SILACFilter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Lars Nilse $
// $Authors: Steffen Sass, Holger Plattfaut, Bastian Blank $
// --------------------------------------------------------------------------

#ifndef OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H
#define OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SILACFiltering.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SILACPattern.h>
#include <OpenMS/FILTERING/DATAREDUCTION/IsotopeDistributionCache.h>
#include <gsl/gsl_interp.h>
#include <gsl/gsl_spline.h>
#include <queue>
#include <list>

namespace OpenMS
{
  class OPENMS_DLLAPI SILACFilter
  {
private:
    friend class SILACFiltering;

    typedef IsotopeDistributionCache::TheoreticalIsotopePattern TheoreticalIsotopePattern;

    std::vector<DoubleReal> mass_separations_;

    Int charge_;

    DoubleReal model_deviation_;

    Size isotopes_per_peptide_;

    DoubleReal intensity_cutoff_;

    DoubleReal intensity_correlation_;

    bool allow_missing_peaks_;

    static IsotopeDistributionCache * isotope_distribution_;

    Size number_of_peptides_;

    std::vector<DoubleReal> peak_positions_;

    std::vector<DoubleReal> mz_peptide_separations_;

    std::vector<DoubleReal> expected_mz_shifts_;

    DoubleReal isotope_distance_;

    std::vector<SILACPattern> elements_;

    DoubleReal current_mz_;

    std::vector<std::vector<DoubleReal> > exact_shifts_;

    std::vector<std::vector<DoubleReal> > exact_mz_positions_;

    std::vector<std::vector<DoubleReal> > exact_intensities_;

    std::vector<std::vector<DoubleReal> > expected_shifts_;

    bool isSILACPattern_(const MSSpectrum<Peak1D> &, const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, DoubleReal picked_mz, const SILACFiltering &, MSSpectrum<Peak1D> & debug, SILACPattern & pattern);

    bool isSILACPatternPicked_(const MSSpectrum<Peak1D> &, DoubleReal mz, const SILACFiltering &, MSSpectrum<Peak1D> & debug);

    bool extractMzShiftsAndIntensities_(const MSSpectrum<Peak1D> &, const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, DoubleReal picked_mz, const SILACFiltering &);

    bool extractMzShiftsAndIntensitiesPicked_(const MSSpectrum<Peak1D> &, DoubleReal mz, const SILACFiltering &);

    bool extractMzShiftsAndIntensitiesPickedToPattern_(const MSSpectrum<Peak1D> &, DoubleReal mz, const SILACFiltering &, SILACPattern & pattern);

    bool intensityFilter_();

    bool correlationFilter1_(const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &);

    bool correlationFilter2_(const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &);

    bool averageneFilter_(DoubleReal mz);

public:
    SILACFilter(std::vector<DoubleReal> mass_separations, Int charge, DoubleReal model_deviation, Int isotopes_per_peptide,
                DoubleReal intensity_cutoff, DoubleReal intensity_correlation, bool allow_missing_peaks);

    std::vector<DoubleReal> getPeakPositions();

    const std::vector<DoubleReal> & getExpectedMzShifts();

    std::vector<SILACPattern> & getElements();

    Int getCharge();

    std::vector<DoubleReal> & getMassSeparations();
  };
}

#endif /* SILACFILTER_H_ */