| 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 | |
| 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 &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~OpenPepXLAlgorithm() override | OpenPepXLAlgorithm | |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.1 
