TheoreticalSpectrumGeneratorXLMS.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 2002-2017.
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
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#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 TheoreticalSpectrumGeneratorXLMS :
    public DefaultParamHandler
  {
    public:

      TheoreticalSpectrumGeneratorXLMS();

      TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS & source);

      ~TheoreticalSpectrumGeneratorXLMS() override;

      TheoreticalSpectrumGeneratorXLMS & operator=(const TheoreticalSpectrumGeneratorXLMS & tsg);

      virtual void getCommonIonSpectrum(PeakSpectrum & spectrum, AASequence peptide, Size link_pos, bool frag_alpha, int charge = 1, Size link_pos_2 = 0) const;

      virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, AASequence peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2 = 0) const;

      void updateMembers_() override;

    protected:

      virtual void addCommonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, int charge = 1, Size link_pos_2 = 0) const;

      virtual void addXLinkIonPeaks_(PeakSpectrum& spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence peptide, Size link_pos, double precursor_mass, bool frag_alpha, Residue::ResidueType res_type, int charge, Size link_pos_2 = 0) const;


      void addPeak_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double pos, double intensity, Residue::ResidueType res_type, Size ion_index, int charge, String ion_type) const;

      // TODO copied from normal TSG, but it is protected over there. Move it to Residue class maybe?
      char residueTypeToIonLetter_(Residue::ResidueType res_type) const;

//      /// TODO helper to add full neutral loss ladders
//      //void addLosses_(RichPeakSpectrum & spectrum, const AASequence & ion, double intensity, Residue::ResidueType res_type, int charge, bool fragment_alpha_chain) 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_abundant_immonium_ions_;
      bool multiple_fragmentation_mode_;
      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_;
  };
}