OpenMS  3.0.0
TheoreticalSpectrumGeneratorXLMS.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
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34 
35 
36 #pragma once
37 
43 
44 
45 namespace OpenMS
46 {
47  class AASequence;
48 
65  class OPENMS_DLLAPI TheoreticalSpectrumGeneratorXLMS :
66  public DefaultParamHandler
67  {
68  public:
69 
70  struct LossIndex
71  {
72  bool has_H2O_loss = false;
73  bool has_NH3_loss = false;
74  };
75 
81 
84 
88 
91 
108  virtual void getLinearIonSpectrum(PeakSpectrum & spectrum, AASequence & peptide, Size link_pos, bool frag_alpha, int charge = 1, Size link_pos_2 = 0) const;
109 
133  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;
134 
152  virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, int mincharge, int maxcharge) const;
153 
155  void updateMembers_() override;
156 
157  protected:
158 
173  virtual void addLinearPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, int charge = 1, Size link_pos_2 = 0) const;
174 
192  virtual 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;
193 
203  virtual void addPrecursorPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double precursor_mass, int charge) const;
204 
219  virtual void addLinearIonLosses_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray& charges, DataArrays::StringDataArray& ion_names, double mono_weight, Residue::ResidueType res_type, Size frag_index, double intensity, int charge, String ion_type, LossIndex & losses) const;
220 
235  virtual void addXLinkIonLosses_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray& charges, DataArrays::StringDataArray& ion_names, double mono_weight, double intensity, int charge, String ion_name, LossIndex & losses) const;
236 
253  virtual void addKLinkedIonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, int charge) const;
254 
273  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, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, int charge, Size link_pos_2 = 0) const;
274 
291  virtual void addXLinkIonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, 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;
292 
300  std::vector< LossIndex > getForwardLosses_(AASequence & peptide) const;
301 
309  std::vector< LossIndex > getBackwardLosses_(AASequence & peptide) const;
310 
324  double a_intensity_;
325  double b_intensity_;
326  double c_intensity_;
327  double x_intensity_;
328  double y_intensity_;
329  double z_intensity_;
332  double pre_int_;
333  double pre_int_H2O_;
334  double pre_int_NH3_;
336 
337  std::map< String, LossIndex > loss_db_;
338  double loss_H2O_ = 0;
339  double loss_NH3_ = 0;
340  };
341 }
DefaultParamHandler.h
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_x_ions_
bool add_x_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:315
OpenMS::TheoreticalSpectrumGeneratorXLMS::loss_db_
std::map< String, LossIndex > loss_db_
Definition: TheoreticalSpectrumGeneratorXLMS.h:337
DataArrays.h
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_precursor_peaks_
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:322
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_charges_
bool add_charges_
Definition: TheoreticalSpectrumGeneratorXLMS.h:320
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TheoreticalSpectrumGeneratorXLMS::max_isotope_
Int max_isotope_
Definition: TheoreticalSpectrumGeneratorXLMS.h:330
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::TheoreticalSpectrumGeneratorXLMS::rel_loss_intensity_
double rel_loss_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:331
OpenMS::TheoreticalSpectrumGeneratorXLMS::x_intensity_
double x_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:327
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_y_ions_
bool add_y_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:312
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OPXLDataStructs.h
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_b_ions_
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:311
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:317
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_isotopes_
bool add_isotopes_
Definition: TheoreticalSpectrumGeneratorXLMS.h:321
OpenMS::TheoreticalSpectrumGeneratorXLMS::z_intensity_
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:329
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_abundant_immonium_ions_
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:323
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_z_ions_
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:316
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:151
OpenMS::DataArrays::StringDataArray
String data array class.
Definition: DataArrays.h:59
OpenMS::TheoreticalSpectrumGeneratorXLMS::a_intensity_
double a_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:324
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_a_ions_
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:313
Residue.h
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_c_ions_
bool add_c_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:314
OpenMS::TheoreticalSpectrumGeneratorXLMS::y_intensity_
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:328
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_losses_
bool add_losses_
Definition: TheoreticalSpectrumGeneratorXLMS.h:318
OpenMS::TheoreticalSpectrumGeneratorXLMS::pre_int_NH3_
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:334
OpenMS::TheoreticalSpectrumGeneratorXLMS::c_intensity_
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:326
OpenMS::TheoreticalSpectrumGeneratorXLMS::b_intensity_
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:325
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::TheoreticalSpectrumGeneratorXLMS
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:65
OpenMS::TheoreticalSpectrumGeneratorXLMS::pre_int_H2O_
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:333
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_metainfo_
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:319
OpenMS::TheoreticalSpectrumGeneratorXLMS::pre_int_
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:332
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
OpenMS::TheoreticalSpectrumGeneratorXLMS::LossIndex
Definition: TheoreticalSpectrumGeneratorXLMS.h:70
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_k_linked_ions_
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:335