IsotopeGrouperParameters.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.isotopes.isotopegrouper;

import java.util.Arrays;

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.BooleanParameter;
import io.github.mzmine.parameters.parametertypes.ComboParameter;
import io.github.mzmine.parameters.parametertypes.IntegerParameter;
import io.github.mzmine.parameters.parametertypes.StringParameter;
import io.github.mzmine.parameters.parametertypes.selectors.FeatureTablesParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.RTToleranceParameter;

public class IsotopeGrouperParameters extends ParameterSet {

  public static final FeatureTablesParameter featureTables = new FeatureTablesParameter();

  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 IntegerParameter maximumCharge = new IntegerParameter("Maximum charge",
      "Maximum charge to consider for detecting the isotope patterns.", "Algorithm Parameters",
      ParameterValidator.createNonEmptyValidator(), 2);

  public static final ComboParameter<RepresentativeIsotope> representativeIsotope =
      new ComboParameter<>("Representative isotope",
          "Which peak should represent the whole isotope pattern.\n"
              + "For small molecular weight compounds with monotonically decreasing isotope pattern, the most intense isotope should be representative.\n"
              + "For high molecular weight peptides, the lowest m/z isotope may be the representative.",
          "Algorithm Parameters", Arrays.asList(RepresentativeIsotope.values()),
          RepresentativeIsotope.MOST_INTENSE);

  public static final BooleanParameter monotonicShape = new BooleanParameter("Monotonic shape?",
      "If checked, a monotonically decreasing height of the isotope pattern in required.",
      "Algorithm Parameters", false);

  public static final StringParameter nameSuffix = new StringParameter("Name suffix",
      "Suffix to be added to the feature table name.", "Output", " deisotoped");

  public static final BooleanParameter removeOldTable =
      new BooleanParameter("Remove original table?",
          "If checked, the original feature table will be removed.", "Output", false);

  /**
   * Create the parameter set.
   */
  public IsotopeGrouperParameters() {
    super(featureTables, mzTolerance, rtTolerance, maximumCharge, representativeIsotope,
        monotonicShape, nameSuffix, removeOldTable);
  }

}