add_a_ions_ | OpenPepXLAlgorithm | private |
add_b_ions_ | OpenPepXLAlgorithm | private |
add_c_ions_ | OpenPepXLAlgorithm | private |
add_losses_ | OpenPepXLAlgorithm | private |
add_x_ions_ | OpenPepXLAlgorithm | private |
add_y_ions_ | OpenPepXLAlgorithm | private |
add_z_ions_ | OpenPepXLAlgorithm | private |
check_defaults_ | DefaultParamHandler | protected |
CMD enum value | ProgressLogger | |
cross_link_mass_iso_shift_ | OpenPepXLAlgorithm | private |
cross_link_mass_light_ | OpenPepXLAlgorithm | private |
cross_link_mass_mono_link_ | OpenPepXLAlgorithm | private |
cross_link_name_ | OpenPepXLAlgorithm | private |
cross_link_residue1_ | OpenPepXLAlgorithm | private |
cross_link_residue2_ | OpenPepXLAlgorithm | private |
current_logger_ | ProgressLogger | mutableprotected |
decoy_prefix_ | OpenPepXLAlgorithm | private |
decoy_string_ | OpenPepXLAlgorithm | private |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
DefaultParamHandler() | DefaultParamHandler | private |
defaults_ | DefaultParamHandler | protected |
defaultsToParam_() | DefaultParamHandler | protected |
deisotope_mode_ | OpenPepXLAlgorithm | private |
endProgress() const | ProgressLogger | |
enzyme_name_ | OpenPepXLAlgorithm | private |
error_name_ | DefaultParamHandler | protected |
EXECUTION_OK enum value | OpenPepXLAlgorithm | |
ExitCodes enum name | OpenPepXLAlgorithm | |
fixedModNames_ | OpenPepXLAlgorithm | private |
fragment_mass_tolerance_ | OpenPepXLAlgorithm | private |
fragment_mass_tolerance_unit_ppm_ | OpenPepXLAlgorithm | private |
fragment_mass_tolerance_xlinks_ | OpenPepXLAlgorithm | private |
getDefaults() const | DefaultParamHandler | |
getLogType() const | ProgressLogger | |
getName() const | DefaultParamHandler | |
getParameters() const | DefaultParamHandler | |
getSubsections() const | DefaultParamHandler | |
GUI enum value | ProgressLogger | |
ILLEGAL_PARAMETERS enum value | OpenPepXLAlgorithm | |
INCOMPATIBLE_INPUT_DATA enum value | OpenPepXLAlgorithm | |
last_invoke_ | ProgressLogger | mutableprotected |
LogType enum name | ProgressLogger | |
logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
max_precursor_charge_ | OpenPepXLAlgorithm | private |
max_variable_mods_per_peptide_ | OpenPepXLAlgorithm | private |
min_precursor_charge_ | OpenPepXLAlgorithm | private |
missed_cleavages_ | OpenPepXLAlgorithm | private |
nextProgress() const | ProgressLogger | |
NONE enum value | ProgressLogger | |
number_top_hits_ | OpenPepXLAlgorithm | private |
OpenPepXLAlgorithm() | OpenPepXLAlgorithm | |
OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
param_ | DefaultParamHandler | protected |
peptide_min_size_ | OpenPepXLAlgorithm | private |
precursor_correction_steps_ | OpenPepXLAlgorithm | private |
precursor_mass_tolerance_ | OpenPepXLAlgorithm | private |
precursor_mass_tolerance_unit_ppm_ | OpenPepXLAlgorithm | private |
preprocessPairs_(const PeakMap &spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, bool deisotope) | OpenPepXLAlgorithm | privatestatic |
ProgressLogger() | ProgressLogger | |
ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
recursion_depth_ | ProgressLogger | protectedstatic |
run(PeakMap &unprocessed_spectra, ConsensusMap &cfeatures, std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, std::vector< std::pair< Size, Size > > &spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, PeakMap &spectra) | OpenPepXLAlgorithm | |
setLogType(LogType type) const | ProgressLogger | |
setName(const String &name) | DefaultParamHandler | |
setParameters(const Param ¶m) | DefaultParamHandler | |
setProgress(SignedSize value) const | ProgressLogger | |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
subsections_ | DefaultParamHandler | protected |
type_ | ProgressLogger | mutableprotected |
UNEXPECTED_RESULT enum value | OpenPepXLAlgorithm | |
updateMembers_() override | OpenPepXLAlgorithm | privatevirtual |
varModNames_ | OpenPepXLAlgorithm | private |
warn_empty_defaults_ | DefaultParamHandler | protected |
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") | DefaultParamHandler | static |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~OpenPepXLAlgorithm() override | OpenPepXLAlgorithm | |
~ProgressLogger() | ProgressLogger | |