ChromatogramBuilderParameters.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.chromatogrambuilder;

import io.github.msdk.util.tolerances.MaximumMzTolerance;
import io.github.mzmine.main.MZmineCore;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.ParameterValidator;
import io.github.mzmine.parameters.parametertypes.DoubleParameter;
import io.github.mzmine.parameters.parametertypes.StringParameter;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesParameter;
import io.github.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;

public class ChromatogramBuilderParameters extends ParameterSet {

  public static final RawDataFilesParameter rawDataFiles = new RawDataFilesParameter();

  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 DoubleParameter noiseLevel =
      new DoubleParameter("Noise level", "Data points below this intensity will be ignored",
          "Algorithm Parameters", MZmineCore.getConfiguration().getIntensityFormat(),
          ParameterValidator.createNonEmptyValidator(), null);

  public static final DoubleParameter minDuration = new DoubleParameter("Min peak duration",
      "Minimum time span over which the same ion must be observed in order to be recognized as a peaks.",
      "Algorithm Parameters", MZmineCore.getConfiguration().getRTFormat(),
      ParameterValidator.createNonEmptyValidator(), 5d);

  public static final DoubleParameter minHeight = new DoubleParameter("Min peak height",
      "Peaks with intensities less than this value are interpreted as noise",
      "Algorithm Parameters", MZmineCore.getConfiguration().getIntensityFormat(),
      ParameterValidator.createNonEmptyValidator(), 5000d);

  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",
      " chromatograms");

  /**
   * Create the parameter set.
   */
  public ChromatogramBuilderParameters() {
    super(rawDataFiles, mzTolerance, noiseLevel, minDuration, minHeight, nameSuffix);
  }

}