, including all inherited members.
| 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 | |
| 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, bool sequential_order) | 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 | [protected, virtual] |
| 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] |