| OpenMS 2.5.0

TheoreticalSpectrumGeneratorXLMS Member List

This is the complete list of members for TheoreticalSpectrumGeneratorXLMS, including all inherited members.

a_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
add_a_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_abundant_immonium_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_b_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_c_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_charges_ | TheoreticalSpectrumGeneratorXLMS | protected
add_first_prefix_ion_ | TheoreticalSpectrumGeneratorXLMS | protected
add_isotopes_ | TheoreticalSpectrumGeneratorXLMS | protected
add_k_linked_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_losses_ | TheoreticalSpectrumGeneratorXLMS | protected
add_metainfo_ | TheoreticalSpectrumGeneratorXLMS | protected
add_precursor_peaks_ | TheoreticalSpectrumGeneratorXLMS | protected
add_x_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_y_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
add_z_ions_ | TheoreticalSpectrumGeneratorXLMS | protected
addKLinkedIonPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int charge) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addLinearIonLosses_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double mono_weight, Residue::ResidueType res_type, Size frag_index, double intensity, int charge, String ion_type, LossIndex &losses) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addLinearPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge=1, Size link_pos_2=0) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addPeak_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double pos, double intensity, Residue::ResidueType res_type, Size ion_index, int charge, String ion_type) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addPrecursorPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double precursor_mass, int charge) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addXLinkIonLosses_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double mono_weight, double intensity, int charge, String ion_name, LossIndex &losses) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addXLinkIonPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, int charge, Size link_pos_2=0) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
addXLinkIonPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > &forward_losses, std::vector< LossIndex > &backward_losses, LossIndex &losses_peptide2, int charge) const | TheoreticalSpectrumGeneratorXLMS | protected virtual
b_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
c_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
check_defaults_ | DefaultParamHandler | protected
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
error_name_ | DefaultParamHandler | protected
getBackwardLosses_(AASequence &peptide) const | TheoreticalSpectrumGeneratorXLMS | protected
getDefaults() const | DefaultParamHandler |
getForwardLosses_(AASequence &peptide) const | TheoreticalSpectrumGeneratorXLMS | protected
getLinearIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) const | TheoreticalSpectrumGeneratorXLMS | virtual
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
getXLinkIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2=0) const | TheoreticalSpectrumGeneratorXLMS | virtual
getXLinkIonSpectrum(PeakSpectrum &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int mincharge, int maxcharge) const | TheoreticalSpectrumGeneratorXLMS | virtual
loss_db_ | TheoreticalSpectrumGeneratorXLMS | protected
loss_H2O_ | TheoreticalSpectrumGeneratorXLMS | protected
loss_NH3_ | TheoreticalSpectrumGeneratorXLMS | protected
max_isotope_ | TheoreticalSpectrumGeneratorXLMS | protected
operator=(const TheoreticalSpectrumGeneratorXLMS &tsg) | TheoreticalSpectrumGeneratorXLMS |
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
param_ | DefaultParamHandler | protected
pre_int_ | TheoreticalSpectrumGeneratorXLMS | protected
pre_int_H2O_ | TheoreticalSpectrumGeneratorXLMS | protected
pre_int_NH3_ | TheoreticalSpectrumGeneratorXLMS | protected
rel_loss_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
subsections_ | DefaultParamHandler | protected
TheoreticalSpectrumGeneratorXLMS() | TheoreticalSpectrumGeneratorXLMS |
TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS &source) | TheoreticalSpectrumGeneratorXLMS |
updateMembers_() override | TheoreticalSpectrumGeneratorXLMS | virtual
warn_empty_defaults_ | DefaultParamHandler | protected
x_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
y_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
z_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected
~DefaultParamHandler() | DefaultParamHandler | virtual
~TheoreticalSpectrumGeneratorXLMS() override | TheoreticalSpectrumGeneratorXLMS |