matchesValidator.attachPeptideProbabilities(identification, waitingHandler);
matchesValidator.fillProteinMap(identification, waitingHandler);
proteinMap.estimateProbabilities(waitingHandler);
matchesValidator.attachProteinProbabilities(identification, metrics, waitingHandler, identificationParameters.getFractionSettings());
ProteinInference proteinInference = new ProteinInference();
<BUG>proteinInference.retainBestScoringGroups(identification, metrics, proteinMap, shotgunProtocol, identificationParameters, identificationFeaturesGenerator, waitingHandler);
}</BUG>
public void peptideMapChanged(Identification identification, WaitingHandler waitingHandler,
<BUG>ShotgunProtocol shotgunProtocol, IdentificationParameters identificationParameters) throws Exception {
ProteinMap proteinMap = new ProteinMap();</BUG>
matchesValidator.setProteinMap(proteinMap);

matchesValidator.attachPeptideProbabilities(identification, waitingHandler);
matchesValidator.fillProteinMap(identification, waitingHandler);
proteinMap.estimateProbabilities(waitingHandler);
matchesValidator.attachProteinProbabilities(identification, metrics, waitingHandler, identificationParameters.getFractionSettings());
ProteinInference proteinInference = new ProteinInference();
proteinInference.retainBestScoringGroups(identification, metrics, proteinMap, identificationParameters, identificationFeaturesGenerator, waitingHandler);
}
public void peptideMapChanged(Identification identification, WaitingHandler waitingHandler,
IdentificationParameters identificationParameters) throws Exception {
ProteinMap proteinMap = new ProteinMap();
