NucleicAcidSpectrumGenerator.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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
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#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/METADATA/DataArrays.h>
#include <OpenMS/CHEMISTRY/NASequence.h>

namespace OpenMS
{
  class NASequence;

  class OPENMS_DLLAPI NucleicAcidSpectrumGenerator :
    public DefaultParamHandler
  {
    public:

    NucleicAcidSpectrumGenerator();

    NucleicAcidSpectrumGenerator(const NucleicAcidSpectrumGenerator& source);

    ~NucleicAcidSpectrumGenerator() override;

    NucleicAcidSpectrumGenerator& operator=(const NucleicAcidSpectrumGenerator& source);

    void getSpectrum(MSSpectrum& spectrum, const NASequence& oligo, Int min_charge, Int max_charge) const;

    void getMultipleSpectra(std::map<Int, MSSpectrum>& spectra, const NASequence& oligo, const std::set<Int>& charges, Int base_charge = 1) const;

    void updateMembers_() override;

    protected:

    void addFragmentPeaks_(MSSpectrum& spectrum, const std::vector<double>& fragment_masses, const String& ion_type, double offset, double intensity, Size start = 0) const;

    void addAMinusBPeaks_(MSSpectrum& spectrum, const std::vector<double>& fragment_masses, const NASequence& oligo, Size start = 0) const;

    MSSpectrum getUnchargedSpectrum_(const NASequence& oligo) const;

    void addChargedSpectrum_(MSSpectrum& spectrum, const MSSpectrum& uncharged_spectrum, Int charge, bool add_precursor) const;

    bool add_a_ions_;
    bool add_b_ions_;
    bool add_c_ions_;
    bool add_d_ions_;
    bool add_w_ions_;
    bool add_x_ions_;
    bool add_y_ions_;
    bool add_z_ions_;
    bool add_aB_ions_;
    bool add_first_prefix_ion_;
    bool add_metainfo_;
    bool add_precursor_peaks_;
    bool add_all_precursor_charges_ ;
    double a_intensity_;
    double b_intensity_;
    double c_intensity_;
    double d_intensity_;
    double w_intensity_;
    double x_intensity_;
    double y_intensity_;
    double z_intensity_;
    double aB_intensity_;
    double precursor_intensity_;
  };
}