| a_intensity_ | TheoreticalSpectrumGenerator | protected |
| add_a_ions_ | TheoreticalSpectrumGenerator | protected |
| add_abundant_immonium_ions_ | TheoreticalSpectrumGenerator | protected |
| add_all_precursor_charges_ | TheoreticalSpectrumGenerator | protected |
| add_b_ions_ | TheoreticalSpectrumGenerator | protected |
| add_c_ions_ | TheoreticalSpectrumGenerator | protected |
| add_first_prefix_ion_ | TheoreticalSpectrumGenerator | protected |
| add_isotopes_ | TheoreticalSpectrumGenerator | protected |
| add_losses_ | TheoreticalSpectrumGenerator | protected |
| add_metainfo_ | TheoreticalSpectrumGenerator | protected |
| add_precursor_peaks_ | TheoreticalSpectrumGenerator | protected |
| add_x_ions_ | TheoreticalSpectrumGenerator | protected |
| add_y_ions_ | TheoreticalSpectrumGenerator | protected |
| add_z_ions_ | TheoreticalSpectrumGenerator | protected |
| addAbundantImmoniumIons_(PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges) const | TheoreticalSpectrumGenerator | protected |
| addIsotopeCluster_(PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, const Residue::ResidueType res_type, Int charge, double intensity) const | TheoreticalSpectrumGenerator | protected |
| addLosses_(PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, double intensity, const Residue::ResidueType res_type, int charge) const | TheoreticalSpectrumGenerator | protected |
| 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 | TheoreticalSpectrumGenerator | protected |
| 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 | TheoreticalSpectrumGenerator | protectedvirtual |
| addPrecursorPeaks_(PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, Int charge=1) const | TheoreticalSpectrumGenerator | protectedvirtual |
| b_intensity_ | TheoreticalSpectrumGenerator | protected |
| c_intensity_ | TheoreticalSpectrumGenerator | protected |
| check_defaults_ | DefaultParamHandler | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| error_name_ | DefaultParamHandler | protected |
| generateSpectrum(const Precursor::ActivationMethod &fm, const AASequence &seq, int precursor_charge) | TheoreticalSpectrumGenerator | static |
| getDefaults() const | DefaultParamHandler | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSpectrum(PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge, Int precursor_charge=0) const | TheoreticalSpectrumGenerator | virtual |
| getSubsections() const | DefaultParamHandler | |
| isotope_model_ | TheoreticalSpectrumGenerator | protected |
| max_isotope_ | TheoreticalSpectrumGenerator | protected |
| max_isotope_probability_ | TheoreticalSpectrumGenerator | protected |
| operator=(const TheoreticalSpectrumGenerator &tsg) | TheoreticalSpectrumGenerator | |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| pre_int_ | TheoreticalSpectrumGenerator | protected |
| pre_int_H2O_ | TheoreticalSpectrumGenerator | protected |
| pre_int_NH3_ | TheoreticalSpectrumGenerator | protected |
| rel_loss_intensity_ | TheoreticalSpectrumGenerator | protected |
| residueTypeToIonLetter_(const Residue::ResidueType res_type) | TheoreticalSpectrumGenerator | protectedstatic |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| sort_by_position_ | TheoreticalSpectrumGenerator | protected |
| subsections_ | DefaultParamHandler | protected |
| TheoreticalSpectrumGenerator() | TheoreticalSpectrumGenerator | |
| TheoreticalSpectrumGenerator(const TheoreticalSpectrumGenerator &source) | TheoreticalSpectrumGenerator | |
| updateMembers_() override | TheoreticalSpectrumGenerator | virtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") | DefaultParamHandler | static |
| x_intensity_ | TheoreticalSpectrumGenerator | protected |
| y_intensity_ | TheoreticalSpectrumGenerator | protected |
| z_intensity_ | TheoreticalSpectrumGenerator | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~TheoreticalSpectrumGenerator() override | TheoreticalSpectrumGenerator | |
1.9.1
