void NormaliseByCurrent::exec() {
// Get the input workspace
MatrixWorkspace_sptr inputWS = getProperty("InputWorkspace");
MatrixWorkspace_sptr outputWS = getProperty("OutputWorkspace");
// Get the good proton charge and check it's valid
double charge = extractCharge(inputWS);
if (charge == 0) {
throw std::domain_error("The proton charge is zero");
}
g_log.information() << "Normalisation current: " << charge << " uamps"
<< std::endl;
charge = 1.0 / charge; // Inverse of the charge to be multiplied by
// The operator overloads properly take into account of both EventWorkspaces
// and doing it in place or not.
if (inputWS != outputWS) {
outputWS = inputWS * charge;
setProperty("OutputWorkspace", outputWS);
} else {
inputWS *= charge;
}
outputWS->setYUnitLabel("Counts per microAmp.hour");
}
/* Creates a map: ("peptide" + "_" + "charge") => ScanMergeInfo(scanNr, PEP,
isDecoy, charge, peptide) of all PSMs under qvalue_thresh */
void parsePercOutfile(std::string percOutFN, SpectraMergeMap& peptideScanMap,
bool isDecoy, double qvalue_thresh = 0.01) {
std::ifstream percOut(percOutFN.c_str());
std::string line, tmp, id, peptide;
double qvalue, pep;
if (percOut.is_open()) {
getline(percOut, line); /* remove header line */
while (getline(percOut, line)) {
std::istringstream iss(line);
iss >> id >> tmp >> qvalue >> pep >> peptide;
std::string key = peptide + "_" + extractCharge(id);
if (qvalue > qvalue_thresh) break;
peptideScanMap[key].push_back(ScanMergeInfo(extractScannr(id), pep,
isDecoy, extractIntCharge(id), peptide));
/* std::cerr << "Inserting peptide " << peptide << " with scannr " <<
scannr << std::endl; */
}
} else {
