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OpenMS
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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 | protectedvirtual |
| 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 | protectedvirtual |
| 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 | protectedvirtual |
| 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 | protectedvirtual |
| addPrecursorPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double precursor_mass, int charge) const | TheoreticalSpectrumGeneratorXLMS | protectedvirtual |
| addXLinkIonLosses_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double mono_weight, double intensity, int charge, String ion_type, LossIndex &losses) const | TheoreticalSpectrumGeneratorXLMS | protectedvirtual |
| 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 | protectedvirtual |
| 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 | protectedvirtual |
| b_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected |
| c_intensity_ | TheoreticalSpectrumGeneratorXLMS | 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 |
| 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 | |
| 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 ¶m) | DefaultParamHandler | |
| subsections_ | DefaultParamHandler | protected |
| TheoreticalSpectrumGeneratorXLMS() | TheoreticalSpectrumGeneratorXLMS | |
| TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS &source) | TheoreticalSpectrumGeneratorXLMS | |
| updateMembers_() override | TheoreticalSpectrumGeneratorXLMS | virtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| x_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected |
| y_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected |
| z_intensity_ | TheoreticalSpectrumGeneratorXLMS | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~TheoreticalSpectrumGeneratorXLMS() override | TheoreticalSpectrumGeneratorXLMS |
1.9.1 
