nightly/html/NucleicAcidSpectrumGenerator_8h_source.html

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//                   OpenMS -- Open-Source Mass Spectrometry

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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,

// ETH Zurich, and Freie Universitaet Berlin 2002-2022.

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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_;

  };

}