ElutionPeakDetection.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Erhan Kenar$
// $Authors: Erhan Kenar, Holger Franken $
// --------------------------------------------------------------------------


#ifndef OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H
#define OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MassTrace.h>


namespace OpenMS
{
  class OPENMS_DLLAPI ElutionPeakDetection :
    public DefaultParamHandler, public ProgressLogger
  {
public:
    ElutionPeakDetection();

    virtual ~ElutionPeakDetection();



    void detectPeaks(MassTrace &, std::vector<MassTrace> &);

    void detectPeaks(std::vector<MassTrace> &, std::vector<MassTrace> &);

    void filterByPeakWidth(std::vector<MassTrace> &, std::vector<MassTrace> &);
    DoubleReal computeMassTraceNoise(const MassTrace&);
    DoubleReal computeMassTraceSNR(const MassTrace&);
    DoubleReal computeApexSNR(const MassTrace&);
    void findLocalExtrema(const MassTrace&, const Size&, std::vector<Size>&, std::vector<Size>&);

protected:
    virtual void updateMembers_();

private:
    DoubleReal chrom_fwhm_;
    // DoubleReal scan_time_;
    DoubleReal chrom_peak_snr_;
    DoubleReal noise_threshold_int_;
    DoubleReal sample_rate_;

    DoubleReal min_fwhm_;
    DoubleReal max_fwhm_;
    DoubleReal min_trace_length_;
    DoubleReal max_trace_length_;

    String pw_filtering_;
    bool mt_snr_filtering_;

    void detectElutionPeaks_(MassTrace &, std::vector<MassTrace> &);
  };
} // namespace OpenMS
#endif // OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H