FIAMSDataProcessor.h

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//---------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// This software is released under a three-clause BSD license:
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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
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// 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"
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// --------------------------------------------------------------------------
// $Maintainer: Svetlana Kutuzova, Douglas McCloskey $
// $Authors: Svetlana Kutuzova, Douglas McCloskey $
// --------------------------------------------------------------------------
 
#pragma once
#include <OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/FORMAT/MzTab.h>
#include <OpenMS/FORMAT/MzTabM.h>
#include <OpenMS/FORMAT/MzTabFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI FIAMSDataProcessor  :
    public DefaultParamHandler
  {
public:
    FIAMSDataProcessor();
 
    ~FIAMSDataProcessor() override = default;
 
    FIAMSDataProcessor(const FIAMSDataProcessor& cp) = default;
 
    FIAMSDataProcessor& operator=(const FIAMSDataProcessor& fdp) = default;
 
    bool run(const MSExperiment& experiment, const float n_seconds, OpenMS::MzTab& output, const bool load_cached_spectrum = true);
 
    void cutForTime(const MSExperiment& experiment, const float n_seconds, std::vector<MSSpectrum>& output);
 
    MSSpectrum mergeAlongTime(const std::vector<OpenMS::MSSpectrum>& input);
 
    MSSpectrum extractPeaks(const MSSpectrum& input);
 
    FeatureMap convertToFeatureMap(const MSSpectrum& input);
 
    MSSpectrum trackNoise(const MSSpectrum& input);
 
    void runAccurateMassSearch(FeatureMap& input, OpenMS::MzTab& output);
 
    const std::vector<float>& getMZs();
 
    const std::vector<float>& getBinSizes();
 
protected:
    void updateMembers_() override;
 
private:
    void storeSpectrum_(const MSSpectrum& input, const String& filename);
 
    std::vector<float> mzs_; 
    std::vector<float> bin_sizes_;
    SavitzkyGolayFilter sgfilter_;
    PeakPickerHiRes picker_;
  };
} // namespace OpenMS