TargetedSpectraExtractor.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
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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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// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h> // OPENMS_DLLAPI
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FILTERING/SMOOTHING/GaussFilter.h>
#include <OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>

namespace OpenMS
{
  class OPENMS_DLLAPI TargetedSpectraExtractor :
    public DefaultParamHandler
  {
public:
    TargetedSpectraExtractor();
    virtual ~TargetedSpectraExtractor();

    void getDefaultParameters(Param& params);

    void annotateSpectra(
      const std::vector<MSSpectrum>& spectra,
      const TargetedExperiment& targeted_exp,
      std::vector<MSSpectrum>& annotated_spectra,
      FeatureMap& features
    );

    void pickSpectrum(const MSSpectrum& spectrum, MSSpectrum& picked_spectrum);

    void scoreSpectra(
      const std::vector<MSSpectrum>& annotated_spectra,
      const std::vector<MSSpectrum>& picked_spectra,
      FeatureMap& features,
      std::vector<MSSpectrum>& scored_spectra
    );

    void selectSpectra(
      const std::vector<MSSpectrum>& scored_spectra,
      const FeatureMap& features,
      std::vector<MSSpectrum>& selected_spectra,
      FeatureMap& selected_features
    );

    void selectSpectra(
      const std::vector<MSSpectrum>& scored_spectra,
      std::vector<MSSpectrum>& selected_spectra
    );

    void extractSpectra(
      const MSExperiment& experiment,
      const TargetedExperiment& targeted_exp,
      std::vector<MSSpectrum>& extracted_spectra,
      FeatureMap& extracted_features
    );

protected:
    void updateMembers_();

private:
    bool mz_unit_is_Da_;

    double rt_window_;

    double mz_tolerance_;

    double peak_height_min_;

    double peak_height_max_;

    double fwhm_threshold_;

    double tic_weight_; 
    double fwhm_weight_; 
    double snr_weight_; 
    double min_score_;

    bool use_gauss_;
  };
}