouping_);
proteinGraph_->setMultipleLabeledPeptides(kAddPeptideDecoyLabel);
if (fname.size() > 0) {
proteinGraph_->read(fin);
} else {
proteinGraph_->read(peptideScores_);
}
if (trivialGrouping_) updateTargetDecoySizes();
}
proteinGraph_->setAlphaBetaGamma(alpha_, beta_, gamma_);
proteinGraph_->getProteinProbs();
pepProteinMap_.clear();
proteinGraph_->getProteinProbsPercolator(pepProteinMap_);
}
//NOTE almost entirely duplicated of computeProbabilities, it could be refactored
void FidoInterface::computeProbabilitiesFromFile(ifstream &fin)
{
proteinGraph->read(fin);
time_t startTime;
clock_t startClock;
time(&startTime);
startClock = clock();
if(mayufdr)
{
computeFDR();
}
if(dogridSearch)
{
if(VERB > 1)
{
std::cerr << "The parameters for the model will be estimated by grid search.\n" << std::endl;
}
if(optimize)
gridSearchOptimize();
else
gridSearch();
time_t procStart;
clock_t procStartClock = clock();
time(&procStart);
double diff = difftime(procStart, startTime);
if (VERB > 1) cerr << "Estimating the parameters took : "
<< ((double)(procStartClock - startClock)) / (double)CLOCKS_PER_SEC
<< " cpu seconds or " << diff << " seconds wall time" << endl;
}
if(VERB > 1)
{
cerr << "The following parameters have been chosen:\n";
std::cerr.precision(10);
cerr << "gamma = " << gamma << endl;
cerr << "alpha = " << alpha << endl;
cerr << "beta = " << beta << endl;
std::cerr.unsetf(std::ios::floatfield);
cerr << "\nProtein level probabilities will now be estimated";
}
if(dogridSearch && reduceTree)
{
//NOTE lets create the tree again with all the members
double local_protein_threshold = proteinThreshold;
if(truncate) local_protein_threshold = 0.0;
proteinGraph->setProteinThreshold(local_protein_threshold);
proteinGraph->setPsmThreshold(psmThreshold);
proteinGraph->setPeptideThreshold(peptideThreshold);
proteinGraph->setGroupProteins(nogroupProteins);
proteinGraph->setSeparateProteins(noseparate);
proteinGraph->setPruneProteins(noprune);
proteinGraph->setMultipleLabeledPeptides(allow_multiple_labeled_peptides);
proteinGraph->read(fin);
}
proteinGraph->setAlphaBetaGamma(alpha,beta,gamma);
proteinGraph->getProteinProbs();
pepProteins.clear();
proteinGraph->getProteinProbsPercolator(pepProteins);
}
