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 $
// --------------------------------------------------------------------------

#pragma once

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

#include <string.h>

namespace OpenMS
{

class MSSpectrum;

class OPENMS_DLLAPI Deisotoper
{
  public:

    static void deisotopeWithAveragineModel(MSSpectrum& spectrum,
                                            double fragment_tolerance,
                                            bool fragment_unit_ppm,
                                            int number_of_final_peaks = 5000,
                                            int min_charge = 1,
                                            int max_charge = 3,
                                            bool keep_only_deisotoped = false,
                                            unsigned int min_isopeaks = 2,
                                            unsigned int max_isopeaks = 10,
                                            bool make_single_charged = true,
                                            bool annotate_charge = false,
                                            bool annotate_iso_peak_count = false,
                                            bool add_up_intensity = false);

    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,
                                         bool annotate_iso_peak_count = false,
                                         bool use_decreasing_model = true,
                                         unsigned int start_intensity_check = 2,
                                         bool add_up_intensity = false);
};

}