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 |
getDefaults() const | DefaultParamHandler | |
getName() const | DefaultParamHandler | |
getParameters() const | DefaultParamHandler | |
getSpectrum(PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge) 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 | |