OPXLSpectrumProcessingAlgorithms.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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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/METADATA/DataArrays.h>
#include <OpenMS/CHEMISTRY/SimpleTSGXLMS.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, bool fragment_mass_tolerance_unit_ppm, Size peptide_min_size, Int min_precursor_charge, Int max_precursor_charge, std::vector<Size>& discarded_spectra, bool deisotope, bool labeled);

      static void getSpectrumAlignmentFastCharge(
            std::vector<std::pair<Size, Size> > & alignment, double fragment_mass_tolerance,
            bool fragment_mass_tolerance_unit_ppm,
            const PeakSpectrum& theo_spectrum,
            const PeakSpectrum& exp_spectrum,
            const DataArrays::IntegerDataArray& theo_charges,
            const DataArrays::IntegerDataArray& exp_charges,
            DataArrays::FloatDataArray& ppm_error_array,
            double intensity_cutoff = 0.0);

            static void getSpectrumAlignmentSimple(
                  std::vector<std::pair<Size, Size> > & alignment,
                  double fragment_mass_tolerance,
                  bool fragment_mass_tolerance_unit_ppm,
                  const std::vector< SimpleTSGXLMS::SimplePeak >& theo_spectrum,
                  const PeakSpectrum& exp_spectrum,
                  const DataArrays::IntegerDataArray& exp_charges);

      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);

  };

}