ChromatogramExtractorAlgorithm.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#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; 
      double ion_mobility; 
      double mz_precursor; 
      double rt_start; 
      double rt_end; 
      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,
        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, 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, bool ppm);

private:

    int getFilterNr_(String filter);

  };

}