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 2002-2021.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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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
//    without specific prior written permission.
// 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"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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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> &, const Size max_traces = 0);
 
        void run(PeakMap::ConstAreaIterator & begin, PeakMap::ConstAreaIterator & end, std::vector<MassTrace> & found_masstraces);
 
    protected:
        void updateMembers_() override;
 
    private:
 
        struct Apex
        {
          Apex(double intensity, Size scan_idx, Size peak_idx);
          double intensity;
          Size scan_idx;
          Size peak_idx;
        };
 
        void run_(const std::vector<Apex>& chrom_apices,
                  const Size peak_count,
                  const PeakMap & work_exp,
                  const std::vector<Size>& spec_offsets,
                  std::vector<MassTrace> & found_masstraces,
                  const Size max_traces = 0);
 
        // 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_;
    };
}