PeakMapExtractor.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractorAlgorithm.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
 
#include <limits>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI PeakMapExtractor :
    public ProgressLogger
  {
  public:
    using ExtractionCoordinates = ChromatogramExtractorAlgorithm::ExtractionCoordinates;
 
    struct OPENMS_DLLAPI ExtractedPeakMap
    {
      std::string native_id;
      double target_mz{0.0};
      double target_rt{std::numeric_limits<double>::quiet_NaN()};
      double target_ion_mobility{-1.0};
      double rt_start{0.0};
      double rt_end{-1.0};
 
      std::vector<double> mz;
      std::vector<double> rt;
      std::vector<double> ion_mobility;
      std::vector<double> intensity;
    };
 
    void extractPeakMaps(const OpenSwath::SpectrumAccessPtr& input,
                         std::vector<ExtractedPeakMap>& output,
                         const std::vector<ExtractionCoordinates>& extraction_coordinates,
                         double mz_extraction_window,
                         bool ppm,
                         double im_extraction_window,
                         const std::string& filter = "tophat");
 
  private:
    int getFilterNr_(const std::string& filter) const;
  };
} // namespace OpenMS