RowFilterParameters.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.rowfilter;

import com.google.common.collect.Range;

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.DoubleParameter;
import io.github.mzmine.parameters.parametertypes.IntegerParameter;
import io.github.mzmine.parameters.parametertypes.OptionalModuleParameter;
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.selectors.FeatureTablesParameter;

public class RowFilterParameters extends ParameterSet {

  public static final FeatureTablesParameter featureTables = new FeatureTablesParameter();

  public static final OptionalParameter<DoubleRangeParameter> mzRange =
      new OptionalParameter<DoubleRangeParameter>(
          new DoubleRangeParameter("m/z range", "Range of acceptable m/z values.", "Filters",
              ParameterValidator.createNonEmptyValidator(), Range.closed(200.0, 1700.0)));

  public static final OptionalParameter<DoubleRangeParameter> rtRange =
      new OptionalParameter<DoubleRangeParameter>(new DoubleRangeParameter(
          "Retention time range (min)", "Range of acceptable retention time values.", "Filters",
          ParameterValidator.createNonEmptyValidator(), Range.closed(0.0, 30.0)));

  public static final OptionalParameter<DoubleRangeParameter> durationRange =
      new OptionalParameter<DoubleRangeParameter>(new DoubleRangeParameter("Duration range (sec)",
          "Range of acceptable average feature duration.", "Filters",
          ParameterValidator.createNonEmptyValidator(), Range.closed(0.0, 60.0)));

  public static final OptionalParameter<DoubleParameter> minCount =
      new OptionalParameter<DoubleParameter>(new DoubleParameter("Minimum features in a row",
          "Minimum number of feature detections required per row.\nValues <1 will be interpreted as a %-value of the total # samples in the feature table. The value will be rounded down to the nearest whole number.",
          "Filters", ParameterValidator.createNonEmptyValidator()));

  public static final OptionalParameter<IntegerParameter> minIsotopes =
      new OptionalParameter<IntegerParameter>(
          new IntegerParameter("Minimum peaks in isotope pattern",
              "Minimum number of peaks required in an isotope pattern.", "Filters",
              ParameterValidator.createNonEmptyValidator()));

  public static final OptionalParameter<StringParameter> ionAnnotation =
      new OptionalParameter<StringParameter>(new StringParameter("Text in ion annotation",
          "Required text in feature annoation.", "Filters", ""));

  public static final BooleanParameter requireAnnotation =
      new BooleanParameter("Remove non-identified features?",
          "If selected, non-identified features will be removed.", "Filters", false);

  public static final OptionalModuleParameter removeDuplicates =
      new OptionalModuleParameter("Remove duplicate features?",
          "Remove duplicate features from the feature list?\nDuplicates are found based on m/z, RT and feature annotation.",
          "Filters", new DuplicateFilterParameters());

  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 RowFilterParameters() {
    super(featureTables, mzRange, rtRange, durationRange, minCount, minIsotopes, ionAnnotation,
        requireAnnotation, removeDuplicates, nameSuffix, removeOldTable);
  }

}