TheoreticalSpectrumGenerator.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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);
 
 
    void getPrefixAndSuffixIonsMZ(std::vector<float>& spectrum, const AASequence& peptide, int charge) const;
 
    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);
 
    bool getIonSeriesSpectrum(PeakSpectrum& spectrum, std::vector<uint8_t>& ion_series, const AASequence& peptide, Int min_charge, Int max_charge) const;
 
    bool getIonSeriesSpectrum(PeakSpectrum& spectrum, std::vector<uint8_t>& ion_series, std::vector<UInt>& ion_ordinals,
                              std::vector<Int>& ion_charges, const AASequence& peptide, Int min_charge, Int max_charge) const;
 
    bool getIonSeriesSpectrum(PeakSpectrum& spectrum, std::vector<uint8_t>& ion_series, std::vector<UInt>& ion_ordinals,
                              std::vector<Int>& ion_charges, std::vector<Residue::ResidueType>& ion_types, const AASequence& peptide,
                              Int min_charge, Int max_charge) const;
 
 
    void updateMembers_() override;
 
    protected:
    bool getIonSeriesSpectrum_(PeakSpectrum& spectrum, std::vector<uint8_t>& ion_series, std::vector<UInt>* ion_ordinals,
                               std::vector<Int>* ion_charges, std::vector<Residue::ResidueType>* ion_types, const AASequence& peptide,
                               Int min_charge, Int max_charge) const;
 
 
    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;
 
    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, std::string>& formula_str_cache, double intensity, const std::string& annotation_prefix_string, bool add_metainfo, int charge) const;
 
    static void addPrefixAndSuffixIons_(std::vector<float>& spectrum, const AASequence& peptide, Residue::ResidueType res_type, int charge);
    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_zp1_ions_;
    bool add_zp2_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_ = 0;
    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_;
  };
}