OpenMS  2.7.0
TheoreticalSpectrumGeneratorXLMS Member List

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

a_intensity_TheoreticalSpectrumGeneratorXLMSprotected
add_a_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_abundant_immonium_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_b_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_c_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_charges_TheoreticalSpectrumGeneratorXLMSprotected
add_first_prefix_ion_TheoreticalSpectrumGeneratorXLMSprotected
add_isotopes_TheoreticalSpectrumGeneratorXLMSprotected
add_k_linked_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_losses_TheoreticalSpectrumGeneratorXLMSprotected
add_metainfo_TheoreticalSpectrumGeneratorXLMSprotected
add_precursor_peaks_TheoreticalSpectrumGeneratorXLMSprotected
add_x_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_y_ions_TheoreticalSpectrumGeneratorXLMSprotected
add_z_ions_TheoreticalSpectrumGeneratorXLMSprotected
addKLinkedIonPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int charge) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
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) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
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) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
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) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
addPrecursorPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double precursor_mass, int charge) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
addXLinkIonLosses_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double mono_weight, double intensity, int charge, String ion_name, LossIndex &losses) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
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) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
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) constTheoreticalSpectrumGeneratorXLMSprotectedvirtual
b_intensity_TheoreticalSpectrumGeneratorXLMSprotected
c_intensity_TheoreticalSpectrumGeneratorXLMSprotected
check_defaults_DefaultParamHandlerprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
getBackwardLosses_(AASequence &peptide) constTheoreticalSpectrumGeneratorXLMSprotected
getDefaults() constDefaultParamHandler
getForwardLosses_(AASequence &peptide) constTheoreticalSpectrumGeneratorXLMSprotected
getLinearIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) constTheoreticalSpectrumGeneratorXLMSvirtual
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
getXLinkIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2=0) constTheoreticalSpectrumGeneratorXLMSvirtual
getXLinkIonSpectrum(PeakSpectrum &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int mincharge, int maxcharge) constTheoreticalSpectrumGeneratorXLMSvirtual
loss_db_TheoreticalSpectrumGeneratorXLMSprotected
loss_H2O_TheoreticalSpectrumGeneratorXLMSprotected
loss_NH3_TheoreticalSpectrumGeneratorXLMSprotected
max_isotope_TheoreticalSpectrumGeneratorXLMSprotected
operator=(const TheoreticalSpectrumGeneratorXLMS &tsg)TheoreticalSpectrumGeneratorXLMS
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandlervirtual
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
pre_int_TheoreticalSpectrumGeneratorXLMSprotected
pre_int_H2O_TheoreticalSpectrumGeneratorXLMSprotected
pre_int_NH3_TheoreticalSpectrumGeneratorXLMSprotected
rel_loss_intensity_TheoreticalSpectrumGeneratorXLMSprotected
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
subsections_DefaultParamHandlerprotected
TheoreticalSpectrumGeneratorXLMS()TheoreticalSpectrumGeneratorXLMS
TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS &source)TheoreticalSpectrumGeneratorXLMS
updateMembers_() overrideTheoreticalSpectrumGeneratorXLMSvirtual
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")DefaultParamHandlerstatic
x_intensity_TheoreticalSpectrumGeneratorXLMSprotected
y_intensity_TheoreticalSpectrumGeneratorXLMSprotected
z_intensity_TheoreticalSpectrumGeneratorXLMSprotected
~DefaultParamHandler()DefaultParamHandlervirtual
~TheoreticalSpectrumGeneratorXLMS() overrideTheoreticalSpectrumGeneratorXLMS
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