MsMsDetectionParameters.java

/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 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 3 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 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.modules.featuredetection.msmsdetection;

import io.github.msdk.util.tolerances.MaximumMzTolerance;
import io.github.msdk.util.tolerances.RTTolerance;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.ParameterValidator;
import io.github.mzmine.parameters.parametertypes.PercentParameter;
import io.github.mzmine.parameters.parametertypes.StringParameter;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
import io.github.mzmine.parameters.parametertypes.selectors.ScanSelection;
import io.github.mzmine.parameters.parametertypes.selectors.ScanSelectionParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.RTToleranceParameter;

public class MsMsDetectionParameters extends ParameterSet {

  public static final RawDataFilesParameter rawDataFiles = new RawDataFilesParameter();

  public static final ScanSelectionParameter scanSelection =
      new ScanSelectionParameter(new ScanSelection(2));

  public static final MZToleranceParameter mzTolerance = new MZToleranceParameter("m/z tolerance",
      "Maximum allowed difference between two m/z values to be considered same.\n"
          + "The value is specified both as absolute tolerance (in m/z) and relative tolerance (in ppm).\n"
          + "The tolerance range is calculated using maximum of the absolute and relative tolerances.",
      "Algorithm Parameters", ParameterValidator.createNonEmptyValidator(),
      new MaximumMzTolerance(0.001, 5.0));

  public static final RTToleranceParameter rtTolerance = new RTToleranceParameter("RT tolerance",
      "Maximum allowed retention time difference between the peak apex and the retention times in the above feature input list.",
      "Algorithm Parameters", ParameterValidator.createNonEmptyValidator(),
      new RTTolerance(10, true));

  public static final PercentParameter intensityTolerance =
      new PercentParameter("Intensity tolerance",
          "Maximum allowed deviation of the peak chromatogram from the expected /\\ shape.",
          "Algorithm Parameters", ParameterValidator.createNonEmptyValidator(), 0.15);

  public static final StringParameter nameSuffix = new StringParameter("Name suffix",
      "Suffix to be added to the raw data file(s) when creating the feature table(s)", "Output",
      " msmsDetection");

  /**
   * Create the parameter set.
   */
  public MsMsDetectionParameters() {
    super(rawDataFiles, scanSelection, mzTolerance, rtTolerance, intensityTolerance, nameSuffix);
  }

}