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TheoreticalSpectrumGenerator.h
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34 
35 #ifndef OPENMS_CHEMISTRY_THEORETICALSPECTRUMGENERATOR_H
36 #define OPENMS_CHEMISTRY_THEORETICALSPECTRUMGENERATOR_H
37 
42 
43 namespace OpenMS
44 {
45  class AASequence;
46 
64  class OPENMS_DLLAPI TheoreticalSpectrumGenerator :
65  public DefaultParamHandler
66  {
67  public:
68 
74 
77 
81 
84 
88  virtual void getSpectrum(PeakSpectrum & spec, const AASequence & peptide, Int min_charge, Int max_charge) const;
90 
92  void updateMembers_();
93 
95 
96  protected:
98  virtual void addPeaks_(PeakSpectrum & spectrum, const AASequence & peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Residue::ResidueType res_type, Int charge = 1) const;
99 
101  virtual void addPrecursorPeaks_(PeakSpectrum & spec, const AASequence & peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Int charge = 1) const;
102 
104  void addAbundantImmoniumIons_(PeakSpectrum & spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges) const;
105 
107  void addIsotopeCluster_(PeakSpectrum & spectrum, const AASequence & ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Residue::ResidueType res_type, Int charge, double intensity) const;
108 
110  char residueTypeToIonLetter_(Residue::ResidueType res_type) const;
111 
113  void addLosses_(PeakSpectrum & spectrum, const AASequence & ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, Residue::ResidueType res_type, int charge) const;
114 
128  double a_intensity_;
129  double b_intensity_;
130  double c_intensity_;
131  double x_intensity_;
132  double y_intensity_;
133  double z_intensity_;
136  double pre_int_;
137  double pre_int_H2O_;
138  double pre_int_NH3_;
139  };
140 }
141 #endif // THEORETICALSPECTRUMGENERATORRPLESS_H
double y_intensity_
Definition: TheoreticalSpectrumGenerator.h:132
double c_intensity_
Definition: TheoreticalSpectrumGenerator.h:130
bool add_y_ions_
Definition: TheoreticalSpectrumGenerator.h:116
double pre_int_
Definition: TheoreticalSpectrumGenerator.h:136
double pre_int_NH3_
Definition: TheoreticalSpectrumGenerator.h:138
double a_intensity_
Definition: TheoreticalSpectrumGenerator.h:128
double rel_loss_intensity_
Definition: TheoreticalSpectrumGenerator.h:135
double x_intensity_
Definition: TheoreticalSpectrumGenerator.h:131
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:64
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGenerator.h:125
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGenerator.h:121
bool add_x_ions_
Definition: TheoreticalSpectrumGenerator.h:119
Integer data array class.
Definition: DataArrays.h:52
bool add_z_ions_
Definition: TheoreticalSpectrumGenerator.h:120
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
bool add_losses_
Definition: TheoreticalSpectrumGenerator.h:122
Int max_isotope_
Definition: TheoreticalSpectrumGenerator.h:134
bool add_isotopes_
Definition: TheoreticalSpectrumGenerator.h:124
bool add_a_ions_
Definition: TheoreticalSpectrumGenerator.h:117
double b_intensity_
Definition: TheoreticalSpectrumGenerator.h:129
bool add_all_precursor_charges_
Definition: TheoreticalSpectrumGenerator.h:126
bool add_b_ions_
Definition: TheoreticalSpectrumGenerator.h:115
ResidueType
Definition: Residue.h:144
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGenerator.h:127
double z_intensity_
Definition: TheoreticalSpectrumGenerator.h:133
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
String data array class.
Definition: DataArrays.h:58
int Int
Signed integer type.
Definition: Types.h:103
bool add_metainfo_
Definition: TheoreticalSpectrumGenerator.h:123
double pre_int_H2O_
Definition: TheoreticalSpectrumGenerator.h:137
bool add_c_ions_
Definition: TheoreticalSpectrumGenerator.h:118

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:04 using doxygen 1.8.13