SimpleTSGXLMS.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
// --------------------------------------------------------------------------


#pragma once

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


namespace OpenMS
{
  class AASequence;

  class OPENMS_DLLAPI SimpleTSGXLMS :
    public DefaultParamHandler
  {
    public:

      struct SimplePeak
      {
        double mz = 0;
        int charge = 0;
      };

      struct SimplePeakComparator
      {
        bool operator() (const SimplePeak& a, const SimplePeak& b)
        {
          return a.mz < b.mz;
        }
      };

      struct LossIndex
      {
        bool has_H2O_loss = false;
        bool has_NH3_loss = false;
      };

      SimpleTSGXLMS();

      SimpleTSGXLMS(const SimpleTSGXLMS & source);

      ~SimpleTSGXLMS() override;

      SimpleTSGXLMS & operator=(const SimpleTSGXLMS & tsg);

      virtual void getLinearIonSpectrum(std::vector< SimplePeak >& spectrum, AASequence& peptide, Size link_pos, int charge = 1, Size link_pos_2 = 0) const;

      virtual void getXLinkIonSpectrum(std::vector< SimplePeak >& spectrum, AASequence& peptide, Size link_pos, double precursor_mass, int mincharge, int maxcharge, Size link_pos_2 = 0) const;

      virtual void getXLinkIonSpectrum(std::vector< SimplePeak >& spectrum, OPXLDataStructs::ProteinProteinCrossLink& crosslink, bool frag_alpha, int mincharge, int maxcharge) const;

      void updateMembers_() override;

    protected:

      virtual void addLinearPeaks_(std::vector< SimplePeak >& spectrum, AASequence& peptide, Size link_pos, Residue::ResidueType res_type, std::vector< LossIndex >& forward_losses, std::vector< LossIndex >& backward_losses, int charge = 1, Size link_pos_2 = 0) const;

      virtual void addPeak_(std::vector< SimplePeak >&, double pos, int charge) const;

      virtual void addPrecursorPeaks_(std::vector< SimplePeak >& spectrum, double precursor_mass, int charge) const;

      virtual void addLosses_(std::vector< SimplePeak >& spectrum, double mono_weight, int charge, LossIndex & losses) const;

      virtual void addKLinkedIonPeaks_(std::vector< SimplePeak >& spectrum, AASequence & peptide, Size link_pos, double precursor_mass, int charge) const;

      virtual void addXLinkIonPeaks_(std::vector< SimplePeak >& spectrum, AASequence & peptide, Size link_pos, double precursor_mass, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, int charge, Size link_pos_2 = 0) const;

      virtual void addXLinkIonPeaks_(std::vector< SimplePeak >& spectrum, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, LossIndex & losses_peptide2, int charge) const;

      std::vector< LossIndex > getForwardLosses_(AASequence & peptide) const;

      std::vector< LossIndex > getBackwardLosses_(AASequence & peptide) 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_charges_;
      bool add_isotopes_;
      bool add_precursor_peaks_;
      bool add_abundant_immonium_ions_;
      Int max_isotope_;
      double pre_int_;
      double pre_int_H2O_;
      double pre_int_NH3_;
      bool add_k_linked_ions_;

      std::map< String, LossIndex > loss_db_;
      double loss_H2O_ = 0;
      double loss_NH3_ = 0;
  };
}