openms/include/OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
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#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Constants.h>

namespace OpenMS
{

class MSSpectrum;

class OPENMS_DLLAPI Deisotoper
{
  public:

  /* @brief Detect isotopic clusters in a fragment spectrum.

    Deisotoping is done in-place and if @p annotate_charge is true,
    an additional IntegerDataArray "charge" will be appended.
    Existing DataArrays are kept and shrunken to the peaks which
    remain in the spectrum.

   * @param [spectra] Input spectra (sorted by m/z)
   * @param [fragment_tolerance] The tolerance used to match isotopic peaks
   * @oaram [fragment_unit_ppm] Whether ppm or m/z is used as tolerance
   * @param [min_charge] The minimum charge considered
   * @param [max_charge] The maximum charge considered
   * @param [keep_only_deisotoped] Only monoisotopic peaks of fragments with isotopic pattern are retained
   * @param [min_isopeaks] The minimum number of isotopic peaks (at least 2) required for an isotopic cluster
   * @param [max_isopeaks] The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster
   * @param [make_single_charged] Convert deisotoped monoisotopic peak to single charge
   * @param [annotate_charge] Annotate the charge to the peaks in the IntegerDataArray: "charge" (0 for unknown charge)
   *        Note: If @p make_single_charged is selected, the original charge (>=1) gets annotated.
   */
  static void deisotopeAndSingleCharge(MSSpectrum& spectrum,
            double fragment_tolerance,
            bool fragment_unit_ppm,
            int min_charge = 1,
            int max_charge = 3,
            bool keep_only_deisotoped = false,
            unsigned int min_isopeaks = 3,
            unsigned int max_isopeaks = 10,
            bool make_single_charged = true,
            bool annotate_charge = false);
};

}