PrecursorCorrection.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg, Oliver Alka $
// --------------------------------------------------------------------------
//

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>

#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>

#include <OpenMS/METADATA/Precursor.h>

#include <string>
#include <vector>
#include <set>

namespace OpenMS
{
class OPENMS_DLLAPI PrecursorCorrection
{
     public:

     static const std::string csv_header;

     static void getPrecursors(const MSExperiment & exp,
                              std::vector<Precursor> & precursors,
                              std::vector<double> & precursors_rt,
                              std::vector<Size> & precursor_scan_index);


     static void writeHist(const String& out_csv,
                           const std::vector<double> & delta_mzs,
                           const std::vector<double> & mzs,
                           const std::vector<double> & rts);
     static std::set<Size> correctToNearestMS1Peak(MSExperiment & exp,
                                                   double mz_tolerance,
                                                   bool ppm,
                                                   std::vector<double> & delta_mzs,
                                                   std::vector<double> & mzs,
                                                   std::vector<double> & rts);

     static std::set<Size> correctToHighestIntensityMS1Peak(MSExperiment & exp,
                                                            double mz_tolerance,
                                                            bool ppm,
                                                            std::vector<double> & delta_mzs,
                                                            std::vector<double> & mzs,
                                                            std::vector<double> & rts);


     static std::set<Size> correctToNearestFeature(const FeatureMap& features,
                                                   MSExperiment & exp,
                                                   double rt_tolerance_s = 0.0,
                                                   double mz_tolerance = 0.0,
                                                   bool ppm = true,
                                                   bool believe_charge = false,
                                                   bool keep_original = false,
                                                   bool all_matching_features = false,
                                                   int max_trace = 2,
                                                   int debug_level = 0);

  protected:

      static bool overlaps_(const Feature& feature,
                            const double rt,
                            const double pc_mz,
                            const double rt_tolerance);

      static bool compatible_(const Feature& feature,
                              double pc_mz,
                              double mz_tolerance,
                              Size max_trace_number = 2,
                              int debug_level = 0);

};
}