package eu.isas.peptideshaker.cmd;
import com.compomics.software.CompomicsWrapper;
<BUG>import com.compomics.software.settings.UtilitiesPathPreferences;
import static eu.isas.peptideshaker.cmd.PeptideShakerCLI.redirectErrorStream;</BUG>
import eu.isas.peptideshaker.preferences.PeptideShakerPathPreferences;
import java.io.File;
import java.io.PrintWriter;

package eu.isas.peptideshaker.cmd;
import com.compomics.software.CompomicsWrapper;
import com.compomics.software.settings.UtilitiesPathPreferences;
import com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl;
import com.compomics.util.waiting.WaitingHandler;
import static eu.isas.peptideshaker.cmd.PeptideShakerCLI.redirectErrorStream;
import eu.isas.peptideshaker.preferences.PeptideShakerPathPreferences;
import java.io.File;
import java.io.PrintWriter;
