FeatureFinderAlgorithmIsotopeWavelet.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 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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#pragma once

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>

namespace OpenMS
{
  class OPENMS_DLLAPI FeatureFinderAlgorithmIsotopeWavelet :
    public FeatureFinderAlgorithm
  {
public:

    typedef FeatureFinderAlgorithm Base;
    typedef Peak1D PeakType;

    FeatureFinderAlgorithmIsotopeWavelet();

    ~FeatureFinderAlgorithmIsotopeWavelet() override;

    MSSpectrum* createHRData(const UInt i);

    void run() override;

    static const String getProductName();

    static FeatureFinderAlgorithm* create();

protected:

    struct BoxElement
    {
      double mz;
      UInt c; 
      double score;
      double intens;
      double RT; 
    };

    typedef std::map<UInt, BoxElement> Box; 

    UInt max_charge_; 
    double intensity_threshold_; 
    UInt RT_votes_cutoff_, real_RT_votes_cutoff_, RT_interleave_; 
    String use_gpus_, intensity_type_;
    bool check_PPMs_, hr_data_;
    std::vector<UInt> gpu_ids_; 

    Int progress_counter_;

    void updateMembers_() override;

  };

} //namespace