annotate_psm_ | SimpleSearchEngineAlgorithm | protected |
check_defaults_ | DefaultParamHandler | protected |
CMD enum value | ProgressLogger | |
current_logger_ | ProgressLogger | mutableprotected |
decoys_ | SimpleSearchEngineAlgorithm | protected |
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) const | SimpleSearchEngineAlgorithm | protected |
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 |
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") | DefaultParamHandler | static |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~ProgressLogger() | ProgressLogger | |