MultiplexFiltering.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.
//
// 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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//    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"
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// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredPeak.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>

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

#include <boost/serialization/strong_typedef.hpp>

namespace OpenMS
{
  class OPENMS_DLLAPI MultiplexFiltering :
    public ProgressLogger
  {
public:
    typedef std::vector<std::map<int, int> > White2Original;

    MultiplexFiltering(const MSExperiment& exp_centroided, 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");
    MSExperiment& getCentroidedExperiment();

protected:
    void updateWhiteMSExperiment_();

    int checkForSignificantPeak_(double mz, double mz_tolerance, MSExperiment::ConstIterator& it_rt, double intensity_first_peak) const;

    bool filterPeakPositions_(const MSSpectrum::ConstIterator& it_mz, const MSExperiment::ConstIterator& it_rt_begin, const MSExperiment::ConstIterator& it_rt_band_begin, const MSExperiment::ConstIterator& it_rt_band_end, const MultiplexIsotopicPeakPattern& pattern, MultiplexFilteredPeak& peak) const;

    void blacklistPeak_(const MultiplexFilteredPeak& peak);

    void blacklistPeak_(const MultiplexFilteredPeak& peak, unsigned pattern_idx);

    bool filterAveragineModel_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak) const;
    
    bool filterPeptideCorrelation_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak) const;

    MSExperiment exp_centroided_;

    std::vector<std::vector<int> > blacklist_;
    
    MSExperiment exp_centroided_white_;
    
    White2Original exp_centroided_mapping_;

    std::vector<MultiplexIsotopicPeakPattern> patterns_;

    size_t isotopes_per_peptide_min_;

    size_t isotopes_per_peptide_max_;

    double intensity_cutoff_;

    double rt_band_;
    
    double mz_tolerance_;

    bool mz_tolerance_unit_in_ppm_;

    double peptide_similarity_;

    double averagine_similarity_;

    double averagine_similarity_scaling_;

    String averagine_type_;

  };

}