// create a shaker which will perform the analysis
PeptideShaker peptideShaker = new PeptideShaker(experiment, sample, replicateNumber);
// import the files
peptideShaker.importFiles(waitingHandler, idFilter, identificationFiles, spectrumFiles, searchParameters,
annotationPreferences, projectDetails, processingPreferences, ptmScoringPreferences,
spectrumCountingPreferences, sequenceMatchingPreferences, false);
// show the warnings
Iterator<String> iterator = peptideShaker.getWarnings().keySet().iterator();