import com.compomics.util.db.DerbyUtil;</BUG>
import com.compomics.util.experiment.biology.EnzymeFactory;
import com.compomics.util.experiment.biology.PTMFactory;
import com.compomics.util.experiment.biology.taxonomy.SpeciesFactory;
<BUG>import com.compomics.util.experiment.identification.protein_sequences.SequenceFactory;
import com.compomics.util.experiment.massspectrometry.SpectrumFactory;</BUG>
import com.compomics.util.waiting.WaitingHandler;
import com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl;
import com.compomics.util.preferences.UtilitiesUserPreferences;
import eu.isas.peptideshaker.PeptideShaker;

package eu.isas.peptideshaker.cmd;
import com.compomics.software.settings.PathKey;
import com.compomics.software.settings.UtilitiesPathPreferences;
import com.compomics.util.experiment.biology.EnzymeFactory;
import com.compomics.util.experiment.biology.PTMFactory;
import com.compomics.util.experiment.biology.taxonomy.SpeciesFactory;
import com.compomics.util.waiting.WaitingHandler;
import com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl;
import com.compomics.util.preferences.UtilitiesUserPreferences;
import eu.isas.peptideshaker.PeptideShaker;
