MultiplexFilteringProfile.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: Lars Nilse $
// $Authors: Lars Nilse $
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#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/SplineSpectrum.h>

#include <vector>
#include <algorithm>
#include <iostream>

namespace OpenMS
{
  class OPENMS_DLLAPI MultiplexFilteringProfile :
    public MultiplexFiltering
  {
public:
    MultiplexFilteringProfile(MSExperiment& exp_profile, const MSExperiment& exp_picked, 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();

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<SplineSpectrum> exp_spline_profile_;
    std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_;

  };

}