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

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#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:
 
  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);
};
 
}