import com.compomics.util.experiment.massspectrometry.Spectrum;
import com.compomics.util.experiment.massspectrometry.SpectrumFactory;
import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
import com.compomics.util.preferences.IdentificationParameters;
import com.compomics.util.experiment.identification.identification_parameters.PtmSettings;
<BUG>import com.compomics.util.experiment.identification.identification_parameters.SearchParameters;
import com.compomics.util.preferences.PTMScoringPreferences;</BUG>
import com.compomics.util.preferences.SequenceMatchingPreferences;
import eu.isas.peptideshaker.gui.PeptideShakerGUI;
import eu.isas.peptideshaker.parameters.PSParameter;

import com.compomics.util.experiment.massspectrometry.Spectrum;
import com.compomics.util.experiment.massspectrometry.SpectrumFactory;
import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
import com.compomics.util.preferences.IdentificationParameters;
import com.compomics.util.experiment.identification.identification_parameters.PtmSettings;
import com.compomics.util.experiment.identification.identification_parameters.SearchParameters;
import com.compomics.util.preferences.DigestionPreferences;
import com.compomics.util.preferences.PTMScoringPreferences;
import com.compomics.util.preferences.SequenceMatchingPreferences;
import eu.isas.peptideshaker.gui.PeptideShakerGUI;
import eu.isas.peptideshaker.parameters.PSParameter;
