/*
 * Copyright 2006-2018 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the
 * terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 2 of the License, or (at your option) any later
 * version.
 * 
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY
 * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
 * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with
 * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
 * Fifth Floor, Boston, MA 02110-1301 USA
 */

package net.sf.mzmine.modules.peaklistmethods.identification.sirius;

import java.util.Collection;
import javax.annotation.Nonnull;
import net.sf.mzmine.datamodel.MZmineProject;
import net.sf.mzmine.datamodel.PeakList;
import net.sf.mzmine.datamodel.PeakListRow;
import net.sf.mzmine.main.MZmineCore;
import net.sf.mzmine.modules.MZmineModuleCategory;
import net.sf.mzmine.modules.MZmineProcessingModule;
import net.sf.mzmine.parameters.ParameterSet;
import net.sf.mzmine.taskcontrol.Task;
import net.sf.mzmine.util.ExitCode;

public class SiriusProcessingModule implements MZmineProcessingModule {

  private static final String MODULE_NAME = "Sirius";
  private static final String MODULE_DESCRIPTION = "Sirius identification method.";

  @Override
  public @Nonnull
  String getName() {
    return MODULE_NAME;
  }

  @Override
  public @Nonnull
  String getDescription() {
    return MODULE_DESCRIPTION;
  }

  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull MZmineProject project,
      @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {

    final PeakList[] peakLists = parameters
        .getParameter(PeakListIdentificationParameters.peakLists)
        .getValue().getMatchingPeakLists();
    for (final PeakList peakList : peakLists) {
      Task newTask = new PeakListIdentificationTask(parameters, peakList);
      tasks.add(newTask);
    }

    return ExitCode.OK;
  }

  /**
   * Show dialog for identifying a single peak-list row.
   *
   * @param row the peak list row.
   */
  public static void showSingleRowIdentificationDialog(final PeakListRow row) {

    final ParameterSet parameters = new SingleRowIdentificationParameters();

//         Set m/z.
    parameters.getParameter(SingleRowIdentificationParameters.NEUTRAL_MASS)
        .setIonMass(row.getAverageMZ());

    // Set charge.
    final int charge = row.getBestPeak().getCharge();
    if (charge > 0) {
      //TODO: auto update the mass value on charge update
      parameters.getParameter(
          SingleRowIdentificationParameters.NEUTRAL_MASS).setCharge(
          charge);
    }

    // Run task.
    if (parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(),
        true) == ExitCode.OK) {

      MZmineCore.getTaskController().addTask(
          new SingleRowIdentificationTask(parameters
              .cloneParameterSet(), row));
    }
  }

  @Override
  public @Nonnull
  MZmineModuleCategory getModuleCategory() {
    return MZmineModuleCategory.IDENTIFICATION;
  }

  @Override
  public @Nonnull
  Class<? extends ParameterSet> getParameterSetClass() {
    return SingleRowIdentificationParameters.class;
  }
}

@@ -3395,25 +3395,24 @@
  return 
-SingleRow
+PeakList
 Identifi

Set proper parameter set