waitingHandler.increasePrimaryProgressCounter();
if (waitingHandler.isRunCanceled()) {
return;
}
waitingHandler.appendReport("Resolving protein inference issues, inferring peptide and protein PI status.", true, true); // could be slow
<BUG>proteinInference.retainBestScoringGroups(identification, metrics, matchesValidator.getProteinMap(), shotgunProtocol, identificationParameters, identificationFeaturesGenerator, waitingHandler);
waitingHandler.increasePrimaryProgressCounter();</BUG>
if (waitingHandler.isRunCanceled()) {
return;
}

waitingHandler.increasePrimaryProgressCounter();
if (waitingHandler.isRunCanceled()) {
return;
}
