| OpenMS 2.5.0

TheoreticalSpectrumGenerator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg, Eugen Netz $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CHEMISTRY/Residue.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/KERNEL/StandardTypes.h>
40 #include <OpenMS/METADATA/DataArrays.h>
41
42 namespace OpenMS
43 {
44 class AASequence;
45
67 class OPENMS_DLLAPI TheoreticalSpectrumGenerator :
68 public DefaultParamHandler
69 {
70 public:
71
75 TheoreticalSpectrumGenerator();
77
79 TheoreticalSpectrumGenerator(const TheoreticalSpectrumGenerator& source);
80
82 ~TheoreticalSpectrumGenerator() override;
84
86 TheoreticalSpectrumGenerator& operator=(const TheoreticalSpectrumGenerator& tsg);
87
91 virtual void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, Int min_charge, Int max_charge) const;
93
95 void updateMembers_() override;
97
98 protected:
99
101 virtual void addPeaks_(PeakSpectrum& spectrum, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Residue::ResidueType res_type, Int charge = 1) const;
102
104 virtual void addPrecursorPeaks_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Int charge = 1) const;
105
107 void addAbundantImmoniumIons_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges) const;
108
110 void addIsotopeCluster_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Residue::ResidueType res_type, Int charge, double intensity) const;
111
113 static char residueTypeToIonLetter_(Residue::ResidueType res_type);
114
116 void addLosses_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, Residue::ResidueType res_type, int charge) const;
117
118 bool add_b_ions_;
119 bool add_y_ions_;
120 bool add_a_ions_;
121 bool add_c_ions_;
122 bool add_x_ions_;
123 bool add_z_ions_;
124 bool add_first_prefix_ion_;
125 bool add_losses_;
126 bool add_metainfo_;
127 bool add_isotopes_;
128 int isotope_model_;
129 bool add_precursor_peaks_;
130 bool add_all_precursor_charges_ ;
131 bool add_abundant_immonium_ions_;
132 bool sort_by_position_;
133 double a_intensity_;
134 double b_intensity_;
135 double c_intensity_;
136 double x_intensity_;
137 double y_intensity_;
138 double z_intensity_;
139
140 Int max_isotope_;
141 double rel_loss_intensity_;
142 double max_isotope_probability_;
143 double pre_int_;
144 double pre_int_H2O_;
145 double pre_int_NH3_;
146 };
147 }
OpenMS::TheoreticalSpectrumGenerator::add_b_ions_
bool add_b_ions_
Definition: TheoreticalSpectrumGenerator.h:118
OpenMS::TheoreticalSpectrumGenerator::add_isotopes_
bool add_isotopes_
Definition: TheoreticalSpectrumGenerator.h:127
OpenMS::TheoreticalSpectrumGenerator::c_intensity_
double c_intensity_
Definition: TheoreticalSpectrumGenerator.h:135
OpenMS::TheoreticalSpectrumGenerator::x_intensity_
double x_intensity_
Definition: TheoreticalSpectrumGenerator.h:136
OpenMS::TheoreticalSpectrumGenerator::max_isotope_
Int max_isotope_
Definition: TheoreticalSpectrumGenerator.h:140
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::TheoreticalSpectrumGenerator::a_intensity_
double a_intensity_
Definition: TheoreticalSpectrumGenerator.h:133
OpenMS::TheoreticalSpectrumGenerator::add_y_ions_
bool add_y_ions_
Definition: TheoreticalSpectrumGenerator.h:119
OpenMS::TheoreticalSpectrumGenerator::pre_int_NH3_
double pre_int_NH3_
Definition: TheoreticalSpectrumGenerator.h:145
Residue.h
StandardTypes.h
OpenMS::TheoreticalSpectrumGenerator::max_isotope_probability_
double max_isotope_probability_
Definition: TheoreticalSpectrumGenerator.h:142
DataArrays.h
OpenMS::TheoreticalSpectrumGenerator::add_metainfo_
bool add_metainfo_
Definition: TheoreticalSpectrumGenerator.h:126
OpenMS::TheoreticalSpectrumGenerator::pre_int_
double pre_int_
Definition: TheoreticalSpectrumGenerator.h:143
OpenMS::TheoreticalSpectrumGenerator::add_x_ions_
bool add_x_ions_
Definition: TheoreticalSpectrumGenerator.h:122
OpenMS::DataArrays::StringDataArray
String data array class.
Definition: DataArrays.h:59
OpenMS::TheoreticalSpectrumGenerator::add_abundant_immonium_ions_
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGenerator.h:131
OpenMS::TheoreticalSpectrumGenerator::z_intensity_
double z_intensity_
Definition: TheoreticalSpectrumGenerator.h:138
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TheoreticalSpectrumGenerator::b_intensity_
double b_intensity_
Definition: TheoreticalSpectrumGenerator.h:134
OpenMS::TheoreticalSpectrumGenerator::y_intensity_
double y_intensity_
Definition: TheoreticalSpectrumGenerator.h:137
OpenMS::TheoreticalSpectrumGenerator::add_a_ions_
bool add_a_ions_
Definition: TheoreticalSpectrumGenerator.h:120
OpenMS::TheoreticalSpectrumGenerator::add_losses_
bool add_losses_
Definition: TheoreticalSpectrumGenerator.h:125
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
OpenMS::TheoreticalSpectrumGenerator::rel_loss_intensity_
double rel_loss_intensity_
Definition: TheoreticalSpectrumGenerator.h:141
DefaultParamHandler.h
OpenMS::TheoreticalSpectrumGenerator::sort_by_position_
bool sort_by_position_
Definition: TheoreticalSpectrumGenerator.h:132
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:67
OpenMS::TheoreticalSpectrumGenerator::add_precursor_peaks_
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGenerator.h:129
int
OpenMS::TheoreticalSpectrumGenerator::add_c_ions_
bool add_c_ions_
Definition: TheoreticalSpectrumGenerator.h:121
OpenMS::TheoreticalSpectrumGenerator::add_z_ions_
bool add_z_ions_
Definition: TheoreticalSpectrumGenerator.h:123
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:150
OpenMS::TheoreticalSpectrumGenerator::add_all_precursor_charges_
bool add_all_precursor_charges_
Definition: TheoreticalSpectrumGenerator.h:130
OpenMS::TheoreticalSpectrumGenerator::pre_int_H2O_
double pre_int_H2O_
Definition: TheoreticalSpectrumGenerator.h:144
OpenMS::TheoreticalSpectrumGenerator::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGenerator.h:124
OpenMS::TheoreticalSpectrumGenerator::isotope_model_
int isotope_model_
Definition: TheoreticalSpectrumGenerator.h:128