OpenMS  3.0.0
TheoreticalSpectrumGenerator.h
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32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
45  class AASequence;
46 
68  class OPENMS_DLLAPI TheoreticalSpectrumGenerator :
69  public DefaultParamHandler
70  {
71  public:
72 
78 
81 
83  ~TheoreticalSpectrumGenerator() override;
85 
88 
92  virtual void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, Int min_charge, Int max_charge, Int precursor_charge = 0) const;
96 
102  static MSSpectrum generateSpectrum(const Precursor::ActivationMethod& fm, const AASequence& seq, int precursor_charge);
103 
105  void updateMembers_() override;
107 
108  protected:
109 
111  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;
112 
114  virtual void addPrecursorPeaks_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Int charge = 1) const;
115 
117  void addAbundantImmoniumIons_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges) const;
118 
120  void addIsotopeCluster_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, const Residue::ResidueType res_type, Int charge, double intensity) const;
121 
123  static char residueTypeToIonLetter_(const Residue::ResidueType res_type);
124 
126  void addLosses_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, const Residue::ResidueType res_type, int charge) const;
127 
129  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, String>& formula_str_cache, double intensity, const Residue::ResidueType res_type, bool add_metainfo, int charge) const;
130 
146  double a_intensity_;
147  double b_intensity_;
148  double c_intensity_;
149  double x_intensity_;
150  double y_intensity_;
151  double z_intensity_;
152 
156  double pre_int_;
157  double pre_int_H2O_;
158  double pre_int_NH3_;
159  };
160 }
DefaultParamHandler.h
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
OpenMS::TheoreticalSpectrumGenerator::rel_loss_intensity_
double rel_loss_intensity_
Definition: TheoreticalSpectrumGenerator.h:154
DataArrays.h
OpenMS::TheoreticalSpectrumGenerator::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGenerator.h:137
OpenMS::TheoreticalSpectrumGenerator::pre_int_H2O_
double pre_int_H2O_
Definition: TheoreticalSpectrumGenerator.h:157
OpenMS::TheoreticalSpectrumGenerator::add_isotopes_
bool add_isotopes_
Definition: TheoreticalSpectrumGenerator.h:140
OpenMS::TheoreticalSpectrumGenerator::b_intensity_
double b_intensity_
Definition: TheoreticalSpectrumGenerator.h:147
OpenMS::TheoreticalSpectrumGenerator::max_isotope_
Int max_isotope_
Definition: TheoreticalSpectrumGenerator.h:153
OpenMS::TheoreticalSpectrumGenerator::add_z_ions_
bool add_z_ions_
Definition: TheoreticalSpectrumGenerator.h:136
OpenMS::TheoreticalSpectrumGenerator::add_metainfo_
bool add_metainfo_
Definition: TheoreticalSpectrumGenerator.h:139
OpenMS::TheoreticalSpectrumGenerator::add_x_ions_
bool add_x_ions_
Definition: TheoreticalSpectrumGenerator.h:135
OpenMS::TheoreticalSpectrumGenerator::add_a_ions_
bool add_a_ions_
Definition: TheoreticalSpectrumGenerator.h:133
OpenMS::TheoreticalSpectrumGenerator::add_abundant_immonium_ions_
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGenerator.h:144
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TheoreticalSpectrumGenerator::x_intensity_
double x_intensity_
Definition: TheoreticalSpectrumGenerator.h:149
OpenMS::TheoreticalSpectrumGenerator::add_b_ions_
bool add_b_ions_
Definition: TheoreticalSpectrumGenerator.h:131
OpenMS::TheoreticalSpectrumGenerator::a_intensity_
double a_intensity_
Definition: TheoreticalSpectrumGenerator.h:146
OpenMS::TheoreticalSpectrumGenerator::isotope_model_
int isotope_model_
Definition: TheoreticalSpectrumGenerator.h:141
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:151
OpenMS::DataArrays::StringDataArray
String data array class.
Definition: DataArrays.h:59
OpenMS::TheoreticalSpectrumGenerator::pre_int_
double pre_int_
Definition: TheoreticalSpectrumGenerator.h:156
OpenMS::TheoreticalSpectrumGenerator::add_precursor_peaks_
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGenerator.h:142
Residue.h
OpenMS::TheoreticalSpectrumGenerator::add_all_precursor_charges_
bool add_all_precursor_charges_
Definition: TheoreticalSpectrumGenerator.h:143
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:68
OpenMS::TheoreticalSpectrumGenerator::add_c_ions_
bool add_c_ions_
Definition: TheoreticalSpectrumGenerator.h:134
OpenMS::TheoreticalSpectrumGenerator::max_isotope_probability_
double max_isotope_probability_
Definition: TheoreticalSpectrumGenerator.h:155
OpenMS::TheoreticalSpectrumGenerator::add_losses_
bool add_losses_
Definition: TheoreticalSpectrumGenerator.h:138
OpenMS::TheoreticalSpectrumGenerator::add_y_ions_
bool add_y_ions_
Definition: TheoreticalSpectrumGenerator.h:132
OpenMS::TheoreticalSpectrumGenerator::pre_int_NH3_
double pre_int_NH3_
Definition: TheoreticalSpectrumGenerator.h:158
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::TheoreticalSpectrumGenerator::c_intensity_
double c_intensity_
Definition: TheoreticalSpectrumGenerator.h:148
OpenMS::TheoreticalSpectrumGenerator::y_intensity_
double y_intensity_
Definition: TheoreticalSpectrumGenerator.h:150
OpenMS::TheoreticalSpectrumGenerator::sort_by_position_
bool sort_by_position_
Definition: TheoreticalSpectrumGenerator.h:145
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::Precursor::ActivationMethod
ActivationMethod
Method of activation.
Definition: Precursor.h:84
StandardTypes.h
MSSpectrum.h
OpenMS::TheoreticalSpectrumGenerator::z_intensity_
double z_intensity_
Definition: TheoreticalSpectrumGenerator.h:151
OpenMS::MSSpectrum::Chunks
Definition: MSSpectrum.h:87