| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| current_logger_ | ProgressLogger | mutableprotected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| endProgress() const | ProgressLogger | |
| enzyme_ | SimpleSearchEngineAlgorithm | protected |
| error_name_ | DefaultParamHandler | protected |
| ExitCodes enum name | SimpleSearchEngineAlgorithm | |
| fragment_mass_tolerance_ | SimpleSearchEngineAlgorithm | protected |
| fragment_mass_tolerance_unit_ | SimpleSearchEngineAlgorithm | protected |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| modifications_fixed_ | SimpleSearchEngineAlgorithm | protected |
| modifications_max_variable_mods_per_peptide_ | SimpleSearchEngineAlgorithm | protected |
| modifications_variable_ | SimpleSearchEngineAlgorithm | protected |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| 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_max_size_ | SimpleSearchEngineAlgorithm | protected |
| peptide_min_size_ | SimpleSearchEngineAlgorithm | protected |
| peptide_missed_cleavages_ | SimpleSearchEngineAlgorithm | protected |
| peptide_motif_ | SimpleSearchEngineAlgorithm | protected |
| postProcessHits_(const PeakMap &exp, std::vector< std::vector< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, Size top_hits, const ModifiedPeptideGenerator::MapToResidueType &fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType &variable_modifications, Size max_variable_mods_per_peptide, const StringList &modifications_fixed, const StringList &modifications_variable, Int peptide_missed_cleavages, double precursor_mass_tolerance, double fragment_mass_tolerance, const String &precursor_mass_tolerance_unit_ppm, const String &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const String &enzyme, const String &database_name) | SimpleSearchEngineAlgorithm | protectedstatic |
| precursor_isotopes_ | SimpleSearchEngineAlgorithm | protected |
| precursor_mass_tolerance_ | SimpleSearchEngineAlgorithm | protected |
| precursor_mass_tolerance_unit_ | SimpleSearchEngineAlgorithm | protected |
| precursor_max_charge_ | SimpleSearchEngineAlgorithm | protected |
| precursor_min_charge_ | SimpleSearchEngineAlgorithm | protected |
| preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm) | SimpleSearchEngineAlgorithm | protectedstatic |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| report_top_hits_ | SimpleSearchEngineAlgorithm | protected |
| search(const String &in_mzML, const String &in_db, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids) const | SimpleSearchEngineAlgorithm | |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| SimpleSearchEngineAlgorithm() | SimpleSearchEngineAlgorithm | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| subsections_ | DefaultParamHandler | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() override | SimpleSearchEngineAlgorithm | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProgressLogger() | ProgressLogger | |
1.8.16
