| check_defaults_ | DefaultParamHandler | protected | 
  | checkForRequiredUserParams_(FeatureMap<> &features) | PrecursorIonSelection | private | 
  | convertPeptideIdScores_(std::vector< PeptideIdentification > &pep_ids) | PrecursorIonSelection | private | 
  | DefaultParamHandler(const String &name) | DefaultParamHandler |  | 
  | DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | DEX enum value | PrecursorIonSelection |  | 
  | DOWNSHIFT enum value | PrecursorIonSelection |  | 
  | error_name_ | DefaultParamHandler | protected | 
  | filterPeptideIds_(std::vector< PeptideIdentification > &pep_ids) | PrecursorIonSelection | private | 
  | filterProtIds_(std::vector< ProteinIdentification > &prot_ids) | PrecursorIonSelection | private | 
  | fraction_counter_ | PrecursorIonSelection | private | 
  | getDefaults() const | DefaultParamHandler |  | 
  | getLPSolver() | PrecursorIonSelection | inline | 
  | getMaxScore() const | PrecursorIonSelection |  | 
  | getName() const | DefaultParamHandler |  | 
  | getNextPrecursors(FeatureMap<> &features, FeatureMap<> &next_features, UInt number) | PrecursorIonSelection |  | 
  | getNextPrecursors(std::vector< Int > &solution_indices, std::vector< PSLPFormulation::IndexTriple > &variable_indices, std::set< Int > &measured_variables, FeatureMap<> &features, FeatureMap<> &new_features, UInt step_size, PSLPFormulation &ilp) | PrecursorIonSelection |  | 
  | getNextPrecursorsSeq(FeatureMap<> &features, FeatureMap<> &next_features, UInt number, DoubleReal &rt) | PrecursorIonSelection |  | 
  | getParameters() const | DefaultParamHandler |  | 
  | getPeptideProteinCounter() | PrecursorIonSelection | inline | 
  | getSubsections() const | DefaultParamHandler |  | 
  | ILP_IPS enum value | PrecursorIonSelection |  | 
  | IPS enum value | PrecursorIonSelection |  | 
  | max_iteration_ | PrecursorIonSelection | private | 
  | max_score_ | PrecursorIonSelection | private | 
  | min_pep_ids_ | PrecursorIonSelection | private | 
  | mz_tolerance_ | PrecursorIonSelection | private | 
  | mz_tolerance_unit_ | PrecursorIonSelection | private | 
  | operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | PrecursorIonSelection() | PrecursorIonSelection |  | 
  | PrecursorIonSelection(const PrecursorIonSelection &source) | PrecursorIonSelection |  | 
  | prot_id_counter_ | PrecursorIonSelection | private | 
  | rescore(FeatureMap<> &features, std::vector< PeptideIdentification > &new_pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, bool check_meta_values=true) | PrecursorIonSelection |  | 
  | rescore_(FeatureMap<> &features, std::vector< PeptideIdentification > &new_pep_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, PSProteinInference &protein_inference) | PrecursorIonSelection | private | 
  | reset() | PrecursorIonSelection |  | 
  | setLPSolver(LPWrapper::SOLVER solver) | PrecursorIonSelection | inline | 
  | setMaxScore(const DoubleReal &max_score) | PrecursorIonSelection |  | 
  | setName(const String &name) | DefaultParamHandler |  | 
  | setParameters(const Param ¶m) | DefaultParamHandler |  | 
  | shiftDown_(FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc) | PrecursorIonSelection | private | 
  | shiftUp_(FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc) | PrecursorIonSelection | private | 
  | simulateILPBasedIPSRun_(FeatureMap<> &features, MSExperiment<> &experiment, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String output_path, String precursor_path="") | PrecursorIonSelection | private | 
  | simulateRun(FeatureMap<> &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, MSExperiment<> &experiment, String precursor_path="") | PrecursorIonSelection |  | 
  | simulateRun_(FeatureMap<> &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, String precursor_path="") | PrecursorIonSelection | private | 
  | solver_ | PrecursorIonSelection | private | 
  | sortByTotalScore(FeatureMap<> &features) | PrecursorIonSelection | inline | 
  | SPS enum value | PrecursorIonSelection |  | 
  | subsections_ | DefaultParamHandler | protected | 
  | Type enum name | PrecursorIonSelection |  | 
  | type_ | PrecursorIonSelection | private | 
  | updateMembers_() | PrecursorIonSelection | privatevirtual | 
  | UPSHIFT enum value | PrecursorIonSelection |  | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | x_variable_number_ | PrecursorIonSelection | private | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~PrecursorIonSelection() | PrecursorIonSelection |  |