| calculateXICs_(const FeatureMap<> &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, DoubleReal > > > &xics) | OfflinePrecursorIonSelection | private | 
  | check_defaults_ | DefaultParamHandler | protected | 
  | checkMassRanges_(std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment) | OfflinePrecursorIonSelection | private | 
  | createProteinSequenceBasedLPInclusionList(String include, String rt_model_file, String pt_model_file, FeatureMap<> &precursors) | OfflinePrecursorIonSelection |  | 
  | DefaultParamHandler(const String &name) | DefaultParamHandler |  | 
  | DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | error_name_ | DefaultParamHandler | protected | 
  | getDefaults() const | DefaultParamHandler |  | 
  | getLPSolver() | OfflinePrecursorIonSelection | inline | 
  | getMassRanges(const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< std::vector< std::pair< Size, Size > > > &indices) | OfflinePrecursorIonSelection |  | 
  | getName() const | DefaultParamHandler |  | 
  | getParameters() const | DefaultParamHandler |  | 
  | getSubsections() const | DefaultParamHandler |  | 
  | IndexTriple typedef | OfflinePrecursorIonSelection |  | 
  | makePrecursorSelectionForKnownLCMSMap(const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, MSExperiment< InputPeakType > &ms2, std::set< Int > &charges_set, bool feature_based) | OfflinePrecursorIonSelection |  | 
  | OfflinePrecursorIonSelection() | OfflinePrecursorIonSelection |  | 
  | operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | setLPSolver(LPWrapper::SOLVER solver) | OfflinePrecursorIonSelection | inline | 
  | setName(const String &name) | DefaultParamHandler |  | 
  | setParameters(const Param ¶m) | DefaultParamHandler |  | 
  | solver_ | OfflinePrecursorIonSelection | private | 
  | subsections_ | DefaultParamHandler | protected | 
  | updateExclusionList_(std::vector< std::pair< T, Size > > &exclusion_list) | OfflinePrecursorIonSelection | private | 
  | updateExclusionList_(std::map< std::pair< DoubleReal, DoubleReal >, Size, PairComparatorSecondElement< std::pair< DoubleReal, DoubleReal > > > &exclusion_list) | OfflinePrecursorIonSelection | inlineprivate | 
  | updateMembers_() | DefaultParamHandler | protectedvirtual | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~OfflinePrecursorIonSelection() | OfflinePrecursorIonSelection | virtual |