MultiplexFilteringProfile.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFiltering.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredPeak.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SplineInterpolatedPeaks.h>
 
#include <vector>
#include <algorithm>
#include <iostream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MultiplexFilteringProfile :
    public MultiplexFiltering
  {
public:
    MultiplexFilteringProfile(MSExperiment& exp_profile, const MSExperiment& exp_centroided, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries,
                              const std::vector<MultiplexIsotopicPeakPattern>& patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band,
                              double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide");
 
    std::vector<MultiplexFilteredMSExperiment> filter();
 
    std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& getPeakBoundaries();
 
private:
    bool filterAveragineModel_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites_profile) const;
 
    bool filterPeptideCorrelation_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites_profile) const;
    
    std::vector<SplineInterpolatedPeaks> exp_spline_profile_;
    std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_;
 
  };
 
}