PSLPFormulation Member List

This is the complete list of members for PSLPFormulation, 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< double > >::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< double > > &xics, const FeatureMap &features, const PeakMap &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< double > > &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 PeakMap &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< double > > &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 PeakMap &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
DefaultParamHandler()	DefaultParamHandler	private
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< double > &weights, const PeakMap &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 &param)	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
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual
~PSLPFormulation() override	PSLPFormulation