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 2002-2021.
//
// 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
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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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 <fstream>
#include <iostream>
#include <string>
#include <algorithm>
 
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);
 
};
}