FeatureFilterParameters.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.filtering.featurefilter;

import com.google.common.collect.Range;

import io.github.mzmine.main.MZmineCore;
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.OptionalParameter;
import io.github.mzmine.parameters.parametertypes.StringParameter;
import io.github.mzmine.parameters.parametertypes.ranges.DoubleRangeParameter;
import io.github.mzmine.parameters.parametertypes.ranges.IntegerRangeParameter;
import io.github.mzmine.parameters.parametertypes.selectors.FeatureTablesParameter;

public class FeatureFilterParameters extends ParameterSet {

  public static final FeatureTablesParameter featureTables = new FeatureTablesParameter();

  public static final OptionalParameter<DoubleRangeParameter> duration =
      new OptionalParameter<DoubleRangeParameter>(
          new DoubleRangeParameter("Duration (sec)", "Permissible range of peak durations.",
              "Filters", MZmineCore.getConfiguration().getRTFormat(),
              ParameterValidator.createNonEmptyValidator(), Range.closed(0.0, 20.0)));

  public static final OptionalParameter<DoubleRangeParameter> area =
      new OptionalParameter<DoubleRangeParameter>(
          new DoubleRangeParameter("Area", "Permissible range of peak areas.", "Filters",
              MZmineCore.getConfiguration().getIntensityFormat(),
              ParameterValidator.createNonEmptyValidator(), Range.closed(0.0, 1E7)));

  public static final OptionalParameter<DoubleRangeParameter> height =
      new OptionalParameter<DoubleRangeParameter>(
          new DoubleRangeParameter("Height", "Permissible range of peak heights.", "Filters",
              MZmineCore.getConfiguration().getIntensityFormat(),
              ParameterValidator.createNonEmptyValidator(), Range.closed(0.0, 1E7)));

  public static final OptionalParameter<IntegerRangeParameter> dataPoints =
      new OptionalParameter<IntegerRangeParameter>(new IntegerRangeParameter("# data points",
          "Permissible range of the number of data points over the peak.", "Filters",
          ParameterValidator.createNonEmptyValidator(), Range.closed(8, 999)));

  public static final OptionalParameter<DoubleRangeParameter> fwhm =
      new OptionalParameter<DoubleRangeParameter>(new DoubleRangeParameter("FWHM (sec)",
          "Permissible range of full width at half maximum (FWHM) for a peak.", "Filters",
          MZmineCore.getConfiguration().getRTFormat(), ParameterValidator.createNonEmptyValidator(),
          Range.closed(0.0, 10.0)));

  public static final OptionalParameter<DoubleRangeParameter> tailingFactor =
      new OptionalParameter<DoubleRangeParameter>(new DoubleRangeParameter("Tailing factor",
          "Permissible range of tailing factor for a peak.", "Filters",
          ParameterValidator.createNonEmptyValidator(), Range.closed(0.5, 2.0)));

  public static final OptionalParameter<DoubleRangeParameter> asymmetryFactor =
      new OptionalParameter<DoubleRangeParameter>(new DoubleRangeParameter("Asymmetry factor",
          "Permissible range of asymmetry factor for a peak.", "Filters",
          ParameterValidator.createNonEmptyValidator(), Range.closed(0.5, 2.0)));

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

  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 FeatureFilterParameters() {
    super(featureTables, duration, area, height, dataPoints, fwhm, tailingFactor, asymmetryFactor,
        nameSuffix, removeOldTable);
  }

}