OpenMS
TheoreticalSpectrumGenerator.h
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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 
85 
88 
95  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 
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 }
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Integer data array class.
Definition: DataArrays.h:55
String data array class.
Definition: DataArrays.h:62
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
ActivationMethod
Method of activation.
Definition: Precursor.h:85
ResidueType
Definition: Residue.h:152
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:70
bool add_x_ions_
Definition: TheoreticalSpectrumGenerator.h:135
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGenerator.h:142
void addLosses_(PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, double intensity, const Residue::ResidueType res_type, int charge) const
helper to add full neutral loss ladders (for isotope clusters), also adds charges and ion names to th...
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
adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity, also adds charges and...
TheoreticalSpectrumGenerator()
default constructor
double rel_loss_intensity_
Definition: TheoreticalSpectrumGenerator.h:154
bool add_all_precursor_charges_
Definition: TheoreticalSpectrumGenerator.h:143
bool add_losses_
Definition: TheoreticalSpectrumGenerator.h:138
bool add_a_ions_
Definition: TheoreticalSpectrumGenerator.h:133
double max_isotope_probability_
Definition: TheoreticalSpectrumGenerator.h:155
static char residueTypeToIonLetter_(const Residue::ResidueType res_type)
helper for mapping residue type to letter
double c_intensity_
Definition: TheoreticalSpectrumGenerator.h:148
bool add_b_ions_
Definition: TheoreticalSpectrumGenerator.h:131
double z_intensity_
Definition: TheoreticalSpectrumGenerator.h:151
~TheoreticalSpectrumGenerator() override
destructor
bool sort_by_position_
Definition: TheoreticalSpectrumGenerator.h:145
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGenerator.h:144
bool add_y_ions_
Definition: TheoreticalSpectrumGenerator.h:132
bool add_isotopes_
Definition: TheoreticalSpectrumGenerator.h:140
double pre_int_NH3_
Definition: TheoreticalSpectrumGenerator.h:158
TheoreticalSpectrumGenerator(const TheoreticalSpectrumGenerator &source)
copy constructor
virtual void addPrecursorPeaks_(PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, Int charge=1) const
adds the precursor peaks to the spectrum, also adds charges and ion names to the DataArrays,...
double x_intensity_
Definition: TheoreticalSpectrumGenerator.h:149
TheoreticalSpectrumGenerator & operator=(const TheoreticalSpectrumGenerator &tsg)
assignment operator
double a_intensity_
Definition: TheoreticalSpectrumGenerator.h:146
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGenerator.h:137
double b_intensity_
Definition: TheoreticalSpectrumGenerator.h:147
void addIsotopeCluster_(PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, const Residue::ResidueType res_type, Int charge, double intensity) const
helper to add an isotope cluster to a spectrum, also adds charges and ion names to the DataArrays,...
int isotope_model_
Definition: TheoreticalSpectrumGenerator.h:141
static MSSpectrum generateSpectrum(const Precursor::ActivationMethod &fm, const AASequence &seq, int precursor_charge)
void updateMembers_() override
overwrite
double pre_int_
Definition: TheoreticalSpectrumGenerator.h:156
double y_intensity_
Definition: TheoreticalSpectrumGenerator.h:150
void addAbundantImmoniumIons_(PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges) const
Adds the common, most abundant immonium ions to the theoretical spectra if the residue is contained i...
virtual void getSpectrum(PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge, Int precursor_charge=0) const
Int max_isotope_
Definition: TheoreticalSpectrumGenerator.h:153
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
helper to add full neutral loss ladders (for single peaks), also adds charges and ion names to the Da...
bool add_c_ions_
Definition: TheoreticalSpectrumGenerator.h:134
bool add_z_ions_
Definition: TheoreticalSpectrumGenerator.h:136
bool add_metainfo_
Definition: TheoreticalSpectrumGenerator.h:139
double pre_int_H2O_
Definition: TheoreticalSpectrumGenerator.h:157
int Int
Signed integer type.
Definition: Types.h:102
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Definition: MSSpectrum.h:93