TheoreticalSpectrumGenerator.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: Timo Sachsenberg, Eugen Netz $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

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

namespace OpenMS
{
  class AASequence;

  class OPENMS_DLLAPI TheoreticalSpectrumGenerator :
    public DefaultParamHandler
  {
    public:

    TheoreticalSpectrumGenerator();

    TheoreticalSpectrumGenerator(const TheoreticalSpectrumGenerator& source);

    ~TheoreticalSpectrumGenerator() override;

    TheoreticalSpectrumGenerator& operator=(const TheoreticalSpectrumGenerator& tsg);

    virtual void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, Int min_charge, Int max_charge, Int precursor_charge = 0) const;

    static MSSpectrum generateSpectrum(const Precursor::ActivationMethod& fm, const AASequence& seq, int precursor_charge);

    void updateMembers_() override;

    protected:

    virtual void addPeaks_(PeakSpectrum& spectrum, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, MSSpectrum::Chunks& chunks, const Residue::ResidueType res_type, Int charge = 1) const;

    virtual void addPrecursorPeaks_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Int charge = 1) const;

    void addAbundantImmoniumIons_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges) const;

    void addIsotopeCluster_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, const Residue::ResidueType res_type, Int charge, double intensity) const;

    static char residueTypeToIonLetter_(const Residue::ResidueType res_type);

    void addLosses_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, const Residue::ResidueType res_type, int charge) const;

    void addLossesFaster_(PeakSpectrum& spectrum, double mz, const std::set<EmpiricalFormula>& f_losses, int ion_ordinal, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, const std::map<EmpiricalFormula, String>& formula_str_cache, double intensity, const String& annotation_prefix_string, bool add_metainfo, int charge) const;

    void addInternalFragmentPeaks_(PeakSpectrum& spectrum,
                                   const AASequence& peptide,
                                   DataArrays::StringDataArray& ion_names,
                                   DataArrays::IntegerDataArray& charges,
                                   MSSpectrum::Chunks& chunks,
                                   const Residue::ResidueType res_type,
                                   Int charge) const;
 
    bool add_b_ions_;
    bool add_y_ions_;
    bool add_a_ions_;
    bool add_c_ions_;
    bool add_x_ions_;
    bool add_z_ions_;
    bool add_first_prefix_ion_;
    bool add_losses_;
    bool add_term_losses_;
    bool add_metainfo_;
    bool add_isotopes_;
    bool add_internal_fragments_;
    int isotope_model_;
    bool add_precursor_peaks_;
    bool add_all_precursor_charges_ ;
    bool add_abundant_immonium_ions_;
    bool sort_by_position_;
    double a_intensity_;
    double b_intensity_;
    double c_intensity_;
    double x_intensity_;
    double y_intensity_;
    double z_intensity_;

    Int max_isotope_;
    double rel_loss_intensity_;
    double max_isotope_probability_;
    double pre_int_;
    double pre_int_H2O_;
    double pre_int_NH3_;
  };
}