psmThreshold = targetDecoyResults.getScoreLimit();
confidenceThreshold = targetDecoyResults.getConfidenceLimit() + targetDecoyMap.getResolution();
if (confidenceThreshold > 100) {
confidenceThreshold = 100;
}
noValidated = targetDecoyResults.noValidated();
}
if (!noValidated && psParameter.getPsmProbabilityScore() <= psmThreshold) {
String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);