OPXLSpectrumProcessingAlgorithms.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: Eugen Netz $
// $Authors: Eugen Netz $
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#ifndef OPENMS_ANALYSIS_XLMS_OPXLSPECTRUMPROCESSINGALGORITHMS_H
#define OPENMS_ANALYSIS_XLMS_OPXLSPECTRUMPROCESSINGALGORITHMS_H

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <numeric>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI OPXLSpectrumProcessingAlgorithms
  {
    public:

      static PeakSpectrum mergeAnnotatedSpectra(PeakSpectrum & first_spectrum, PeakSpectrum & second_spectrum);

      static PeakMap preprocessSpectra(PeakMap& exp, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, Size peptide_min_size, Int min_precursor_charge, Int max_precursor_charge, bool labeled);

      static void getSpectrumAlignment(std::vector <std::pair <Size, Size> >& alignment, const PeakSpectrum & s1, const PeakSpectrum & s2, double tolerance, bool relative_tolerance, double intensity_cutoff = 0.0);

      static PeakSpectrum deisotopeAndSingleChargeMSSpectrum(PeakSpectrum& old_spectrum, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_tolerance_unit_ppm, bool keep_only_deisotoped = false, Size min_isopeaks = 3, Size max_isopeaks = 10, bool make_single_charged = false);

  };

}

#endif // OPXLSPECTRUMPROCESSINGALGORITHMS_H