| addMaxInclusionListSizeConstraints_(std::vector< IndexTriple > &variable_indices, UInt max_list_size) | PSLPFormulation | protected | 
  | addPrecursorAcquisitionNumberConstraint_(std::vector< IndexTriple > &variable_indices, Size number_of_features, UInt number_of_msms_per_precursor) | PSLPFormulation | protected | 
  | addProteinCoverageConstraint_(std::vector< IndexTriple > &variable_indices, PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, Size > protein_variable_index_map) | PSLPFormulation | protected | 
  | addProteinToILP_(PrecursorIonSelectionPreprocessing &preprocessing, std::map< String, std::vector< DoubleReal > >::const_iterator map_iter, Size &counter, Size &pep_counter, Size &feature_counter, std::vector< IndexTriple > &variable_indices, std::map< String, Size > &protein_penalty_index_map, FeatureMap<> &precursors) | PSLPFormulation | protected | 
  | addRTBinCapacityConstraint_(std::vector< IndexTriple > &variable_indices, Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order=false) | PSLPFormulation | protected | 
  | addStepSizeConstraint_(std::vector< IndexTriple > &variable_indices, UInt step_size) | PSLPFormulation | protected | 
  | assembleInclusionListForProteinBasedLP_(std::vector< IndexTriple > &variable_indices, FeatureMap<> &precursors, std::vector< int > &solution_indices, PrecursorIonSelectionPreprocessing &preprocessing) | PSLPFormulation | protected | 
  | calculateXICs_(std::vector< std::vector< DoubleReal > > &xics, const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const bool normalize) | PSLPFormulation | protected | 
  | check_defaults_ | DefaultParamHandler | protected | 
  | createAndSolveCombinedLPFeatureBased_(const FeatureMap<> &features, std::vector< std::vector< DoubleReal > > &intensity_weights, std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::vector< IndexTriple > &variable_indices, std::vector< Int > &solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans, Size step_size=0, bool sequential_order=false) | PSLPFormulation | protected | 
  | createAndSolveCombinedLPForKnownLCMSMapFeatureBased(const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< IndexTriple > &variable_indices, std::vector< int > &solution_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, Size step_size=0, bool sequential_order=false) | PSLPFormulation |  | 
  | createAndSolveILP_(const FeatureMap<> &features, std::vector< std::vector< DoubleReal > > &intensity_weights, std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::vector< IndexTriple > &variable_indices, std::vector< int > &solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans) | PSLPFormulation | protected | 
  | createAndSolveILPForInclusionListCreation(PrecursorIonSelectionPreprocessing &preprocessing, UInt ms2_spectra_per_rt_bin, UInt max_list_size, FeatureMap<> &precursors, bool solve_ILP=true) | PSLPFormulation |  | 
  | createAndSolveILPForKnownLCMSMapFeatureBased(const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, std::vector< IndexTriple > &variable_indices, std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, std::set< Int > &charges_set, UInt ms2_spectra_per_rt_bin, std::vector< int > &solution_indices) | PSLPFormulation |  | 
  | DefaultParamHandler(const String &name) | DefaultParamHandler |  | 
  | DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | error_name_ | DefaultParamHandler | protected | 
  | getDefaults() const | DefaultParamHandler |  | 
  | getLPSolver() | PSLPFormulation | inline | 
  | getName() const | DefaultParamHandler |  | 
  | getNumberOfPrecsInSpectrum_(Int constr_idx) | PSLPFormulation | protected | 
  | getParameters() const | DefaultParamHandler |  | 
  | getSubsections() const | DefaultParamHandler |  | 
  | getXIC_(const std::vector< std::pair< Size, Size > > &end_points, std::vector< DoubleReal > &weights, const MSExperiment< InputPeakType > &experiment, const bool normalize) | PSLPFormulation | protected | 
  | model_ | PSLPFormulation | protected | 
  | operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | PSLPFormulation() | PSLPFormulation |  | 
  | setLPSolver(LPWrapper::SOLVER solver) | PSLPFormulation | inline | 
  | setName(const String &name) | DefaultParamHandler |  | 
  | setParameters(const Param ¶m) | DefaultParamHandler |  | 
  | solveILP(std::vector< int > &solution_indices) | PSLPFormulation |  | 
  | solver_ | PSLPFormulation | protected | 
  | subsections_ | DefaultParamHandler | protected | 
  | updateCombinedILP(FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices, std::vector< String > &new_protein_accs, std::vector< String > &protein_accs, PSProteinInference &prot_inference, Size &variable_counter, std::map< String, std::vector< Size > > &protein_feature_map, Feature &new_feature, std::map< String, Size > &protein_variable_index_map, std::map< String, std::set< String > > &prot_id_counter) | PSLPFormulation |  | 
  | updateFeatureILPVariables(FeatureMap<> &new_features, std::vector< IndexTriple > &variable_indices, std::map< Size, std::vector< String > > &feature_constraints_map) | PSLPFormulation |  | 
  | updateMembers_() | DefaultParamHandler | protectedvirtual | 
  | updateObjFunction_(String acc, FeatureMap<> &features, PrecursorIonSelectionPreprocessing &preprocessed_db, std::vector< IndexTriple > &variable_indices) | PSLPFormulation | protected | 
  | updateRTConstraintsForSequentialILP(Size &rt_index, UInt ms2_spectra_per_rt_bin, Size max_rt_index) | PSLPFormulation |  | 
  | updateStepSizeConstraint(Size iteration, UInt step_size) | PSLPFormulation |  | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~PSLPFormulation() | PSLPFormulation | virtual |