TheoreticalSpectrumGenerator.h

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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 2002-2018.
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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>

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) const;

    void updateMembers_() override;


    protected:
      virtual void addPeaks_(PeakSpectrum & spectrum, const AASequence & peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, 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, Residue::ResidueType res_type, Int charge, double intensity) const;

      char residueTypeToIonLetter_(Residue::ResidueType res_type) const;

      void addLosses_(PeakSpectrum & spectrum, const AASequence & ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, 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_metainfo_;
      bool add_isotopes_;
      bool add_precursor_peaks_;
      bool add_all_precursor_charges_ ;
      bool add_abundant_immonium_ions_;
      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 pre_int_;
      double pre_int_H2O_;
      double pre_int_NH3_;
  };
}