ChromatogramExtractorAlgorithm.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI ChromatogramExtractorAlgorithm :
    public ProgressLogger
  {
 
public:
 
    struct ExtractionCoordinates
    {
      double mz = 0.0; 
      double ion_mobility = 0.0; 
      double mz_precursor = 0.0; 
      double rt_start = 0.0; 
      double rt_end = 0.0; 
      std::string id; 
 
      static bool SortExtractionCoordinatesByMZ(
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& left,
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& right)
      {
        return left.mz < right.mz;
      }
      static bool SortExtractionCoordinatesReverseByMZ(
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& left,
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& right)
      {
        return left.mz > right.mz;
      }
    };
 
    void extractChromatograms(const OpenSwath::SpectrumAccessPtr& input,
        std::vector< OpenSwath::ChromatogramPtr >& output,
        const std::vector<ExtractionCoordinates>& extraction_coordinates,
        double mz_extraction_window,
        bool ppm,
        double im_extraction_window,
        const String& filter);
 
    void extract_value_tophat(const std::vector<double>::const_iterator& mz_start,
                              std::vector<double>::const_iterator& mz_it,
                              const std::vector<double>::const_iterator& mz_end,
                              std::vector<double>::const_iterator& int_it,
                              const double mz,
                              double& integrated_intensity,
                              const double mz_extraction_window,
                              const bool ppm);
 
    void extract_value_tophat(const std::vector<double>::const_iterator& mz_start,
                              std::vector<double>::const_iterator& mz_it,
                              const std::vector<double>::const_iterator& mz_end,
                              std::vector<double>::const_iterator& int_it,
                              std::vector<double>::const_iterator& im_it,
                              const double mz,
                              const double im,
                              double& integrated_intensity,
                              const double mz_extraction_window,
                              const double im_extraction_window,
                              const bool ppm);
 
private:
 
    int getFilterNr_(const String& filter);
 
  };
 
}