MassTraceDetection.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
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//  * Redistributions in binary form must reproduce the above copyright
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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: Timo Sachsenberg $
// $Authors: Erhan Kenar, Holger Franken $
// --------------------------------------------------------------------------

#pragma once

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

namespace OpenMS
{

  class OPENMS_DLLAPI MassTraceDetection :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MassTraceDetection();

    ~MassTraceDetection() override;

    void updateIterativeWeightedMeanMZ(const double &, const double &, double &, double &, double &);

    void run(const PeakMap &, std::vector<MassTrace> &);

    void run(PeakMap::ConstAreaIterator & begin, PeakMap::ConstAreaIterator & end, std::vector<MassTrace> & found_masstraces);

protected:
    void updateMembers_() override;

private:

    typedef std::multimap<double, std::pair<Size, Size> > MapIdxSortedByInt;

    void run_(const MapIdxSortedByInt& chrom_apices,
              const Size peak_count, 
              const PeakMap & work_exp,
              const std::vector<Size>& spec_offsets,
              std::vector<MassTrace> & found_masstraces);

    // parameter stuff
    double mass_error_ppm_;
    double noise_threshold_int_;
    double chrom_peak_snr_;
    MassTrace::MT_QUANTMETHOD quant_method_;

    String trace_termination_criterion_;
    Size trace_termination_outliers_;
    double min_sample_rate_;
    double min_trace_length_;
    double max_trace_length_;

    bool reestimate_mt_sd_;
  };
}