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 |